=============================================================================== About this build: this rebuild has been done as part of reproduce.debian.net where we aim to reproduce Debian binary packages distributed via ftp.debian.org, by rebuilding using the exact same packages as the original build on the buildds, as described in the relevant .buildinfo file from buildinfos.debian.net. For more information please go to https://reproduce.debian.net or join #debian-reproducible on irc.debian.org =============================================================================== Preparing download of sources for /srv/rebuilderd/tmp/rebuilderdkS7JpC/inputs/python-cogent_2024.5.7a1+dfsg-3_all.buildinfo Source: python-cogent Version: 2024.5.7a1+dfsg-3 rebuilderd-worker node: ionos25-amd64 +------------------------------------------------------------------------------+ | Downloading sources Sat, 04 Oct 2025 11:00:17 +0000 | +------------------------------------------------------------------------------+ Get:1 https://deb.debian.org/debian trixie InRelease [140 kB] Get:2 https://deb.debian.org/debian-security trixie-security InRelease [43.4 kB] Get:3 https://deb.debian.org/debian trixie-updates InRelease [47.3 kB] Get:4 https://deb.debian.org/debian trixie-proposed-updates InRelease [55.8 kB] Get:5 https://deb.debian.org/debian trixie-backports InRelease [53.8 kB] Get:6 https://deb.debian.org/debian forky InRelease [147 kB] Get:7 https://deb.debian.org/debian sid InRelease [207 kB] Get:8 https://deb.debian.org/debian experimental InRelease [101 kB] Get:9 https://deb.debian.org/debian trixie/non-free-firmware Sources [6536 B] Get:10 https://deb.debian.org/debian trixie/main Sources [10.5 MB] Get:11 https://deb.debian.org/debian-security trixie-security/main Sources [55.5 kB] Get:12 https://deb.debian.org/debian trixie-updates/main Sources [2788 B] Get:13 https://deb.debian.org/debian trixie-proposed-updates/main Sources [22.3 kB] Get:14 https://deb.debian.org/debian trixie-backports/main Sources [54.0 kB] Get:15 https://deb.debian.org/debian trixie-backports/non-free-firmware Sources [1052 B] Get:16 https://deb.debian.org/debian forky/non-free-firmware Sources [7128 B] Get:17 https://deb.debian.org/debian forky/main Sources [10.7 MB] Get:18 https://deb.debian.org/debian sid/non-free-firmware Sources [9100 B] Get:19 https://deb.debian.org/debian sid/main Sources [11.1 MB] Get:20 https://deb.debian.org/debian experimental/main Sources [370 kB] Get:21 https://deb.debian.org/debian experimental/non-free-firmware Sources [2572 B] Fetched 33.7 MB in 3s (10.9 MB/s) Reading package lists... 'https://deb.debian.org/debian/pool/main/p/python-cogent/python-cogent_2024.5.7a1%2bdfsg-3.dsc' python-cogent_2024.5.7a1+dfsg-3.dsc 2634 SHA256:1333faf81544141e442359a86c91c451e7ae021e38b47ad5c09d2f6ccd32358e 'https://deb.debian.org/debian/pool/main/p/python-cogent/python-cogent_2024.5.7a1%2bdfsg.orig.tar.xz' python-cogent_2024.5.7a1+dfsg.orig.tar.xz 14846556 SHA256:e4fe6bc1d1ce9df1f91ca84123df8427c37327847564244c0abc97ccc3357f2c 'https://deb.debian.org/debian/pool/main/p/python-cogent/python-cogent_2024.5.7a1%2bdfsg-3.debian.tar.xz' python-cogent_2024.5.7a1+dfsg-3.debian.tar.xz 12180 SHA256:4d5837beed17582651dabe60b4b6ce0f2781a68e4c2ab57fad48a5befb2a9c2c e4fe6bc1d1ce9df1f91ca84123df8427c37327847564244c0abc97ccc3357f2c python-cogent_2024.5.7a1+dfsg.orig.tar.xz 4d5837beed17582651dabe60b4b6ce0f2781a68e4c2ab57fad48a5befb2a9c2c python-cogent_2024.5.7a1+dfsg-3.debian.tar.xz 1333faf81544141e442359a86c91c451e7ae021e38b47ad5c09d2f6ccd32358e python-cogent_2024.5.7a1+dfsg-3.dsc +------------------------------------------------------------------------------+ | Calling debrebuild Sat, 04 Oct 2025 11:00:21 +0000 | +------------------------------------------------------------------------------+ Rebuilding python-cogent=2024.5.7a1+dfsg-3 in /srv/rebuilderd/tmp/rebuilderdkS7JpC/inputs now. + nice /usr/bin/debrebuild --buildresult=/srv/rebuilderd/tmp/rebuilderdkS7JpC/out --builder=sbuild+unshare --cache=/srv/rebuilderd/cache -- /srv/rebuilderd/tmp/rebuilderdkS7JpC/inputs/python-cogent_2024.5.7a1+dfsg-3_all.buildinfo /srv/rebuilderd/tmp/rebuilderdkS7JpC/inputs/python-cogent_2024.5.7a1+dfsg-3_all.buildinfo contains a GPG signature which has NOT been validated Using defined Build-Path: /build/reproducible-path/python-cogent-2024.5.7a1+dfsg I: verifying dsc... successful! Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid InRelease [198 kB] Get:2 http://snapshot.debian.org/archive/debian/20240712T203746Z sid InRelease [198 kB] Get:3 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 Packages [9945 kB] Get:4 http://snapshot.debian.org/archive/debian/20240712T203746Z sid/main amd64 Packages [9962 kB] Fetched 20.3 MB in 3s (7710 kB/s) Reading package lists... W: http://snapshot.debian.org/archive/debian/20240704T022806Z/dists/sid/InRelease: Loading /etc/apt/trusted.gpg from deprecated option Dir::Etc::Trusted W: http://snapshot.debian.org/archive/debian/20240712T203746Z/dists/sid/InRelease: Loading /etc/apt/trusted.gpg from deprecated option Dir::Etc::Trusted Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 unicode-data all 15.1.0-1 [8547 kB] Fetched 8547 kB in 0s (150 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsiylmt0a/unicode-data_15.1.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-webencodings all 0.5.1-5 [11.1 kB] Fetched 11.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp27_80ri8/python3-webencodings_0.5.1-5_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3.11-dev amd64 3.11.9-1 [501 kB] Fetched 501 kB in 0s (2143 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzo9k3x2y/python3.11-dev_3.11.9-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libunistring5 amd64 1.2-1 [425 kB] Fetched 425 kB in 0s (32.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpoer4l5op/libunistring5_1.2-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libllvm14t64 amd64 1:14.0.6-20 [21.9 MB] Fetched 21.9 MB in 1s (39.8 MB/s) dpkg-name: info: moved 'libllvm14t64_1%3a14.0.6-20_amd64.deb' to '/srv/rebuilderd/tmp/tmpa9k1ggif/libllvm14t64_14.0.6-20_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-build all 1.2.1-1 [34.1 kB] Fetched 34.1 kB in 0s (189 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphba1ac22/python3-build_1.2.1-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libexpat1-dev amd64 2.6.2-1 [155 kB] Fetched 155 kB in 0s (549 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdn12c7n9/libexpat1-dev_2.6.2-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-pil amd64 10.3.0-2 [564 kB] Fetched 564 kB in 0s (2363 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwb4mynak/python3-pil_10.3.0-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Fetched 8952 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpspywyu0g/libkeyutils1_1.6.3-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3.11-minimal amd64 3.11.9-1 [1879 kB] Fetched 1879 kB in 0s (6239 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpay_rws2r/python3.11-minimal_3.11.9-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libblkid1 amd64 2.40.1-9 [166 kB] Fetched 166 kB in 0s (813 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpak54urty/libblkid1_2.40.1-9_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 g++-13 amd64 13.3.0-1 [16.2 kB] Fetched 16.2 kB in 0s (105 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpa9xkegqs/g++-13_13.3.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 dpkg amd64 1.22.6 [1510 kB] Fetched 1510 kB in 0s (91.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpujs1t6pc/dpkg_1.22.6_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-dateutil all 2.9.0-2 [79.4 kB] Fetched 79.4 kB in 0s (398 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbgqjb1f1/python3-dateutil_2.9.0-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 liblz4-1 amd64 1.9.4-2 [61.4 kB] Fetched 61.4 kB in 0s (324 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplzpqdnbz/liblz4-1_1.9.4-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-pytest-xdist all 3.6.1-1 [44.4 kB] Fetched 44.4 kB in 0s (170 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwr06l3_n/python3-pytest-xdist_3.6.1-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libgssapi-krb5-2 amd64 1.21.2-1 [136 kB] Fetched 136 kB in 0s (638 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcvwlgy_i/libgssapi-krb5-2_1.21.2-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 base-files amd64 13.3 [72.3 kB] Fetched 72.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgnd4fq1a/base-files_13.3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-tabulate all 0.9.0-1 [45.9 kB] Fetched 45.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2l8n_npc/python3-tabulate_0.9.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 blt amd64 2.5.3+dfsg-7 [6024 B] Fetched 6024 B in 0s (36.3 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2axyo3h8/blt_2.5.3+dfsg-7_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python-tinycss2-common all 1.3.0-1 [31.9 kB] Fetched 31.9 kB in 0s (213 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpov_x3zbw/python-tinycss2-common_1.3.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libcurl4t64 amd64 8.8.0-2 [445 kB] Fetched 445 kB in 0s (1809 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpoghrqwf7/libcurl4t64_8.8.0-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-decorator all 5.1.1-5 [15.1 kB] Fetched 15.1 kB in 0s (97.1 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpavrgqn4t/python3-decorator_5.1.1-5_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libpam0g amd64 1.5.3-7 [67.7 kB] Fetched 67.7 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpko2vanrw/libpam0g_1.5.3-7_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-isort all 5.6.4-1 [63.2 kB] Fetched 63.2 kB in 0s (323 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9d8d8hoo/python3-isort_5.6.4-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 liblerc4 amd64 4.0.0+ds-4+b1 [171 kB] Fetched 171 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkxoihp_m/liblerc4_4.0.0+ds-4+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 file amd64 1:5.45-3 [42.9 kB] Fetched 42.9 kB in 0s (0 B/s) dpkg-name: info: moved 'file_1%3a5.45-3_amd64.deb' to '/srv/rebuilderd/tmp/tmp4iedm2_8/file_5.45-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-minimal amd64 3.12.2-1 [26.5 kB] Fetched 26.5 kB in 0s (147 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp02bltppd/python3-minimal_3.12.2-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-setuptools-scm all 8.1.0-1 [40.5 kB] Fetched 40.5 kB in 0s (236 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd46z_p04/python3-setuptools-scm_8.1.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libpam-runtime all 1.5.3-7 [140 kB] Fetched 140 kB in 0s (11.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpw9jjpp0y/libpam-runtime_1.5.3-7_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 coreutils amd64 9.4-3.1 [2950 kB] Fetched 2950 kB in 0s (119 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpy_hy9dfu/coreutils_9.4-3.1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libpng16-16t64 amd64 1.6.43-5 [278 kB] Fetched 278 kB in 0s (24.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7h3xsrz8/libpng16-16t64_1.6.43-5_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-execnet all 2.1.1-1 [40.2 kB] Fetched 40.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpeu4fv5vi/python3-execnet_2.1.1-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libseccomp2 amd64 2.5.5-1 [47.0 kB] Fetched 47.0 kB in 0s (4640 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmps2cvhb3_/libseccomp2_2.5.5-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 pandoc-data all 3.1.3-2 [445 kB] Fetched 445 kB in 0s (1854 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpp8px_5rv/pandoc-data_3.1.3-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-toml all 0.10.2-1 [16.2 kB] Fetched 16.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9c_9pluy/python3-toml_0.10.2-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libcc1-0 amd64 14.1.0-3 [42.7 kB] Fetched 42.7 kB in 0s (246 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8dz_loj6/libcc1-0_14.1.0-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-tenacity all 8.4.2-1 [46.0 kB] Fetched 46.0 kB in 0s (246 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbmxbub1b/python3-tenacity_8.4.2-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-6 [56.9 kB] Fetched 56.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpe4khv5dp/libsasl2-2_2.1.28+dfsg1-6_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Fetched 103 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5rcla7vb/libexpat1_2.6.2-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 automake all 1:1.16.5-1.3 [823 kB] Fetched 823 kB in 0s (58.6 MB/s) dpkg-name: info: moved 'automake_1%3a1.16.5-1.3_all.deb' to '/srv/rebuilderd/tmp/tmps0jmle3s/automake_1.16.5-1.3_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-jupyter-client all 7.4.9-2 [103 kB] Fetched 103 kB in 0s (539 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpa8tuep30/python3-jupyter-client_7.4.9-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libxau6 amd64 1:1.0.9-1+b1 [18.1 kB] Fetched 18.1 kB in 0s (0 B/s) dpkg-name: info: moved 'libxau6_1%3a1.0.9-1+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmpv3vicmn1/libxau6_1.0.9-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 cpp-x86-64-linux-gnu amd64 4:13.2.0-7 [4724 B] Fetched 4724 B in 0s (0 B/s) dpkg-name: info: moved 'cpp-x86-64-linux-gnu_4%3a13.2.0-7_amd64.deb' to '/srv/rebuilderd/tmp/tmpwel7khhv/cpp-x86-64-linux-gnu_13.2.0-7_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libxml2 amd64 2.12.7+dfsg-3 [670 kB] Fetched 670 kB in 0s (53.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1kil7gtn/libxml2_2.12.7+dfsg-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python-babel-localedata all 2.14.0-1 [5701 kB] Fetched 5701 kB in 0s (13.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplf4p769z/python-babel-localedata_2.14.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libfreetype6 amd64 2.13.2+dfsg-1+b4 [439 kB] Fetched 439 kB in 0s (40.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpiy0uzthe/libfreetype6_2.13.2+dfsg-1+b4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libk5crypto3 amd64 1.21.2-1 [80.0 kB] Fetched 80.0 kB in 0s (406 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpenxmbf3k/libk5crypto3_1.21.2-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 readline-common all 8.2-4 [69.3 kB] Fetched 69.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpu13k6fw1/readline-common_8.2-4_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libopenjp2-7 amd64 2.5.0-2+b3 [190 kB] Fetched 190 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpz_z4ybi5/libopenjp2-7_2.5.0-2+b3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-json5 all 0.9.25-1 [21.9 kB] Fetched 21.9 kB in 0s (89.4 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2yknyiz1/python3-json5_0.9.25-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-stevedore all 5.2.0-2 [20.8 kB] Fetched 20.8 kB in 0s (124 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpz87itqrm/python3-stevedore_5.2.0-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libaudit-common all 1:3.1.2-4 [11.5 kB] Fetched 11.5 kB in 0s (0 B/s) dpkg-name: info: moved 'libaudit-common_1%3a3.1.2-4_all.deb' to '/srv/rebuilderd/tmp/tmpa2yx0cy2/libaudit-common_3.1.2-4_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libpython3.11t64 amd64 3.11.9-1 [1960 kB] Fetched 1960 kB in 0s (5236 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplxu6wy0l/libpython3.11t64_3.11.9-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Fetched 116 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpu9v1jnl1/libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-commonmark all 0.9.1-6 [45.3 kB] Fetched 45.3 kB in 0s (170 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmfubjk3c/python3-commonmark_0.9.1-6_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libuuid1 amd64 2.40.1-9 [34.9 kB] Fetched 34.9 kB in 0s (211 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd2wm2z8e/libuuid1_2.40.1-9_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Fetched 68.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4p9o4xur/libuchardet0_0.0.8-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libbinutils amd64 2.42.50.20240625-1 [523 kB] Fetched 523 kB in 0s (2092 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4kf1e4si/libbinutils_2.42.50.20240625-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libkrb5support0 amd64 1.21.2-1 [32.2 kB] Fetched 32.2 kB in 0s (191 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5owxc0fr/libkrb5support0_1.21.2-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libc-bin amd64 2.38-13 [613 kB] Fetched 613 kB in 0s (46.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8txh1rm7/libc-bin_2.38-13_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-nest-asyncio all 1.5.4-1 [6248 B] Fetched 6248 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpl9vcnt2j/python3-nest-asyncio_1.5.4-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-soupsieve all 2.5-1 [38.1 kB] Fetched 38.1 kB in 0s (206 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpf7govkk1/python3-soupsieve_2.5-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libgprofng0 amd64 2.42.50.20240625-1 [776 kB] Fetched 776 kB in 0s (1716 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpn5o5068d/libgprofng0_2.42.50.20240625-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-coverage amd64 7.2.7+dfsg1-1+b1 [170 kB] Fetched 170 kB in 0s (537 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpppyei4h2/python3-coverage_7.2.7+dfsg1-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 bash amd64 5.2.21-2.1 [1492 kB] Fetched 1492 kB in 0s (88.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp89_yfa8t/bash_5.2.21-2.1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 docutils-common all 0.20.1+dfsg-3 [128 kB] Fetched 128 kB in 1s (163 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpftsnsgjd/docutils-common_0.20.1+dfsg-3_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 build-essential amd64 12.10 [4516 B] Fetched 4516 B in 0s (202 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp16dkxcc0/build-essential_12.10_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-appdirs all 1.4.4-4 [12.5 kB] Fetched 12.5 kB in 0s (55.9 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmqxclbos/python3-appdirs_1.4.4-4_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-sniffio all 1.3.1-1 [7120 B] Fetched 7120 B in 1s (12.3 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjbubqd9g/python3-sniffio_1.3.1-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libjs-sphinxdoc all 7.3.7-3 [154 kB] Fetched 154 kB in 0s (381 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwbd5n_hm/libjs-sphinxdoc_7.3.7-3_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Fetched 2407 kB in 1s (4570 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4_cdrq1_/liblapack3_3.12.0-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libc6 amd64 2.38-13 [2775 kB] Fetched 2775 kB in 0s (112 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7ptu1456/libc6_2.38-13_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 x11-common all 1:7.7+23 [252 kB] Fetched 252 kB in 0s (24.7 MB/s) dpkg-name: info: moved 'x11-common_1%3a7.7+23_all.deb' to '/srv/rebuilderd/tmp/tmpqwpxfvq0/x11-common_7.7+23_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Fetched 58.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyo63gtju/python3-snowballstemmer_2.2.0-4_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-tomli-w all 1.0.0-2 [8012 B] Fetched 8012 B in 0s (47.6 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpa2zb2qwt/python3-tomli-w_1.0.0-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 sysvinit-utils amd64 3.09-2 [32.5 kB] Fetched 32.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0w551h47/sysvinit-utils_3.09-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libjpeg62-turbo amd64 1:2.1.5-3 [167 kB] Fetched 167 kB in 0s (12.4 MB/s) dpkg-name: info: moved 'libjpeg62-turbo_1%3a2.1.5-3_amd64.deb' to '/srv/rebuilderd/tmp/tmpkn6op108/libjpeg62-turbo_2.1.5-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libcrypt-dev amd64 1:4.4.36-4 [119 kB] Fetched 119 kB in 0s (0 B/s) dpkg-name: info: moved 'libcrypt-dev_1%3a4.4.36-4_amd64.deb' to '/srv/rebuilderd/tmp/tmp2k0wuj7q/libcrypt-dev_4.4.36-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-distutils all 3.12.3-3.1 [131 kB] Fetched 131 kB in 0s (691 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpj90soz1d/python3-distutils_3.12.3-3.1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-hatchling all 1.25.0-1 [53.8 kB] Fetched 53.8 kB in 0s (214 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkdh4ts9k/python3-hatchling_1.25.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 flit all 3.9.0-2 [93.4 kB] Fetched 93.4 kB in 0s (565 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpabyosug2/flit_3.9.0-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-cffi-backend amd64 1.16.0-2+b2 [112 kB] Fetched 112 kB in 0s (533 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8qirfyhx/python3-cffi-backend_1.16.0-2+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-charset-normalizer all 3.3.2-1 [51.6 kB] Fetched 51.6 kB in 0s (265 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_lygld83/python3-charset-normalizer_3.3.2-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-roman all 3.3-3 [9880 B] Fetched 9880 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpnjbireb8/python3-roman_3.3-3_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 sgml-base all 1.31 [15.4 kB] Fetched 15.4 kB in 0s (1420 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpih6yu1so/sgml-base_1.31_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [162 kB] Fetched 162 kB in 0s (13.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfixpkbox/fonts-glyphicons-halflings_1.009~3.4.1+dfsg-3_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 diffutils amd64 1:3.10-1 [375 kB] Fetched 375 kB in 0s (32.3 MB/s) dpkg-name: info: moved 'diffutils_1%3a3.10-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpzfczwdi9/diffutils_3.10-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 ncurses-base all 6.5-2 [270 kB] Fetched 270 kB in 0s (25.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4aoxkouk/ncurses-base_6.5-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 pybuild-plugin-pyproject all 6.20240603 [11.2 kB] Fetched 11.2 kB in 0s (87.3 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjicaqwxl/pybuild-plugin-pyproject_6.20240603_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-scipy amd64 1.12.0-2 [21.0 MB] Fetched 21.0 MB in 0s (44.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwwzwfrnk/python3-scipy_1.12.0-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libtinfo6 amd64 6.5-2 [344 kB] Fetched 344 kB in 0s (32.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1o2krox1/libtinfo6_6.5-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 tar amd64 1.35+dfsg-3 [813 kB] Fetched 813 kB in 0s (60.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2fp8pfld/tar_1.35+dfsg-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 gcc-13-x86-64-linux-gnu amd64 13.3.0-1 [19.2 MB] Fetched 19.2 MB in 0s (67.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp69cvcy9z/gcc-13-x86-64-linux-gnu_13.3.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-docutils all 0.20.1+dfsg-3 [389 kB] Fetched 389 kB in 0s (2450 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp17_kidlf/python3-docutils_0.20.1+dfsg-3_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-typing-extensions all 4.12.2-1 [72.9 kB] Fetched 72.9 kB in 0s (514 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpez86txju/python3-typing-extensions_4.12.2-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libpython3.12-dev amd64 3.12.4-1 [5067 kB] Fetched 5067 kB in 0s (13.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqeahueuo/libpython3.12-dev_3.12.4-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-pytest all 8.2.2-2 [248 kB] Fetched 248 kB in 0s (1441 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmr7qaida/python3-pytest_8.2.2-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-nbconvert all 7.16.4-1 [175 kB] Fetched 175 kB in 0s (860 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0tocb3tf/python3-nbconvert_7.16.4-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libnghttp2-14 amd64 1.62.1-1 [75.5 kB] Fetched 75.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjb28fb0z/libnghttp2-14_1.62.1-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-babel all 2.14.0-1 [111 kB] Fetched 111 kB in 0s (669 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwvttkcwl/python3-babel_2.14.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 man-db amd64 2.12.1-2 [1411 kB] Fetched 1411 kB in 0s (84.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptf6c66zt/man-db_2.12.1-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 architecture-properties amd64 0.1.1+b1 [1888 B] Fetched 1888 B in 0s (13.8 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqobzeof7/architecture-properties_0.1.1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-requests all 2.32.3+dfsg-1 [71.9 kB] Fetched 71.9 kB in 0s (482 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxzdo5y6u/python3-requests_2.32.3+dfsg-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 m4 amd64 1.4.19-4 [287 kB] Fetched 287 kB in 0s (27.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpy6ildpvx/m4_1.4.19-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-jupyter-server all 1.23.3-2 [165 kB] Fetched 165 kB in 0s (1074 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbs60pwnw/python3-jupyter-server_1.23.3-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-markupsafe amd64 2.1.5-1 [14.5 kB] Fetched 14.5 kB in 0s (124 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxvqktoiu/python3-markupsafe_2.1.5-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libstdc++6 amd64 14.1.0-3 [713 kB] Fetched 713 kB in 0s (4458 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkdqawvab/libstdc++6_14.1.0-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libtiff6 amd64 4.5.1+git230720-4 [322 kB] Fetched 322 kB in 0s (29.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp885sx63z/libtiff6_4.5.1+git230720-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libacl1 amd64 2.3.2-2 [32.4 kB] Fetched 32.4 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvh_p7vff/libacl1_2.3.2-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-cycler all 0.12.1-1 [9496 B] Fetched 9496 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpi67huz01/python3-cycler_0.12.1-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libjbig0 amd64 2.1-6.1+b1 [32.0 kB] Fetched 32.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4tqp_jzd/libjbig0_2.1-6.1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-sphinx-bootstrap-theme all 0.8.1-5 [422 kB] Fetched 422 kB in 0s (1469 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpv45kthlk/python3-sphinx-bootstrap-theme_0.8.1-5_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libpython3.11-stdlib amd64 3.11.9-1 [1792 kB] Fetched 1792 kB in 0s (10.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptrp2bliq/libpython3.11-stdlib_3.11.9-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libpython3.11-dev amd64 3.11.9-1 [4513 kB] Fetched 4513 kB in 0s (17.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpv6xou31m/libpython3.11-dev_3.11.9-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libtool all 2.4.7-7 [517 kB] Fetched 517 kB in 0s (43.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9w72tdau/libtool_2.4.7-7_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Fetched 19.5 kB in 0s (1947 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7gosh941/libfile-stripnondeterminism-perl_1.14.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-dev amd64 3.12.2-1 [26.2 kB] Fetched 26.2 kB in 0s (152 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpk3lyv033/python3-dev_3.12.2-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-send2trash all 1.8.2-1 [16.5 kB] Fetched 16.5 kB in 0s (145 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpr4iyor4_/python3-send2trash_1.8.2-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libglib2.0-0t64 amd64 2.80.3-1 [1485 kB] Fetched 1485 kB in 0s (81.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpixaa7jyv/libglib2.0-0t64_2.80.3-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Fetched 148 kB in 0s (13.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpn74dvj8g/libblas3_3.12.0-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 sphinx-common all 7.3.7-3 [731 kB] Fetched 731 kB in 0s (4395 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpee0xjbqr/sphinx-common_7.3.7-3_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libxslt1.1 amd64 1.1.35-1+b1 [232 kB] Fetched 232 kB in 0s (901 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6usx3c6s/libxslt1.1_1.1.35-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libxss1 amd64 1:1.2.3-1+b1 [17.0 kB] Fetched 17.0 kB in 0s (0 B/s) dpkg-name: info: moved 'libxss1_1%3a1.2.3-1+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmpavy1whpl/libxss1_1.2.3-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Fetched 250 kB in 0s (24.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2rdlo1i1/libjs-jquery-ui_1.13.2+dfsg-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-pbr all 6.0.0-2 [55.8 kB] Fetched 55.8 kB in 0s (287 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_wmq5ftg/python3-pbr_6.0.0-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libjs-jquery-isonscreen all 1.2.0-1.1 [3196 B] Fetched 3196 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzi1de2c4/libjs-jquery-isonscreen_1.2.0-1.1_all.deb' Downloading dependency 1 of 425: unicode-data:amd64=15.1.0-1 Downloading dependency 2 of 425: python3-webencodings:amd64=0.5.1-5 Downloading dependency 3 of 425: python3.11-dev:amd64=3.11.9-1 Downloading dependency 4 of 425: libunistring5:amd64=1.2-1 Downloading dependency 5 of 425: libllvm14t64:amd64=1:14.0.6-20 Downloading dependency 6 of 425: python3-build:amd64=1.2.1-1 Downloading dependency 7 of 425: libexpat1-dev:amd64=2.6.2-1 Downloading dependency 8 of 425: python3-pil:amd64=10.3.0-2 Downloading dependency 9 of 425: libkeyutils1:amd64=1.6.3-3 Downloading dependency 10 of 425: python3.11-minimal:amd64=3.11.9-1 Downloading dependency 11 of 425: libblkid1:amd64=2.40.1-9 Downloading dependency 12 of 425: g++-13:amd64=13.3.0-1 Downloading dependency 13 of 425: dpkg:amd64=1.22.6 Downloading dependency 14 of 425: python3-dateutil:amd64=2.9.0-2 Downloading dependency 15 of 425: liblz4-1:amd64=1.9.4-2 Downloading dependency 16 of 425: python3-pytest-xdist:amd64=3.6.1-1 Downloading dependency 17 of 425: libgssapi-krb5-2:amd64=1.21.2-1 Downloading dependency 18 of 425: base-files:amd64=13.3 Downloading dependency 19 of 425: python3-tabulate:amd64=0.9.0-1 Downloading dependency 20 of 425: blt:amd64=2.5.3+dfsg-7 Downloading dependency 21 of 425: python-tinycss2-common:amd64=1.3.0-1 Downloading dependency 22 of 425: libcurl4t64:amd64=8.8.0-2 Downloading dependency 23 of 425: python3-decorator:amd64=5.1.1-5 Downloading dependency 24 of 425: libpam0g:amd64=1.5.3-7 Downloading dependency 25 of 425: python3-isort:amd64=5.6.4-1 Downloading dependency 26 of 425: liblerc4:amd64=4.0.0+ds-4+b1 Downloading dependency 27 of 425: file:amd64=1:5.45-3 Downloading dependency 28 of 425: python3-minimal:amd64=3.12.2-1 Downloading dependency 29 of 425: python3-setuptools-scm:amd64=8.1.0-1 Downloading dependency 30 of 425: libpam-runtime:amd64=1.5.3-7 Downloading dependency 31 of 425: coreutils:amd64=9.4-3.1 Downloading dependency 32 of 425: libpng16-16t64:amd64=1.6.43-5 Downloading dependency 33 of 425: python3-execnet:amd64=2.1.1-1 Downloading dependency 34 of 425: libseccomp2:amd64=2.5.5-1 Downloading dependency 35 of 425: pandoc-data:amd64=3.1.3-2 Downloading dependency 36 of 425: python3-toml:amd64=0.10.2-1 Downloading dependency 37 of 425: libcc1-0:amd64=14.1.0-3 Downloading dependency 38 of 425: python3-tenacity:amd64=8.4.2-1 Downloading dependency 39 of 425: libsasl2-2:amd64=2.1.28+dfsg1-6 Downloading dependency 40 of 425: libexpat1:amd64=2.6.2-1 Downloading dependency 41 of 425: automake:amd64=1:1.16.5-1.3 Downloading dependency 42 of 425: python3-jupyter-client:amd64=7.4.9-2 Downloading dependency 43 of 425: libxau6:amd64=1:1.0.9-1+b1 Downloading dependency 44 of 425: cpp-x86-64-linux-gnu:amd64=4:13.2.0-7 Downloading dependency 45 of 425: libxml2:amd64=2.12.7+dfsg-3 Downloading dependency 46 of 425: python-babel-localedata:amd64=2.14.0-1 Downloading dependency 47 of 425: libfreetype6:amd64=2.13.2+dfsg-1+b4 Downloading dependency 48 of 425: libk5crypto3:amd64=1.21.2-1 Downloading dependency 49 of 425: readline-common:amd64=8.2-4 Downloading dependency 50 of 425: libopenjp2-7:amd64=2.5.0-2+b3 Downloading dependency 51 of 425: python3-json5:amd64=0.9.25-1 Downloading dependency 52 of 425: python3-stevedore:amd64=5.2.0-2 Downloading dependency 53 of 425: libaudit-common:amd64=1:3.1.2-4 Downloading dependency 54 of 425: libpython3.11t64:amd64=3.11.9-1 Downloading dependency 55 of 425: libjs-underscore:amd64=1.13.4~dfsg+~1.11.4-3 Downloading dependency 56 of 425: python3-commonmark:amd64=0.9.1-6 Downloading dependency 57 of 425: libuuid1:amd64=2.40.1-9 Downloading dependency 58 of 425: libuchardet0:amd64=0.0.8-1+b1 Downloading dependency 59 of 425: libbinutils:amd64=2.42.50.20240625-1 Downloading dependency 60 of 425: libkrb5support0:amd64=1.21.2-1 Downloading dependency 61 of 425: libc-bin:amd64=2.38-13 Downloading dependency 62 of 425: python3-nest-asyncio:amd64=1.5.4-1 Downloading dependency 63 of 425: python3-soupsieve:amd64=2.5-1 Downloading dependency 64 of 425: libgprofng0:amd64=2.42.50.20240625-1 Downloading dependency 65 of 425: python3-coverage:amd64=7.2.7+dfsg1-1+b1 Downloading dependency 66 of 425: bash:amd64=5.2.21-2.1 Downloading dependency 67 of 425: docutils-common:amd64=0.20.1+dfsg-3 Downloading dependency 68 of 425: build-essential:amd64=12.10 Downloading dependency 69 of 425: python3-appdirs:amd64=1.4.4-4 Downloading dependency 70 of 425: python3-sniffio:amd64=1.3.1-1 Downloading dependency 71 of 425: libjs-sphinxdoc:amd64=7.3.7-3 Downloading dependency 72 of 425: liblapack3:amd64=3.12.0-3 Downloading dependency 73 of 425: libc6:amd64=2.38-13 Downloading dependency 74 of 425: x11-common:amd64=1:7.7+23 Downloading dependency 75 of 425: python3-snowballstemmer:amd64=2.2.0-4 Downloading dependency 76 of 425: python3-tomli-w:amd64=1.0.0-2 Downloading dependency 77 of 425: sysvinit-utils:amd64=3.09-2 Downloading dependency 78 of 425: libjpeg62-turbo:amd64=1:2.1.5-3 Downloading dependency 79 of 425: libcrypt-dev:amd64=1:4.4.36-4 Downloading dependency 80 of 425: python3-distutils:amd64=3.12.3-3.1 Downloading dependency 81 of 425: python3-hatchling:amd64=1.25.0-1 Downloading dependency 82 of 425: flit:amd64=3.9.0-2 Downloading dependency 83 of 425: python3-cffi-backend:amd64=1.16.0-2+b2 Downloading dependency 84 of 425: python3-charset-normalizer:amd64=3.3.2-1 Downloading dependency 85 of 425: python3-roman:amd64=3.3-3 Downloading dependency 86 of 425: sgml-base:amd64=1.31 Downloading dependency 87 of 425: fonts-glyphicons-halflings:amd64=1.009~3.4.1+dfsg-3 Downloading dependency 88 of 425: diffutils:amd64=1:3.10-1 Downloading dependency 89 of 425: ncurses-base:amd64=6.5-2 Downloading dependency 90 of 425: pybuild-plugin-pyproject:amd64=6.20240603 Downloading dependency 91 of 425: python3-scipy:amd64=1.12.0-2 Downloading dependency 92 of 425: libtinfo6:amd64=6.5-2 Downloading dependency 93 of 425: tar:amd64=1.35+dfsg-3 Downloading dependency 94 of 425: gcc-13-x86-64-linux-gnu:amd64=13.3.0-1 Downloading dependency 95 of 425: python3-docutils:amd64=0.20.1+dfsg-3 Downloading dependency 96 of 425: python3-typing-extensions:amd64=4.12.2-1 Downloading dependency 97 of 425: libpython3.12-dev:amd64=3.12.4-1 Downloading dependency 98 of 425: python3-pytest:amd64=8.2.2-2 Downloading dependency 99 of 425: python3-nbconvert:amd64=7.16.4-1 Downloading dependency 100 of 425: libnghttp2-14:amd64=1.62.1-1 Downloading dependency 101 of 425: python3-babel:amd64=2.14.0-1 Downloading dependency 102 of 425: man-db:amd64=2.12.1-2 Downloading dependency 103 of 425: architecture-properties:amd64=0.1.1+b1 Downloading dependency 104 of 425: python3-requests:amd64=2.32.3+dfsg-1 Downloading dependency 105 of 425: m4:amd64=1.4.19-4 Downloading dependency 106 of 425: python3-jupyter-server:amd64=1.23.3-2 Downloading dependency 107 of 425: python3-markupsafe:amd64=2.1.5-1 Downloading dependency 108 of 425: libstdc++6:amd64=14.1.0-3 Downloading dependency 109 of 425: libtiff6:amd64=4.5.1+git230720-4 Downloading dependency 110 of 425: libacl1:amd64=2.3.2-2 Downloading dependency 111 of 425: python3-cycler:amd64=0.12.1-1 Downloading dependency 112 of 425: libjbig0:amd64=2.1-6.1+b1 Downloading dependency 113 of 425: python3-sphinx-bootstrap-theme:amd64=0.8.1-5 Downloading dependency 114 of 425: libpython3.11-stdlib:amd64=3.11.9-1 Downloading dependency 115 of 425: libpython3.11-dev:amd64=3.11.9-1 Downloading dependency 116 of 425: libtool:amd64=2.4.7-7 Downloading dependency 117 of 425: libfile-stripnondeterminism-perl:amd64=1.14.0-1 Downloading dependency 118 of 425: python3-dev:amd64=3.12.2-1 Downloading dependency 119 of 425: python3-send2trash:amd64=1.8.2-1 Downloading dependency 120 of 425: libglib2.0-0t64:amd64=2.80.3-1 Downloading dependency 121 of 425: libblas3:amd64=3.12.0-3 Downloading dependency 122 of 425: sphinx-common:amd64=7.3.7-3 Downloading dependency 123 of 425: libxslt1.1:amd64=1.1.35-1+b1 Downloading dependency 124 of 425: libxss1:amd64=1:1.2.3-1+b1 Downloading dependency 125 of 425: libjs-jquery-ui:amd64=1.13.2+dfsg-1 Downloading dependency 126 of 425: python3-pbr:amd64=6.0.0-2 Downloading dependency 127 of 425: libjs-jquery-isonscreen:amd64=1.2.0-1.1 Downloading dependency 128 of 425: libtbb12:amd64=2021.11.0-2Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libtbb12 amd64 2021.11.0-2 [87.6 kB] Fetched 87.6 kB in 0s (382 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9v9pzume/libtbb12_2021.11.0-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libjs-jquery-throttle-debounce all 1.1+dfsg.1-2 [12.2 kB] Fetched 12.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpc107h6y6/libjs-jquery-throttle-debounce_1.1+dfsg.1-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-pytest-cov all 5.0.0-1 [26.8 kB] Fetched 26.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpf9mer03a/python3-pytest-cov_5.0.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-ufolib2 all 0.16.0+dfsg1-1 [32.9 kB] Fetched 32.9 kB in 0s (250 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsuz68c_6/python3-ufolib2_0.16.0+dfsg1-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-pkg-resources all 68.1.2-2 [241 kB] Fetched 241 kB in 0s (18.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmph0afb832/python3-pkg-resources_68.1.2-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libgnutls30t64 amd64 3.8.5-4 [1437 kB] Fetched 1437 kB in 0s (78.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbz1q1sd3/libgnutls30t64_3.8.5-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python-matplotlib-data all 3.6.3-2 [2744 kB] Fetched 2744 kB in 0s (8371 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3wlmvfu_/python-matplotlib-data_3.6.3-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libp11-kit0 amd64 0.25.3-5 [417 kB] Fetched 417 kB in 0s (37.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpr3oly0ix/libp11-kit0_0.25.3-5_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 cpp-13-x86-64-linux-gnu amd64 13.3.0-1 [9931 kB] Fetched 9931 kB in 0s (40.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4bokbb16/cpp-13-x86-64-linux-gnu_13.3.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-fs all 2.4.16-4 [95.4 kB] Fetched 95.4 kB in 0s (230 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4wu8r_ms/python3-fs_2.4.16-4_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 sensible-utils all 0.0.24 [24.8 kB] Fetched 24.8 kB in 0s (2432 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprg59bd0a/sensible-utils_0.0.24_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libpam-modules-bin amd64 1.5.3-7 [54.4 kB] Fetched 54.4 kB in 0s (5276 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpuw8ut5yi/libpam-modules-bin_1.5.3-7_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-imagesize all 1.4.1-1 [6688 B] Fetched 6688 B in 0s (599 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4b5i1rvu/python3-imagesize_1.4.1-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-pybtex-docutils all 1.0.2-1 [8064 B] Fetched 8064 B in 0s (69.9 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppbb3b8do/python3-pybtex-docutils_1.0.2-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 rpcsvc-proto amd64 1.4.3-1 [63.3 kB] Fetched 63.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcf03sh6q/rpcsvc-proto_1.4.3-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 g++-x86-64-linux-gnu amd64 4:13.2.0-7 [1200 B] Fetched 1200 B in 0s (95.7 kB/s) dpkg-name: info: moved 'g++-x86-64-linux-gnu_4%3a13.2.0-7_amd64.deb' to '/srv/rebuilderd/tmp/tmpxur6jwol/g++-x86-64-linux-gnu_13.2.0-7_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 binutils-x86-64-linux-gnu amd64 2.42.50.20240625-1 [2235 kB] Fetched 2235 kB in 0s (7629 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprzkyaoew/binutils-x86-64-linux-gnu_2.42.50.20240625-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Fetched 489 kB in 0s (38.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpv52jea2n/fonts-dejavu-mono_2.37-8_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240712T203746Z sid/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Fetched 1181 kB in 0s (76.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8or_6bac/groff-base_1.23.0-5_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libpcre2-8-0 amd64 10.42-4+b1 [262 kB] Fetched 262 kB in 0s (25.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplpua821n/libpcre2-8-0_10.42-4+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libx11-6 amd64 2:1.8.7-1+b1 [799 kB] Fetched 799 kB in 0s (57.5 MB/s) dpkg-name: info: moved 'libx11-6_2%3a1.8.7-1+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmpipejg9xk/libx11-6_1.8.7-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libtasn1-6 amd64 4.19.0-3+b2 [48.9 kB] Fetched 48.9 kB in 0s (4286 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpehg4euvj/libtasn1-6_4.19.0-3+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libgmp10 amd64 2:6.3.0+dfsg-2+b1 [559 kB] Fetched 559 kB in 0s (42.8 MB/s) dpkg-name: info: moved 'libgmp10_2%3a6.3.0+dfsg-2+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmpzqvgxcet/libgmp10_6.3.0+dfsg-2+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 openssl amd64 3.2.2-1 [1364 kB] Fetched 1364 kB in 0s (82.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptkz0li0z/openssl_3.2.2-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libzstd1 amd64 1.5.6+dfsg-1 [303 kB] Fetched 303 kB in 0s (25.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwv1xtlfk/libzstd1_1.5.6+dfsg-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 ncurses-bin amd64 6.5-2 [433 kB] Fetched 433 kB in 0s (36.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_ao5koeq/ncurses-bin_6.5-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 gcc-13 amd64 13.3.0-1 [492 kB] Fetched 492 kB in 0s (2970 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpga9xz3e2/gcc-13_13.3.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 debianutils amd64 5.19 [89.3 kB] Fetched 89.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzwqu291w/debianutils_5.19_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libtbbbind-2-5 amd64 2021.11.0-2 [14.1 kB] Fetched 14.1 kB in 0s (104 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpu860l0s_/libtbbbind-2-5_2021.11.0-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libpython3-stdlib amd64 3.12.2-1 [9432 B] Fetched 9432 B in 0s (74.6 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpydv8dvow/libpython3-stdlib_3.12.2-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-brotli amd64 1.1.0-2+b3 [312 kB] Fetched 312 kB in 0s (2155 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3hdz6vkm/python3-brotli_1.1.0-2+b3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libjs-jquery-tablesorter all 1:2.31.3+dfsg1-3 [184 kB] Fetched 184 kB in 0s (792 kB/s) dpkg-name: info: moved 'libjs-jquery-tablesorter_1%3a2.31.3+dfsg1-3_all.deb' to '/srv/rebuilderd/tmp/tmp0dlexpl4/libjs-jquery-tablesorter_2.31.3+dfsg1-3_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-bs4 all 4.12.3-1 [133 kB] Fetched 133 kB in 0s (325 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5eu2pqfk/python3-bs4_4.12.3-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-prometheus-client all 0.19.0+ds1-1 [35.0 kB] Fetched 35.0 kB in 0s (133 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpiptofy6q/python3-prometheus-client_0.19.0+ds1-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 bsdutils amd64 1:2.40.1-9 [104 kB] Fetched 104 kB in 0s (546 kB/s) dpkg-name: info: moved 'bsdutils_1%3a2.40.1-9_amd64.deb' to '/srv/rebuilderd/tmp/tmp_325xn7p/bsdutils_2.40.1-9_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libcom-err2 amd64 1.47.1-1 [22.9 kB] Fetched 22.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpk6dqyu3p/libcom-err2_1.47.1-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3.12 amd64 3.12.4-1 [664 kB] Fetched 664 kB in 0s (3799 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqu3v8v09/python3.12_3.12.4-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Fetched 840 kB in 0s (64.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxqn8hr69/fonts-dejavu-core_2.37-8_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Fetched 328 kB in 0s (26.0 MB/s) dpkg-name: info: moved 'libx11-data_2%3a1.8.7-1_all.deb' to '/srv/rebuilderd/tmp/tmp8d2ec132/libx11-data_1.8.7-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-pil.imagetk amd64 10.3.0-2 [79.5 kB] Fetched 79.5 kB in 0s (649 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2g2qwwnn/python3-pil.imagetk_10.3.0-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-jupyterlab-server all 2.25.2-1 [50.9 kB] Fetched 50.9 kB in 0s (254 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp57surpey/python3-jupyterlab-server_2.25.2-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-tz all 2024.1-2 [30.9 kB] Fetched 30.9 kB in 0s (180 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpino_vohf/python3-tz_2024.1-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-pydata-sphinx-theme all 0.15.2.is.0.7.2-1 [1076 kB] Fetched 1076 kB in 0s (3552 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpx4zbq8x9/python3-pydata-sphinx-theme_0.15.2.is.0.7.2-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 cpp-13 amd64 13.3.0-1 [1276 B] Fetched 1276 B in 0s (10.4 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2n902joy/cpp-13_13.3.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libwebpmux3 amd64 1.4.0-0.1 [123 kB] Fetched 123 kB in 0s (12.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpq7iuqhix/libwebpmux3_1.4.0-0.1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libz3-4 amd64 4.8.12-3.1+b2 [7346 kB] Fetched 7346 kB in 0s (139 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpszk7enwo/libz3-4_4.8.12-3.1+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 perl-modules-5.38 all 5.38.2-5 [2905 kB] Fetched 2905 kB in 0s (114 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqfi8x7ko/perl-modules-5.38_5.38.2-5_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 util-linux amd64 2.40.1-9 [1209 kB] Fetched 1209 kB in 0s (4923 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwojr7eza/util-linux_2.40.1-9_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libcrypt1 amd64 1:4.4.36-4 [89.8 kB] Fetched 89.8 kB in 0s (0 B/s) dpkg-name: info: moved 'libcrypt1_1%3a4.4.36-4_amd64.deb' to '/srv/rebuilderd/tmp/tmp_lbb8con/libcrypt1_4.4.36-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libhwloc15 amd64 2.11.0-2 [162 kB] Fetched 162 kB in 0s (1158 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2c5fgia5/libhwloc15_2.11.0-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libtbbmalloc2 amd64 2021.11.0-2 [48.6 kB] Fetched 48.6 kB in 0s (248 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1rvmrd1o/libtbbmalloc2_2021.11.0-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libisl23 amd64 0.26-3+b2 [652 kB] Fetched 652 kB in 0s (49.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7mb6axcz/libisl23_0.26-3+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 liblzma5 amd64 5.6.2-1 [254 kB] Fetched 254 kB in 0s (24.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppehjfpq9/liblzma5_5.6.2-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-sphinxcontrib.bibtex all 2.6.2-1 [32.4 kB] Fetched 32.4 kB in 0s (247 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphmelud2q/python3-sphinxcontrib.bibtex_2.6.2-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libgdbm-compat4t64 amd64 1.23-6 [48.7 kB] Fetched 48.7 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2qto7bsq/libgdbm-compat4t64_1.23-6_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Fetched 58.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7f_ms78n/librtmp1_2.4+20151223.gitfa8646d.1-2+b4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libssl3t64 amd64 3.2.2-1 [2246 kB] Fetched 2246 kB in 0s (101 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpt9bkoita/libssl3t64_3.2.2-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Fetched 107 kB in 0s (821 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpc7x_8jis/python3-chardet_5.2.0+dfsg-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-pyparsing all 3.1.2-1 [146 kB] Fetched 146 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd6uv4leu/python3-pyparsing_3.1.2-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 linux-libc-dev all 6.9.7-1 [2338 kB] Fetched 2338 kB in 0s (11.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppuhwd_vv/linux-libc-dev_6.9.7-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-all-dev amd64 3.12.2-1 [1080 B] Fetched 1080 B in 0s (6859 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpw00py45y/python3-all-dev_3.12.2-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libc-dev-bin amd64 2.38-13 [50.3 kB] Fetched 50.3 kB in 0s (4312 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdw7fwg1m/libc-dev-bin_2.38-13_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-pathspec all 0.12.1-1 [28.1 kB] Fetched 28.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpl9k9g243/python3-pathspec_0.12.1-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 binutils amd64 2.42.50.20240625-1 [81.0 kB] Fetched 81.0 kB in 0s (440 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpz14zmm_b/binutils_2.42.50.20240625-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libfribidi0 amd64 1.0.13-3+b1 [71.4 kB] Fetched 71.4 kB in 0s (6255 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1gfghoja/libfribidi0_1.0.13-3+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-argon2 amd64 21.1.0-2 [22.8 kB] Fetched 22.8 kB in 0s (153 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdmgkam2t/python3-argon2_21.1.0-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libffi8 amd64 3.4.6-1 [23.6 kB] Fetched 23.6 kB in 0s (2153 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpa3gsnjhi/libffi8_3.4.6-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-tornado amd64 6.4.1-1 [348 kB] Fetched 348 kB in 0s (1277 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbybnv65k/python3-tornado_6.4.1-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-pandocfilters all 1.5.1-1 [23.7 kB] Fetched 23.7 kB in 0s (2243 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptf9s4uc0/python3-pandocfilters_1.5.1-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libxft2 amd64 2.3.6-1+b1 [54.2 kB] Fetched 54.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6k15e958/libxft2_2.3.6-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-numba amd64 0.59.1+dfsg-1 [1767 kB] Fetched 1767 kB in 0s (4809 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpo1lnpznl/python3-numba_0.59.1+dfsg-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Fetched 105 kB in 0s (9196 kB/s) dpkg-name: info: moved 'libmagic1t64_1%3a5.45-3_amd64.deb' to '/srv/rebuilderd/tmp/tmpe5r7i6nx/libmagic1t64_5.45-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libssh2-1t64 amd64 1.11.0-5 [215 kB] Fetched 215 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwguy0nfk/libssh2-1t64_1.11.0-5_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-jupyterlab-pygments all 0.2.2-3 [6096 B] Fetched 6096 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6pyxxdfk/python3-jupyterlab-pygments_0.2.2-3_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 g++-13-x86-64-linux-gnu amd64 13.3.0-1 [10.9 MB] Fetched 10.9 MB in 1s (15.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpljyrkiul/g++-13-x86-64-linux-gnu_13.3.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-numpy amd64 1:1.26.4+ds-10 [5465 kB] Fetched 5465 kB in 0s (15.8 MB/s) dpkg-name: info: moved 'python3-numpy_1%3a1.26.4+ds-10_amd64.deb' to '/srv/rebuilderd/tmp/tmp006p_ib1/python3-numpy_1.26.4+ds-10_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-nbsphinx all 0.9.4+ds-1 [39.5 kB] Fetched 39.5 kB in 0s (295 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpc6w4_v8c/python3-nbsphinx_0.9.4+ds-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Fetched 326 kB in 0s (30.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptizncr9_/libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-mpmath all 1.3.0-1 [419 kB] Fetched 419 kB in 0s (36.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpextcx_ft/python3-mpmath_1.3.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-rpds-py amd64 0.12.0-3 [276 kB] Fetched 276 kB in 0s (1976 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvqixz90e/python3-rpds-py_0.12.0-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1 [919 kB] Fetched 919 kB in 0s (71.0 MB/s) dpkg-name: info: moved 'zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpqhkv1avw/zlib1g-dev_1.3.dfsg+really1.3.1-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libitm1 amd64 14.1.0-3 [25.8 kB] Fetched 25.8 kB in 0s (113 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmocppjcb/libitm1_14.1.0-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libgpg-error0 amd64 1.49-2 [79.9 kB] Fetched 79.9 kB in 0s (662 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpj79hzi_8/libgpg-error0_1.49-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libpython3.11-minimal amd64 3.11.9-1 [817 kB] Fetched 817 kB in 0s (5494 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpp0iewnco/libpython3.11-minimal_3.11.9-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 fontconfig-config amd64 2.15.0-1.1 [317 kB] Fetched 317 kB in 0s (27.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprtnbpzk9/fontconfig-config_2.15.0-1.1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Fetched 27.9 kB in 0s (2549 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpd5cakzxl/python3-alabaster_0.7.16-0.1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libfontconfig1 amd64 2.15.0-1.1 [388 kB] Fetched 388 kB in 0s (30.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpobrjpkme/libfontconfig1_2.15.0-1.1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libbsd0 amd64 0.12.2-1 [131 kB] Fetched 131 kB in 0s (11.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptmrtsc34/libbsd0_0.12.2-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libjansson4 amd64 2.14-2+b2 [39.9 kB] Fetched 39.9 kB in 0s (3693 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0cvyx3wx/libjansson4_2.14-2+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-lz4 amd64 4.0.2+dfsg-1+b3 [25.5 kB] Fetched 25.5 kB in 0s (115 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpeosdvj7m/python3-lz4_4.0.2+dfsg-1+b3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 cython3 amd64 3.0.10+dfsg-5 [3571 kB] Fetched 3571 kB in 0s (11.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9hmhtxjv/cython3_3.0.10+dfsg-5_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 autotools-dev all 20220109.1 [51.6 kB] Fetched 51.6 kB in 0s (4917 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3gw166v2/autotools-dev_20220109.1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 gcc-x86-64-linux-gnu amd64 4:13.2.0-7 [1440 B] Fetched 1440 B in 0s (0 B/s) dpkg-name: info: moved 'gcc-x86-64-linux-gnu_4%3a13.2.0-7_amd64.deb' to '/srv/rebuilderd/tmp/tmpyis8zfcm/gcc-x86-64-linux-gnu_13.2.0-7_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-tinycss2 all 1.3.0-1 [22.1 kB] Fetched 22.1 kB in 0s (67.0 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprjex9pgv/python3-tinycss2_1.3.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libsmartcols1 amd64 2.40.1-9 [138 kB] Fetched 138 kB in 0s (873 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmy_rb_mx/libsmartcols1_2.40.1-9_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libnettle8t64 amd64 3.10-1 [303 kB] Fetched 303 kB in 0s (24.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcxoeujq4/libnettle8t64_3.10-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-nbclient all 0.8.0-1 [64.0 kB] Fetched 64.0 kB in 0s (261 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpj92e7rj2/python3-nbclient_0.8.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-wheel all 0.43.0-1 [52.5 kB] Fetched 52.5 kB in 0s (388 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqzd10rst/python3-wheel_0.43.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libkrb5-3 amd64 1.21.2-1 [324 kB] Fetched 324 kB in 0s (2192 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpdd1sxr9m/libkrb5-3_1.21.2-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 llvm-14 amd64 1:14.0.6-20 [11.8 MB] Fetched 11.8 MB in 1s (11.1 MB/s) dpkg-name: info: moved 'llvm-14_1%3a14.0.6-20_amd64.deb' to '/srv/rebuilderd/tmp/tmpvn_htzgs/llvm-14_14.0.6-20_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-certifi all 2024.6.2-1 [157 kB] Fetched 157 kB in 0s (880 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpr7xvmrkk/python3-certifi_2024.6.2-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-iniconfig all 1.1.1-2 [6396 B] Fetched 6396 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmps_wuypam/python3-iniconfig_1.1.1-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libbz2-1.0 amd64 1.0.8-5.1 [38.0 kB] Fetched 38.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6qy7qgx5/libbz2-1.0_1.0.8-5.1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 debhelper all 13.16 [891 kB] Fetched 891 kB in 0s (59.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptoome7h8/debhelper_13.16_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3 amd64 3.12.2-1 [27.5 kB] Fetched 27.5 kB in 0s (137 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpksl_tlxl/python3_3.12.2-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libdpkg-perl all 1.22.6 [631 kB] Fetched 631 kB in 0s (47.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwsclrp15/libdpkg-perl_1.22.6_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-numpydoc all 1.6.0-2 [49.6 kB] Fetched 49.6 kB in 0s (336 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpeto0c26y/python3-numpydoc_1.6.0-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 ca-certificates all 20240203 [158 kB] Fetched 158 kB in 0s (14.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1w5jrnu3/ca-certificates_20240203_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 gettext-base amd64 0.22.5-1 [199 kB] Fetched 199 kB in 0s (18.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwz9v3im1/gettext-base_0.22.5-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libidn2-0 amd64 2.3.7-2 [128 kB] Fetched 128 kB in 0s (12.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp41o6trwd/libidn2-0_2.3.7-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 xml-core all 0.19 [20.1 kB] Fetched 20.1 kB in 0s (1749 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphft_ry2h/xml-core_0.19_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libgcrypt20 amd64 1.10.3-3 [708 kB] Fetched 708 kB in 0s (3093 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptoll21xw/libgcrypt20_1.10.3-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libdebconfclient0 amd64 0.272 [10.0 kB] Fetched 10.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprie7_037/libdebconfclient0_0.272_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Fetched 8448 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpb3u988qy/dh-strip-nondeterminism_1.14.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-referencing all 0.31.0-1 [22.2 kB] Fetched 22.2 kB in 0s (177 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0ceohmvt/python3-referencing_0.31.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-sphinx-gallery all 0.16.0-1 [392 kB] Fetched 392 kB in 0s (2397 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpogikan0_/python3-sphinx-gallery_0.16.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 jupyter-sphinx-theme-common all 0.0.6+ds1-11 [13.2 kB] Fetched 13.2 kB in 0s (55.9 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpykn9hbsc/jupyter-sphinx-theme-common_0.0.6+ds1-11_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-tinydb all 3.15.2-4 [20.8 kB] Fetched 20.8 kB in 0s (103 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7dalgufp/python3-tinydb_3.15.2-4_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 gcc-13-base amd64 13.3.0-1 [46.0 kB] Fetched 46.0 kB in 0s (184 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpoirckhv7/gcc-13-base_13.3.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 dash amd64 0.5.12-9 [93.2 kB] Fetched 93.2 kB in 0s (9142 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_rpkya6o/dash_0.5.12-9_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 liblsan0 amd64 14.1.0-3 [1205 kB] Fetched 1205 kB in 0s (6460 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmllm94oo/liblsan0_14.1.0-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libimagequant0 amd64 2.18.0-1+b1 [35.3 kB] Fetched 35.3 kB in 0s (3272 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxwz2xqkz/libimagequant0_2.18.0-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libtk8.6 amd64 8.6.14-1 [784 kB] Fetched 784 kB in 0s (53.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvv8dpoeb/libtk8.6_8.6.14-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libstdc++-13-dev amd64 13.3.0-1 [2290 kB] Fetched 2290 kB in 0s (11.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpi0hv8t5v/libstdc++-13-dev_13.3.0-1_amd64.deb' Downloading dependency 129 of 425: libjs-jquery-throttle-debounce:amd64=1.1+dfsg.1-2 Downloading dependency 130 of 425: python3-pytest-cov:amd64=5.0.0-1 Downloading dependency 131 of 425: python3-ufolib2:amd64=0.16.0+dfsg1-1 Downloading dependency 132 of 425: python3-pkg-resources:amd64=68.1.2-2 Downloading dependency 133 of 425: libgnutls30t64:amd64=3.8.5-4 Downloading dependency 134 of 425: python-matplotlib-data:amd64=3.6.3-2 Downloading dependency 135 of 425: libp11-kit0:amd64=0.25.3-5 Downloading dependency 136 of 425: cpp-13-x86-64-linux-gnu:amd64=13.3.0-1 Downloading dependency 137 of 425: python3-fs:amd64=2.4.16-4 Downloading dependency 138 of 425: sensible-utils:amd64=0.0.24 Downloading dependency 139 of 425: libpam-modules-bin:amd64=1.5.3-7 Downloading dependency 140 of 425: python3-imagesize:amd64=1.4.1-1 Downloading dependency 141 of 425: python3-pybtex-docutils:amd64=1.0.2-1 Downloading dependency 142 of 425: rpcsvc-proto:amd64=1.4.3-1 Downloading dependency 143 of 425: g++-x86-64-linux-gnu:amd64=4:13.2.0-7 Downloading dependency 144 of 425: binutils-x86-64-linux-gnu:amd64=2.42.50.20240625-1 Downloading dependency 145 of 425: fonts-dejavu-mono:amd64=2.37-8 Downloading dependency 146 of 425: groff-base:amd64=1.23.0-5 Downloading dependency 147 of 425: libpcre2-8-0:amd64=10.42-4+b1 Downloading dependency 148 of 425: libx11-6:amd64=2:1.8.7-1+b1 Downloading dependency 149 of 425: libtasn1-6:amd64=4.19.0-3+b2 Downloading dependency 150 of 425: libgmp10:amd64=2:6.3.0+dfsg-2+b1 Downloading dependency 151 of 425: openssl:amd64=3.2.2-1 Downloading dependency 152 of 425: libzstd1:amd64=1.5.6+dfsg-1 Downloading dependency 153 of 425: ncurses-bin:amd64=6.5-2 Downloading dependency 154 of 425: gcc-13:amd64=13.3.0-1 Downloading dependency 155 of 425: debianutils:amd64=5.19 Downloading dependency 156 of 425: libtbbbind-2-5:amd64=2021.11.0-2 Downloading dependency 157 of 425: libpython3-stdlib:amd64=3.12.2-1 Downloading dependency 158 of 425: python3-brotli:amd64=1.1.0-2+b3 Downloading dependency 159 of 425: libjs-jquery-tablesorter:amd64=1:2.31.3+dfsg1-3 Downloading dependency 160 of 425: python3-bs4:amd64=4.12.3-1 Downloading dependency 161 of 425: python3-prometheus-client:amd64=0.19.0+ds1-1 Downloading dependency 162 of 425: bsdutils:amd64=1:2.40.1-9 Downloading dependency 163 of 425: libcom-err2:amd64=1.47.1-1 Downloading dependency 164 of 425: python3.12:amd64=3.12.4-1 Downloading dependency 165 of 425: fonts-dejavu-core:amd64=2.37-8 Downloading dependency 166 of 425: libx11-data:amd64=2:1.8.7-1 Downloading dependency 167 of 425: python3-pil.imagetk:amd64=10.3.0-2 Downloading dependency 168 of 425: python3-jupyterlab-server:amd64=2.25.2-1 Downloading dependency 169 of 425: python3-tz:amd64=2024.1-2 Downloading dependency 170 of 425: python3-pydata-sphinx-theme:amd64=0.15.2.is.0.7.2-1 Downloading dependency 171 of 425: cpp-13:amd64=13.3.0-1 Downloading dependency 172 of 425: libwebpmux3:amd64=1.4.0-0.1 Downloading dependency 173 of 425: libz3-4:amd64=4.8.12-3.1+b2 Downloading dependency 174 of 425: perl-modules-5.38:amd64=5.38.2-5 Downloading dependency 175 of 425: util-linux:amd64=2.40.1-9 Downloading dependency 176 of 425: libcrypt1:amd64=1:4.4.36-4 Downloading dependency 177 of 425: libhwloc15:amd64=2.11.0-2 Downloading dependency 178 of 425: libtbbmalloc2:amd64=2021.11.0-2 Downloading dependency 179 of 425: libisl23:amd64=0.26-3+b2 Downloading dependency 180 of 425: liblzma5:amd64=5.6.2-1 Downloading dependency 181 of 425: python3-sphinxcontrib.bibtex:amd64=2.6.2-1 Downloading dependency 182 of 425: libgdbm-compat4t64:amd64=1.23-6 Downloading dependency 183 of 425: librtmp1:amd64=2.4+20151223.gitfa8646d.1-2+b4 Downloading dependency 184 of 425: libssl3t64:amd64=3.2.2-1 Downloading dependency 185 of 425: python3-chardet:amd64=5.2.0+dfsg-1 Downloading dependency 186 of 425: python3-pyparsing:amd64=3.1.2-1 Downloading dependency 187 of 425: linux-libc-dev:amd64=6.9.7-1 Downloading dependency 188 of 425: python3-all-dev:amd64=3.12.2-1 Downloading dependency 189 of 425: libc-dev-bin:amd64=2.38-13 Downloading dependency 190 of 425: python3-pathspec:amd64=0.12.1-1 Downloading dependency 191 of 425: binutils:amd64=2.42.50.20240625-1 Downloading dependency 192 of 425: libfribidi0:amd64=1.0.13-3+b1 Downloading dependency 193 of 425: python3-argon2:amd64=21.1.0-2 Downloading dependency 194 of 425: libffi8:amd64=3.4.6-1 Downloading dependency 195 of 425: python3-tornado:amd64=6.4.1-1 Downloading dependency 196 of 425: python3-pandocfilters:amd64=1.5.1-1 Downloading dependency 197 of 425: libxft2:amd64=2.3.6-1+b1 Downloading dependency 198 of 425: python3-numba:amd64=0.59.1+dfsg-1 Downloading dependency 199 of 425: libmagic1t64:amd64=1:5.45-3 Downloading dependency 200 of 425: libssh2-1t64:amd64=1.11.0-5 Downloading dependency 201 of 425: python3-jupyterlab-pygments:amd64=0.2.2-3 Downloading dependency 202 of 425: g++-13-x86-64-linux-gnu:amd64=13.3.0-1 Downloading dependency 203 of 425: python3-numpy:amd64=1:1.26.4+ds-10 Downloading dependency 204 of 425: python3-nbsphinx:amd64=0.9.4+ds-1 Downloading dependency 205 of 425: libjs-jquery:amd64=3.6.1+dfsg+~3.5.14-1 Downloading dependency 206 of 425: python3-mpmath:amd64=1.3.0-1 Downloading dependency 207 of 425: python3-rpds-py:amd64=0.12.0-3 Downloading dependency 208 of 425: zlib1g-dev:amd64=1:1.3.dfsg+really1.3.1-1 Downloading dependency 209 of 425: libitm1:amd64=14.1.0-3 Downloading dependency 210 of 425: libgpg-error0:amd64=1.49-2 Downloading dependency 211 of 425: libpython3.11-minimal:amd64=3.11.9-1 Downloading dependency 212 of 425: fontconfig-config:amd64=2.15.0-1.1 Downloading dependency 213 of 425: python3-alabaster:amd64=0.7.16-0.1 Downloading dependency 214 of 425: libfontconfig1:amd64=2.15.0-1.1 Downloading dependency 215 of 425: libbsd0:amd64=0.12.2-1 Downloading dependency 216 of 425: libjansson4:amd64=2.14-2+b2 Downloading dependency 217 of 425: python3-lz4:amd64=4.0.2+dfsg-1+b3 Downloading dependency 218 of 425: cython3:amd64=3.0.10+dfsg-5 Downloading dependency 219 of 425: autotools-dev:amd64=20220109.1 Downloading dependency 220 of 425: gcc-x86-64-linux-gnu:amd64=4:13.2.0-7 Downloading dependency 221 of 425: python3-tinycss2:amd64=1.3.0-1 Downloading dependency 222 of 425: libsmartcols1:amd64=2.40.1-9 Downloading dependency 223 of 425: libnettle8t64:amd64=3.10-1 Downloading dependency 224 of 425: python3-nbclient:amd64=0.8.0-1 Downloading dependency 225 of 425: python3-wheel:amd64=0.43.0-1 Downloading dependency 226 of 425: libkrb5-3:amd64=1.21.2-1 Downloading dependency 227 of 425: llvm-14:amd64=1:14.0.6-20 Downloading dependency 228 of 425: python3-certifi:amd64=2024.6.2-1 Downloading dependency 229 of 425: python3-iniconfig:amd64=1.1.1-2 Downloading dependency 230 of 425: libbz2-1.0:amd64=1.0.8-5.1 Downloading dependency 231 of 425: debhelper:amd64=13.16 Downloading dependency 232 of 425: python3:amd64=3.12.2-1 Downloading dependency 233 of 425: libdpkg-perl:amd64=1.22.6 Downloading dependency 234 of 425: python3-numpydoc:amd64=1.6.0-2 Downloading dependency 235 of 425: ca-certificates:amd64=20240203 Downloading dependency 236 of 425: gettext-base:amd64=0.22.5-1 Downloading dependency 237 of 425: libidn2-0:amd64=2.3.7-2 Downloading dependency 238 of 425: xml-core:amd64=0.19 Downloading dependency 239 of 425: libgcrypt20:amd64=1.10.3-3 Downloading dependency 240 of 425: libdebconfclient0:amd64=0.272 Downloading dependency 241 of 425: dh-strip-nondeterminism:amd64=1.14.0-1 Downloading dependency 242 of 425: python3-referencing:amd64=0.31.0-1 Downloading dependency 243 of 425: python3-sphinx-gallery:amd64=0.16.0-1 Downloading dependency 244 of 425: jupyter-sphinx-theme-common:amd64=0.0.6+ds1-11 Downloading dependency 245 of 425: python3-tinydb:amd64=3.15.2-4 Downloading dependency 246 of 425: gcc-13-base:amd64=13.3.0-1 Downloading dependency 247 of 425: dash:amd64=0.5.12-9 Downloading dependency 248 of 425: liblsan0:amd64=14.1.0-3 Downloading dependency 249 of 425: libimagequant0:amd64=2.18.0-1+b1 Downloading dependency 250 of 425: libtk8.6:amd64=8.6.14-1 Downloading dependency 251 of 425: libstdc++-13-dev:amd64=13.3.0-1 Downloading dependency 252 of 425: libelf1t64:amd64=0.191-1+b1Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Fetched 189 kB in 0s (17.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_3kb3mvt/libelf1t64_0.191-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-jsonschema all 4.19.2-3 [71.3 kB] Fetched 71.3 kB in 0s (484 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpm9816qlc/python3-jsonschema_4.19.2-3_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libgcc-s1 amd64 14.1.0-3 [72.7 kB] Fetched 72.7 kB in 0s (502 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptfwfsc_i/libgcc-s1_14.1.0-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-setuptools all 68.1.2-2 [468 kB] Fetched 468 kB in 0s (2986 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp92_g_cmm/python3-setuptools_68.1.2-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libattr1 amd64 1:2.5.2-1 [22.5 kB] Fetched 22.5 kB in 0s (0 B/s) dpkg-name: info: moved 'libattr1_1%3a2.5.2-1_amd64.deb' to '/srv/rebuilderd/tmp/tmpdw85mzui/libattr1_2.5.2-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-ptyprocess all 0.7.0-5 [14.7 kB] Fetched 14.7 kB in 0s (96.3 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphfm4pqyu/python3-ptyprocess_0.7.0-5_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 dwz amd64 0.15-1+b1 [110 kB] Fetched 110 kB in 0s (10.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbx1zl15p/dwz_0.15-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Fetched 56.8 kB in 0s (5415 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprii8cqyb/libpsl5t64_0.21.2-1.1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 dh-autoreconf all 20 [17.1 kB] Fetched 17.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4ac5gx_1/dh-autoreconf_20_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-lxml amd64 5.2.1-1 [1995 kB] Fetched 1995 kB in 0s (6549 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_ts84qg_/python3-lxml_5.2.1-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-traitlets all 5.14.3-1 [70.7 kB] Fetched 70.7 kB in 0s (492 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpc08j8pne/python3-traitlets_5.14.3-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libpython3-dev amd64 3.12.2-1 [9680 B] Fetched 9680 B in 0s (64.7 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp__cr4l6k/libpython3-dev_3.12.2-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libxrender1 amd64 1:0.9.10-1.1+b1 [27.9 kB] Fetched 27.9 kB in 0s (0 B/s) dpkg-name: info: moved 'libxrender1_1%3a0.9.10-1.1+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmpnk1cqwsy/libxrender1_0.9.10-1.1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 liblcms2-2 amd64 2.14-2+b1 [154 kB] Fetched 154 kB in 0s (14.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmqs14jvh/liblcms2-2_2.14-2+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-pluggy all 1.5.0-1 [26.9 kB] Fetched 26.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7ye3o9dh/python3-pluggy_1.5.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libgdbm6t64 amd64 1.23-6 [72.8 kB] Fetched 72.8 kB in 0s (6599 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7gjykgxi/libgdbm6t64_1.23-6_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Fetched 22.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpumeb0i9k/intltool-debian_0.35.0+20060710.6_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [113 kB] Fetched 113 kB in 0s (10.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsxuiuhd_/libsharpyuv0_1.4.0-0.1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libperl5.38t64 amd64 5.38.2-5 [4275 kB] Fetched 4275 kB in 0s (124 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpug9js85k/libperl5.38t64_5.38.2-5_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libcap2 amd64 1:2.66-5 [27.4 kB] Fetched 27.4 kB in 0s (2722 kB/s) dpkg-name: info: moved 'libcap2_1%3a2.66-5_amd64.deb' to '/srv/rebuilderd/tmp/tmp448gcgyo/libcap2_2.66-5_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1+b1 [29.1 kB] Fetched 29.1 kB in 0s (156 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9rijtndh/liblbfgsb0_3.0+dfsg.4-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-jupyter-core all 5.3.2-2 [31.6 kB] Fetched 31.6 kB in 0s (245 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphnw3_bv8/python3-jupyter-core_5.3.2-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-scitrack all 2021.5.3-3 [9272 B] Fetched 9272 B in 0s (46.1 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpr1fh7ul5/python3-scitrack_2021.5.3-3_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-yaml amd64 6.0.1-2 [177 kB] Fetched 177 kB in 0s (16.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp0e28lecr/python3-yaml_6.0.1-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libpython3-all-dev amd64 3.12.2-1 [1072 B] Fetched 1072 B in 0s (8433 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfg1gkijb/libpython3-all-dev_3.12.2-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-installer all 0.7.0+dfsg1-3 [18.6 kB] Fetched 18.6 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpk_4ka3cj/python3-installer_0.7.0+dfsg1-3_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 binutils-common amd64 2.42.50.20240625-1 [2605 kB] Fetched 2605 kB in 0s (14.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpu2xkhu5g/binutils-common_2.42.50.20240625-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-trove-classifiers all 2024.4.10-1 [10.1 kB] Fetched 10.1 kB in 0s (81.2 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpz39gkizh/python3-trove-classifiers_2024.4.10-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libudev1 amd64 256.1-2 [143 kB] Fetched 143 kB in 0s (1328 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_b5v85tb/libudev1_256.1-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libc6-dev amd64 2.38-13 [1917 kB] Fetched 1917 kB in 0s (101 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp8ktkdee5/libc6-dev_2.38-13_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-pyproject-hooks all 1.1.0-1 [11.3 kB] Fetched 11.3 kB in 0s (25.9 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmph74fyleg/python3-pyproject-hooks_1.1.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 gcc amd64 4:13.2.0-7 [5152 B] Fetched 5152 B in 0s (0 B/s) dpkg-name: info: moved 'gcc_4%3a13.2.0-7_amd64.deb' to '/srv/rebuilderd/tmp/tmptzay72kq/gcc_13.2.0-7_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-html5lib all 1.1-6 [90.5 kB] Fetched 90.5 kB in 0s (702 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptjwv2r0v/python3-html5lib_1.1-6_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libedit2 amd64 3.1-20240517-1 [93.3 kB] Fetched 93.3 kB in 0s (451 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzmfmuqhv/libedit2_3.1-20240517-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libharfbuzz0b amd64 8.3.0-2+b1 [2214 kB] Fetched 2214 kB in 0s (92.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqiu3tgtm/libharfbuzz0b_8.3.0-2+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 llvm-14-runtime amd64 1:14.0.6-20 [481 kB] Fetched 481 kB in 0s (2933 kB/s) dpkg-name: info: moved 'llvm-14-runtime_1%3a14.0.6-20_amd64.deb' to '/srv/rebuilderd/tmp/tmpfhba_yd6/llvm-14-runtime_14.0.6-20_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-terminado all 0.18.1-1 [17.3 kB] Fetched 17.3 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzfo85soh/python3-terminado_0.18.1-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-entrypoints all 0.4-2 [7184 B] Fetched 7184 B in 0s (37.8 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfegsy28u/python3-entrypoints_0.4-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libpython3.12-minimal amd64 3.12.4-1 [811 kB] Fetched 811 kB in 0s (4316 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbqbamsiw/libpython3.12-minimal_3.12.4-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 perl amd64 5.38.2-5 [236 kB] Fetched 236 kB in 0s (22.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpgoc1yai_/perl_5.38.2-5_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libncursesw6 amd64 6.5-2 [135 kB] Fetched 135 kB in 0s (13.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpx86do3u0/libncursesw6_6.5-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-six all 1.16.0-6 [16.3 kB] Fetched 16.3 kB in 0s (132 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpp7pbkwx4/python3-six_1.16.0-6_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-packaging all 24.0-1 [45.5 kB] Fetched 45.5 kB in 0s (370 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjsqfqzk3/python3-packaging_24.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libgcc-13-dev amd64 13.3.0-1 [2538 kB] Fetched 2538 kB in 0s (11.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprrbabupi/libgcc-13-dev_13.3.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libsqlite3-0 amd64 3.46.0-1 [902 kB] Fetched 902 kB in 0s (3257 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplvdswyfg/libsqlite3-0_3.46.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libctf-nobfd0 amd64 2.42.50.20240625-1 [153 kB] Fetched 153 kB in 0s (988 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpu76dvo59/libctf-nobfd0_2.42.50.20240625-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libqhull-r8.0 amd64 2020.2-6+b1 [245 kB] Fetched 245 kB in 0s (1679 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4n9akule/libqhull-r8.0_2020.2-6+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 sed amd64 4.9-2 [329 kB] Fetched 329 kB in 0s (29.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp05e9i5e8/sed_4.9-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 media-types all 10.1.0 [26.9 kB] Fetched 26.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6y4_odtx/media-types_10.1.0_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-platformdirs all 4.2.1-1 [16.0 kB] Fetched 16.0 kB in 0s (127 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpndpp6pk_/python3-platformdirs_4.2.1-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libjs-requirejs all 2.3.6+ds+~2.1.37-1 [196 kB] Fetched 196 kB in 0s (797 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4c5zm_oa/libjs-requirejs_2.3.6+ds+~2.1.37-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-anyio all 4.4.0-1 [57.3 kB] Fetched 57.3 kB in 0s (177 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqor79m75/python3-anyio_4.4.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 zlib1g amd64 1:1.3.dfsg+really1.3.1-1 [87.9 kB] Fetched 87.9 kB in 0s (8674 kB/s) dpkg-name: info: moved 'zlib1g_1%3a1.3.dfsg+really1.3.1-1_amd64.deb' to '/srv/rebuilderd/tmp/tmp6l8qnwbw/zlib1g_1.3.dfsg+really1.3.1-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 dpkg-dev all 1.22.6 [1317 kB] Fetched 1317 kB in 0s (80.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpei0qie_0/dpkg-dev_1.22.6_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libaudit1 amd64 1:3.1.2-4 [48.8 kB] Fetched 48.8 kB in 0s (4515 kB/s) dpkg-name: info: moved 'libaudit1_1%3a3.1.2-4_amd64.deb' to '/srv/rebuilderd/tmp/tmp361pxou7/libaudit1_3.1.2-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libubsan1 amd64 14.1.0-3 [1075 kB] Fetched 1075 kB in 0s (2592 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1o91hxpp/libubsan1_14.1.0-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libjs-bootswatch all 3.3.7+dfsg2-1.1 [133 kB] Fetched 133 kB in 0s (648 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpt851_88k/libjs-bootswatch_3.3.7+dfsg2-1.1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-websocket all 1.7.0-1 [45.0 kB] Fetched 45.0 kB in 0s (331 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6cdqmmcz/python3-websocket_1.7.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 hostname amd64 3.23+nmu2 [10.6 kB] Fetched 10.6 kB in 0s (1032 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1paxoqxy/hostname_3.23+nmu2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libmount1 amd64 2.40.1-9 [197 kB] Fetched 197 kB in 0s (1337 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp93v3cizc/libmount1_2.40.1-9_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-jupyter-sphinx-theme all 0.0.6+ds1-11 [2976 B] Fetched 2976 B in 0s (25.9 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpp90_9681/python3-jupyter-sphinx-theme_0.0.6+ds1-11_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-matplotlib amd64 3.6.3-2 [8167 kB] Fetched 8167 kB in 1s (15.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6pcbeuyj/python3-matplotlib_3.6.3-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 llvm-14-linker-tools amd64 1:14.0.6-20 [1292 kB] Fetched 1292 kB in 0s (4167 kB/s) dpkg-name: info: moved 'llvm-14-linker-tools_1%3a14.0.6-20_amd64.deb' to '/srv/rebuilderd/tmp/tmpy9ur0qvm/llvm-14-linker-tools_14.0.6-20_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 make amd64 4.3-4.1 [396 kB] Fetched 396 kB in 0s (34.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpw97gvwa0/make_4.3-4.1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libasan8 amd64 14.1.0-3 [2727 kB] Fetched 2727 kB in 0s (9535 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmps8519kct/libasan8_14.1.0-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-1 [186 kB] Fetched 186 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsyd0zxhn/libldap-2.5-0_2.5.18+dfsg-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 mawk amd64 1.3.4.20240622-1 [136 kB] Fetched 136 kB in 0s (648 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmps0cphmj4/mawk_1.3.4.20240622-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-defusedxml all 0.7.1-2 [43.3 kB] Fetched 43.3 kB in 0s (229 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwxt2vi7o/python3-defusedxml_0.7.1-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-idna all 3.6-2.1 [38.6 kB] Fetched 38.6 kB in 0s (199 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfriw5a9f/python3-idna_3.6-2.1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [110 kB] Fetched 110 kB in 0s (10.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpswf4ygaz/libwebpdemux2_1.4.0-0.1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-pandas all 2.1.4+dfsg-8 [3015 kB] Fetched 3015 kB in 0s (8139 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp93yvguju/python3-pandas_2.1.4+dfsg-8_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-pandas-lib amd64 2.1.4+dfsg-8 [7882 kB] Fetched 7882 kB in 0s (18.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpf2tjze8g/python3-pandas-lib_2.1.4+dfsg-8_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-pybtex all 0.24.0-4 [74.6 kB] Fetched 74.6 kB in 0s (380 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppfha0mzc/python3-pybtex_0.24.0-4_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libsystemd0 amd64 256.1-2 [376 kB] Fetched 376 kB in 0s (1110 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxh6gii8g/libsystemd0_256.1-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-contourpy amd64 1.0.7-3 [285 kB] Fetched 285 kB in 0s (976 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpqpcmras9/python3-contourpy_1.0.7-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-hatch-vcs all 0.4.0-1 [8336 B] Fetched 8336 B in 0s (56.7 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmgfd43ng/python3-hatch-vcs_0.4.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-kiwisolver amd64 1.4.5-1 [80.7 kB] Fetched 80.7 kB in 0s (426 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpf51xxy5d/python3-kiwisolver_1.4.5-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-recommonmark all 0.7.1+ds-5 [17.3 kB] Fetched 17.3 kB in 0s (102 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpazodea4i/python3-recommonmark_0.7.1+ds-5_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 xz-utils amd64 5.6.2-1 [522 kB] Fetched 522 kB in 0s (48.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprlze9pk2/xz-utils_5.6.2-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libpgm-5.3-0t64 amd64 5.3.128~dfsg-2.1 [161 kB] Fetched 161 kB in 0s (777 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptklb39np/libpgm-5.3-0t64_5.3.128~dfsg-2.1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libjs-bootstrap all 3.4.1+dfsg-3 [172 kB] Fetched 172 kB in 0s (15.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfdyiw78k/libjs-bootstrap_3.4.1+dfsg-3_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Fetched 38.0 kB in 0s (3392 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmxufgr68/libpipeline1_1.5.7-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 tzdata all 2024a-4 [255 kB] Fetched 255 kB in 0s (22.3 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpweamx9bu/tzdata_2024a-4_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 pandoc amd64 3.1.3+ds-3 [24.3 MB] Fetched 24.3 MB in 0s (55.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsgjhk9mv/pandoc_3.1.3+ds-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 bzip2 amd64 1.0.8-5.1 [40.3 kB] Fetched 40.3 kB in 0s (3934 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpo7lwbh58/bzip2_1.0.8-5.1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libargon2-1 amd64 0~20190702+dfsg-4+b1 [21.1 kB] Fetched 21.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp39_7h1a4/libargon2-1_0~20190702+dfsg-4+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 gcc-14-base amd64 14.1.0-3 [44.9 kB] Fetched 44.9 kB in 0s (256 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpggtksnse/gcc-14-base_14.1.0-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libdb5.3t64 amd64 5.3.28+dfsg2-7 [697 kB] Fetched 697 kB in 0s (59.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp5in17fhs/libdb5.3t64_5.3.28+dfsg2-7_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-fastjsonschema all 2.20.0-1 [21.8 kB] Fetched 21.8 kB in 0s (117 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpcg3l7_b3/python3-fastjsonschema_2.20.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libjson-perl all 4.10000-1 [87.5 kB] Fetched 87.5 kB in 0s (7245 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpasjialbm/libjson-perl_4.10000-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-sphinx-design all 0.6.0-2 [883 kB] Fetched 883 kB in 0s (3343 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpk6zc_9ma/python3-sphinx-design_0.6.0-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-plotly all 5.20.0+dfsg-1 [2726 kB] Fetched 2726 kB in 0s (123 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpxbpwd8mt/python3-plotly_5.20.0+dfsg-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-jsonschema-specifications all 2023.12.1-1 [8976 B] Fetched 8976 B in 0s (57.8 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjmocbpzp/python3-jsonschema-specifications_2023.12.1-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-pygments all 2.18.0+dfsg-1 [836 kB] Fetched 836 kB in 0s (3346 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_s4kdpiz/python3-pygments_2.18.0+dfsg-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 autoconf all 2.71-3 [332 kB] Fetched 332 kB in 0s (31.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjznguk_5/autoconf_2.71-3_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-attr all 23.2.0-2 [65.5 kB] Fetched 65.5 kB in 0s (263 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2q2o70io/python3-attr_23.2.0-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 gzip amd64 1.12-1.1 [133 kB] Fetched 133 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp9ig8dkyy/gzip_1.12-1.1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libgraphite2-3 amd64 1.3.14-2 [74.9 kB] Fetched 74.9 kB in 0s (6955 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpsws6u40x/libgraphite2-3_1.3.14-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libquadmath0 amd64 14.1.0-3 [145 kB] Fetched 145 kB in 0s (677 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpvdfvmfaq/libquadmath0_14.1.0-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libzmq5 amd64 4.3.5-1+b2 [281 kB] Fetched 281 kB in 0s (924 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp66f53wdw/libzmq5_4.3.5-1+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-sympy all 1.12.1-1 [3869 kB] Fetched 3869 kB in 0s (13.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpu73825dn/python3-sympy_1.12.1-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libcap-ng0 amd64 0.8.5-1 [17.1 kB] Fetched 17.1 kB in 0s (1707 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp17gyuo6d/libcap-ng0_0.8.5-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 gettext amd64 0.22.5-1 [1593 kB] Fetched 1593 kB in 0s (95.7 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptvk_vm28/gettext_0.22.5-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libpfm4 amd64 4.13.0+git32-g0d4ed0e-1 [341 kB] Fetched 341 kB in 0s (1569 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpi2er3en9/libpfm4_4.13.0+git32-g0d4ed0e-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Fetched 167 kB in 0s (16.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpz18d4hll/libreadline8t64_8.2-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-sphinx all 7.3.7-3 [569 kB] Fetched 569 kB in 0s (2235 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpm19qhmn8/python3-sphinx_7.3.7-3_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-urllib3 all 2.0.7-2 [111 kB] Fetched 111 kB in 0s (528 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmps9263yuf/python3-urllib3_2.0.7-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libtsan2 amd64 14.1.0-3 [2460 kB] Fetched 2460 kB in 0s (7802 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpiyfzzss8/libtsan2_14.1.0-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3.12-minimal amd64 3.12.4-1 [2136 kB] Fetched 2136 kB in 0s (7403 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpscbd2zur/python3.12-minimal_3.12.4-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libicu72 amd64 72.1-5 [9396 kB] Fetched 9396 kB in 0s (160 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp017dx7ix/libicu72_72.1-5_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libhogweed6t64 amd64 3.10-1 [334 kB] Fetched 334 kB in 0s (32.6 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3hetv3ls/libhogweed6t64_3.10-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libmd0 amd64 1.1.0-2 [35.8 kB] Fetched 35.8 kB in 0s (3226 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpf3vmkgj_/libmd0_1.1.0-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-lib2to3 all 3.12.3-3.1 [77.7 kB] Fetched 77.7 kB in 0s (406 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpo55y4tx6/python3-lib2to3_3.12.3-3.1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 bsdextrautils amd64 2.40.1-9 [96.2 kB] Fetched 96.2 kB in 0s (460 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpre9yujrv/bsdextrautils_2.40.1-9_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Fetched 248 kB in 0s (21.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplcnde7dm/po-debconf_1.0.21+nmu1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 autopoint all 0.22.5-1 [723 kB] Fetched 723 kB in 0s (64.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpb8mnu7e6/autopoint_0.22.5-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-nbformat all 5.9.1-1 [45.1 kB] Fetched 45.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7zg0url5/python3-nbformat_5.9.1-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Fetched 104 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpkri98lkx/libarchive-zip-perl_1.68-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libjs-jquery-metadata all 12-4 [6532 B] Fetched 6532 B in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpq1xmk4cc/libjs-jquery-metadata_12-4_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 g++ amd64 4:13.2.0-7 [1348 B] Fetched 1348 B in 0s (0 B/s) dpkg-name: info: moved 'g++_4%3a13.2.0-7_amd64.deb' to '/srv/rebuilderd/tmp/tmpt9p14wj7/g++_13.2.0-7_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libnorm1t64 amd64 1.5.9+dfsg-3.1 [221 kB] Fetched 221 kB in 0s (1050 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmbg2qaz5/libnorm1t64_1.5.9+dfsg-3.1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 init-system-helpers all 1.66 [39.0 kB] Fetched 39.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphhjcamtd/init-system-helpers_1.66_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-tk amd64 3.12.3-3.1 [113 kB] Fetched 113 kB in 0s (583 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpoxquac21/python3-tk_3.12.3-3.1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libgfortran5 amd64 14.1.0-3 [837 kB] Fetched 837 kB in 0s (3131 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1tjc8u_8/libgfortran5_14.1.0-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-py all 1.11.0-2 [88.7 kB] Fetched 88.7 kB in 0s (322 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1j1i1yav/python3-py_1.11.0-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libpython3.12-stdlib amd64 3.12.4-1 [1948 kB] Fetched 1948 kB in 0s (6754 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpwk9bvtgb/libpython3.12-stdlib_3.12.4-1_amd64.deb' Downloading dependency 253 of 425: python3-jsonschema:amd64=4.19.2-3 Downloading dependency 254 of 425: libgcc-s1:amd64=14.1.0-3 Downloading dependency 255 of 425: python3-setuptools:amd64=68.1.2-2 Downloading dependency 256 of 425: libattr1:amd64=1:2.5.2-1 Downloading dependency 257 of 425: python3-ptyprocess:amd64=0.7.0-5 Downloading dependency 258 of 425: dwz:amd64=0.15-1+b1 Downloading dependency 259 of 425: libpsl5t64:amd64=0.21.2-1.1 Downloading dependency 260 of 425: dh-autoreconf:amd64=20 Downloading dependency 261 of 425: python3-lxml:amd64=5.2.1-1 Downloading dependency 262 of 425: python3-traitlets:amd64=5.14.3-1 Downloading dependency 263 of 425: libpython3-dev:amd64=3.12.2-1 Downloading dependency 264 of 425: libxrender1:amd64=1:0.9.10-1.1+b1 Downloading dependency 265 of 425: liblcms2-2:amd64=2.14-2+b1 Downloading dependency 266 of 425: python3-pluggy:amd64=1.5.0-1 Downloading dependency 267 of 425: libgdbm6t64:amd64=1.23-6 Downloading dependency 268 of 425: intltool-debian:amd64=0.35.0+20060710.6 Downloading dependency 269 of 425: libsharpyuv0:amd64=1.4.0-0.1 Downloading dependency 270 of 425: libperl5.38t64:amd64=5.38.2-5 Downloading dependency 271 of 425: libcap2:amd64=1:2.66-5 Downloading dependency 272 of 425: liblbfgsb0:amd64=3.0+dfsg.4-1+b1 Downloading dependency 273 of 425: python3-jupyter-core:amd64=5.3.2-2 Downloading dependency 274 of 425: python3-scitrack:amd64=2021.5.3-3 Downloading dependency 275 of 425: python3-yaml:amd64=6.0.1-2 Downloading dependency 276 of 425: libpython3-all-dev:amd64=3.12.2-1 Downloading dependency 277 of 425: python3-installer:amd64=0.7.0+dfsg1-3 Downloading dependency 278 of 425: binutils-common:amd64=2.42.50.20240625-1 Downloading dependency 279 of 425: python3-trove-classifiers:amd64=2024.4.10-1 Downloading dependency 280 of 425: libudev1:amd64=256.1-2 Downloading dependency 281 of 425: libc6-dev:amd64=2.38-13 Downloading dependency 282 of 425: python3-pyproject-hooks:amd64=1.1.0-1 Downloading dependency 283 of 425: gcc:amd64=4:13.2.0-7 Downloading dependency 284 of 425: python3-html5lib:amd64=1.1-6 Downloading dependency 285 of 425: libedit2:amd64=3.1-20240517-1 Downloading dependency 286 of 425: libharfbuzz0b:amd64=8.3.0-2+b1 Downloading dependency 287 of 425: llvm-14-runtime:amd64=1:14.0.6-20 Downloading dependency 288 of 425: python3-terminado:amd64=0.18.1-1 Downloading dependency 289 of 425: python3-entrypoints:amd64=0.4-2 Downloading dependency 290 of 425: libpython3.12-minimal:amd64=3.12.4-1 Downloading dependency 291 of 425: perl:amd64=5.38.2-5 Downloading dependency 292 of 425: libncursesw6:amd64=6.5-2 Downloading dependency 293 of 425: python3-six:amd64=1.16.0-6 Downloading dependency 294 of 425: python3-packaging:amd64=24.0-1 Downloading dependency 295 of 425: libgcc-13-dev:amd64=13.3.0-1 Downloading dependency 296 of 425: libsqlite3-0:amd64=3.46.0-1 Downloading dependency 297 of 425: libctf-nobfd0:amd64=2.42.50.20240625-1 Downloading dependency 298 of 425: libqhull-r8.0:amd64=2020.2-6+b1 Downloading dependency 299 of 425: sed:amd64=4.9-2 Downloading dependency 300 of 425: media-types:amd64=10.1.0 Downloading dependency 301 of 425: python3-platformdirs:amd64=4.2.1-1 Downloading dependency 302 of 425: libjs-requirejs:amd64=2.3.6+ds+~2.1.37-1 Downloading dependency 303 of 425: python3-anyio:amd64=4.4.0-1 Downloading dependency 304 of 425: zlib1g:amd64=1:1.3.dfsg+really1.3.1-1 Downloading dependency 305 of 425: dpkg-dev:amd64=1.22.6 Downloading dependency 306 of 425: libaudit1:amd64=1:3.1.2-4 Downloading dependency 307 of 425: libubsan1:amd64=14.1.0-3 Downloading dependency 308 of 425: libjs-bootswatch:amd64=3.3.7+dfsg2-1.1 Downloading dependency 309 of 425: python3-websocket:amd64=1.7.0-1 Downloading dependency 310 of 425: hostname:amd64=3.23+nmu2 Downloading dependency 311 of 425: libmount1:amd64=2.40.1-9 Downloading dependency 312 of 425: python3-jupyter-sphinx-theme:amd64=0.0.6+ds1-11 Downloading dependency 313 of 425: python3-matplotlib:amd64=3.6.3-2 Downloading dependency 314 of 425: llvm-14-linker-tools:amd64=1:14.0.6-20 Downloading dependency 315 of 425: make:amd64=4.3-4.1 Downloading dependency 316 of 425: libasan8:amd64=14.1.0-3 Downloading dependency 317 of 425: libldap-2.5-0:amd64=2.5.18+dfsg-1 Downloading dependency 318 of 425: mawk:amd64=1.3.4.20240622-1 Downloading dependency 319 of 425: python3-defusedxml:amd64=0.7.1-2 Downloading dependency 320 of 425: python3-idna:amd64=3.6-2.1 Downloading dependency 321 of 425: libwebpdemux2:amd64=1.4.0-0.1 Downloading dependency 322 of 425: python3-pandas:amd64=2.1.4+dfsg-8 Downloading dependency 323 of 425: python3-pandas-lib:amd64=2.1.4+dfsg-8 Downloading dependency 324 of 425: python3-pybtex:amd64=0.24.0-4 Downloading dependency 325 of 425: libsystemd0:amd64=256.1-2 Downloading dependency 326 of 425: python3-contourpy:amd64=1.0.7-3 Downloading dependency 327 of 425: python3-hatch-vcs:amd64=0.4.0-1 Downloading dependency 328 of 425: python3-kiwisolver:amd64=1.4.5-1 Downloading dependency 329 of 425: python3-recommonmark:amd64=0.7.1+ds-5 Downloading dependency 330 of 425: xz-utils:amd64=5.6.2-1 Downloading dependency 331 of 425: libpgm-5.3-0t64:amd64=5.3.128~dfsg-2.1 Downloading dependency 332 of 425: libjs-bootstrap:amd64=3.4.1+dfsg-3 Downloading dependency 333 of 425: libpipeline1:amd64=1.5.7-2 Downloading dependency 334 of 425: tzdata:amd64=2024a-4 Downloading dependency 335 of 425: pandoc:amd64=3.1.3+ds-3 Downloading dependency 336 of 425: bzip2:amd64=1.0.8-5.1 Downloading dependency 337 of 425: libargon2-1:amd64=0~20190702+dfsg-4+b1 Downloading dependency 338 of 425: gcc-14-base:amd64=14.1.0-3 Downloading dependency 339 of 425: libdb5.3t64:amd64=5.3.28+dfsg2-7 Downloading dependency 340 of 425: python3-fastjsonschema:amd64=2.20.0-1 Downloading dependency 341 of 425: libjson-perl:amd64=4.10000-1 Downloading dependency 342 of 425: python3-sphinx-design:amd64=0.6.0-2 Downloading dependency 343 of 425: python3-plotly:amd64=5.20.0+dfsg-1 Downloading dependency 344 of 425: python3-jsonschema-specifications:amd64=2023.12.1-1 Downloading dependency 345 of 425: python3-pygments:amd64=2.18.0+dfsg-1 Downloading dependency 346 of 425: autoconf:amd64=2.71-3 Downloading dependency 347 of 425: python3-attr:amd64=23.2.0-2 Downloading dependency 348 of 425: gzip:amd64=1.12-1.1 Downloading dependency 349 of 425: libgraphite2-3:amd64=1.3.14-2 Downloading dependency 350 of 425: libquadmath0:amd64=14.1.0-3 Downloading dependency 351 of 425: libzmq5:amd64=4.3.5-1+b2 Downloading dependency 352 of 425: python3-sympy:amd64=1.12.1-1 Downloading dependency 353 of 425: libcap-ng0:amd64=0.8.5-1 Downloading dependency 354 of 425: gettext:amd64=0.22.5-1 Downloading dependency 355 of 425: libpfm4:amd64=4.13.0+git32-g0d4ed0e-1 Downloading dependency 356 of 425: libreadline8t64:amd64=8.2-4 Downloading dependency 357 of 425: python3-sphinx:amd64=7.3.7-3 Downloading dependency 358 of 425: python3-urllib3:amd64=2.0.7-2 Downloading dependency 359 of 425: libtsan2:amd64=14.1.0-3 Downloading dependency 360 of 425: python3.12-minimal:amd64=3.12.4-1 Downloading dependency 361 of 425: libicu72:amd64=72.1-5 Downloading dependency 362 of 425: libhogweed6t64:amd64=3.10-1 Downloading dependency 363 of 425: libmd0:amd64=1.1.0-2 Downloading dependency 364 of 425: python3-lib2to3:amd64=3.12.3-3.1 Downloading dependency 365 of 425: bsdextrautils:amd64=2.40.1-9 Downloading dependency 366 of 425: po-debconf:amd64=1.0.21+nmu1 Downloading dependency 367 of 425: autopoint:amd64=0.22.5-1 Downloading dependency 368 of 425: python3-nbformat:amd64=5.9.1-1 Downloading dependency 369 of 425: libarchive-zip-perl:amd64=1.68-1 Downloading dependency 370 of 425: libjs-jquery-metadata:amd64=12-4 Downloading dependency 371 of 425: g++:amd64=4:13.2.0-7 Downloading dependency 372 of 425: libnorm1t64:amd64=1.5.9+dfsg-3.1 Downloading dependency 373 of 425: init-system-helpers:amd64=1.66 Downloading dependency 374 of 425: python3-tk:amd64=3.12.3-3.1 Downloading dependency 375 of 425: libgfortran5:amd64=14.1.0-3 Downloading dependency 376 of 425: python3-py:amd64=1.11.0-2 Downloading dependency 377 of 425: libpython3.12-stdlib:amd64=3.12.4-1 Downloading dependency 378 of 425: python3.11:amd64=3.11.9-1Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3.11 amd64 3.11.9-1 [602 kB] Fetched 602 kB in 0s (1909 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpc4xusk0q/python3.11_3.11.9-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-jinja2 all 3.1.3-1 [119 kB] Fetched 119 kB in 0s (616 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpccufhhuq/python3-jinja2_3.1.3-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libdebhelper-perl all 13.16 [88.6 kB] Fetched 88.6 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_eztzlqn/libdebhelper-perl_13.16_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 liblua5.4-0 amd64 5.4.6-3+b1 [147 kB] Fetched 147 kB in 0s (679 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmprmuj_y_8/liblua5.4-0_5.4.6-3+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-latexcodec all 3.0.0-1 [17.5 kB] Fetched 17.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp_ca6rmsi/python3-latexcodec_3.0.0-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-6 [19.5 kB] Fetched 19.5 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyhl3vnoz/libsasl2-modules-db_2.1.28+dfsg1-6_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Fetched 52.9 kB in 0s (4870 kB/s) dpkg-name: info: moved 'libxext6_2%3a1.3.4-1+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmphqazx1tq/libxext6_1.3.4-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Fetched 314 kB in 0s (26.3 MB/s) dpkg-name: info: moved 'libmagic-mgc_1%3a5.45-3_amd64.deb' to '/srv/rebuilderd/tmp/tmp7d6xazgv/libmagic-mgc_5.45-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-zmq amd64 24.0.1-5+b1 [356 kB] Fetched 356 kB in 0s (1498 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbdnljur2/python3-zmq_24.0.1-5+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libsodium23 amd64 1.0.18-1+b1 [163 kB] Fetched 163 kB in 0s (795 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3a01o31k/libsodium23_1.0.18-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libsframe1 amd64 2.42.50.20240625-1 [76.1 kB] Fetched 76.1 kB in 0s (497 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyqhf4qxw/libsframe1_2.42.50.20240625-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 usr-is-merged all 39 [5572 B] Fetched 5572 B in 0s (541 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7z947tjx/usr-is-merged_39_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-fonttools amd64 4.46.0-1 [1623 kB] Fetched 1623 kB in 0s (4721 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpf2eu0y_h/python3-fonttools_4.46.0-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libmpc3 amd64 1.3.1-1+b2 [52.1 kB] Fetched 52.1 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpt4s1lvai/libmpc3_1.3.1-1+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 netbase all 6.4 [12.8 kB] Fetched 12.8 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp36866cfw/netbase_6.4_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libgomp1 amd64 14.1.0-3 [137 kB] Fetched 137 kB in 0s (730 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmput9dgi5k/libgomp1_14.1.0-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 debconf all 1.5.86 [119 kB] Fetched 119 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpg1b3texu/debconf_1.5.86_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libdeflate0 amd64 1.20-1 [46.0 kB] Fetched 46.0 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpiy21vltz/libdeflate0_1.20-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libtcl8.6 amd64 8.6.14+dfsg-1 [1034 kB] Fetched 1034 kB in 0s (68.4 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpzw_o94j7/libtcl8.6_8.6.14+dfsg-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libxdmcp6 amd64 1:1.1.2-3+b1 [24.3 kB] Fetched 24.3 kB in 0s (0 B/s) dpkg-name: info: moved 'libxdmcp6_1%3a1.1.2-3+b1_amd64.deb' to '/srv/rebuilderd/tmp/tmp5pntx29p/libxdmcp6_1.1.2-3+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libraqm0 amd64 0.10.1-1+b1 [14.2 kB] Fetched 14.2 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpbwvo92sx/libraqm0_0.10.1-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-bleach all 6.1.0-2 [50.7 kB] Fetched 50.7 kB in 0s (293 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjue_jwud/python3-bleach_6.1.0-2_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3.12-dev amd64 3.12.4-1 [499 kB] Fetched 499 kB in 0s (2030 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpj_lxc0b1/python3.12-dev_3.12.4-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libxcb1 amd64 1.17.0-2 [144 kB] Fetched 144 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp4ntks4gt/libxcb1_1.17.0-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7 [586 kB] Fetched 586 kB in 0s (2247 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpmi5n8sxn/tk8.6-blt2.5_2.5.3+dfsg-7_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libpam-modules amd64 1.5.3-7 [265 kB] Fetched 265 kB in 0s (25.1 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2l_mypc8/libpam-modules_1.5.3-7_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-mistune all 3.0.2-1 [33.1 kB] Fetched 33.1 kB in 0s (138 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp3w548fhu/python3-mistune_3.0.2-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Fetched 305 kB in 0s (29.9 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmphfqpzcwa/libbrotli1_1.1.0-2+b3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 perl-base amd64 5.38.2-5 [1643 kB] Fetched 1643 kB in 0s (99.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp7v1acwl2/perl-base_5.38.2-5_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libhwasan0 amd64 14.1.0-3 [1489 kB] Fetched 1489 kB in 0s (3998 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp45wf0qeb/libhwasan0_14.1.0-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libatomic1 amd64 14.1.0-3 [9180 B] Fetched 9180 B in 0s (54.1 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmplw7q4t8w/libatomic1_14.1.0-3_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 patch amd64 2.7.6-7 [128 kB] Fetched 128 kB in 0s (11.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpznjfwf86/patch_2.7.6-7_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libmpfr6 amd64 4.2.1-1+b1 [714 kB] Fetched 714 kB in 0s (61.8 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptcwzcy1q/libmpfr6_4.2.1-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-all amd64 3.12.2-1 [1060 B] Fetched 1060 B in 0s (5983 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpyw8s2jga/python3-all_3.12.2-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libyaml-0-2 amd64 0.2.5-1+b1 [52.6 kB] Fetched 52.6 kB in 0s (189 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpx9vmemhn/libyaml-0-2_0.2.5-1+b1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libpython3.12t64 amd64 3.12.4-1 [2111 kB] Fetched 2111 kB in 0s (6152 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp46tgz0au/libpython3.12t64_3.12.4-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 grep amd64 3.11-4 [431 kB] Fetched 431 kB in 0s (41.2 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpjl3cublm/grep_3.11-4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libwebp7 amd64 1.4.0-0.1 [311 kB] Fetched 311 kB in 0s (30.5 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpb80gzifq/libwebp7_1.4.0-0.1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 cpp amd64 4:13.2.0-7 [1564 B] Fetched 1564 B in 0s (0 B/s) dpkg-name: info: moved 'cpp_4%3a13.2.0-7_amd64.deb' to '/srv/rebuilderd/tmp/tmpy3ylfj9_/cpp_13.2.0-7_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libselinux1 amd64 3.5-2+b2 [74.9 kB] Fetched 74.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpfv51atpv/libselinux1_3.5-2+b2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 findutils amd64 4.10.0-2 [699 kB] Fetched 699 kB in 0s (59.0 MB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpp182vixd/findutils_4.10.0-2_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-tqdm all 4.66.4-1 [90.8 kB] Fetched 90.8 kB in 0s (265 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2rr53quq/python3-tqdm_4.66.4-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240712T203746Z sid/main amd64 fonts-lyx all 2.4.1-1 [189 kB] Fetched 189 kB in 0s (865 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp6d2a36dl/fonts-lyx_2.4.1-1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 base-passwd amd64 3.6.4 [50.9 kB] Fetched 50.9 kB in 0s (0 B/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp2xcfvys8/base-passwd_3.6.4_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 dh-python all 6.20240603 [109 kB] Fetched 109 kB in 0s (546 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmptw2y4wu0/dh-python_6.20240603_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libjs-jquery-hotkeys all 0~20130707+git2d51e3a9+dfsg-2.1 [11.5 kB] Fetched 11.5 kB in 0s (70.7 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmp1ke8mpf8/libjs-jquery-hotkeys_0~20130707+git2d51e3a9+dfsg-2.1_all.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 libctf0 amd64 2.42.50.20240625-1 [88.5 kB] Fetched 88.5 kB in 0s (441 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmppefgjjbz/libctf0_2.42.50.20240625-1_amd64.deb' Get:1 http://snapshot.debian.org/archive/debian/20240704T022806Z sid/main amd64 python3-llvmlite amd64 0.42.0-1+b1 [180 kB] Fetched 180 kB in 0s (901 kB/s) dpkg-name: warning: skipping '/srv/rebuilderd/tmp/tmpf6chv50m/python3-llvmlite_0.42.0-1+b1_amd64.deb' dpkg-buildpackage: info: source package debootsnap-dummy dpkg-buildpackage: info: source version 1.0 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Equivs Dummy Package Generator dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/debootsnap-dummy/ dh_install dh_installdocs dh_installchangelogs dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'debootsnap-dummy' in '../debootsnap-dummy_1.0_all.deb'. dpkg-genbuildinfo --build=binary -O../debootsnap-dummy_1.0_amd64.buildinfo dpkg-genchanges --build=binary -O../debootsnap-dummy_1.0_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) The package has been created. Attention, the package has been created in the /srv/rebuilderd/tmp/tmpm_77abw2/cache directory, not in ".." as indicated by the message above! I: automatically chosen mode: unshare I: chroot architecture amd64 is equal to the host's architecture I: using /srv/rebuilderd/tmp/mmdebstrap.VJnVd3ufE1 as tempdir I: running --setup-hook directly: /usr/share/mmdebstrap/hooks/maybe-merged-usr/setup00.sh /srv/rebuilderd/tmp/mmdebstrap.VJnVd3ufE1 127.0.0.1 - - [04/Oct/2025 11:03:41] code 404, message File not found 127.0.0.1 - - [04/Oct/2025 11:03:41] "GET /./InRelease HTTP/1.1" 404 - Ign:1 http://localhost:43041 ./ InRelease 127.0.0.1 - - [04/Oct/2025 11:03:41] "GET /./Release HTTP/1.1" 200 - Get:2 http://localhost:43041 ./ Release [462 B] 127.0.0.1 - - [04/Oct/2025 11:03:41] code 404, message File not found 127.0.0.1 - - [04/Oct/2025 11:03:41] "GET /./Release.gpg HTTP/1.1" 404 - Ign:3 http://localhost:43041 ./ Release.gpg 127.0.0.1 - - [04/Oct/2025 11:03:41] "GET /./Packages HTTP/1.1" 200 - Get:4 http://localhost:43041 ./ Packages [531 kB] Fetched 531 kB in 0s (16.9 MB/s) Reading package lists... usr-is-merged found -- running merged-usr setup hook dpkg-deb: building package 'usr-is-merged' in '/srv/rebuilderd/tmp/mmdebstrap.VJnVd3ufE1/tmp/tmp.gIUCZld1Vg/usr-is-merged.deb'. Selecting previously unselected package usr-is-merged. (Reading database ... 0 files and directories currently installed.) Preparing to unpack .../usr-is-merged.deb ... Unpacking usr-is-merged (1) ... touch: cannot touch '/run/needrestart/unpacked': Permission denied Setting up usr-is-merged (1) ... I: skipping apt-get update because it was already run I: downloading packages with apt... 127.0.0.1 - - [04/Oct/2025 11:03:42] "GET /./gcc-14-base_14.1.0-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Oct/2025 11:03:42] "GET /./libc6_2.38-13_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Oct/2025 11:03:42] "GET /./libgcc-s1_14.1.0-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Oct/2025 11:03:42] "GET /./mawk_1.3.4.20240622-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Oct/2025 11:03:42] "GET /./base-files_13.3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Oct/2025 11:03:42] "GET /./libtinfo6_6.5-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Oct/2025 11:03:42] "GET /./debianutils_5.19_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Oct/2025 11:03:42] "GET /./bash_5.2.21-2.1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Oct/2025 11:03:42] "GET /./libcap2_2.66-5_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Oct/2025 11:03:42] "GET /./libsystemd0_256.1-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Oct/2025 11:03:42] "GET /./bsdutils_2.40.1-9_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Oct/2025 11:03:42] "GET /./libacl1_2.3.2-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Oct/2025 11:03:42] "GET /./libattr1_2.5.2-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Oct/2025 11:03:42] "GET /./libgmp10_6.3.0%2bdfsg-2%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Oct/2025 11:03:42] "GET /./libpcre2-8-0_10.42-4%2bb1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Oct/2025 11:03:42] "GET /./libselinux1_3.5-2%2bb2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Oct/2025 11:03:42] "GET /./libzstd1_1.5.6%2bdfsg-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Oct/2025 11:03:42] "GET /./zlib1g_1.3.dfsg%2breally1.3.1-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Oct/2025 11:03:42] "GET /./libssl3t64_3.2.2-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Oct/2025 11:03:42] "GET /./coreutils_9.4-3.1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Oct/2025 11:03:42] "GET /./dash_0.5.12-9_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Oct/2025 11:03:42] "GET /./diffutils_3.10-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Oct/2025 11:03:42] "GET /./libbz2-1.0_1.0.8-5.1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Oct/2025 11:03:42] "GET /./liblzma5_5.6.2-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Oct/2025 11:03:42] "GET /./libmd0_1.1.0-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Oct/2025 11:03:42] "GET /./tar_1.35%2bdfsg-3_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Oct/2025 11:03:42] "GET /./dpkg_1.22.6_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Oct/2025 11:03:42] "GET /./findutils_4.10.0-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Oct/2025 11:03:42] "GET /./grep_3.11-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Oct/2025 11:03:42] "GET /./gzip_1.12-1.1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Oct/2025 11:03:42] "GET /./hostname_3.23%2bnmu2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Oct/2025 11:03:42] "GET /./ncurses-bin_6.5-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Oct/2025 11:03:42] "GET /./libcrypt1_4.4.36-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Oct/2025 11:03:42] "GET /./perl-base_5.38.2-5_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Oct/2025 11:03:42] "GET /./sed_4.9-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Oct/2025 11:03:42] "GET /./libaudit-common_3.1.2-4_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Oct/2025 11:03:42] "GET /./libcap-ng0_0.8.5-1_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Oct/2025 11:03:42] "GET /./libaudit1_3.1.2-4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Oct/2025 11:03:42] "GET /./libdb5.3t64_5.3.28%2bdfsg2-7_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Oct/2025 11:03:42] "GET /./debconf_1.5.86_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Oct/2025 11:03:42] "GET /./libpam0g_1.5.3-7_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Oct/2025 11:03:42] "GET /./libpam-modules-bin_1.5.3-7_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Oct/2025 11:03:42] "GET /./libpam-modules_1.5.3-7_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Oct/2025 11:03:42] "GET /./libpam-runtime_1.5.3-7_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Oct/2025 11:03:42] "GET /./libblkid1_2.40.1-9_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Oct/2025 11:03:42] "GET /./libmount1_2.40.1-9_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Oct/2025 11:03:42] "GET /./libsmartcols1_2.40.1-9_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Oct/2025 11:03:42] "GET /./libudev1_256.1-2_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Oct/2025 11:03:42] "GET /./libuuid1_2.40.1-9_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Oct/2025 11:03:42] "GET /./util-linux_2.40.1-9_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Oct/2025 11:03:42] "GET /./libdebconfclient0_0.272_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Oct/2025 11:03:42] "GET /./base-passwd_3.6.4_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Oct/2025 11:03:42] "GET /./init-system-helpers_1.66_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Oct/2025 11:03:42] "GET /./libc-bin_2.38-13_amd64.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Oct/2025 11:03:42] "GET /./ncurses-base_6.5-2_all.deb HTTP/1.1" 200 - 127.0.0.1 - - [04/Oct/2025 11:03:42] "GET /./sysvinit-utils_3.09-2_amd64.deb HTTP/1.1" 200 - I: extracting archives... I: running --extract-hook directly: /usr/share/mmdebstrap/hooks/maybe-merged-usr/extract00.sh /srv/rebuilderd/tmp/mmdebstrap.VJnVd3ufE1 127.0.0.1 - - [04/Oct/2025 11:03:43] code 404, message File not found 127.0.0.1 - - [04/Oct/2025 11:03:43] "GET /./InRelease HTTP/1.1" 404 - Ign:1 http://localhost:43041 ./ InRelease 127.0.0.1 - - [04/Oct/2025 11:03:43] "GET /./Release HTTP/1.1" 304 - Hit:2 http://localhost:43041 ./ Release 127.0.0.1 - - [04/Oct/2025 11:03:43] code 404, message File not found 127.0.0.1 - - [04/Oct/2025 11:03:43] "GET /./Release.gpg HTTP/1.1" 404 - Ign:3 http://localhost:43041 ./ Release.gpg Reading package lists... usr-is-merged found -- running merged-usr extract hook I: installing essential packages... I: running --essential-hook directly: /usr/share/mmdebstrap/hooks/maybe-merged-usr/essential00.sh /srv/rebuilderd/tmp/mmdebstrap.VJnVd3ufE1 dummy usr-is-merged package installed -- running merged-usr essential hook Reading package lists... Building dependency tree... The following packages will be upgraded: usr-is-merged 127.0.0.1 - - [04/Oct/2025 11:03:48] "GET /./usr-is-merged_39_all.deb HTTP/1.1" 200 - 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 5572 B of archives. After this operation, 13.3 kB of additional disk space will be used. Get:1 http://localhost:43041 ./ usr-is-merged 39 [5572 B] Fetched 5572 B in 0s (242 kB/s) Chrooting into /srv/rebuilderd/tmp/mmdebstrap.VJnVd3ufE1/ (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 3520 files and directories currently installed.) Preparing to unpack .../usr-is-merged_39_all.deb ... Unpacking usr-is-merged (39) over (1) ... Chrooting into /srv/rebuilderd/tmp/mmdebstrap.VJnVd3ufE1/ Setting up usr-is-merged (39) ... 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- [04/Oct/2025 11:03:52] "GET /./debootsnap-dummy_1.0_all.deb HTTP/1.1" 200 - I: running --customize-hook directly: /srv/rebuilderd/tmp/tmpm_77abw2/apt_install.sh /srv/rebuilderd/tmp/mmdebstrap.VJnVd3ufE1 Reading package lists... Building dependency tree... Reading state information... unicode-data is already the newest version (15.1.0-1). unicode-data set to manually installed. python3-webencodings is already the newest version (0.5.1-5). python3-webencodings set to manually installed. python3.11-dev is already the newest version (3.11.9-1). python3.11-dev set to manually installed. libunistring5 is already the newest version (1.2-1). libunistring5 set to manually installed. libllvm14t64 is already the newest version (1:14.0.6-20). libllvm14t64 set to manually installed. python3-build is already the newest version (1.2.1-1). python3-build set to manually installed. libexpat1-dev is already the newest version (2.6.2-1). libexpat1-dev set to manually installed. python3-pil is already the newest version (10.3.0-2). python3-pil set to manually installed. libkeyutils1 is already the newest version (1.6.3-3). libkeyutils1 set to manually installed. python3.11-minimal is already the newest version (3.11.9-1). python3.11-minimal set to manually installed. libblkid1 is already the newest version (2.40.1-9). g++-13 is already the newest version (13.3.0-1). g++-13 set to manually installed. dpkg is already the newest version (1.22.6). python3-dateutil is already the newest version (2.9.0-2). python3-dateutil set to manually installed. liblz4-1 is already the newest version (1.9.4-2). liblz4-1 set to manually installed. python3-pytest-xdist is already the newest version (3.6.1-1). python3-pytest-xdist set to manually installed. libgssapi-krb5-2 is already the newest version (1.21.2-1). libgssapi-krb5-2 set to manually installed. base-files is already the newest version (13.3). python3-tabulate is already the newest version (0.9.0-1). python3-tabulate set to manually installed. blt is already the newest version (2.5.3+dfsg-7). blt set to manually installed. python-tinycss2-common is already the newest version (1.3.0-1). python-tinycss2-common set to manually installed. libcurl4t64 is already the newest version (8.8.0-2). libcurl4t64 set to manually installed. python3-decorator is already the newest version (5.1.1-5). python3-decorator set to manually installed. libpam0g is already the newest version (1.5.3-7). python3-isort is already the newest version (5.6.4-1). python3-isort set to manually installed. liblerc4 is already the newest version (4.0.0+ds-4+b1). liblerc4 set to manually installed. file is already the newest version (1:5.45-3). file set to manually installed. python3-minimal is already the newest version (3.12.2-1). python3-minimal set to manually installed. python3-setuptools-scm is already the newest version (8.1.0-1). python3-setuptools-scm set to manually installed. libpam-runtime is already the newest version (1.5.3-7). coreutils is already the newest version (9.4-3.1). libpng16-16t64 is already the newest version (1.6.43-5). libpng16-16t64 set to manually installed. python3-execnet is already the newest version (2.1.1-1). python3-execnet set to manually installed. libseccomp2 is already the newest version (2.5.5-1). libseccomp2 set to manually installed. pandoc-data is already the newest version (3.1.3-2). pandoc-data set to manually installed. python3-toml is already the newest version (0.10.2-1). python3-toml set to manually installed. libcc1-0 is already the newest version (14.1.0-3). libcc1-0 set to manually installed. python3-tenacity is already the newest version (8.4.2-1). python3-tenacity set to manually installed. libsasl2-2 is already the newest version (2.1.28+dfsg1-6). libsasl2-2 set to manually installed. libexpat1 is already the newest version (2.6.2-1). libexpat1 set to manually installed. automake is already the newest version (1:1.16.5-1.3). automake set to manually installed. python3-jupyter-client is already the newest version (7.4.9-2). python3-jupyter-client set to manually installed. libxau6 is already the newest version (1:1.0.9-1+b1). libxau6 set to manually installed. cpp-x86-64-linux-gnu is already the newest version (4:13.2.0-7). cpp-x86-64-linux-gnu set to manually installed. libxml2 is already the newest version (2.12.7+dfsg-3). libxml2 set to manually installed. python-babel-localedata is already the newest version (2.14.0-1). python-babel-localedata set to manually installed. libfreetype6 is already the newest version (2.13.2+dfsg-1+b4). libfreetype6 set to manually installed. libk5crypto3 is already the newest version (1.21.2-1). libk5crypto3 set to manually installed. readline-common is already the newest version (8.2-4). readline-common set to manually installed. libopenjp2-7 is already the newest version (2.5.0-2+b3). libopenjp2-7 set to manually installed. python3-json5 is already the newest version (0.9.25-1). python3-json5 set to manually installed. python3-stevedore is already the newest version (5.2.0-2). python3-stevedore set to manually installed. libaudit-common is already the newest version (1:3.1.2-4). libpython3.11t64 is already the newest version (3.11.9-1). libpython3.11t64 set to manually installed. libjs-underscore is already the newest version (1.13.4~dfsg+~1.11.4-3). libjs-underscore set to manually installed. python3-commonmark is already the newest version (0.9.1-6). python3-commonmark set to manually installed. libuuid1 is already the newest version (2.40.1-9). libuchardet0 is already the newest version (0.0.8-1+b1). libuchardet0 set to manually installed. libbinutils is already the newest version (2.42.50.20240625-1). libbinutils set to manually installed. libkrb5support0 is already the newest version (1.21.2-1). libkrb5support0 set to manually installed. libc-bin is already the newest version (2.38-13). python3-nest-asyncio is already the newest version (1.5.4-1). python3-nest-asyncio set to manually installed. python3-soupsieve is already the newest version (2.5-1). python3-soupsieve set to manually installed. libgprofng0 is already the newest version (2.42.50.20240625-1). libgprofng0 set to manually installed. python3-coverage is already the newest version (7.2.7+dfsg1-1+b1). python3-coverage set to manually installed. bash is already the newest version (5.2.21-2.1). docutils-common is already the newest version (0.20.1+dfsg-3). docutils-common set to manually installed. build-essential is already the newest version (12.10). build-essential set to manually installed. python3-appdirs is already the newest version (1.4.4-4). python3-appdirs set to manually installed. python3-sniffio is already the newest version (1.3.1-1). python3-sniffio set to manually installed. libjs-sphinxdoc is already the newest version (7.3.7-3). libjs-sphinxdoc set to manually installed. liblapack3 is already the newest version (3.12.0-3). liblapack3 set to manually installed. libc6 is already the newest version (2.38-13). x11-common is already the newest version (1:7.7+23). x11-common set to manually installed. python3-snowballstemmer is already the newest version (2.2.0-4). python3-snowballstemmer set to manually installed. python3-tomli-w is already the newest version (1.0.0-2). python3-tomli-w set to manually installed. sysvinit-utils is already the newest version (3.09-2). libjpeg62-turbo is already the newest version (1:2.1.5-3). libjpeg62-turbo set to manually installed. libcrypt-dev is already the newest version (1:4.4.36-4). libcrypt-dev set to manually installed. python3-distutils is already the newest version (3.12.3-3.1). python3-distutils set to manually installed. python3-hatchling is already the newest version (1.25.0-1). python3-hatchling set to manually installed. flit is already the newest version (3.9.0-2). flit set to manually installed. python3-cffi-backend is already the newest version (1.16.0-2+b2). python3-cffi-backend set to manually installed. python3-charset-normalizer is already the newest version (3.3.2-1). python3-charset-normalizer set to manually installed. python3-roman is already the newest version (3.3-3). python3-roman set to manually installed. sgml-base is already the newest version (1.31). sgml-base set to manually installed. fonts-glyphicons-halflings is already the newest version (1.009~3.4.1+dfsg-3). fonts-glyphicons-halflings set to manually installed. diffutils is already the newest version (1:3.10-1). ncurses-base is already the newest version (6.5-2). pybuild-plugin-pyproject is already the newest version (6.20240603). pybuild-plugin-pyproject set to manually installed. python3-scipy is already the newest version (1.12.0-2). python3-scipy set to manually installed. libtinfo6 is already the newest version (6.5-2). tar is already the newest version (1.35+dfsg-3). gcc-13-x86-64-linux-gnu is already the newest version (13.3.0-1). gcc-13-x86-64-linux-gnu set to manually installed. python3-docutils is already the newest version (0.20.1+dfsg-3). python3-docutils set to manually installed. python3-typing-extensions is already the newest version (4.12.2-1). python3-typing-extensions set to manually installed. libpython3.12-dev is already the newest version (3.12.4-1). libpython3.12-dev set to manually installed. python3-pytest is already the newest version (8.2.2-2). python3-pytest set to manually installed. python3-nbconvert is already the newest version (7.16.4-1). python3-nbconvert set to manually installed. libnghttp2-14 is already the newest version (1.62.1-1). libnghttp2-14 set to manually installed. python3-babel is already the newest version (2.14.0-1). python3-babel set to manually installed. man-db is already the newest version (2.12.1-2). man-db set to manually installed. architecture-properties is already the newest version (0.1.1+b1). architecture-properties set to manually installed. python3-requests is already the newest version (2.32.3+dfsg-1). python3-requests set to manually installed. m4 is already the newest version (1.4.19-4). m4 set to manually installed. python3-jupyter-server is already the newest version (1.23.3-2). python3-jupyter-server set to manually installed. python3-markupsafe is already the newest version (2.1.5-1). python3-markupsafe set to manually installed. libstdc++6 is already the newest version (14.1.0-3). libstdc++6 set to manually installed. libtiff6 is already the newest version (4.5.1+git230720-4). libtiff6 set to manually installed. libacl1 is already the newest version (2.3.2-2). python3-cycler is already the newest version (0.12.1-1). python3-cycler set to manually installed. libjbig0 is already the newest version (2.1-6.1+b1). libjbig0 set to manually installed. python3-sphinx-bootstrap-theme is already the newest version (0.8.1-5). python3-sphinx-bootstrap-theme set to manually installed. libpython3.11-stdlib is already the newest version (3.11.9-1). libpython3.11-stdlib set to manually installed. libpython3.11-dev is already the newest version (3.11.9-1). libpython3.11-dev set to manually installed. libtool is already the newest version (2.4.7-7). libtool set to manually installed. libfile-stripnondeterminism-perl is already the newest version (1.14.0-1). libfile-stripnondeterminism-perl set to manually installed. python3-dev is already the newest version (3.12.2-1). python3-dev set to manually installed. python3-send2trash is already the newest version (1.8.2-1). python3-send2trash set to manually installed. libglib2.0-0t64 is already the newest version (2.80.3-1). libglib2.0-0t64 set to manually installed. libblas3 is already the newest version (3.12.0-3). libblas3 set to manually installed. sphinx-common is already the newest version (7.3.7-3). sphinx-common set to manually installed. libxslt1.1 is already the newest version (1.1.35-1+b1). libxslt1.1 set to manually installed. libxss1 is already the newest version (1:1.2.3-1+b1). libxss1 set to manually installed. libjs-jquery-ui is already the newest version (1.13.2+dfsg-1). libjs-jquery-ui set to manually installed. python3-pbr is already the newest version (6.0.0-2). python3-pbr set to manually installed. libjs-jquery-isonscreen is already the newest version (1.2.0-1.1). libjs-jquery-isonscreen set to manually installed. libtbb12 is already the newest version (2021.11.0-2). libtbb12 set to manually installed. libjs-jquery-throttle-debounce is already the newest version (1.1+dfsg.1-2). libjs-jquery-throttle-debounce set to manually installed. python3-pytest-cov is already the newest version (5.0.0-1). python3-pytest-cov set to manually installed. python3-ufolib2 is already the newest version (0.16.0+dfsg1-1). python3-ufolib2 set to manually installed. python3-pkg-resources is already the newest version (68.1.2-2). python3-pkg-resources set to manually installed. libgnutls30t64 is already the newest version (3.8.5-4). libgnutls30t64 set to manually installed. python-matplotlib-data is already the newest version (3.6.3-2). python-matplotlib-data set to manually installed. libp11-kit0 is already the newest version (0.25.3-5). libp11-kit0 set to manually installed. cpp-13-x86-64-linux-gnu is already the newest version (13.3.0-1). cpp-13-x86-64-linux-gnu set to manually installed. python3-fs is already the newest version (2.4.16-4). python3-fs set to manually installed. sensible-utils is already the newest version (0.0.24). sensible-utils set to manually installed. libpam-modules-bin is already the newest version (1.5.3-7). python3-imagesize is already the newest version (1.4.1-1). python3-imagesize set to manually installed. python3-pybtex-docutils is already the newest version (1.0.2-1). python3-pybtex-docutils set to manually installed. rpcsvc-proto is already the newest version (1.4.3-1). rpcsvc-proto set to manually installed. g++-x86-64-linux-gnu is already the newest version (4:13.2.0-7). g++-x86-64-linux-gnu set to manually installed. binutils-x86-64-linux-gnu is already the newest version (2.42.50.20240625-1). binutils-x86-64-linux-gnu set to manually installed. fonts-dejavu-mono is already the newest version (2.37-8). fonts-dejavu-mono set to manually installed. groff-base is already the newest version (1.23.0-5). groff-base set to manually installed. libpcre2-8-0 is already the newest version (10.42-4+b1). libx11-6 is already the newest version (2:1.8.7-1+b1). libx11-6 set to manually installed. libtasn1-6 is already the newest version (4.19.0-3+b2). libtasn1-6 set to manually installed. libgmp10 is already the newest version (2:6.3.0+dfsg-2+b1). openssl is already the newest version (3.2.2-1). openssl set to manually installed. libzstd1 is already the newest version (1.5.6+dfsg-1). ncurses-bin is already the newest version (6.5-2). gcc-13 is already the newest version (13.3.0-1). gcc-13 set to manually installed. debianutils is already the newest version (5.19). libtbbbind-2-5 is already the newest version (2021.11.0-2). libtbbbind-2-5 set to manually installed. libpython3-stdlib is already the newest version (3.12.2-1). libpython3-stdlib set to manually installed. python3-brotli is already the newest version (1.1.0-2+b3). python3-brotli set to manually installed. libjs-jquery-tablesorter is already the newest version (1:2.31.3+dfsg1-3). libjs-jquery-tablesorter set to manually installed. python3-bs4 is already the newest version (4.12.3-1). python3-bs4 set to manually installed. python3-prometheus-client is already the newest version (0.19.0+ds1-1). python3-prometheus-client set to manually installed. bsdutils is already the newest version (1:2.40.1-9). libcom-err2 is already the newest version (1.47.1-1). libcom-err2 set to manually installed. python3.12 is already the newest version (3.12.4-1). python3.12 set to manually installed. fonts-dejavu-core is already the newest version (2.37-8). fonts-dejavu-core set to manually installed. libx11-data is already the newest version (2:1.8.7-1). libx11-data set to manually installed. python3-pil.imagetk is already the newest version (10.3.0-2). python3-pil.imagetk set to manually installed. python3-jupyterlab-server is already the newest version (2.25.2-1). python3-jupyterlab-server set to manually installed. python3-tz is already the newest version (2024.1-2). python3-tz set to manually installed. python3-pydata-sphinx-theme is already the newest version (0.15.2.is.0.7.2-1). python3-pydata-sphinx-theme set to manually installed. cpp-13 is already the newest version (13.3.0-1). cpp-13 set to manually installed. libwebpmux3 is already the newest version (1.4.0-0.1). libwebpmux3 set to manually installed. libz3-4 is already the newest version (4.8.12-3.1+b2). libz3-4 set to manually installed. perl-modules-5.38 is already the newest version (5.38.2-5). perl-modules-5.38 set to manually installed. util-linux is already the newest version (2.40.1-9). libcrypt1 is already the newest version (1:4.4.36-4). libhwloc15 is already the newest version (2.11.0-2). libhwloc15 set to manually installed. libtbbmalloc2 is already the newest version (2021.11.0-2). libtbbmalloc2 set to manually installed. libisl23 is already the newest version (0.26-3+b2). libisl23 set to manually installed. liblzma5 is already the newest version (5.6.2-1). python3-sphinxcontrib.bibtex is already the newest version (2.6.2-1). python3-sphinxcontrib.bibtex set to manually installed. libgdbm-compat4t64 is already the newest version (1.23-6). libgdbm-compat4t64 set to manually installed. librtmp1 is already the newest version (2.4+20151223.gitfa8646d.1-2+b4). librtmp1 set to manually installed. libssl3t64 is already the newest version (3.2.2-1). python3-chardet is already the newest version (5.2.0+dfsg-1). python3-chardet set to manually installed. python3-pyparsing is already the newest version (3.1.2-1). python3-pyparsing set to manually installed. linux-libc-dev is already the newest version (6.9.7-1). linux-libc-dev set to manually installed. python3-all-dev is already the newest version (3.12.2-1). python3-all-dev set to manually installed. libc-dev-bin is already the newest version (2.38-13). libc-dev-bin set to manually installed. python3-pathspec is already the newest version (0.12.1-1). python3-pathspec set to manually installed. binutils is already the newest version (2.42.50.20240625-1). binutils set to manually installed. libfribidi0 is already the newest version (1.0.13-3+b1). libfribidi0 set to manually installed. python3-argon2 is already the newest version (21.1.0-2). python3-argon2 set to manually installed. libffi8 is already the newest version (3.4.6-1). libffi8 set to manually installed. python3-tornado is already the newest version (6.4.1-1). python3-tornado set to manually installed. python3-pandocfilters is already the newest version (1.5.1-1). python3-pandocfilters set to manually installed. libxft2 is already the newest version (2.3.6-1+b1). libxft2 set to manually installed. python3-numba is already the newest version (0.59.1+dfsg-1). python3-numba set to manually installed. libmagic1t64 is already the newest version (1:5.45-3). libmagic1t64 set to manually installed. libssh2-1t64 is already the newest version (1.11.0-5). libssh2-1t64 set to manually installed. python3-jupyterlab-pygments is already the newest version (0.2.2-3). python3-jupyterlab-pygments set to manually installed. g++-13-x86-64-linux-gnu is already the newest version (13.3.0-1). g++-13-x86-64-linux-gnu set to manually installed. python3-numpy is already the newest version (1:1.26.4+ds-10). python3-numpy set to manually installed. python3-nbsphinx is already the newest version (0.9.4+ds-1). python3-nbsphinx set to manually installed. libjs-jquery is already the newest version (3.6.1+dfsg+~3.5.14-1). libjs-jquery set to manually installed. python3-mpmath is already the newest version (1.3.0-1). python3-mpmath set to manually installed. python3-rpds-py is already the newest version (0.12.0-3). python3-rpds-py set to manually installed. zlib1g-dev is already the newest version (1:1.3.dfsg+really1.3.1-1). zlib1g-dev set to manually installed. libitm1 is already the newest version (14.1.0-3). libitm1 set to manually installed. libgpg-error0 is already the newest version (1.49-2). libgpg-error0 set to manually installed. libpython3.11-minimal is already the newest version (3.11.9-1). libpython3.11-minimal set to manually installed. fontconfig-config is already the newest version (2.15.0-1.1). fontconfig-config set to manually installed. python3-alabaster is already the newest version (0.7.16-0.1). python3-alabaster set to manually installed. libfontconfig1 is already the newest version (2.15.0-1.1). libfontconfig1 set to manually installed. libbsd0 is already the newest version (0.12.2-1). libbsd0 set to manually installed. libjansson4 is already the newest version (2.14-2+b2). libjansson4 set to manually installed. python3-lz4 is already the newest version (4.0.2+dfsg-1+b3). python3-lz4 set to manually installed. cython3 is already the newest version (3.0.10+dfsg-5). cython3 set to manually installed. autotools-dev is already the newest version (20220109.1). autotools-dev set to manually installed. gcc-x86-64-linux-gnu is already the newest version (4:13.2.0-7). gcc-x86-64-linux-gnu set to manually installed. python3-tinycss2 is already the newest version (1.3.0-1). python3-tinycss2 set to manually installed. libsmartcols1 is already the newest version (2.40.1-9). libnettle8t64 is already the newest version (3.10-1). libnettle8t64 set to manually installed. python3-nbclient is already the newest version (0.8.0-1). python3-nbclient set to manually installed. python3-wheel is already the newest version (0.43.0-1). python3-wheel set to manually installed. libkrb5-3 is already the newest version (1.21.2-1). libkrb5-3 set to manually installed. llvm-14 is already the newest version (1:14.0.6-20). llvm-14 set to manually installed. python3-certifi is already the newest version (2024.6.2-1). python3-certifi set to manually installed. python3-iniconfig is already the newest version (1.1.1-2). python3-iniconfig set to manually installed. libbz2-1.0 is already the newest version (1.0.8-5.1). debhelper is already the newest version (13.16). debhelper set to manually installed. python3 is already the newest version (3.12.2-1). python3 set to manually installed. libdpkg-perl is already the newest version (1.22.6). libdpkg-perl set to manually installed. python3-numpydoc is already the newest version (1.6.0-2). python3-numpydoc set to manually installed. ca-certificates is already the newest version (20240203). ca-certificates set to manually installed. gettext-base is already the newest version (0.22.5-1). gettext-base set to manually installed. libidn2-0 is already the newest version (2.3.7-2). libidn2-0 set to manually installed. xml-core is already the newest version (0.19). xml-core set to manually installed. libgcrypt20 is already the newest version (1.10.3-3). libgcrypt20 set to manually installed. libdebconfclient0 is already the newest version (0.272). dh-strip-nondeterminism is already the newest version (1.14.0-1). dh-strip-nondeterminism set to manually installed. python3-referencing is already the newest version (0.31.0-1). python3-referencing set to manually installed. python3-sphinx-gallery is already the newest version (0.16.0-1). python3-sphinx-gallery set to manually installed. jupyter-sphinx-theme-common is already the newest version (0.0.6+ds1-11). jupyter-sphinx-theme-common set to manually installed. python3-tinydb is already the newest version (3.15.2-4). python3-tinydb set to manually installed. gcc-13-base is already the newest version (13.3.0-1). gcc-13-base set to manually installed. dash is already the newest version (0.5.12-9). liblsan0 is already the newest version (14.1.0-3). liblsan0 set to manually installed. libimagequant0 is already the newest version (2.18.0-1+b1). libimagequant0 set to manually installed. libtk8.6 is already the newest version (8.6.14-1). libtk8.6 set to manually installed. libstdc++-13-dev is already the newest version (13.3.0-1). libstdc++-13-dev set to manually installed. libelf1t64 is already the newest version (0.191-1+b1). libelf1t64 set to manually installed. python3-jsonschema is already the newest version (4.19.2-3). python3-jsonschema set to manually installed. libgcc-s1 is already the newest version (14.1.0-3). python3-setuptools is already the newest version (68.1.2-2). python3-setuptools set to manually installed. libattr1 is already the newest version (1:2.5.2-1). python3-ptyprocess is already the newest version (0.7.0-5). python3-ptyprocess set to manually installed. dwz is already the newest version (0.15-1+b1). dwz set to manually installed. libpsl5t64 is already the newest version (0.21.2-1.1). libpsl5t64 set to manually installed. dh-autoreconf is already the newest version (20). dh-autoreconf set to manually installed. python3-lxml is already the newest version (5.2.1-1). python3-lxml set to manually installed. python3-traitlets is already the newest version (5.14.3-1). python3-traitlets set to manually installed. libpython3-dev is already the newest version (3.12.2-1). libpython3-dev set to manually installed. libxrender1 is already the newest version (1:0.9.10-1.1+b1). libxrender1 set to manually installed. liblcms2-2 is already the newest version (2.14-2+b1). liblcms2-2 set to manually installed. python3-pluggy is already the newest version (1.5.0-1). python3-pluggy set to manually installed. libgdbm6t64 is already the newest version (1.23-6). libgdbm6t64 set to manually installed. intltool-debian is already the newest version (0.35.0+20060710.6). intltool-debian set to manually installed. libsharpyuv0 is already the newest version (1.4.0-0.1). libsharpyuv0 set to manually installed. libperl5.38t64 is already the newest version (5.38.2-5). libperl5.38t64 set to manually installed. libcap2 is already the newest version (1:2.66-5). liblbfgsb0 is already the newest version (3.0+dfsg.4-1+b1). liblbfgsb0 set to manually installed. python3-jupyter-core is already the newest version (5.3.2-2). python3-jupyter-core set to manually installed. python3-scitrack is already the newest version (2021.5.3-3). python3-scitrack set to manually installed. python3-yaml is already the newest version (6.0.1-2). python3-yaml set to manually installed. libpython3-all-dev is already the newest version (3.12.2-1). libpython3-all-dev set to manually installed. python3-installer is already the newest version (0.7.0+dfsg1-3). python3-installer set to manually installed. binutils-common is already the newest version (2.42.50.20240625-1). binutils-common set to manually installed. python3-trove-classifiers is already the newest version (2024.4.10-1). python3-trove-classifiers set to manually installed. libudev1 is already the newest version (256.1-2). libc6-dev is already the newest version (2.38-13). libc6-dev set to manually installed. python3-pyproject-hooks is already the newest version (1.1.0-1). python3-pyproject-hooks set to manually installed. gcc is already the newest version (4:13.2.0-7). gcc set to manually installed. python3-html5lib is already the newest version (1.1-6). python3-html5lib set to manually installed. libedit2 is already the newest version (3.1-20240517-1). libedit2 set to manually installed. libharfbuzz0b is already the newest version (8.3.0-2+b1). libharfbuzz0b set to manually installed. llvm-14-runtime is already the newest version (1:14.0.6-20). llvm-14-runtime set to manually installed. python3-terminado is already the newest version (0.18.1-1). python3-terminado set to manually installed. python3-entrypoints is already the newest version (0.4-2). python3-entrypoints set to manually installed. libpython3.12-minimal is already the newest version (3.12.4-1). libpython3.12-minimal set to manually installed. perl is already the newest version (5.38.2-5). perl set to manually installed. libncursesw6 is already the newest version (6.5-2). libncursesw6 set to manually installed. python3-six is already the newest version (1.16.0-6). python3-six set to manually installed. python3-packaging is already the newest version (24.0-1). python3-packaging set to manually installed. libgcc-13-dev is already the newest version (13.3.0-1). libgcc-13-dev set to manually installed. libsqlite3-0 is already the newest version (3.46.0-1). libsqlite3-0 set to manually installed. libctf-nobfd0 is already the newest version (2.42.50.20240625-1). libctf-nobfd0 set to manually installed. libqhull-r8.0 is already the newest version (2020.2-6+b1). libqhull-r8.0 set to manually installed. sed is already the newest version (4.9-2). media-types is already the newest version (10.1.0). media-types set to manually installed. python3-platformdirs is already the newest version (4.2.1-1). python3-platformdirs set to manually installed. libjs-requirejs is already the newest version (2.3.6+ds+~2.1.37-1). libjs-requirejs set to manually installed. python3-anyio is already the newest version (4.4.0-1). python3-anyio set to manually installed. zlib1g is already the newest version (1:1.3.dfsg+really1.3.1-1). dpkg-dev is already the newest version (1.22.6). dpkg-dev set to manually installed. libaudit1 is already the newest version (1:3.1.2-4). libubsan1 is already the newest version (14.1.0-3). libubsan1 set to manually installed. libjs-bootswatch is already the newest version (3.3.7+dfsg2-1.1). libjs-bootswatch set to manually installed. python3-websocket is already the newest version (1.7.0-1). python3-websocket set to manually installed. hostname is already the newest version (3.23+nmu2). libmount1 is already the newest version (2.40.1-9). python3-jupyter-sphinx-theme is already the newest version (0.0.6+ds1-11). python3-jupyter-sphinx-theme set to manually installed. python3-matplotlib is already the newest version (3.6.3-2). python3-matplotlib set to manually installed. llvm-14-linker-tools is already the newest version (1:14.0.6-20). llvm-14-linker-tools set to manually installed. make is already the newest version (4.3-4.1). make set to manually installed. libasan8 is already the newest version (14.1.0-3). libasan8 set to manually installed. libldap-2.5-0 is already the newest version (2.5.18+dfsg-1). libldap-2.5-0 set to manually installed. mawk is already the newest version (1.3.4.20240622-1). python3-defusedxml is already the newest version (0.7.1-2). python3-defusedxml set to manually installed. python3-idna is already the newest version (3.6-2.1). python3-idna set to manually installed. libwebpdemux2 is already the newest version (1.4.0-0.1). libwebpdemux2 set to manually installed. python3-pandas is already the newest version (2.1.4+dfsg-8). python3-pandas set to manually installed. python3-pandas-lib is already the newest version (2.1.4+dfsg-8). python3-pandas-lib set to manually installed. python3-pybtex is already the newest version (0.24.0-4). python3-pybtex set to manually installed. libsystemd0 is already the newest version (256.1-2). python3-contourpy is already the newest version (1.0.7-3). python3-contourpy set to manually installed. python3-hatch-vcs is already the newest version (0.4.0-1). python3-hatch-vcs set to manually installed. python3-kiwisolver is already the newest version (1.4.5-1). python3-kiwisolver set to manually installed. python3-recommonmark is already the newest version (0.7.1+ds-5). python3-recommonmark set to manually installed. xz-utils is already the newest version (5.6.2-1). xz-utils set to manually installed. libpgm-5.3-0t64 is already the newest version (5.3.128~dfsg-2.1). libpgm-5.3-0t64 set to manually installed. libjs-bootstrap is already the newest version (3.4.1+dfsg-3). libjs-bootstrap set to manually installed. libpipeline1 is already the newest version (1.5.7-2). libpipeline1 set to manually installed. tzdata is already the newest version (2024a-4). tzdata set to manually installed. pandoc is already the newest version (3.1.3+ds-3). pandoc set to manually installed. bzip2 is already the newest version (1.0.8-5.1). bzip2 set to manually installed. libargon2-1 is already the newest version (0~20190702+dfsg-4+b1). libargon2-1 set to manually installed. gcc-14-base is already the newest version (14.1.0-3). libdb5.3t64 is already the newest version (5.3.28+dfsg2-7). python3-fastjsonschema is already the newest version (2.20.0-1). python3-fastjsonschema set to manually installed. libjson-perl is already the newest version (4.10000-1). libjson-perl set to manually installed. python3-sphinx-design is already the newest version (0.6.0-2). python3-sphinx-design set to manually installed. python3-plotly is already the newest version (5.20.0+dfsg-1). python3-plotly set to manually installed. python3-jsonschema-specifications is already the newest version (2023.12.1-1). python3-jsonschema-specifications set to manually installed. python3-pygments is already the newest version (2.18.0+dfsg-1). python3-pygments set to manually installed. autoconf is already the newest version (2.71-3). autoconf set to manually installed. python3-attr is already the newest version (23.2.0-2). python3-attr set to manually installed. gzip is already the newest version (1.12-1.1). libgraphite2-3 is already the newest version (1.3.14-2). libgraphite2-3 set to manually installed. libquadmath0 is already the newest version (14.1.0-3). libquadmath0 set to manually installed. libzmq5 is already the newest version (4.3.5-1+b2). libzmq5 set to manually installed. python3-sympy is already the newest version (1.12.1-1). python3-sympy set to manually installed. libcap-ng0 is already the newest version (0.8.5-1). gettext is already the newest version (0.22.5-1). gettext set to manually installed. libpfm4 is already the newest version (4.13.0+git32-g0d4ed0e-1). libpfm4 set to manually installed. libreadline8t64 is already the newest version (8.2-4). libreadline8t64 set to manually installed. python3-sphinx is already the newest version (7.3.7-3). python3-sphinx set to manually installed. python3-urllib3 is already the newest version (2.0.7-2). python3-urllib3 set to manually installed. libtsan2 is already the newest version (14.1.0-3). libtsan2 set to manually installed. python3.12-minimal is already the newest version (3.12.4-1). python3.12-minimal set to manually installed. libicu72 is already the newest version (72.1-5). libicu72 set to manually installed. libhogweed6t64 is already the newest version (3.10-1). libhogweed6t64 set to manually installed. libmd0 is already the newest version (1.1.0-2). python3-lib2to3 is already the newest version (3.12.3-3.1). python3-lib2to3 set to manually installed. bsdextrautils is already the newest version (2.40.1-9). bsdextrautils set to manually installed. po-debconf is already the newest version (1.0.21+nmu1). po-debconf set to manually installed. autopoint is already the newest version (0.22.5-1). autopoint set to manually installed. python3-nbformat is already the newest version (5.9.1-1). python3-nbformat set to manually installed. libarchive-zip-perl is already the newest version (1.68-1). libarchive-zip-perl set to manually installed. libjs-jquery-metadata is already the newest version (12-4). libjs-jquery-metadata set to manually installed. g++ is already the newest version (4:13.2.0-7). g++ set to manually installed. libnorm1t64 is already the newest version (1.5.9+dfsg-3.1). libnorm1t64 set to manually installed. init-system-helpers is already the newest version (1.66). python3-tk is already the newest version (3.12.3-3.1). python3-tk set to manually installed. libgfortran5 is already the newest version (14.1.0-3). libgfortran5 set to manually installed. python3-py is already the newest version (1.11.0-2). python3-py set to manually installed. libpython3.12-stdlib is already the newest version (3.12.4-1). libpython3.12-stdlib set to manually installed. python3.11 is already the newest version (3.11.9-1). python3.11 set to manually installed. python3-jinja2 is already the newest version (3.1.3-1). python3-jinja2 set to manually installed. libdebhelper-perl is already the newest version (13.16). libdebhelper-perl set to manually installed. liblua5.4-0 is already the newest version (5.4.6-3+b1). liblua5.4-0 set to manually installed. python3-latexcodec is already the newest version (3.0.0-1). python3-latexcodec set to manually installed. libsasl2-modules-db is already the newest version (2.1.28+dfsg1-6). libsasl2-modules-db set to manually installed. libxext6 is already the newest version (2:1.3.4-1+b1). libxext6 set to manually installed. libmagic-mgc is already the newest version (1:5.45-3). libmagic-mgc set to manually installed. python3-zmq is already the newest version (24.0.1-5+b1). python3-zmq set to manually installed. libsodium23 is already the newest version (1.0.18-1+b1). libsodium23 set to manually installed. libsframe1 is already the newest version (2.42.50.20240625-1). libsframe1 set to manually installed. usr-is-merged is already the newest version (39). python3-fonttools is already the newest version (4.46.0-1). python3-fonttools set to manually installed. libmpc3 is already the newest version (1.3.1-1+b2). libmpc3 set to manually installed. netbase is already the newest version (6.4). netbase set to manually installed. libgomp1 is already the newest version (14.1.0-3). libgomp1 set to manually installed. debconf is already the newest version (1.5.86). libdeflate0 is already the newest version (1.20-1). libdeflate0 set to manually installed. libtcl8.6 is already the newest version (8.6.14+dfsg-1). libtcl8.6 set to manually installed. libxdmcp6 is already the newest version (1:1.1.2-3+b1). libxdmcp6 set to manually installed. libraqm0 is already the newest version (0.10.1-1+b1). libraqm0 set to manually installed. python3-bleach is already the newest version (6.1.0-2). python3-bleach set to manually installed. python3.12-dev is already the newest version (3.12.4-1). python3.12-dev set to manually installed. libxcb1 is already the newest version (1.17.0-2). libxcb1 set to manually installed. tk8.6-blt2.5 is already the newest version (2.5.3+dfsg-7). tk8.6-blt2.5 set to manually installed. libpam-modules is already the newest version (1.5.3-7). python3-mistune is already the newest version (3.0.2-1). python3-mistune set to manually installed. libbrotli1 is already the newest version (1.1.0-2+b3). libbrotli1 set to manually installed. perl-base is already the newest version (5.38.2-5). libhwasan0 is already the newest version (14.1.0-3). libhwasan0 set to manually installed. libatomic1 is already the newest version (14.1.0-3). libatomic1 set to manually installed. patch is already the newest version (2.7.6-7). patch set to manually installed. libmpfr6 is already the newest version (4.2.1-1+b1). libmpfr6 set to manually installed. python3-all is already the newest version (3.12.2-1). python3-all set to manually installed. libyaml-0-2 is already the newest version (0.2.5-1+b1). libyaml-0-2 set to manually installed. libpython3.12t64 is already the newest version (3.12.4-1). libpython3.12t64 set to manually installed. grep is already the newest version (3.11-4). libwebp7 is already the newest version (1.4.0-0.1). libwebp7 set to manually installed. cpp is already the newest version (4:13.2.0-7). cpp set to manually installed. libselinux1 is already the newest version (3.5-2+b2). findutils is already the newest version (4.10.0-2). python3-tqdm is already the newest version (4.66.4-1). python3-tqdm set to manually installed. fonts-lyx is already the newest version (2.4.1-1). fonts-lyx set to manually installed. base-passwd is already the newest version (3.6.4). dh-python is already the newest version (6.20240603). dh-python set to manually installed. libjs-jquery-hotkeys is already the newest version (0~20130707+git2d51e3a9+dfsg-2.1). libjs-jquery-hotkeys set to manually installed. libctf0 is already the newest version (2.42.50.20240625-1). libctf0 set to manually installed. python3-llvmlite is already the newest version (0.42.0-1+b1). python3-llvmlite set to manually installed. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: running --customize-hook in shell: sh -c 'chroot "$1" dpkg -r debootsnap-dummy' exec /srv/rebuilderd/tmp/mmdebstrap.VJnVd3ufE1 (Reading database ... 49031 files and directories currently installed.) Removing debootsnap-dummy (1.0) ... I: running --customize-hook in shell: sh -c 'chroot "$1" dpkg-query --showformat '${binary:Package}=${Version}\n' --show > "$1/pkglist"' exec /srv/rebuilderd/tmp/mmdebstrap.VJnVd3ufE1 I: running special hook: download /pkglist ./pkglist I: running --customize-hook in shell: sh -c 'rm "$1/pkglist"' exec /srv/rebuilderd/tmp/mmdebstrap.VJnVd3ufE1 I: running special hook: upload sources.list /etc/apt/sources.list I: waiting for background processes to finish... I: PID 9401 exited with exit code 0 I: cleaning package lists and apt cache... I: skipping cleanup/reproducible as requested I: creating tarball... I: done I: removing tempdir /srv/rebuilderd/tmp/mmdebstrap.VJnVd3ufE1... I: success in 195.7587 seconds Downloading dependency 379 of 425: python3-jinja2:amd64=3.1.3-1 Downloading dependency 380 of 425: libdebhelper-perl:amd64=13.16 Downloading dependency 381 of 425: liblua5.4-0:amd64=5.4.6-3+b1 Downloading dependency 382 of 425: python3-latexcodec:amd64=3.0.0-1 Downloading dependency 383 of 425: libsasl2-modules-db:amd64=2.1.28+dfsg1-6 Downloading dependency 384 of 425: libxext6:amd64=2:1.3.4-1+b1 Downloading dependency 385 of 425: libmagic-mgc:amd64=1:5.45-3 Downloading dependency 386 of 425: python3-zmq:amd64=24.0.1-5+b1 Downloading dependency 387 of 425: libsodium23:amd64=1.0.18-1+b1 Downloading dependency 388 of 425: libsframe1:amd64=2.42.50.20240625-1 Downloading dependency 389 of 425: usr-is-merged:amd64=39 Downloading dependency 390 of 425: python3-fonttools:amd64=4.46.0-1 Downloading dependency 391 of 425: libmpc3:amd64=1.3.1-1+b2 Downloading dependency 392 of 425: netbase:amd64=6.4 Downloading dependency 393 of 425: libgomp1:amd64=14.1.0-3 Downloading dependency 394 of 425: debconf:amd64=1.5.86 Downloading dependency 395 of 425: libdeflate0:amd64=1.20-1 Downloading dependency 396 of 425: libtcl8.6:amd64=8.6.14+dfsg-1 Downloading dependency 397 of 425: libxdmcp6:amd64=1:1.1.2-3+b1 Downloading dependency 398 of 425: libraqm0:amd64=0.10.1-1+b1 Downloading dependency 399 of 425: python3-bleach:amd64=6.1.0-2 Downloading dependency 400 of 425: python3.12-dev:amd64=3.12.4-1 Downloading dependency 401 of 425: libxcb1:amd64=1.17.0-2 Downloading dependency 402 of 425: tk8.6-blt2.5:amd64=2.5.3+dfsg-7 Downloading dependency 403 of 425: libpam-modules:amd64=1.5.3-7 Downloading dependency 404 of 425: python3-mistune:amd64=3.0.2-1 Downloading dependency 405 of 425: libbrotli1:amd64=1.1.0-2+b3 Downloading dependency 406 of 425: perl-base:amd64=5.38.2-5 Downloading dependency 407 of 425: libhwasan0:amd64=14.1.0-3 Downloading dependency 408 of 425: libatomic1:amd64=14.1.0-3 Downloading dependency 409 of 425: patch:amd64=2.7.6-7 Downloading dependency 410 of 425: libmpfr6:amd64=4.2.1-1+b1 Downloading dependency 411 of 425: python3-all:amd64=3.12.2-1 Downloading dependency 412 of 425: libyaml-0-2:amd64=0.2.5-1+b1 Downloading dependency 413 of 425: libpython3.12t64:amd64=3.12.4-1 Downloading dependency 414 of 425: grep:amd64=3.11-4 Downloading dependency 415 of 425: libwebp7:amd64=1.4.0-0.1 Downloading dependency 416 of 425: cpp:amd64=4:13.2.0-7 Downloading dependency 417 of 425: libselinux1:amd64=3.5-2+b2 Downloading dependency 418 of 425: findutils:amd64=4.10.0-2 Downloading dependency 419 of 425: python3-tqdm:amd64=4.66.4-1 Downloading dependency 420 of 425: fonts-lyx:amd64=2.4.1-1 Downloading dependency 421 of 425: base-passwd:amd64=3.6.4 Downloading dependency 422 of 425: dh-python:amd64=6.20240603 Downloading dependency 423 of 425: libjs-jquery-hotkeys:amd64=0~20130707+git2d51e3a9+dfsg-2.1 Downloading dependency 424 of 425: libctf0:amd64=2.42.50.20240625-1 Downloading dependency 425 of 425: python3-llvmlite:amd64=0.42.0-1+b1 env --chdir=/srv/rebuilderd/tmp/rebuilderdkS7JpC/out DEB_BUILD_OPTIONS=parallel=6 LANG=C.UTF-8 LC_ALL=C.UTF-8 LC_COLLATE=C.UTF-8 SOURCE_DATE_EPOCH=1720197900 SBUILD_CONFIG=/srv/rebuilderd/tmp/debrebuildiv09G6/debrebuild.sbuildrc.dy7k8zOjcD2P sbuild --build=amd64 --host=amd64 --no-source --no-arch-any --arch-all --chroot=/srv/rebuilderd/tmp/debrebuildiv09G6/debrebuild.tar.JPP1ybqHeZZI --chroot-mode=unshare --dist=unstable --no-run-lintian --no-run-piuparts --no-run-autopkgtest --no-apt-update --no-apt-upgrade --no-apt-distupgrade --starting-build-commands=grep -iq "^Rules-Requires-Root:" "%p/debian/control" || sed -i "1iRules-Requires-Root: no" "%p/debian/control" --verbose --nolog --bd-uninstallable-explainer= --build-path=/build/reproducible-path --dsc-dir=python-cogent-2024.5.7a1+dfsg /srv/rebuilderd/tmp/rebuilderdkS7JpC/inputs/python-cogent_2024.5.7a1+dfsg-3.dsc I: consider moving your ~/.sbuildrc to /srv/rebuilderd/.config/sbuild/config.pl The Debian buildds switched to the "unshare" backend and sbuild will default to it in the future. To start using "unshare" add this to your `~/.config/sbuild/config.pl`: $chroot_mode = "unshare"; If you want to keep the old "schroot" mode even in the future, add the following to your `~/.config/sbuild/config.pl`: $chroot_mode = "schroot"; $schroot = "schroot"; sbuild (Debian sbuild) 0.89.3+deb13u1 (16 August 2025) on ionos25-amd64.debian.net +==============================================================================+ | python-cogent 2024.5.7a1+dfsg-3 (amd64) Sat, 04 Oct 2025 11:06:57 +0000 | +==============================================================================+ Package: python-cogent Version: 2024.5.7a1+dfsg-3 Source Version: 2024.5.7a1+dfsg-3 Distribution: unstable Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: all I: No tarballs found in /srv/rebuilderd/.cache/sbuild I: Unpacking /srv/rebuilderd/tmp/debrebuildiv09G6/debrebuild.tar.JPP1ybqHeZZI to /srv/rebuilderd/tmp/tmp.sbuild.UXS6SsaLI3... I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... I: Setting up apt archive... +------------------------------------------------------------------------------+ | Fetch source files Sat, 04 Oct 2025 11:07:09 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/rebuilderd/tmp/rebuilderdkS7JpC/inputs/python-cogent_2024.5.7a1+dfsg-3.dsc exists in /srv/rebuilderd/tmp/rebuilderdkS7JpC/inputs; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Sat, 04 Oct 2025 11:07:10 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: architecture-is-64-bit, architecture-is-little-endian, cython3, debhelper-compat (= 13), dh-sequence-python3, flit, libjs-requirejs, pandoc, pybuild-plugin-pyproject, python3-all-dev, python3-chardet, python3-isort, python3-jupyter-sphinx-theme, python3-jupyterlab-server, python3-matplotlib, python3-nbsphinx, python3-numba, python3-numpy, python3-numpydoc, python3-pandas, python3-plotly, python3-pydata-sphinx-theme, python3-pytest, python3-pytest-cov, python3-pytest-xdist, python3-scipy, python3-scitrack, python3-sphinx, python3-sphinx-bootstrap-theme, python3-sphinx-design, python3-sphinx-gallery, python3-sphinxcontrib.bibtex, python3-stevedore, python3-tinydb, python3-tqdm, python3-typing-extensions, build-essential Filtered Build-Depends: architecture-is-64-bit, architecture-is-little-endian, cython3, debhelper-compat (= 13), dh-sequence-python3, flit, libjs-requirejs, pandoc, pybuild-plugin-pyproject, python3-all-dev, python3-chardet, python3-isort, python3-jupyter-sphinx-theme, python3-jupyterlab-server, python3-matplotlib, python3-nbsphinx, python3-numba, python3-numpy, python3-numpydoc, python3-pandas, python3-plotly, python3-pydata-sphinx-theme, python3-pytest, python3-pytest-cov, python3-pytest-xdist, python3-scipy, python3-scitrack, python3-sphinx, python3-sphinx-bootstrap-theme, python3-sphinx-design, python3-sphinx-gallery, python3-sphinxcontrib.bibtex, python3-stevedore, python3-tinydb, python3-tqdm, python3-typing-extensions, build-essential dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/reproducible-path/resolver-RjYPha/apt_archive/sbuild-build-depends-main-dummy.deb'. Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies +------------------------------------------------------------------------------+ | Check architectures Sat, 04 Oct 2025 11:07:14 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Build environment Sat, 04 Oct 2025 11:07:15 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.12.48+deb13-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) amd64 (x86_64) Toolchain package versions: binutils_2.42.50.20240625-1 dpkg-dev_1.22.6 g++-13_13.3.0-1 gcc-13_13.3.0-1 libc6-dev_2.38-13 libstdc++-13-dev_13.3.0-1 libstdc++6_14.1.0-3 linux-libc-dev_6.9.7-1 Package versions: architecture-properties_0.1.1+b1 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.22.5-1 autotools-dev_20220109.1 base-files_13.3 base-passwd_3.6.4 bash_5.2.21-2.1 binutils_2.42.50.20240625-1 binutils-common_2.42.50.20240625-1 binutils-x86-64-linux-gnu_2.42.50.20240625-1 blt_2.5.3+dfsg-7 bsdextrautils_2.40.1-9 bsdutils_1:2.40.1-9 build-essential_12.10 bzip2_1.0.8-5.1 ca-certificates_20240203 coreutils_9.4-3.1 cpp_4:13.2.0-7 cpp-13_13.3.0-1 cpp-13-x86-64-linux-gnu_13.3.0-1 cpp-x86-64-linux-gnu_4:13.2.0-7 cython3_3.0.10+dfsg-5 dash_0.5.12-9 debconf_1.5.86 debhelper_13.16 debianutils_5.19 dh-autoreconf_20 dh-python_6.20240603 dh-strip-nondeterminism_1.14.0-1 diffutils_1:3.10-1 docutils-common_0.20.1+dfsg-3 dpkg_1.22.6 dpkg-dev_1.22.6 dwz_0.15-1+b1 file_1:5.45-3 findutils_4.10.0-2 flit_3.9.0-2 fontconfig-config_2.15.0-1.1 fonts-dejavu-core_2.37-8 fonts-dejavu-mono_2.37-8 fonts-glyphicons-halflings_1.009~3.4.1+dfsg-3 fonts-lyx_2.4.1-1 g++_4:13.2.0-7 g++-13_13.3.0-1 g++-13-x86-64-linux-gnu_13.3.0-1 g++-x86-64-linux-gnu_4:13.2.0-7 gcc_4:13.2.0-7 gcc-13_13.3.0-1 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pybuild-plugin-pyproject_6.20240603 python-babel-localedata_2.14.0-1 python-matplotlib-data_3.6.3-2 python-tinycss2-common_1.3.0-1 python3_3.12.2-1 python3-alabaster_0.7.16-0.1 python3-all_3.12.2-1 python3-all-dev_3.12.2-1 python3-anyio_4.4.0-1 python3-appdirs_1.4.4-4 python3-argon2_21.1.0-2 python3-attr_23.2.0-2 python3-babel_2.14.0-1 python3-bleach_6.1.0-2 python3-brotli_1.1.0-2+b3 python3-bs4_4.12.3-1 python3-build_1.2.1-1 python3-certifi_2024.6.2-1 python3-cffi-backend_1.16.0-2+b2 python3-chardet_5.2.0+dfsg-1 python3-charset-normalizer_3.3.2-1 python3-commonmark_0.9.1-6 python3-contourpy_1.0.7-3 python3-coverage_7.2.7+dfsg1-1+b1 python3-cycler_0.12.1-1 python3-dateutil_2.9.0-2 python3-decorator_5.1.1-5 python3-defusedxml_0.7.1-2 python3-dev_3.12.2-1 python3-distutils_3.12.3-3.1 python3-docutils_0.20.1+dfsg-3 python3-entrypoints_0.4-2 python3-execnet_2.1.1-1 python3-fastjsonschema_2.20.0-1 python3-fonttools_4.46.0-1 python3-fs_2.4.16-4 python3-hatch-vcs_0.4.0-1 python3-hatchling_1.25.0-1 python3-html5lib_1.1-6 python3-idna_3.6-2.1 python3-imagesize_1.4.1-1 python3-iniconfig_1.1.1-2 python3-installer_0.7.0+dfsg1-3 python3-isort_5.6.4-1 python3-jinja2_3.1.3-1 python3-json5_0.9.25-1 python3-jsonschema_4.19.2-3 python3-jsonschema-specifications_2023.12.1-1 python3-jupyter-client_7.4.9-2 python3-jupyter-core_5.3.2-2 python3-jupyter-server_1.23.3-2 python3-jupyter-sphinx-theme_0.0.6+ds1-11 python3-jupyterlab-pygments_0.2.2-3 python3-jupyterlab-server_2.25.2-1 python3-kiwisolver_1.4.5-1 python3-latexcodec_3.0.0-1 python3-lib2to3_3.12.3-3.1 python3-llvmlite_0.42.0-1+b1 python3-lxml_5.2.1-1 python3-lz4_4.0.2+dfsg-1+b3 python3-markupsafe_2.1.5-1 python3-matplotlib_3.6.3-2 python3-minimal_3.12.2-1 python3-mistune_3.0.2-1 python3-mpmath_1.3.0-1 python3-nbclient_0.8.0-1 python3-nbconvert_7.16.4-1 python3-nbformat_5.9.1-1 python3-nbsphinx_0.9.4+ds-1 python3-nest-asyncio_1.5.4-1 python3-numba_0.59.1+dfsg-1 python3-numpy_1:1.26.4+ds-10 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python3-sniffio_1.3.1-1 python3-snowballstemmer_2.2.0-4 python3-soupsieve_2.5-1 python3-sphinx_7.3.7-3 python3-sphinx-bootstrap-theme_0.8.1-5 python3-sphinx-design_0.6.0-2 python3-sphinx-gallery_0.16.0-1 python3-sphinxcontrib.bibtex_2.6.2-1 python3-stevedore_5.2.0-2 python3-sympy_1.12.1-1 python3-tabulate_0.9.0-1 python3-tenacity_8.4.2-1 python3-terminado_0.18.1-1 python3-tinycss2_1.3.0-1 python3-tinydb_3.15.2-4 python3-tk_3.12.3-3.1 python3-toml_0.10.2-1 python3-tomli-w_1.0.0-2 python3-tornado_6.4.1-1 python3-tqdm_4.66.4-1 python3-traitlets_5.14.3-1 python3-trove-classifiers_2024.4.10-1 python3-typing-extensions_4.12.2-1 python3-tz_2024.1-2 python3-ufolib2_0.16.0+dfsg1-1 python3-urllib3_2.0.7-2 python3-webencodings_0.5.1-5 python3-websocket_1.7.0-1 python3-wheel_0.43.0-1 python3-yaml_6.0.1-2 python3-zmq_24.0.1-5+b1 python3.11_3.11.9-1 python3.11-dev_3.11.9-1 python3.11-minimal_3.11.9-1 python3.12_3.12.4-1 python3.12-dev_3.12.4-1 python3.12-minimal_3.12.4-1 readline-common_8.2-4 rpcsvc-proto_1.4.3-1 sed_4.9-2 sensible-utils_0.0.24 sgml-base_1.31 sphinx-common_7.3.7-3 sysvinit-utils_3.09-2 tar_1.35+dfsg-3 tk8.6-blt2.5_2.5.3+dfsg-7 tzdata_2024a-4 unicode-data_15.1.0-1 usr-is-merged_39 util-linux_2.40.1-9 x11-common_1:7.7+23 xml-core_0.19 xz-utils_5.6.2-1 zlib1g_1:1.3.dfsg+really1.3.1-1 zlib1g-dev_1:1.3.dfsg+really1.3.1-1 +------------------------------------------------------------------------------+ | Build Sat, 04 Oct 2025 11:07:15 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: python-cogent Binary: python3-cogent3, python-cogent-doc Architecture: any all Version: 2024.5.7a1+dfsg-3 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Andreas Tille , Homepage: https://github.com/cogent3/cogent3 Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/python-cogent Vcs-Git: https://salsa.debian.org/med-team/python-cogent.git Testsuite: autopkgtest, autopkgtest-pkg-python Testsuite-Triggers: python3-pytest Build-Depends: architecture-is-64-bit, architecture-is-little-endian, cython3, debhelper-compat (= 13), dh-sequence-python3, flit, libjs-requirejs, pandoc, pybuild-plugin-pyproject, python3-all-dev, python3-chardet, python3-isort, python3-jupyter-sphinx-theme, python3-jupyterlab-server, python3-matplotlib, python3-nbsphinx, python3-numba, python3-numpy, python3-numpydoc, python3-pandas, python3-plotly , python3-pydata-sphinx-theme, python3-pytest , python3-pytest-cov , python3-pytest-xdist , python3-scipy, python3-scitrack, python3-sphinx, python3-sphinx-bootstrap-theme, python3-sphinx-design, python3-sphinx-gallery, python3-sphinxcontrib.bibtex, python3-stevedore, python3-tinydb, python3-tqdm, python3-typing-extensions Package-List: python-cogent-doc deb doc optional arch=all python3-cogent3 deb python optional arch=any Checksums-Sha1: 4c596fb13b9c8a2e24179e6758c2de76f751a4bd 14846556 python-cogent_2024.5.7a1+dfsg.orig.tar.xz 0d0a703332c2378c2ff0b2a26b0848ca1ef286e3 12180 python-cogent_2024.5.7a1+dfsg-3.debian.tar.xz Checksums-Sha256: e4fe6bc1d1ce9df1f91ca84123df8427c37327847564244c0abc97ccc3357f2c 14846556 python-cogent_2024.5.7a1+dfsg.orig.tar.xz 4d5837beed17582651dabe60b4b6ce0f2781a68e4c2ab57fad48a5befb2a9c2c 12180 python-cogent_2024.5.7a1+dfsg-3.debian.tar.xz Files: 21ad4f0d79bc3a240bf1c58a5fd74099 14846556 python-cogent_2024.5.7a1+dfsg.orig.tar.xz a5479a4fbe9c77308149bbe0ec587ad9 12180 python-cogent_2024.5.7a1+dfsg-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQEzBAEBCgAdFiEE1Uw7+v+wQt44LaXXQc5/C58bizIFAmaIJNgACgkQQc5/C58b izJNMAf/aNfniQYvYU4D1doMXSxHuVgf9Vxtf9ar16FiRyWQJJNZsR2qpy0Pq/rZ gFPeEIHg+M6MnJYxtEXcw6QzT+GCM4guyQViKAk3WZxfgtAC1JLolk9JgZBgfH+v pDYTH7RUNKvhDj897e3Qg/kZry9fA01eAfvcJ2iwmKOo/cLiqMLzg1VrpfgaYxoT VeqvmtcUGYnA3RAjTEkxIRiQJ0QOfv3QTuOXKHXyDiw3f6IYt0kKePdSHkzVCAcv nN3vBQFYWVI8YzjGaVMArn9KEjGU0NFJexEiKi6HYx8v96XLevkQ+nR/TDlh1SLO LyChw5VT4ri1wRn++aof5DwNfKt2KA== =kZpK -----END PGP SIGNATURE----- dpkg-source: warning: cannot verify inline signature for ./python-cogent_2024.5.7a1+dfsg-3.dsc: unsupported subcommand dpkg-source: info: extracting python-cogent in /build/reproducible-path/python-cogent-2024.5.7a1+dfsg dpkg-source: info: unpacking python-cogent_2024.5.7a1+dfsg.orig.tar.xz dpkg-source: info: unpacking python-cogent_2024.5.7a1+dfsg-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying sphinx.patch dpkg-source: info: applying fix_interpreter.patch dpkg-source: info: applying remove-jupyter-sphinx.patch dpkg-source: info: applying ignore_tests_accessing_network.patch dpkg-source: info: applying skip-parallel-tests-on-single-cpu-systems.patch Install fakeroot ---------------- Setup apt archive ----------------- Merged Build-Depends: fakeroot Filtered Build-Depends: fakeroot dpkg-deb: building package 'sbuild-build-depends-fakeroot-dummy' in '/build/reproducible-path/resolver-RjYPha/apt_archive/sbuild-build-depends-fakeroot-dummy.deb'. Install fakeroot build dependencies (apt-based resolver) -------------------------------------------------------- Installing build dependencies Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands Sat, 04 Oct 2025 11:07:20 +0000 | +------------------------------------------------------------------------------+ grep -iq "^Rules-Requires-Root:" "/build/reproducible-path/python-cogent-2024.5.7a1+dfsg/debian/control" || sed -i "1iRules-Requires-Root: no" "/build/reproducible-path/python-cogent-2024.5.7a1+dfsg/debian/control" ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- I: Finished running 'grep -iq "^Rules-Requires-Root:" "/build/reproducible-path/python-cogent-2024.5.7a1+dfsg/debian/control" || sed -i "1iRules-Requires-Root: no" "/build/reproducible-path/python-cogent-2024.5.7a1+dfsg/debian/control"'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=6 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LC_COLLATE=C.UTF-8 LOGNAME=sbuild PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SHELL=/bin/sh SOURCE_DATE_EPOCH=1720197900 USER=sbuild dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -A dpkg-buildpackage: info: source package python-cogent dpkg-buildpackage: info: source version 2024.5.7a1+dfsg-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Santiago Vila dpkg-source --before-build . debian/rules clean dh clean --with sphinxdoc --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild dh_autoreconf_clean -O--buildsystem=pybuild debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/python-cogent-2024.5.7a1+dfsg' #These files are rebuilt on-the-fly for f in `find -name '*.c'` ; do \ head -n 1 "$f" | grep -q '^/\* Generated by Cython' && rm "$f" ; \ done rm -rf build build-stamp rm -rf doc/_build dh_clean make[1]: Leaving directory '/build/reproducible-path/python-cogent-2024.5.7a1+dfsg' debian/rules binary-indep dh binary-indep --with sphinxdoc --buildsystem=pybuild dh_update_autotools_config -i -O--buildsystem=pybuild dh_autoreconf -i -O--buildsystem=pybuild dh_auto_configure -i -O--buildsystem=pybuild dh_auto_build -i -O--buildsystem=pybuild I: pybuild plugin_pyproject:129: Building wheel for python3.11 with "build" module I: pybuild base:311: python3.11 -m build --skip-dependency-check --no-isolation --wheel --outdir /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/.pybuild/cpython3_3.11_cogent3 * Building wheel... Successfully built cogent3-2024.5.7a1-py3-none-any.whl I: pybuild plugin_pyproject:144: Unpacking wheel built for python3.11 with "installer" module I: pybuild plugin_pyproject:129: Building wheel for python3.12 with "build" module I: pybuild base:311: python3.12 -m build --skip-dependency-check --no-isolation --wheel --outdir /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/.pybuild/cpython3_3.12_cogent3 * Building wheel... Successfully built cogent3-2024.5.7a1-py3-none-any.whl I: pybuild plugin_pyproject:144: Unpacking wheel built for python3.12 with "installer" module debian/rules execute_after_dh_auto_build make[1]: Entering directory '/build/reproducible-path/python-cogent-2024.5.7a1+dfsg' set -x; cd doc; PYTHONPATH=/build/reproducible-path/python-cogent-2024.5.7a1+dfsg http_proxy='127.0.0.1:9' /usr/bin/make html + cd doc + PYTHONPATH=/build/reproducible-path/python-cogent-2024.5.7a1+dfsg http_proxy=127.0.0.1:9 /usr/bin/make html make[2]: Entering directory '/build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc' sphinx-build -b html -d _build/doctrees . _build/html Running Sphinx v7.3.7 making output directory... done WARNING: html_static_path entry '_static' does not exist WARNING: The config value `today' has type `date', defaults to `str'. checking bibtex cache... out of date parsing bibtex file /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cogent3.bib... parsed 21 entries building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 176 source files that are out of date updating environment: [new config] 176 added, 0 changed, 0 removed reading sources... [ 1%] COGENT3_LICENSE reading sources... [ 1%] api/__init__/cogent3.__init__.available_apps reading sources... [ 2%] api/__init__/cogent3.__init__.available_codes reading sources... [ 2%] api/__init__/cogent3.__init__.available_models reading sources... [ 3%] api/__init__/cogent3.__init__.available_moltypes reading sources... [ 3%] api/__init__/cogent3.__init__.get_code reading sources... [ 4%] api/__init__/cogent3.__init__.get_model reading sources... [ 5%] api/__init__/cogent3.__init__.get_moltype reading sources... [ 5%] api/__init__/cogent3.__init__.load_aligned_seqs reading sources... [ 6%] api/__init__/cogent3.__init__.load_annotations reading sources... [ 6%] api/__init__/cogent3.__init__.load_delimited reading sources... [ 7%] api/__init__/cogent3.__init__.load_seq reading sources... [ 7%] api/__init__/cogent3.__init__.load_table reading sources... [ 8%] api/__init__/cogent3.__init__.load_tree reading sources... [ 9%] api/__init__/cogent3.__init__.load_unaligned_seqs reading sources... [ 9%] api/__init__/cogent3.__init__.make_aligned_seqs reading sources... [ 10%] api/__init__/cogent3.__init__.make_seq reading sources... [ 10%] api/__init__/cogent3.__init__.make_table reading sources... [ 11%] api/__init__/cogent3.__init__.make_tree reading sources... [ 11%] api/__init__/cogent3.__init__.make_unaligned_seqs reading sources... [ 12%] api/__init__/cogent3.__init__.open_ reading sources... [ 12%] api/__init__/cogent3.__init__.open_data_store reading sources... [ 13%] api/alignment/alignment reading sources... [ 14%] api/alignment/classes/cogent3.core.alignment.Alignment reading sources... [ 14%] api/alignment/classes/cogent3.core.alignment.ArrayAlignment reading sources... [ 15%] api/alignment/classes/cogent3.core.alignment.SequenceCollection reading sources... [ 15%] api/alphabet/alphabet reading sources... [ 16%] api/alphabet/classes/cogent3.core.alphabet.Alphabet reading sources... 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[100%] templates/class WARNING: autodoc: failed to import function '__init__.available_apps' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.available_codes' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.available_models' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.available_moltypes' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.get_code' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.get_model' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.get_moltype' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.load_aligned_seqs' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.load_annotations' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.load_delimited' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.load_seq' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.load_table' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.load_tree' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.load_unaligned_seqs' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.make_aligned_seqs' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.make_seq' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.make_table' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.make_tree' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.make_unaligned_seqs' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.open_' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.open_data_store' from module 'cogent3'; the following exception was raised: No module named 'cogent3' /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/alignment/alignment.rst:6: ERROR: Unknown directive type "autosummary". .. autosummary:: :toctree: classes :template: class.rst SequenceCollection Alignment ArrayAlignment WARNING: autodoc: failed to import class 'core.alignment.Alignment' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import class 'core.alignment.ArrayAlignment' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import class 'core.alignment.SequenceCollection' from module 'cogent3'; the following exception was raised: No module named 'cogent3' /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/alphabet/alphabet.rst:6: ERROR: Unknown directive type "autosummary". .. autosummary:: :toctree: classes :template: class.rst Alphabet WARNING: autodoc: failed to import class 'core.alphabet.Alphabet' from module 'cogent3'; the following exception was raised: No module named 'cogent3' /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/annotation/annotation.rst:6: ERROR: Unknown directive type "autosummary". .. autosummary:: :toctree: classes :template: class.rst Feature WARNING: autodoc: failed to import class 'core.annotation.Feature' from module 'cogent3'; the following exception was raised: No module named 'cogent3' /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/annotation_db/annotation_db.rst:6: ERROR: Unknown directive type "autosummary". .. autosummary:: :toctree: classes :template: class.rst BasicAnnotationDb GffAnnotationDb GenbankAnnotationDb WARNING: autodoc: failed to import class 'core.annotation_db.BasicAnnotationDb' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import class 'core.annotation_db.GenbankAnnotationDb' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import class 'core.annotation_db.GffAnnotationDb' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function 'app.composable.define_app' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import class 'app.data_store.DataMember' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import class 'app.data_store.DataStoreDirectory' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import class 'app.data_store.ReadOnlyDataStoreZipped' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function 'app.io.register_datastore_reader' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import class 'app.sqlite_data_store.DataStoreSqlite' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import class 'core.genetic_code.GeneticCode' from module 'cogent3'; the following exception was raised: No module named 'cogent3' /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/genetic_code/genetic_code.rst:6: ERROR: Unknown directive type "autosummary". .. autosummary:: :toctree: classes :template: class.rst GeneticCode WARNING: autodoc: failed to import class 'core.moltype.MolType' from module 'cogent3'; the following exception was raised: No module named 'cogent3' /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/moltype/moltype.rst:6: ERROR: Unknown directive type "autosummary". .. autosummary:: :toctree: classes :template: class.rst MolType WARNING: autodoc: failed to import class 'core.sequence.DnaSequence' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import class 'core.sequence.ProteinSequence' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import class 'core.sequence.RnaSequence' from module 'cogent3'; the following exception was raised: No module named 'cogent3' /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/sequence/sequence.rst:6: ERROR: Unknown directive type "autosummary". .. autosummary:: :toctree: classes :template: class.rst DnaSequence RnaSequence ProteinSequence WARNING: autodoc: failed to import class 'parse.table.FilteringParser' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import class 'util.table.Columns' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import class 'util.table.Table' from module 'cogent3'; the following exception was raised: No module named 'cogent3' /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/table/table.rst:6: ERROR: Unknown directive type "autosummary". .. autosummary:: :toctree: classes :template: class.rst Table Columns /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/table/table.rst:15: ERROR: Unknown directive type "autosummary". .. autosummary:: :toctree: classes :template: class.rst FilteringParser WARNING: autodoc: failed to import class 'core.tree.PhyloNode' from module 'cogent3'; the following exception was raised: No module named 'cogent3' /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/tree/tree.rst:6: ERROR: Unknown directive type "autosummary". .. autosummary:: :toctree: classes :template: class.rst PhyloNode WARNING: autodoc: failed to import class 'util.deserialise.register_deserialiser' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function 'util.deserialise.deserialise_object' from module 'cogent3'; the following exception was raised: No module named 'cogent3' /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-codon.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-codon.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app loader = get_app("load_unaligned", format="fasta") seqs = loader("data/SCA1-cds.fasta") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-codon.rst:26: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app codon_aligner = get_app("progressive_align", "codon") aligned = codon_aligner(seqs) aligned /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-codon.rst:44: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: nt_aligner = get_app("progressive_align", "codon", distance="paralinear") aligned = nt_aligner(seqs) aligned /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-codon.rst:54: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: tree = "((Chimp:0.001,Human:0.001):0.0076,Macaque:0.01,((Rat:0.01,Mouse:0.01):0.02,Mouse_Lemur:0.02):0.01)" codon_aligner = get_app("progressive_align", "codon", guide_tree=tree) aligned = codon_aligner(seqs) aligned /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-codon.rst:67: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: codon_aligner = get_app("progressive_align", "codon", guide_tree=tree, indel_rate=0.001, indel_length=0.01 ) aligned = codon_aligner(seqs) aligned /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-codon.rst:81: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: codon_aligner = get_app("progressive_align", "CNFHKY", guide_tree=tree, param_vals=dict(omega=0.1, kappa=3) ) aligned = codon_aligner(seqs) aligned /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-codon.rst:97: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aligned.info /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-nucleotide.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-nucleotide.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app loader = get_app("load_unaligned", format="fasta") seqs = loader("data/SCA1-cds.fasta") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-nucleotide.rst:26: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app nt_aligner = get_app("progressive_align", "nucleotide") aligned = nt_aligner(seqs) aligned /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-nucleotide.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: nt_aligner = get_app("progressive_align", "nucleotide", distance="TN93") aligned = nt_aligner(seqs) aligned /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-nucleotide.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: tree = "((Chimp:0.001,Human:0.001):0.0076,Macaque:0.01,((Rat:0.01,Mouse:0.01):0.02,Mouse_Lemur:0.02):0.01)" nt_aligner = get_app("progressive_align", "nucleotide", guide_tree=tree) aligned = nt_aligner(seqs) aligned /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-nucleotide.rst:67: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: tree = "((Chimp:0.001,Human:0.001):0.0076,Macaque:0.01,((Rat:0.01,Mouse:0.01):0.02,Mouse_Lemur:0.02):0.01)" nt_aligner = get_app("progressive_align", "F81", guide_tree=tree) aligned = nt_aligner(seqs) aligned /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-nucleotide.rst:78: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aligned.info /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-protein.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-protein.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app loader = get_app("load_unaligned", format="fasta") to_aa = get_app("translate_seqs") process = loader + to_aa seqs = process("data/SCA1-cds.fasta") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-protein.rst:26: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app aa_aligner = get_app("progressive_align", "protein") aligned = aa_aligner(seqs) aligned /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-protein.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aa_aligner = get_app("progressive_align", "protein", distance="paralinear") aligned = aa_aligner(seqs) aligned /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-protein.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aligned.info /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/index-sample.rst:6: WARNING: toctree contains reference to nonexisting document 'app/app_cookbook/sample-trim-stop' /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/index-writers.rst:5: WARNING: Explicit markup ends without a blank line; unexpected unindent. /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-aligned.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-aligned.rst:16: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app load_aligned_app = get_app("load_aligned", moltype="dna", format="fasta") aln = load_aligned_app("data/brca1-bats.fasta") aln /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-aligned.rst:30: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app load_aligned_app = get_app("load_aligned", moltype="protein", format="phylip") aln = load_aligned_app("data/abglobin_aa.phylip") aln /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-aligned.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from tempfile import TemporaryDirectory tmpdir = TemporaryDirectory(dir=".") path_to_dir = tmpdir.name /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-aligned.rst:59: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import open_data_store fasta_seq_dstore = open_data_store("data", suffix="fasta", mode="r", limit=2) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-aligned.rst:73: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app, open_data_store out_dstore = open_data_store(path_to_dir, suffix="fa", mode="w") loader = get_app("load_aligned", format="fasta", moltype="dna") cpos3 = get_app("take_codon_positions", 3) writer = get_app("write_seqs", out_dstore, format="fasta") process = loader + cpos3 + writer /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-aligned.rst:93: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: result = process.apply_to(fasta_seq_dstore) print(result[0].read()[:50]) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-json.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-json.rst:17: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from cogent3 import get_app, open_data_store from tempfile import TemporaryDirectory tmpdir = TemporaryDirectory(dir=".") path_to_dir = tmpdir.name # create lf object to write load_aligned_app = get_app("load_aligned", moltype="dna", format="fasta") aln = load_aligned_app("data/primate_brca1.fasta") gn_model_app = get_app("model", "GN", tree="data/primate_brca1.tree") lf = gn_model_app(aln).lf out_dstore = open_data_store(path_to_dir, mode="w", suffix="json") # write with the same identifier as the write_json example write_json_app = get_app("write_json", data_store=out_dstore) data_member = write_json_app(lf, identifier="gn_params.json") path_to_dstore = data_member.data_store.source /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-json.rst:39: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app load_json_app = get_app("load_json") lf = load_json_app(f"{path_to_dstore}/gn_params.json") lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-tabular.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-tabular.rst:14: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app load_tsv_app = get_app("load_tabular", sep="\t") tsv_data = load_tsv_app("data/stats.tsv") tsv_data /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-tabular.rst:30: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from tempfile import NamedTemporaryFile tmpdir = NamedTemporaryFile(dir=".") path_to_csv_file = tmpdir.name /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-tabular.rst:40: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app tsv_data.write(path_to_csv_file, sep=",") load_csv_app = get_app("load_tabular", sep=",") csv_data = load_csv_app(path_to_csv_file) csv_data /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-unaligned.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-unaligned.rst:16: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app load_unaligned_app = get_app("load_unaligned", format="fasta", moltype="protein") seqs = load_unaligned_app("data/inseqs_protein.fasta") seqs /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-unaligned.rst:35: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from tempfile import TemporaryDirectory tmpdir = TemporaryDirectory(dir=".") path_to_dir = tmpdir.name /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-unaligned.rst:44: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app, open_data_store fasta_seq_dstore = open_data_store("data", suffix="fasta", mode="r", limit=2) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-unaligned.rst:58: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: out_dstore = open_data_store(path_to_dir, suffix="tsv", mode="w") load_unaligned_app = get_app("load_unaligned", format="fasta", moltype="dna") jdist = get_app("jaccard_dist") writer = get_app("write_tabular", out_dstore, format="tsv") process = load_unaligned_app + jdist + writer /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-unaligned.rst:73: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: result = process.apply_to(fasta_seq_dstore) print(result[1].read()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-concat.rst:6: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app concat_alns_app = get_app("concat", moltype="dna") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-concat.rst:15: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs aln1 = make_aligned_seqs({"s1": "AAA", "s2": "CAA", "s3": "AAA"}, moltype="dna") aln2 = make_aligned_seqs({"s1": "GCG", "s2": "GGG", "s3": "GGT"}, moltype="dna") aln1 /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-concat.rst:24: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aln2 /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-concat.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: result = concat_alns_app([aln1, aln2]) result /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-concat.rst:45: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs, get_app concat_missing = get_app("concat", moltype="dna", intersect=False) aln3 = make_aligned_seqs({"s4": "GCG", "s5": "GGG"}, moltype="dna") result = concat_missing([aln1, aln3]) result /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-concat.rst:60: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app concat_delim = get_app("concat", join_seq="N", moltype="dna") result = concat_delim([aln1, aln2]) result /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-fixed-len.rst:6: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app loader = get_app("load_aligned", moltype="protein", format="phylip") aln = loader("data/abglobin_aa.phylip") aln /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-fixed-len.rst:21: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app first_20 = get_app("fixed_length", length=20) first_20(aln) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-fixed-len.rst:35: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app skip_10_take_20 = get_app("fixed_length", length=20, start=10) skip_10_take_20(aln) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-fixed-len.rst:49: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app random_20 = get_app("fixed_length", length=20, random=True) random_20(aln) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-min-len.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-min-len.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app loader = get_app("load_unaligned", moltype="dna", format="fasta") aln = loader("data/SCA1-cds.fasta") aln /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-min-len.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app over_240s = get_app("min_length", 240) aln_fltrd = over_240s(aln) aln_fltrd /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-min-len.rst:39: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from tempfile import TemporaryDirectory tmpdir = TemporaryDirectory(dir=".") path_to_dir = tmpdir.name /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-min-len.rst:51: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app, open_data_store dstore = open_data_store("data", suffix="fasta", limit=2) reader = get_app("load_aligned", format="fasta", moltype="dna") min_length = get_app("min_length", 300) out_dstore = open_data_store(path_to_dir, mode="w", suffix="fasta") writer = get_app("write_seqs", out_dstore) process = reader + min_length + writer result = process.apply_to(dstore) result.describe /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-bad.rst:8: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( { "s1": "---ACC---TT-", "s2": "---ACC---TT-", "s3": "---ACC---TT-", "s4": "--AACCG-GTT-", "s5": "--AACCGGGTTT", "s6": "AGAACCGGGTT-", "s7": "------------", }, moltype="dna", ) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-bad.rst:31: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app omit_frac_05 = get_app("omit_bad_seqs", gap_fraction=0.5) omit_frac_05(aln) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-bad.rst:44: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app omit_quant_08 = get_app("omit_bad_seqs", quantile=0.8) omit_quant_08(aln) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-degen.rst:10: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs aln = make_aligned_seqs({"s1": "ACGA-GACG", "s2": "GATGATGYT"}, moltype="dna") aln /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-degen.rst:21: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app omit_degens = get_app("omit_degenerates", moltype="dna") result = omit_degens(aln) result /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-degen.rst:36: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app omit_degens_keep_gaps = get_app("omit_degenerates", moltype="dna", gap_is_degen=False) result = omit_degens_keep_gaps(aln) result /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-degen.rst:50: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app omit_degenerates_app = get_app("omit_degenerates", moltype="dna", motif_length=2) result = omit_degenerates_app(aln) result /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-duplicated.rst:8: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs data = { "a": "ACGT", "b": "ACG-", # identical to 'a' except has a gap "c": "ACGG", # duplicate "d": "ACGG", # duplicate "e": "AGTC", # unique } aln = make_aligned_seqs(data, moltype="dna") aln /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-duplicated.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app omit_shorter_duplicate = get_app("omit_duplicated", moltype="dna", choose="longest") omit_shorter_duplicate(aln) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-duplicated.rst:35: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app omit_all_duplicates = get_app("omit_duplicated", moltype="dna", choose=None) omit_all_duplicates(aln) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-duplicated.rst:47: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( { "s1": "ATCG", "s2": "ATYG", # matches s1 with ambiguity "s3": "GGTA", }, moltype="dna", ) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-duplicated.rst:63: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app app_dna = get_app("omit_duplicated", mask_degen=True, choose="longest", moltype="dna") app_dna(aln) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-gap.rst:9: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs aln = make_aligned_seqs({"s1": "ACGA-GA-CG", "s2": "GATGATG-AT"}, moltype="dna") aln /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-gap.rst:22: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app omit_gap_pos_app = get_app("omit_gap_pos", moltype="dna") result = omit_gap_pos_app(aln) result /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-gap.rst:33: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: omit_gap_pos_app = get_app("omit_gap_pos", allowed_frac=0.49, moltype="dna") result = omit_gap_pos_app(aln) result /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-gap.rst:45: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: omit_gap_pos_app = get_app( "omit_gap_pos", allowed_frac=0, motif_length=3, moltype="dna" ) result = omit_gap_pos_app(aln) result /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-n-seqs.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-n-seqs.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app loader = get_app("load_aligned", moltype="dna") aln = loader("data/primate_brca1.fasta") aln /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-n-seqs.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app first_3 = get_app("take_n_seqs", number=3) first_3(aln) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-n-seqs.rst:40: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app random_n = get_app("take_n_seqs", random=True, number=3, seed=1) random_n(aln) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-n-seqs.rst:53: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app loader = get_app("load_aligned", moltype="dna") aln1 = loader("data/primate_brca1.fasta") aln2 = loader("data/brca1.fasta") aln1.names /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-n-seqs.rst:64: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aln2.names /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-n-seqs.rst:69: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: fixed_choice = get_app("take_n_seqs", number=2, random=True, fixed_choice=True) result1 = fixed_choice(aln1).names result2 = fixed_choice(aln2).names result1 == result2 /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-pos.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-pos.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs aln = make_aligned_seqs({"s1": "ACGACGACG", "s2": "GATGATGAT"}, moltype="dna") aln /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-pos.rst:26: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app take_pos3 = get_app("take_codon_positions", 3, moltype="dna") result = take_pos3(aln) result /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-pos.rst:40: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app take_pos12 = get_app("take_codon_positions", 1, 2, moltype="dna") result = take_pos12(aln) result /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-pos.rst:54: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app, make_aligned_seqs aln_ff = make_aligned_seqs({"s1": "GCAAGCGTTTAT", "s2": "GCTTTTGTCAAT"}) take_fourfold = get_app("take_codon_positions", fourfold_degenerate=True, moltype="dna") result = take_fourfold(aln_ff) result /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-pos.rst:67: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from tempfile import TemporaryDirectory tmpdir = TemporaryDirectory(dir=".") path_to_dir = tmpdir.name /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-pos.rst:77: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import open_data_store fasta_seq_dstore = open_data_store("data", suffix="fasta", mode="r", limit=2) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-pos.rst:88: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app, open_data_store out_dstore = open_data_store(path_to_dir, suffix="fa", mode="w") loader = get_app("load_aligned", format="fasta", moltype="dna") cpos3 = get_app("take_codon_positions", 3) writer = get_app("write_seqs", out_dstore, format="fasta") process = loader + cpos3 + writer /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-pos.rst:105: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: out_dstore = process.apply_to(fasta_seq_dstore) out_dstore.describe /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-seqs.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-seqs.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app loader = get_app("load_aligned", moltype="dna") aln = loader("data/primate_brca1.fasta") aln /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-seqs.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app greater_ape_selector = get_app("take_named_seqs", "Human", "Chimpanzee", "Gorilla") ape_aln = greater_ape_selector(aln) ape_aln /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-seqs.rst:37: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_aligned", format="fasta", moltype="dna") select_seqs = get_app("take_named_seqs", "Human", "Rhesus", "Galago") process = loader + select_seqs hrg_aln = process("data/primate_brca1.fasta") hrg_aln.names /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-seqs.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app no_galagos = get_app("take_named_seqs", "Galago", negate=True) no_galago_aln = no_galagos(hrg_aln) no_galago_aln.names /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-trim-stops.rst:6: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app, make_aligned_seqs aln = make_aligned_seqs( data={"seq1": "ACGTAA---", "seq2": "ACGACA---", "seq3": "ACGCAATGA"}, moltype="dna", ) no_stops = get_app("trim_stop_codons", gc=1) no_stops(aln) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-db.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-db.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from tempfile import TemporaryDirectory tmpdir = TemporaryDirectory(dir=".") path_to_dir = tmpdir.name /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-db.rst:21: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app, open_data_store dstore = open_data_store("data", suffix="fasta", limit=2) reader = get_app("load_aligned", format="fasta", moltype="dna") min_length = get_app("min_length", 300) out_dstore = open_data_store(f"{path_to_dir}.sqlitedb", mode="w") writer = get_app("write_db", out_dstore) process = reader + min_length + writer result = process.apply_to(dstore) result.describe /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-db.rst:39: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: out_dstore is result /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-json.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-json.rst:18: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from tempfile import TemporaryDirectory tmpdir = TemporaryDirectory(dir=".") path_to_dir = tmpdir.name /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-json.rst:26: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app # Load the alignment load_aligned_app = get_app("load_aligned", moltype="dna", format="fasta") aln = load_aligned_app("data/primate_brca1.fasta") # Fit the GN model gn_model_app = get_app("model", "GN", tree="data/primate_brca1.tree") model_result = gn_model_app(aln) model_result.lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-json.rst:47: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app, open_data_store # Initialise the write_json app with a data store out_dstore = open_data_store(path_to_dir, mode="w", suffix="json") write_json_app = get_app("write_json", data_store=out_dstore) write_json_app(model_result.lf, identifier="gn_params.json") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-seqs.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-seqs.rst:14: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app load_aligned_app = get_app("load_aligned", moltype="dna", format="fasta") aln = load_aligned_app("data/primate_brca1.fasta") aln /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-seqs.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from tempfile import TemporaryDirectory tmpdir = TemporaryDirectory(dir=".") path_to_dir = tmpdir.name /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-seqs.rst:33: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app, open_data_store seq_dstore = open_data_store(path_to_dir, suffix="phylip", mode="w") write_seqs_app = get_app("write_seqs", data_store=seq_dstore, format="phylip") result = write_seqs_app(aln) result.read()[:50] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-seqs.rst:50: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from tempfile import TemporaryDirectory tmpdir = TemporaryDirectory(dir=".") path_to_dir = tmpdir.name /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-seqs.rst:60: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import open_data_store fasta_seq_dstore = open_data_store("data", suffix="fasta", mode="r") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-seqs.rst:69: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app, open_data_store out_dstore = open_data_store(path_to_dir, suffix="fa", mode="w") loader = get_app("load_unaligned", format="fasta", moltype="dna") keep_translatable = get_app("select_translatable") translate = get_app("translate_seqs") writer = get_app("write_seqs", out_dstore, format="fasta") process = loader + keep_translatable + translate + writer /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-seqs.rst:87: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: result = process.apply_to(fasta_seq_dstore) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-seqs.rst:97: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: result.describe /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-seqs.rst:104: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: result.summary_not_completed /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-tabular.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-tabular.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app # load alignment load_aligned_app = get_app("load_aligned", moltype="dna") aln = load_aligned_app("data/primate_brca1.fasta") # fit GN model gn_model_app = get_app("model", "GN", tree="data/primate_brca1.tree") model_result = gn_model_app(aln) # tabulate the model result tabulator = get_app("tabulate_stats") model_result_tab = tabulator(model_result) motif_params = model_result_tab["motif params"] print(type(motif_params)) motif_params /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-tabular.rst:38: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from tempfile import TemporaryDirectory tmpdir = TemporaryDirectory(dir=".") path_to_dir = tmpdir.name /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-tabular.rst:47: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app, open_data_store out_dstore = open_data_store(path_to_dir, mode="w", suffix="csv") write_tabular_app = get_app("write_tabular", data_store=out_dstore, format="csv") write_tabular_app(motif_params, identifier="gn_model_results.csv") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-tabular.rst:63: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from tempfile import TemporaryDirectory tmpdir = TemporaryDirectory(dir=".") path_to_dir = tmpdir.name /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-tabular.rst:72: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app, open_data_store out_dstore = open_data_store(path_to_dir, mode="w", suffix="tsv") write_tabular_app = get_app("write_tabular", data_store=out_dstore, format="tsv") write_tabular_app(motif_params, identifier="gn_model_results.tsv") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-tabular.rst:87: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from tempfile import TemporaryDirectory tmpdir = TemporaryDirectory(dir=".") path_to_dir = tmpdir.name /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-tabular.rst:96: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app, open_data_store loader = get_app("load_unaligned", moltype="dna") jdist = get_app("jaccard_dist") out_dstore = open_data_store(path_to_dir, mode="w", suffix="tsv") writer = get_app("write_tabular", data_store=out_dstore, format="tsv") process = loader + jdist + writer in_dstore = open_data_store("data", suffix="fasta", mode="r", limit=2) result = process.apply_to(in_dstore) result.describe /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/app-get.rst:8: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app just_nucs = get_app("omit_degenerates", moltype="dna") just_nucs /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/app-help.rst:8: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import app_help app_help("omit_degenerates") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/app-overview.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/app-overview.rst:95: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from tempfile import TemporaryDirectory tmpdir = TemporaryDirectory(dir=".") path_to_dir = tmpdir.name /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/app-overview.rst:106: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app, open_data_store out_dstore = open_data_store(path_to_dir, suffix="fa", mode="w") loader = get_app("load_aligned", format="fasta", moltype="dna") cpos3 = get_app("take_codon_positions", 3) writer = get_app("write_seqs", out_dstore, format="fasta") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/app-overview.rst:121: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data = loader("data/primate_brca1.fasta") just3rd = cpos3(data) m = writer(just3rd) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/app-overview.rst:138: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: process = loader + cpos3 + writer m = process("data/primate_brca1.fasta") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/app-overview.rst:148: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore = open_data_store("data", suffix="fasta", mode="r") result = process.apply_to(dstore) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/app-overview.rst:163: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: out_dstore.summary_logs /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/app-overview.rst:172: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: out_dstore.describe /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/app-overview.rst:178: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: out_dstore.summary_not_completed /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/app-overview.rst:185: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result = process.apply_to(dstore, show_progress=True) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/app-overview.rst:205: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import shutil shutil.rmtree(path_to_dir, ignore_errors=True) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/available-apps.rst:8: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import available_apps available_apps() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/available-apps.rst:16: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: available_apps(name_filter="load") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:66: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import open_data_store dstore = open_data_store("data/raw.zip", suffix="fa", mode="r") print(dstore) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:78: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore.describe /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:92: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: m = dstore[0] m /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:102: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: for m in dstore[:5]: print(m) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:110: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: m.read()[:20] # truncating /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:130: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore = open_data_store("data/demo-locked.sqlitedb") dstore.describe /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:137: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore.unlock(force=True) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:146: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore.summary_logs /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:152: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore.logs /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:158: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(dstore.logs[0].read()[:225]) # truncated for clarity /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:172: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import open_data_store in_dstore = open_data_store("data/raw.zip", suffix="fa") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:180: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: out_dstore = open_data_store("translated.sqlitedb", mode="w") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:189: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app load = get_app("load_unaligned", moltype="dna") translate = get_app("translate_seqs") write = get_app("write_db", data_store=out_dstore) app = load + translate + write app /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:201: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: out_dstore = app.apply_to(in_dstore) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:210: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: out_dstore.describe /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:216: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: out_dstore.validate() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:222: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: out_dstore.summary_not_completed /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:232: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: len(out_dstore.not_completed) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:238: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: out_dstore.not_completed[:2] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:242: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import pathlib fn = pathlib.Path("translated.sqlitedb") fn.unlink() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:11: WARNING: download file not readable: /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/data/raw.zip /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/not-completed.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/not-completed.rst:23: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app reader = get_app("load_aligned", format="fasta") select_seqs = get_app("take_named_seqs", "Mouse", "Human") aln = reader("data/primate_brca1.fasta") result = select_seqs(aln) assert result == False result /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/not-completed.rst:36: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.source /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/not-completed.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.origin /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/not-completed.rst:48: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.message /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/not-completed.rst:58: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: result = reader("primate_brca1.fasta") result /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/not-completed.rst:69: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: app = reader + select_seqs result = app("data/primate_brca1.fasta") result /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/not-completed.rst:77: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: result = app("primate_brca1.fasta") result /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-ancestral-states.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-ancestral-states.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_aligned", format="fasta") aln = loader("data/primate_brca1.fasta") gn = get_app("model", "GN", tree="data/primate_brca1.tree") result = gn(aln) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-ancestral-states.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: reconstuctor = get_app("ancestral_states") states_result = reconstuctor(result) states_result /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-ancestral-states.rst:33: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: states_result["edge.0"] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-ancestral-states.rst:39: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.tree.get_figure(contemporaneous=True).show(width=500, height=500) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-dt-nuc-model.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-dt-nuc-model.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_aligned", format="fasta", moltype="dna") aln = loader("data/primate_brca1.fasta") model = get_app("model", "BH", tree="data/primate_brca1.tree") result = model(aln) result /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-dt-nuc-model.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-dt-nuc-model.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tree = result.tree fig = tree.get_figure() fig.scale_bar = "top right" fig.show(width=500, height=500) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-dt-nuc-model.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tabulator = get_app("tabulate_stats") stats = tabulator(result) stats /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-dt-nuc-model.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: stats["edge motif motif2 params"] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-extract-model-stats.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-extract-model-stats.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_aligned", format="fasta", moltype="dna") aln = loader("data/primate_brca1.fasta") model = get_app("model", "GN", tree="data/primate_brca1.tree") result = model(aln) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-extract-model-stats.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tabulator = get_app("tabulate_stats") tabulated = tabulator(result) tabulated /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-extract-model-stats.rst:38: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tabulated["edge params"] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-extract-model-stats.rst:49: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tabulated["global params"] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-extract-model-stats.rst:58: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tabulated["motif params"] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-hypothesis.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-hypothesis.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_aligned", format="fasta", moltype="dna") aln = loader("data/primate_brca1.fasta") tree = "data/primate_brca1.tree" null = get_app("model", "GTR", tree=tree, optimise_motif_probs=True) alt = get_app("model", "GN", tree=tree, optimise_motif_probs=True) hyp = get_app("hypothesis", null, alt) result = hyp(aln) type(result) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-hypothesis.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-hypothesis.rst:40: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.LR, result.df, result.pvalue /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-hypothesis.rst:49: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.null /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-hypothesis.rst:53: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.null.lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-hypothesis.rst:60: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.alt.lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_aligned", format="fasta", moltype="dna") select_seqs = get_app("take_named_seqs", "Human", "Rhesus", "Galago") process = loader + select_seqs aln = process("data/primate_brca1.fasta") aln.names /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: gn = get_app("model", "GN") gn /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model.rst:32: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted = gn(aln) type(fitted) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model.rst:56: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.lnL, fitted.nfp /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model.rst:60: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.source /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model.rst:66: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.tree, fitted.alignment /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model.rst:72: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.total_length(length_as="paralinear") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model.rst:81: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: gn = get_app("model", "GN", split_codons=True) fitted = gn(aln) fitted /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model.rst:92: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted[3] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model-timehet.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model-timehet.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3 import get_app tree = load_tree("data/primate_brca1.tree") fig = tree.get_figure(contemporaneous=True) fig.style_edges( "Human", tip2="Orangutan", outgroup="Galago", line=dict(color="red") ) fig.show(width=500, height=500) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model-timehet.rst:32: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: time_het = get_app("model", "GN", tree=tree, time_het=[dict(tip_names=["Human", "Orangutan"], outgroup_name="Galago")], ) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model-timehet.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: loader = get_app("load_aligned", format="fasta") aln = loader("data/primate_brca1.fasta") result = time_het(aln) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model-timehet.rst:50: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model-with-tree.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model-with-tree.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_aligned", format="fasta", moltype="dna") aln = loader("data/primate_brca1.fasta") aln.names /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model-with-tree.rst:22: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3 import get_app tree = load_tree("data/primate_brca1.tree") gn = get_app("model", "GN", tree=tree) gn /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model-with-tree.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: gn = get_app("model", "GN", tree="data/primate_brca1.tree") gn /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model-with-tree.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted = gn(aln) fitted /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model-with-tree.rst:51: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-natsel_neutral.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-natsel_neutral.rst:15: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_aligned", format="fasta", moltype="dna") aln = loader("data/primate_brca1.fasta") omega_eq_1 = get_app("natsel_neutral", "GNC", tree="data/primate_brca1.tree", optimise_motif_probs=False ) result = omega_eq_1(aln) type(result) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-natsel_neutral.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-natsel_neutral.rst:32: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.alt.lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-natsel_sitehet.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-natsel_sitehet.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_aligned", format="fasta", moltype="dna") aln = loader("data/primate_brca1.fasta") sites_differ = get_app("natsel_sitehet", "GNC", tree="data/primate_brca1.tree", optimise_motif_probs=False ) result = sites_differ(aln) result /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-natsel_sitehet.rst:29: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.alt.lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-natsel_sitehet.rst:38: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: bprobs = result.alt.lf.get_bin_probs() bprobs[:, :20] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-natsel_timehet.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-natsel_timehet.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_aligned", format="fasta", moltype="dna") aln = loader("data/primate_brca1.fasta") hc_differ = get_app("natsel_timehet", "GNC", tree="data/primate_brca1.tree", optimise_motif_probs=False, tip1="Human", tip2="Chimpanzee", ) result = hc_differ(aln) result /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-natsel_timehet.rst:30: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.alt.lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-natsel_zhang.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-natsel_zhang.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from IPython.core.display import HTML from numpy import array from cogent3 import make_table header = ['Site Class', 'Proportion', 'Background Edges', 'Foreground Edges'] data = {'Site Class': array(['0', '1', '2a', '2b'], dtype=' 1', '0 < omega0 < 1'], dtype=' AlignedSeqsType: return val[:index] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/user_function.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: first4 = up_to(index=4) first4 /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/user_function.rst:51: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data=dict(a="GCAAGCGTTTAT", b="GCTTTTGTCAAT"), array_align=False, moltype="dna" ) result = first4(aln) result /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/user_function.rst:68: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from typing import Union from cogent3.app.composable import define_app from cogent3.app.typing import SeqsCollectionType, SerialisableType T = Union[SeqsCollectionType, SerialisableType] @define_app def rename_seqs(seqs: SeqsCollectionType) -> T: """upper case names""" return seqs.rename_seqs(lambda x: x.upper()) renamer = rename_seqs() result = renamer(aln) result /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/user_function.rst:91: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app.composable import define_app from cogent3.app.typing import AlignedSeqsType, PairwiseDistanceType @define_app def get_dists(aln: AlignedSeqsType, calc="hamming") -> PairwiseDistanceType: return aln.distance_matrix(calc=calc, show_progress=False) percent_dist = get_dists(calc="pdist") result = percent_dist(aln) result /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("AGTACACTGGT") my_seq.moltype.label /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:20: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: my_seq /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:26: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: my_seq = make_seq("AGTACACTGGT", moltype="bytes") my_seq.moltype.label /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:31: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: my_seq /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:47: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("AGTACACTGGT", moltype="dna") my_seq /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:57: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq rnaseq = make_seq("ACGUACGUACGUACGU", moltype="rna") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:66: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("AGTACACTGGT", moltype="dna") my_seq /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:76: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq rnaseq = make_seq("ACGUACGUACGUACGU", moltype="rna") rnaseq /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:88: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("AGTACACTGGT", "my_gene", moltype="dna") my_seq type(my_seq) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:99: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("AGTACACTGGT", moltype="dna") my_seq.name = "my_gene" my_seq /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:110: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("AGTACACTGGT", moltype="dna") my_seq.complement() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:120: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: my_seq.rc() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:129: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("GCTTGGGAAAGTCAAATGGAA", name="s1", moltype="dna") pep = my_seq.get_translation() type(pep) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:137: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: pep /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:144: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("ACGTACGTACGTACGT", moltype="dna") rnaseq = my_seq.to_rna() rnaseq /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:155: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq rnaseq = make_seq("ACGUACGUACGUACGU", moltype="rna") dnaseq = rnaseq.to_dna() dnaseq /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:166: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq a = make_seq("AGTACACTGGT", moltype="dna") a.can_pair(a.complement()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:173: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: a.can_pair(a.rc()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:180: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("AGTACACTGGT", moltype="dna") extra_seq = make_seq("CTGAC", moltype="dna") long_seq = my_seq + extra_seq long_seq /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:192: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: my_seq[1:6] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:201: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq seq = make_seq("ATGATGATGATG", moltype="dna") pos3 = seq[2::3] assert str(pos3) == "GGGG" /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:214: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq seq = make_seq("ATGATGATGATG", moltype="dna") indices = [(i, i + 2) for i in range(len(seq))[::3]] pos12 = seq.add_feature(biotype="pos12", name="pos12", spans=indices) pos12 = pos12.get_slice() assert str(pos12) == "ATATATAT" /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:227: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: rnaseq.shuffle() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:234: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq s = make_seq("--AUUAUGCUAU-UAu--", moltype="rna") s.degap() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs, make_unaligned_seqs dna = {"seq1": "ATGACC", "seq2": "ATCGCC"} seqs = make_aligned_seqs(data=dna, moltype="dna") type(seqs) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:36: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seqs = make_unaligned_seqs(dna, moltype="dna") type(seqs) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:44: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs dna = {"seq1": "ATGACC", "seq2": "ATCGCC"} seqs = make_aligned_seqs(data=dna, moltype="dna", array_align=True) print(type(seqs)) seqs /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:56: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_unaligned_seqs seqs = load_unaligned_seqs("data/test.paml") seqs /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:73: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( [("seq1", "ATGAA------"), ("seq2", "ATG-AGTGATG"), ("seq3", "AT--AG-GATG")], moltype="dna", ) aln /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:83: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: new_seqs = make_aligned_seqs( [("seq0", "ATG-AGT-AGG"), ("seq4", "ATGCC------")], moltype="dna" ) new_aln = aln.add_seqs(new_seqs) new_aln /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:98: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: new_aln = aln.add_seqs(new_seqs, before_name="seq2") new_aln /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:103: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: new_aln = aln.add_seqs(new_seqs, after_name="seq2") new_aln /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:113: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( [("seq1", "ATGAA------"), ("seq2", "ATG-AGTGATG"), ("seq3", "AT--AG-GATG")], moltype="dna", ) ref_aln = make_aligned_seqs( [("seq3", "ATAGGATG"), ("seq0", "ATG-AGCG"), ("seq4", "ATGCTGGG")], moltype="dna", ) new_aln = aln.add_from_ref_aln(ref_aln) new_aln /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:135: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( [("seq1", "ATGAA---TG-"), ("seq2", "ATG-AGTGATG"), ("seq3", "AT--AG-GATG")], moltype="dna", ) new_aln = aln.get_degapped_relative_to("seq1") new_aln /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:154: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( [("seq1", "ATGAA------"), ("seq2", "ATG-AGTGATG"), ("seq3", "AT--AG-GATG")], moltype="dna", array_align=False, ) seq = aln.get_seq("seq1") seq.name type(seq) seq.is_gapped() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:170: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq = aln.get_gapped_seq("seq1") seq.is_gapped() seq /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:178: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln.names /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:187: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_unaligned_seqs fn = "data/long_testseqs.fasta" seqs = load_unaligned_seqs(fn, moltype="dna") my_seq = seqs.seqs[0] my_seq[:24] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:196: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: type(my_seq) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:200: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = load_aligned_seqs(fn, moltype="dna") aln.seqs[0][:24] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:209: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/test.paml", moltype="dna") aln.names /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:216: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: new = aln.take_seqs(["Human", "HowlerMon"]) new.names /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:229: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_unaligned_seqs from cogent3.core.alignment import Alignment seq = load_unaligned_seqs("data/test.paml", moltype="dna") seq /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:237: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = Alignment(seq) aln /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:247: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs data = [("a", "ACG---"), ("b", "CCTGGG")] aln = make_aligned_seqs(data=data) dna = aln.to_dna() dna /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:258: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln.to_moltype("dna") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:264: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs data = [("a", "ACG---"), ("b", "CCUGGG")] aln = make_aligned_seqs(data=data) rna = aln.to_rna() rna /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:275: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs data = [("x", "TYV"), ("y", "TE-")] aln = make_aligned_seqs(data=data) prot = aln.to_protein() prot /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:292: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta") degapped = aln.degap() print(type(degapped)) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:307: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs dna = {"seq1": "ATGACC", "seq2": "ATCGCC"} aln = make_aligned_seqs(data=dna, moltype="dna") aln.write("sample.fasta") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:317: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln.write("sample", format="fasta") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:323: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.io import remove_files remove_files(["sample", "sample.fasta"], error_on_missing=False) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:332: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.core.alignment import Alignment seq = load_aligned_seqs("data/long_testseqs.fasta") aln = Alignment(seq) fasta_align = aln /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:344: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.core.alignment import Alignment seq = load_aligned_seqs("data/test.paml") aln = Alignment(seq) got = aln.to_phylip() print(got) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:357: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.core.alignment import Alignment seq = load_aligned_seqs("data/test.paml") aln = Alignment(seq) string_list = aln.to_dict().values() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:374: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs fn = "data/long_testseqs.fasta" aln = load_aligned_seqs(fn, moltype="dna") aln[:24] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:384: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: TypeError from cogent3 import load_unaligned_seqs fn = "data/long_testseqs.fasta" seqs = load_unaligned_seqs(fn) seqs[:24] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:396: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs seq = load_aligned_seqs("data/test.paml") column_four = aln[3] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:406: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/long_testseqs.fasta") region = aln[50:70] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:416: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta") col = aln[113:115].iter_positions() type(col) list(col) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:430: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data={"seq1": "ATGATGATG---", "seq2": "ATGATGATGATG"}, array_align=False ) list(range(len(aln))[2::3]) indices = [(i, i + 1) for i in range(len(aln))[2::3]] indices /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:441: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: pos3 = aln.add_feature(biotype="pos3", name="pos3", spans=indices) pos3 = pos3.get_slice() pos3 /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:452: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data={"seq1": "ATGATGATG---", "seq2": "ATGATGATGATG"}, array_align=True ) pos3 = aln[2::3] pos3 /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:472: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data={"seq1": "ACGTAA---", "seq2": "ACGACA---", "seq3": "ACGCAATGA"}, moltype="dna", ) new = aln.trim_stop_codons() new /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:485: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aln = make_aligned_seqs( data={ "seq1": "ACGTAA---", "seq2": "ACGAC----", # terminal codon incomplete "seq3": "ACGCAATGA", }, moltype="dna", ) new = aln.trim_stop_codons(strict=True) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:504: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data=[ ("seq1", "ATGAAGGTG---"), ("seq2", "ATGAAGGTGATG"), ("seq3", "ATGAAGGNGATG"), ], moltype="dna", ) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:519: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: nucs = aln.no_degenerates() nucs /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:526: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: trinucs = aln.no_degenerates(motif_length=3) trinucs /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:534: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/long_testseqs.fasta") pos = aln.variable_positions() just_variable_aln = aln.take_positions(pos) just_variable_aln[:10] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:546: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/long_testseqs.fasta") pos = aln.variable_positions() just_constant_aln = aln.take_positions(pos, negate=True) just_constant_aln[:10] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:560: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/long_testseqs.fasta") variable_codons = aln.filtered( lambda x: len(set(map(tuple, x))) > 1, motif_length=3 ) just_variable_aln[:9] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:572: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = aln.to_type(array_align=False) variable_codons = aln.filtered(lambda x: len(set("".join(x))) > 1, motif_length=3) just_variable_aln[:9] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:586: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/long_testseqs.fasta") aln.take_seqs(["Human", "Mouse"]) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:595: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln.take_seqs(["Human", "Mouse"], negate=True) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:604: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data=[ ("seq1", "ATGAAGGTG---"), ("seq2", "ATGAAGGTGATG"), ("seq3", "ATGAAGGNGATG"), ], moltype="dna", ) def no_N_chars(s): return "N" not in s aln.take_seqs_if(no_N_chars) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:624: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln.take_seqs_if(no_N_chars, negate=True) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:636: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data=[ ("seq1", "ATGAAGGTG---"), ("seq2", "ATGAAGGTGATG"), ("seq3", "ATGAAGGNGATG"), ], moltype="dna", ) counts = aln.counts() counts /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:651: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: counts = aln.counts(motif_length=3) counts /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:656: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: counts = aln.counts(include_ambiguity=True) counts /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:670: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta", moltype="dna") motif_probs = aln.get_motif_probs() motif_probs /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:680: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA, load_aligned_seqs trinuc_alphabet = DNA.alphabet.get_word_alphabet(3) aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta", moltype="dna") motif_probs = aln.get_motif_probs(alphabet=trinuc_alphabet) for m in sorted(motif_probs, key=lambda x: motif_probs[x], reverse=True): print("%s %.3f" % (m, motif_probs[m])) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:694: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = make_aligned_seqs(data=[("a", "AACAAC"), ("b", "AAGAAG")], moltype="dna") motif_probs = aln.get_motif_probs() assert motif_probs["T"] == 0.0 motif_probs = aln.get_motif_probs(pseudocount=1e-6) assert 0 < motif_probs["T"] <= 1e-6 /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:706: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seqs = [("a", "AACGTAAG"), ("b", "AACGTAAG")] aln = make_aligned_seqs(data=seqs, moltype="dna") dinuc_alphabet = DNA.alphabet.get_word_alphabet(2) motif_probs = aln.get_motif_probs(alphabet=dinuc_alphabet) assert motif_probs["AA"] == 0.25 /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:716: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seqs = [("my_seq", "AAAGTAAG")] aln = make_aligned_seqs(data=seqs, moltype="dna") my_seq = aln.get_seq("my_seq") my_seq.count("AA") "AAA".count("AA") "AAAA".count("AA") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:727: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq seq = make_seq(moltype="dna", seq="AAAGTAAG") seq di_nucs = [seq[i : i + 2] for i in range(len(seq) - 1)] sum([nn == "AA" for nn in di_nucs]) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:742: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta") col = aln[113:115].iter_positions() c1, c2 = list(col) c1, c2 list(filter(lambda x: x == "-", c1)) list(filter(lambda x: x == "-", c2)) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:756: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta") for column in aln[113:150].iter_positions(): ungapped = list(filter(lambda x: x == "-", column)) gap_fraction = len(ungapped) * 1.0 / len(column) print(gap_fraction) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:771: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data=[ ("seq1", "ATGAAGG-TG--"), ("seq2", "ATG-AGGTGATG"), ("seq3", "ATGAAG--GATG"), ], moltype="dna", ) seq_to_aln_map = aln.get_gapped_seq("seq1").gap_maps()[0] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:787: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq_to_aln_map[3] seq_to_aln_map[8] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:796: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln_to_seq_map = aln.get_gapped_seq("seq1").gap_maps()[1] aln_to_seq_map[3] aln_to_seq_map[8] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:804: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: KeyError seq_pos = aln_to_seq_map[7] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:818: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = make_aligned_seqs( data=[ ("seq1", "ATGAA---TG-"), ("seq2", "ATG-AGTGATG"), ("seq3", "AT--AG-GATG"), ], moltype="dna", ) aln.omit_gap_runs(2) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:832: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = make_aligned_seqs( data=[ ("seq1", "ATGAA---TG-"), ("seq2", "ATG-AGTGATG"), ("seq3", "AT--AG-GATG"), ], moltype="dna", ) aln.omit_gap_pos(0.40) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:846: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = make_aligned_seqs( data=[ ("seq1", "ATGAA------"), ("seq2", "ATG-AGTGATG"), ("seq3", "AT--AG-GATG"), ], moltype="dna", ) filtered_aln = aln.omit_gap_seqs(0.50) filtered_aln /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:861: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: filtered_aln.omit_gap_pos() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alphabet.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA, PROTEIN print(DNA.alphabet) print(PROTEIN.alphabet) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alphabet.rst:20: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: PROTEIN.alphabet.moltype == PROTEIN /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alphabet.rst:29: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dinuc_alphabet = DNA.alphabet.get_word_alphabet(2) print(dinuc_alphabet) trinuc_alphabet = DNA.alphabet.get_word_alphabet(3) print(trinuc_alphabet) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alphabet.rst:39: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq = "TAGT" indices = DNA.alphabet.to_indices(seq) indices /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alphabet.rst:48: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq = DNA.alphabet.from_indices([0, 2, 3, 0]) seq /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:23: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3.core.annotation_db import BasicAnnotationDb anno_db = BasicAnnotationDb() anno_db /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:43: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_annotations gff_db = load_annotations(path="data/mycoplasma-genitalium.gff") gff_db /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:56: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_annotations gb_db = load_annotations(path="data/mycoplasma-genitalium.gb") gb_db /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:69: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: summary = gff_db.describe summary /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:82: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: anno_db.add_feature( seqid="NC_000908", biotype="gene", name="interesting_gene", spans=[(1, 4)], strand="+", ) anno_db.describe /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:96: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: gff_db.add_feature( seqid="seq1", biotype="gene", name="interesting_gene", spans=[(1, 4)], strand="+", ) gff_db.describe[-2:, :] # showing just last two rows /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:143: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: mg_16s = list( gb_db.get_features_matching( name="MG_RS00775", biotype="gene", seqid="NC_000908" ) ) mg_16s /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:160: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: pseudogenes = list(gff_db.get_features_matching(biotype="pseudogene")) pseudogenes[:2] # showing just the first two /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:173: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: operon_cds = list( gff_db.get_features_matching(start=220600, end=229067, biotype="CDS") ) operon_cds /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:188: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: replication_records = list( gff_db.get_records_matching(attributes="replication", biotype="CDS") ) replication_records[0] # showing just the first match /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:208: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: gb_db.num_matches(biotype="gene") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:215: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: total_genes = gb_db.count_distinct(biotype="gene", name=True) single_copy = total_genes[total_genes.columns["count"] == 1, :] len(single_copy) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:226: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: total_genes = gff_db.num_matches(biotype="gene") print("total genes: ", total_genes) genes = gff_db.count_distinct(biotype="gene", name=True) single_copy = genes[genes.columns["count"] == 1, :] print("single copy genes: ", len(single_copy)) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:246: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: children = list(gff_db.get_feature_children(name="gene-MG_RS00035")) children /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:259: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: parents = list(gff_db.get_feature_parent(name="cds-WP_009885556.1")) parents /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:273: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: gff_db.compatible(anno_db) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:282: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: gff_db.compatible(gb_db) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:294: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: union_db = gb_db.union(anno_db) union_db.describe[-2:, :] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:307: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: gff_db.update(anno_db) gff_db.describe[-2:, :] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:318: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3.core.annotation_db import GenbankAnnotationDb new_gb_db = GenbankAnnotationDb(source="m-genitalium-database.gbdb", db=anno_db) new_gb_db /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:331: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_annotations gff_db = load_annotations(path="data/mycoplasma-genitalium.gff") just_cds = gff_db.subset(biotype="CDS") just_cds.describe /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:354: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_seq seq1 = make_seq( "AAGAAGAAGACCCCCAAAAAAAAAATTTTTTTTTTAAAAAGGGAACCCT", name="NC_000908", moltype="dna", ) seq1.annotation_db = anno_db seq1.annotation_db /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:376: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq gb_seq = load_seq("data/mycoplasma-genitalium.gb") gb_seq.annotation_db /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:389: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: gff_seq = load_seq( "data/mycoplasma-genitalium.fa", annotation_path="data/mycoplasma-genitalium.gff", ) gff_seq.annotation_db /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:402: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: seq = load_seq( "data/mycoplasma-genitalium.fa", annotation_path="data/mycoplasma-genitalium.gff", label_to_name=lambda x: x.split()[0], ) seq.annotation_db /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:412: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import pathlib # clean up files path = pathlib.Path("m-genitalium-database.gbdb") path.unlink() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_alignments.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_alignments.rst:17: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_unaligned_seqs, make_tree from cogent3.align.progressive import tree_align /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_alignments.rst:24: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seqs = load_unaligned_seqs("data/test2.fasta", moltype="dna") aln, tree = tree_align("HKY85", seqs, show_progress=False) aln /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_alignments.rst:32: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tree = make_tree( "(((NineBande:0.013,Mouse:0.185):0.023,DogFaced:0.046):0.027,Human:0.034,HowlerMon:0.019)" ) params = {"kappa": 4.0} aln, tree = tree_align( "HKY85", seqs, tree=tree, param_vals=params, show_progress=False ) aln /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_alignments.rst:48: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_unaligned_seqs, make_tree from cogent3.align.progressive import tree_align seqs = load_unaligned_seqs("data/test2.fasta", moltype="dna") tree = make_tree( "((NineBande:0.058,Mouse:0.595):0.079,DogFaced:0.142,(HowlerMon:0.062,Human:0.103):0.079)" ) params = {"kappa": 4.0, "omega": 1.3} aln, tree = tree_align( "MG94HKY", seqs, tree=tree, param_vals=params, show_progress=False ) aln /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_alignments.rst:68: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_unaligned_seqs from cogent3.align.progressive import tree_align from cogent3.evolve.models import get_model seqs = [ ( "hum", "AAGCAGATCCAGGAAAGCAGCGAGAATGGCAGCCTGGCCGCGCGCCAGGAGAGGCAGGCCCAGGTCAACCTCACT", ), ( "mus", "AAGCAGATCCAGGAGAGCGGCGAGAGCGGCAGCCTGGCCGCGCGGCAGGAGAGGCAGGCCCAAGTCAACCTCACG", ), ("rat", "CTGAACAAGCAGCCACTTTCAAACAAGAAA"), ] unaligned_DNA = make_unaligned_seqs(seqs, moltype="dna") unaligned_DNA /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_alignments.rst:88: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: unaligned_DNA.get_translation() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_alignments.rst:94: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aligned_aa_seqs = [ ("hum", "KQIQESSENGSLAARQERQAQVNLT"), ("mus", "KQIQESGESGSLAARQERQAQVNLT"), ("rat", "LNKQ------PLS---------NKK"), ] aligned_aa = make_aligned_seqs(aligned_aa_seqs, moltype="protein") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_alignments.rst:107: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aligned_DNA = aligned_aa.replace_seqs(unaligned_DNA, aa_to_codon=True) aligned_DNA /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_phylogenies.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_phylogenies.rst:18: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna") tree = aln.quick_tree(calc="TN93", show_progress=False) tree = tree.balanced() # purely for display print(tree.ascii_art()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_phylogenies.rst:29: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tree = aln.quick_tree(calc="TN93", bootstrap=100, show_progress=False) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_phylogenies.rst:36: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna") dists = aln.distance_matrix(calc="TN93") tree = dists.quick_tree(show_progress=False) tree = tree.balanced() # purely for display print(tree.ascii_art()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_phylogenies.rst:49: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.phylo import nj aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna") dists = aln.distance_matrix(calc="TN93") tree = nj.nj(dists, show_progress=False) tree = tree.balanced() # purely for display print(tree.ascii_art()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_phylogenies.rst:63: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.phylo import nj dists = {("a", "b"): 2.7, ("c", "b"): 2.33, ("c", "a"): 0.73} tree = nj.nj(dists, show_progress=False) print(tree.ascii_art()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_phylogenies.rst:76: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.phylo.least_squares import WLS from cogent3.util.deserialise import deserialise_object dists = deserialise_object("data/dists_for_phylo.json") ls = WLS(dists) stat, tree = ls.trex(a=5, k=5, show_progress=False) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_phylogenies.rst:92: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.evolve.models import F81 from cogent3.phylo.maximum_likelihood import ML aln = load_aligned_seqs("data/primate_brca1.fasta") ml = ML(F81(), aln) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/calc_genetic_distance.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/calc_genetic_distance.rst:16: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import available_distances available_distances() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/calc_genetic_distance.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna") dists = aln.distance_matrix(calc="tn93", show_progress=False) dists /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/calc_genetic_distance.rst:38: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_distance_calculator, load_aligned_seqs aln = load_aligned_seqs("data/primate_brca1.fasta") dist_calc = get_distance_calculator("tn93", alignment=aln) dist_calc /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/calc_genetic_distance.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dist_calc.run(show_progress=False) dists = dist_calc.get_pairwise_distances() dists /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/calc_genetic_distance.rst:54: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dist_calc.stderr /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/calc_genetic_distance.rst:65: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_model, load_aligned_seqs from cogent3.evolve import distance aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna") d = distance.EstimateDistances(aln, submodel=get_model("F81")) d.run(show_progress=False) dists = d.get_pairwise_distances() dists /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/calc_genetic_distance.rst:82: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna") dists = aln.distance_matrix(calc="tn93", show_progress=False) dists.max_pair() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/calc_genetic_distance.rst:93: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: dists[dists.max_pair()] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/calc_genetic_distance.rst:106: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna") dists = aln.distance_matrix(calc="tn93", show_progress=False) dists.min_pair() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/calc_genetic_distance.rst:117: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: dists[dists.min_pair()] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:18: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import available_models available_models() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import get_model hky = get_model("HKY85") print(hky) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:44: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import get_model sub_mod = get_model("GTR", with_rate=True, distribution="gamma") print(sub_mod) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:56: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import get_model sub_mod = get_model("CNFGTR", with_rate=True, distribution="gamma") print(sub_mod) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:68: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import get_model sub_mod = get_model("JTT92", with_rate=True, distribution="gamma") print(sub_mod) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:80: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_tree from cogent3.evolve.models import get_model sub_mod = get_model("F81") tree = make_tree("(a,b,(c,d))") lf = sub_mod.make_likelihood_function(tree) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:94: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs, make_tree from cogent3.evolve.models import get_model sub_mod = get_model("F81") tree = make_tree("(a,b,(c,d))") lf = sub_mod.make_likelihood_function(tree) aln = make_aligned_seqs( [("a", "ACGT"), ("b", "AC-T"), ("c", "ACGT"), ("d", "AC-T")] ) lf.set_alignment(aln) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:112: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") print(tree.ascii_art()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:120: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: sm = get_model("CNFGTR") lf = sm.make_likelihood_function(tree, digits=2) lf.set_param_rule( "omega", tip_names=["Human", "Orangutan"], outgroup_name="Galago", clade=True, init=0.5, ) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:134: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:145: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") sm = get_model("CNFGTR") lf = sm.make_likelihood_function(tree, digits=2) lf.set_param_rule("omega", is_constant=True) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:160: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") sm = get_model("CNFGTR") lf = sm.make_likelihood_function(tree, digits=2) lf.set_param_rule("omega", init=0.1) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:175: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") sm = get_model("CNFGTR") lf = sm.make_likelihood_function(tree, digits=2) lf.set_param_rule("omega", init=0.1, lower=1e-9, upper=20.0) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:190: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") sm = get_model("F81") lf = sm.make_likelihood_function(tree) lf.set_param_rule("length", upper=1.0) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:207: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.models import get_model sm = get_model("GTR", with_rate=True, distribution="gamma") tree = load_tree("data/primate_brca1.tree") lf = sm.make_likelihood_function(tree, bins=4, digits=2) lf.set_param_rule("bprobs", is_constant=True) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:222: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.models import get_model sm = get_model("GTR", with_rate=True, distribution="gamma") tree = load_tree("data/primate_brca1.tree") lf = sm.make_likelihood_function(tree, bins=4, sites_independent=False, digits=2) lf.set_param_rule("bprobs", is_constant=True) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:239: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") aln = load_aligned_seqs("data/primate_brca1.fasta") sm = get_model("F81") lf = sm.make_likelihood_function(tree, digits=3, space=2) lf.set_alignment(aln) lf.optimise(show_progress=False) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:253: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(local=True, max_restarts=5, show_progress=False) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:259: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(local=False, global_tolerance=1.0, show_progress=False) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:265: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(show_progress=False, max_restarts=5, tolerance=1e-8) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:276: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") aln = load_aligned_seqs("data/primate_brca1.fasta") sm = get_model("F81") lf = sm.make_likelihood_function(tree, digits=3, space=2) lf.set_alignment(aln) try: lf.optimise( show_progress=False, limit_action="raise", max_evaluations=10, return_calculator=True, ) except ArithmeticError as err: print(err) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:303: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model sm = get_model("GTR") tree = load_tree("data/primate_brca1.tree") lf = sm.make_likelihood_function(tree) aln = load_aligned_seqs("data/primate_brca1.fasta") lf.set_alignment(aln) lf.optimise(local=True, show_progress=False) lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:321: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lnL = lf.lnL lnL /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:326: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: nfp = lf.nfp nfp /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:338: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.get_aic() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:344: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.get_aic(second_order=True) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:353: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.get_bic() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:367: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: a_g = lf.get_param_value("A/G") a_g /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:372: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: human = lf.get_param_value("length", "Human") human /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:380: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: mprobs = lf.get_motif_probs() mprobs /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:388: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tables = lf.get_statistics(with_motif_probs=True, with_titles=True) tables[0] # just displaying the first /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:398: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") aln = load_aligned_seqs("data/primate_brca1.fasta") sm = get_model("F81") lf = sm.make_likelihood_function(tree, digits=3, space=2) lf.set_alignment(aln) lf.set_param_rule( "length", tip_names=["Human", "Chimpanzee"], outgroup_name="Galago", clade=True, is_independent=False, ) lf.set_name("Null Hypothesis") lf.optimise(local=True, show_progress=False) null_lnL = lf.lnL null_nfp = lf.nfp lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:423: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule("length", is_independent=True) lf.set_name("Alt Hypothesis") lf.optimise(local=True, show_progress=False) alt_lnL = lf.lnL alt_nfp = lf.nfp lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:434: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from scipy.stats.distributions import chi2 LR = 2 * (alt_lnL - null_lnL) # the likelihood ratio statistic df = alt_nfp - null_nfp # the test degrees of freedom p = chi2.sf(LR, df) print(f"LR={LR:.4f} ; df={df}; p={df:.4f}") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:450: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") aln = load_aligned_seqs("data/primate_brca1.fasta") sm = get_model("F81") lf = sm.make_likelihood_function(tree, digits=3, space=2) lf.set_alignment(aln) lf.set_param_rule( "length", tip_names=["Human", "Chimpanzee"], outgroup_name="Galago", clade=True, is_independent=False, ) lf.set_name("Null Hypothesis") lf.optimise(local=True, show_progress=False) sim_aln = lf.simulate_alignment() sim_aln[:60] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:478: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") aln = load_aligned_seqs("data/primate_brca1.fasta") sm = get_model("HKY85") lf = sm.make_likelihood_function(tree) lf.set_alignment(aln) lf.optimise(local=True, show_progress=False) kappa_lo, kappa_mle, kappa_hi = lf.get_param_interval("kappa") print(f"lo={kappa_lo:.2f} ; mle={kappa_mle:.2f} ; hi={kappa_hi:.2f}") human_lo, human_mle, human_hi = lf.get_param_interval("length", "Human") print(f"lo={human_lo:.2f} ; mle={human_mle:.2f} ; hi={human_hi:.2f}") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:501: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model aln = make_aligned_seqs(data=dict(a="ACGG", b="ATAG", c="ATGG")) tree = make_tree(tip_names=aln.names) sm = get_model("F81") lf = sm.make_likelihood_function(tree) lf.set_alignment(aln) json = lf.to_json() json[:60] # just truncating the displayed string /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:516: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.deserialise import deserialise_object newlf = deserialise_object(json) newlf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:528: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") aln = load_aligned_seqs("data/primate_brca1.fasta") sm = get_model("F81") lf = sm.make_likelihood_function(tree, digits=3, space=2) lf.set_alignment(aln) lf.optimise(show_progress=False) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:542: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: ancestors = lf.likely_ancestral_seqs() ancestors[:60] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:549: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: ancestral_probs = lf.reconstruct_ancestral_seqs() ancestral_probs["root"][:5] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_seq # create an example sequence seq = make_seq( "GCCTAATACTAAGCCTAAGCCTAAGACTAAGCCTAATACTAAGCCTAAGCCTAAGACTAA", name="seq1", moltype="dna", ) # Add a feature seq.add_feature(biotype="gene", name="a_gene", spans=[(12, 48)], seqid="seq1") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:45: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: # Add a feature as a series seq.add_feature( biotype="cpgsite", name="a_cpgsite", spans=[(12, 18), (21, 29), (35, 48)], seqid="seq1", ) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:63: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs # make demo alignment aln1 = make_aligned_seqs( data=[["seq1", "-AAACCCCCA"], ["seq2", "TTTT--TTTT"]], array_align=False ) # add feature to seq1 aln1.add_feature( seqid="seq1", biotype="exon", name="A", spans=[(3, 8)], on_alignment=False ) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:84: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs # make demo alignment aln1 = make_aligned_seqs( data=[["seq1", "-AAACCCCCA"], ["seq2", "TTTT--TTTT"]], array_align=False ) aln1.add_feature( biotype="exon", name="aligned_exon", spans=[(0, 8)], on_alignment=True, ) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:108: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq from cogent3.core.annotation_db import BasicAnnotationDb # init empty db and add feature db = BasicAnnotationDb() db.add_feature(seqid="seq1", biotype="exon", name="C", spans=[(45, 48)]) # make demo seq s1 = make_seq( "AAGAAGAAGACCCCCAAAAAAAAAATTTTTTTTTTAAAAAGGGAACCCT", name="seq1", moltype="dna" ) # assign db to sequence s1.annotation_db = db s1.annotation_db /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:143: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq %timeit load_seq("data/C-elegans-chromosome-I.gb", moltype="dna") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:150: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: :hide-code: seq = load_seq("data/C-elegans-chromosome-I.gb", moltype="dna") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:158: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: seq.annotation_db /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:173: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq seq = load_seq( filename="data/C-elegans-chromosome-I.fa", annotation_path="data/C-elegans-chromosome-I.gff", moltype="dna", ) seq.annotation_db /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:189: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq seq = load_seq( "data/C-elegans-chromosome-I.fa", annotation_path="data/C-elegans-chromosome-I.gff", label_to_name=lambda x: x.split()[0], moltype="dna", ) seq.annotation_db /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:209: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from cogent3 import load_seq loaded_seq = load_seq( "data/C-elegans-chromosome-I.fa", label_to_name=lambda x: x.split()[0], moltype="dna", ) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:220: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: # loaded_seq = < loaded / created the seq> loaded_seq.annotate_from_gff("data/C-elegans-chromosome-I.gff") loaded_seq.annotation_db /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:229: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from cogent3 import make_seq sub_seq = make_seq( "GCCTAATACTAAGCCTAAGCCTAAGACTAAGCCTAATACTAAGCCTAAGCCTAAGACTAAGCCTAAGACTAAGCCTAAGA", name="I", moltype="dna", ) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:240: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: # sub_seq = sub_seq.annotate_from_gff("data/C-elegans-chromosome-I.gff", offset=600) sub_seq.annotation_db /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:254: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_aligned_seqs brca1_aln = load_aligned_seqs( "data/primate_brca1.fasta", array_align=False, moltype="dna" ) brca1_aln /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:266: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: brca1_aln.annotate_from_gff("data/brca1_hsa_shortened.gff", seq_ids=["Human"]) brca1_aln.annotation_db /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:274: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: brca1_aln.get_seq("Human").annotation_db /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:296: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq seq = load_seq("data/C-elegans-chromosome-I.gb", moltype="dna") # note we wrap `get_features` in `list` as generator is returned gene = list(seq.get_features(name="WBGene00021661", biotype="gene")) gene /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:312: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq seq = load_seq("data/C-elegans-chromosome-I.gb", moltype="dna") cds = list(seq.get_features(biotype="CDS")) cds[:3] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:323: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: cds = list(seq.get_features(biotype="CDS", name="WBGene00021661")) cds /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:334: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq seq = load_seq("data/C-elegans-chromosome-I.gb", moltype="dna") region_features = list(seq.get_features(start=10148, stop=26732)) region_features[:3] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:345: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: mRNA = list(seq.get_features(start=10148, stop=29322, biotype="mRNA"))[0] mRNA /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:358: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_aligned_seqs # first load alignment and annotate the human seq aln = load_aligned_seqs( "data/primate_brca1.fasta", array_align=False, moltype="dna" ) aln.annotate_from_gff("data/brca1_hsa_shortened.gff", seq_ids=["Human"]) # query alignment providing seqid of interest human_exons = list(aln.get_features(biotype="exon", seqid="Human")) human_exons /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:383: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs # add a feature to the alignment we created above on difference sequence aln.add_feature(biotype="gene", name="gene:101", spans=[(40, 387)], seqid="Rhesus") any_feature = list(aln.get_features(on_alignment=False)) any_feature /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:405: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs # first we add the feature to the alignment aln.add_feature( biotype="pseudogene", name="pseudogene1", spans=[(420, 666)], on_alignment=True ) # query for features on the alignment aln_features = list(aln.get_features(on_alignment=True)) aln_features /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:426: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs aln3 = make_aligned_seqs( data=[["x", "C-CCCAAAAA"], ["y", "-T----TTTT"]], array_align=False, moltype="dna", ) exon = aln3.add_feature( seqid="x", biotype="exon", name="ex1", spans=[(0, 4)], on_alignment=False ) exon.get_slice() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:441: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aln_exons = list(aln3.get_features(seqid="x", biotype="exon"))[0] aln_exons /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:451: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: exon.get_slice(allow_gaps=True) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:466: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq seq = load_seq( "data/C-elegans-chromosome-I.fa", annotation_path="data/C-elegans-chromosome-I.gff", label_to_name=lambda x: x.split()[0], moltype="dna", ) pseudogene = list(seq.get_features(start=10148, stop=26732, biotype="pseudogene"))[0] seq[pseudogene] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:484: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: pseudogene.get_slice() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:494: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_seq seq = load_seq("data/C-elegans-chromosome-I.gb", moltype="dna") subseq = seq[25000:35000] fig = subseq.get_drawable(biotype=("gene", "mRNA", "CDS", "misc_RNA")) fig.show() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:508: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: pseudogene.get_coordinates() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:515: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq seq = load_seq("data/C-elegans-chromosome-I.gb", moltype="dna") cds = list(seq.get_features(biotype="CDS"))[0] exon_coords = cds.get_coordinates() exon_coords /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:528: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: intron_coords = [] for i in range(len(exon_coords) - 1): intron_coords.append((exon_coords[i][1], exon_coords[i + 1][0])) intron_coords /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:540: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: intron = seq.add_feature( biotype="intron", name="intron:Y74C9A.3.1", seqid="I", spans=intron_coords ) intron /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:553: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq seq = load_seq("data/C-elegans-chromosome-I.gb", moltype="dna") cds = list(seq.get_features(biotype="CDS")) union_cds = cds[0].union(cds[1:]) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:572: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq seq = load_seq("data/C-elegans-chromosome-I.gb", moltype="dna") genes = list(seq.get_features(biotype="gene")) genes = genes[0].union(genes[1:]) genes /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:584: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: intergenic = genes.shadow() intergenic /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:592: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: intergenic.get_slice() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:605: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq seq = load_seq("data/C-elegans-chromosome-I.gb", moltype="dna") no_cds = seq.with_masked_annotations("CDS") no_cds[2575800:2575900] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:621: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data=[["x", "C-CCCAAAAAGGGAA"], ["y", "-T----TTTTG-GTT"]], moltype="dna", array_align=False, ) exon = aln.add_feature( seqid="x", biotype="exon", name="exon-be-gone", spans=[(0, 4)], on_alignment=False, ) aln.with_masked_annotations("exon", mask_char="?") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:642: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: rc = aln.rc() rc /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:650: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: rc.with_masked_annotations("exon", mask_char="?") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:664: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq seq = load_seq( "data/C-elegans-chromosome-I.fa", annotation_path="data/C-elegans-chromosome-I.gff", label_to_name=lambda x: x.split()[0], moltype="dna", ) gene = list(seq.get_features(name="gene:WBGene00022276", biotype="gene"))[0] children = list(gene.get_children()) children /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:686: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: child = list(seq.get_features(name="transcript:Y74C9A.2a.3", biotype="mRNA"))[0] parent = list(child.get_parent()) parent /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:698: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aln2 = make_aligned_seqs( data=[["x", "-AAAAAAAAA"], ["y", "TTTT--TTTT"]], array_align=False, moltype="dna", ) x, y = aln2.get_seq("x"), aln2.get_seq("y") x.annotation_db is y.annotation_db is aln2.annotation_db /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:711: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: seq = make_seq("CCCCCCCCCCCCCCCCCCCC", name="x", moltype="dna") match_exon = seq.add_feature(biotype="exon", name="A", spans=[(3, 8)]) aln2.copy_annotations(seq.annotation_db) aln2.annotation_db /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:721: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: copied = list(aln2.get_features(seqid="x", biotype="exon")) copied /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:732: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: unified = aln_exons.as_one_span() aln3[unified] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:743: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: plus = make_seq("CCCCCAAAAAAAAAATTTTTTTTTTAAAGG", moltype="dna") plus_rpt = plus.add_feature(biotype="blah", name="a", spans=[(5, 15), (25, 28)]) plus[plus_rpt] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:750: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: minus = plus.rc() minus /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:756: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: minus_rpt = list(minus.get_features(biotype="blah"))[0] minus[minus_rpt] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs data = { "s1": "GCTCATGCCAGCTCTTTACAGCATGAGAACA--AGT", "s2": "ACTCATGCCAACTCATTACAGCATGAGAACAGCAGT", "s3": "ACTCATGCCAGCTCATTACAGCATGAGAACAGCAGT", "s4": "ACTCATGCCAGCTCATTACAGCATGAGAACAGCAGT", "s5": "ACTCATGCCAGCTCAGTACAGCATGAGAACAGCAGT", } nt_seqs = make_aligned_seqs(data=data, moltype="dna") nt_seqs /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:30: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: nt_seqs.get_translation(gc=1, incomplete_ok=True) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:38: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code standard_code = get_code(1) standard_code.translate("TTTGCAAAC") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:50: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code, make_seq standard_code = get_code(1) seq = make_seq("ATGCTAACATAAA", moltype="dna") translations = standard_code.sixframes(seq) print(translations) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:62: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code, make_seq standard_code = get_code(1) seq = make_seq("ATGCTAACATAAA", moltype="dna") stops_frame1 = standard_code.get_stop_indices(seq, start=0) stops_frame1 /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:71: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: stop_index = stops_frame1[0] seq[stop_index : stop_index + 3] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:79: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code, make_seq standard_code = get_code(1) standard_code["TTT"] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:88: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: standard_code["A"] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:95: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code standard_code = get_code(1) standard_code["TTT"] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:105: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code standard_code = get_code(1) standard_code["A"] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:115: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: targets = ["A", "C"] codons = [standard_code[aa] for aa in targets] codons /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:121: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: flat_list = sum(codons, []) flat_list /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:129: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code gc = get_code(1) alphabet = gc.get_alphabet() print(alphabet) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:142: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("ATGCACTGGTAA", name="my_gene", moltype="dna") codons = my_seq.get_in_motif_size(3) codons /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:155: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: pep = my_seq.get_translation() pep /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:163: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from cogent3.core.alphabet import AlphabetError /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:170: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_seq seq = make_seq("ATGTGATGGTAA", name="s1", moltype="dna") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:179: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: AlphabetError pep = seq.get_translation() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:186: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: pep = seq.get_translation(include_stop=True) pep /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_seq seq = load_seq("data/mycoplasma-genitalium.fa", moltype="dna") seq /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:22: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq = load_seq("data/brca1-bats.fasta", moltype="dna") seq /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:39: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/long_testseqs.fasta", moltype="dna") type(aln) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:48: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln.info.source /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:61: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_unaligned_seqs seqs = load_unaligned_seqs("data/long_testseqs.fasta", moltype="dna") type(seqs) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:75: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs( "https://raw.githubusercontent.com/cogent3/cogent3/develop/doc/data/long_testseqs.fasta", moltype="dna", ) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:89: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/long_testseqs.fasta", moltype="dna", format="fasta") aln /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:101: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs protein_seqs = {"seq1": "DEKQL-RG", "seq2": "DDK--SRG"} proteins_loaded = make_aligned_seqs(protein_seqs) proteins_loaded.moltype proteins_loaded /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:110: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: proteins_loaded = make_aligned_seqs(protein_seqs, moltype="protein") proteins_loaded /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:123: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs seqs = {"seq1": "AATCG-A", "seq2": "AATCGGA"} seqs_loaded = make_aligned_seqs(seqs) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:133: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs seqs = {"seq1": "AATCG-A", "seq2": "AATCGGA"} seqs_loaded = make_aligned_seqs(seqs) seqs_loaded /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:146: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs DNA_seqs = { "sample1 Mus musculus": "AACCTGC--C", "sample2 Gallus gallus": "AAC-TGCAAC", } loaded_seqs = make_aligned_seqs( DNA_seqs, moltype="dna", label_to_name=lambda x: x.split()[0] ) loaded_seqs /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:164: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_unaligned_seqs seqs = {"seq1": "AATCA", "seq2": "AATCGGA"} seqs = make_unaligned_seqs(data=seqs, moltype="dna") seqs /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:184: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.fasta import MinimalFastaParser f = open("data/long_testseqs.fasta") seqs = [(name, seq) for name, seq in MinimalFastaParser(f)] seqs /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:197: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.fasta import LabelParser def latin_to_common(latin): return {"Homo sapiens": "human", "Pan troglodtyes": "chimp"}[latin] label_parser = LabelParser( "%(species)s", [[1, "species", latin_to_common]], split_with=":" ) for label in ">abcd:Homo sapiens:misc", ">abcd:Pan troglodtyes:misc": label = label_parser(label) print(label, type(label)) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:213: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.fasta import LabelParser, MinimalFastaParser fasta_data = [ ">gi|10047090|ref|NP_055147.1| small muscle protein, X-linked [Homo sapiens]", "MNMSKQPVSNVRAIQANINIPMGAFRPGAGQPPRRKECTPEVEEGVPPTSDEEKKPIPGAKKLPGPAVNL", "SEIQNIKSELKYVPKAEQ", ">gi|10047092|ref|NP_037391.1| neuronal protein [Homo sapiens]", "MANRGPSYGLSREVQEKIEQKYDADLENKLVDWIILQCAEDIEHPPPGRAHFQKWLMDGTVLCKLINSLY", "PPGQEPIPKISESKMAFKQMEQISQFLKAAETYGVRTTDIFQTVDLWEGKDMAAVQRTLMALGSVAVTKD", ] label_to_name = LabelParser( "%(ref)s", [[1, "gi", str], [3, "ref", str], [4, "description", str]], split_with="|", ) for name, seq in MinimalFastaParser(fasta_data, label_to_name=label_to_name): print(name) print(name.info.gi) print(name.info.description) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:54: WARNING: TODO entry found: add cross ref for description of Info class /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv") table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("https://raw.githubusercontent.com/cogent3/cogent3/develop/doc/data/stats.tsv") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:38: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv", sep="\t") table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:55: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import load_delimited header, rows, title, legend = load_delimited("data/CerebellumDukeDNaseSeq.pk", header=False, sep="\t") rows[:4] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:65: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(with_header=False, sep="\t") rows = list(reader("data/CerebellumDukeDNaseSeq.pk")) rows[:4] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:81: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv", limit=2) table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:93: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser( lambda line: float(line[2]) <= 10, with_header=True, sep="\t" ) table = load_table("data/stats.tsv", reader=reader, digits=1) table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:105: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: reader = FilteringParser( lambda line: float(line[2]) <= 10, with_header=True, sep="\t", negate=True ) table = load_table("data/stats.tsv", reader=reader, digits=1) table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:118: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(columns=["Locus", "Ratio"], with_header=True, sep="\t") table = load_table("data/stats.tsv", reader=reader) table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:128: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(columns=[0, -1], with_header=True, sep="\t") table = load_table("data/stats.tsv", reader=reader) table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:143: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(with_header=True, sep="\t") data = list(reader("data/stats.tsv")) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:152: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data[:2] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:161: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table header = ["A", "B", "C"] rows = [range(3), range(3, 6), range(6, 9), range(9, 12)] table = make_table(header=["A", "B", "C"], data=rows) table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:175: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table data = dict(A=[0, 3, 6], B=[1, 4, 7], C=[2, 5, 8]) table = make_table(data=data) table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:186: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = make_table(header=["C", "A", "B"], data=data) table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:196: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv", index_name="Locus") table["NP_055852"] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:201: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table["NP_055852", "Region"] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:210: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from pandas import DataFrame from cogent3 import make_table data = dict(a=[0, 3], b=["a", "c"]) df = DataFrame(data=data) table = make_table(data_frame=df) table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:224: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table(header=["a", "b"], data=[[0, "a"], [3, "c"]]) table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:236: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table data = dict(a=[0, 3], b=["a", "c"]) table = make_table(data=data) table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:247: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table d2D = { "edge.parent": { "NineBande": "root", "edge.1": "root", "DogFaced": "root", "Human": "edge.0", }, "x": { "NineBande": 1.0, "edge.1": 1.0, "DogFaced": 1.0, "Human": 1.0, }, "length": { "NineBande": 4.0, "edge.1": 4.0, "DogFaced": 4.0, "Human": 4.0, }, } table = make_table( data=d2D, ) table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:279: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table( header=["abcd", "data"], data=[[range(1, 6), "0"], ["x", 5.0], ["y", None]], missing_data="*", digits=1, ) table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:294: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table() table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/moltypes.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/moltypes.rst:17: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import available_moltypes available_moltypes() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/moltypes.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs seqs = load_aligned_seqs("data/brca1-bats.fasta", moltype="dna") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/moltypes.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_moltype dna = get_moltype("dna") dna /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/moltypes.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dna.ambiguities /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/moltypes.rst:53: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dna.degenerates /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/moltypes.rst:60: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dna.complement("AGG") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/moltypes.rst:69: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq = dna.make_seq("AGGCTT", name="seq1") seq /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/moltypes.rst:77: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: rna = get_moltype("rna") rna.is_valid("ACGUACGUACGUACGU") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/moltypes.rst:87: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.core import moltype as mt DNAgapped = mt.MolType( seq_constructor=mt.DnaSequence, motifset=mt.IUPAC_DNA_chars, ambiguities=mt.IUPAC_DNA_ambiguities, complements=mt.IUPAC_DNA_ambiguities_complements, pairs=mt.DnaStandardPairs, gaps=".", ) seq = DNAgapped.make_seq("ACG.") seq /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/moltypes.rst:104: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA from cogent3.core.sequence import DnaSequence DnaSequence.moltype = DNA /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/protein_sequences.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/protein_sequences.rst:14: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq p = make_seq("THISISAPRQTEIN", "myProtein", moltype="protein") type(p) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/protein_sequences.rst:21: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: p /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/protein_sequences.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code standard_code = get_code(1) standard_code.translate("TTTGCAAAC") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/protein_sequences.rst:40: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq nuc = make_seq("TTTGCAAAC", moltype="dna") pep = nuc.get_translation() pep /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/protein_sequences.rst:51: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs seq = load_aligned_seqs("data/abglobin_aa.phylip", moltype="protein") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:14: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") print(tr.ascii_art()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:24: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") tr.write("data/temp.tree") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") names = tr.get_node_names() names[:4] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: names[4:] names_nodes = tr.get_nodes_dict() names_nodes["Human"] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:48: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tr.get_node_matching_name("Mouse") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:55: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") hu = tr.get_node_matching_name("Human") tr.name /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:63: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: hu.name /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:70: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") nodes = tr.get_nodes_dict() hu = nodes["Human"] type(hu) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:79: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: type(tr) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:88: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") nodes = tr.get_nodes_dict() for n in nodes.items(): print(n) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:99: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: for n in tr.iter_tips(): print(n) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:106: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") for n in tr.iter_nontips(): print(n.get_newick()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:117: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") edges = tr.get_connecting_edges("edge.1", "Human") for edge in edges: print(edge.name) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:129: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") nodes = tr.get_nodes_dict() hu = nodes["Human"] mu = nodes["Mouse"] hu.distance(mu) hu.is_tip() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:143: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") nodes = tr.get_nodes_dict() hu = nodes["Human"] mu = nodes["Mouse"] lca = hu.last_common_ancestor(mu) lca /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:154: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: type(lca) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:161: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") hu = tr.get_node_matching_name("Human") for a in hu.ancestors(): print(a.name) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:173: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") node = tr.get_node_matching_name("edge.1") children = list(node.iter_tips()) + list(node.iter_nontips()) for child in children: print(child.name) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:186: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") dists = tr.get_distances() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:195: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: human_dists = [names for names in dists if "Human" in names] for dist in human_dists: print(dist, dists[dist]) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:204: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") tr.max_tip_tip_distance() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:214: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") hu = tr.get_node_matching_name("Human") tips = hu.tips_within_distance(0.2) for t in tips: print(t) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:230: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") print(tr.rooted_at("edge.0").ascii_art()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:240: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") print(tr.root_at_midpoint().ascii_art()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:247: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(tr.ascii_art()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:254: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") print(tr.ascii_art()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:261: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(tr.rooted_with_tip("Mouse").ascii_art()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:271: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") tr.get_newick() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:278: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tr.get_newick(with_distances=True) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:285: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") xml = tr.get_xml() for line in xml.splitlines(): print(line) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:299: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") print(tr.ascii_art()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:309: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") for t in tr.preorder(): print(t.get_newick()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:320: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") for t in tr.postorder(): print(t.get_newick()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:334: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") for tip in tr.iter_nontips(): tip_names = tip.get_tip_names() print(tip_names) sub_tree = tr.get_sub_tree(tip_names) print(sub_tree.ascii_art()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:348: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from cogent3.util.io import remove_files remove_files(["data/temp.tree", "data/temp.pdf"], error_on_missing=False) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:364: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_tree simple_tree_string = "(B:0.2,(D:0.4)E:0.5)F;" simple_tree = make_tree(simple_tree_string) print(simple_tree.ascii_art()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:372: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: simple_tree.prune() print(simple_tree.ascii_art()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:377: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(simple_tree) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:384: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr1 = load_tree("data/test.tree") print(tr1.get_newick()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:391: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tr2 = tr1.unrooted_deepcopy() print(tr2.get_newick()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:401: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_tree tree_string = "(B:0.2,H:0.2,(C:0.3,D:0.4,E:0.1)F:0.5)G;" tr = make_tree(tree_string) print(tr.ascii_art()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:409: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(tr.bifurcating().ascii_art()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:422: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") print(tr.ascii_art()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:429: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(tr.balanced().ascii_art()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:438: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_tree tr1 = make_tree("(B:0.2,(C:0.2,D:0.2)F:0.2)G;") tr2 = make_tree("((C:0.1,D:0.1)F:0.1,B:0.1)G;") tr1.same_topology(tr2) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:467: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: # Distance metrics for rooted trees from cogent3 import make_tree tr1 = make_tree(treestring="(a,(b,(c,(d,e))));") tr2 = make_tree(treestring="(e,(d,(c,(b,a))));") mc_distance = tr1.tree_distance(tr2, method="matching_cluster") # or method="mc" or method="matching" rooted_rf_distance = tr1.tree_distance(tr2, method="rooted_robinson_foulds") # or method="rrf" or method="rf" print("Matching Cluster Distance:", mc_distance) print("Rooted Robinson Foulds Distance:", rooted_rf_distance) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:481: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: # Distance metrics for unrooted trees from cogent3 import make_tree tr1 = make_tree(treestring="(a,b,(c,(d,e)));") tr2 = make_tree(treestring="((a,c),(b,d),e);") lrm_distance = tr1.tree_distance(tr2, method="lin_rajan_moret") # or method="lrm" or method="matching" unrooted_rf_distance = tr1.tree_distance(tr2, method="unrooted_robinson_foulds") # or method="urf" or method="rf" print("Lin-Rajan-Moret Distance:", lrm_distance) print("Unrooted Robinson Foulds Distance:", unrooted_rf_distance) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:501: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_tree tr = make_tree("(B:0.2,(C:0.3,D:0.4)F:0.5)G;") print(tr.ascii_art()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:508: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tr.set_tip_distances() for t in tr.preorder(): print(t.name, t.TipDistance) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:517: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_tree tr = make_tree("(B:0.2,(C:0.3,D:0.4)F:0.5)G;") print(tr) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:524: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tr.scale_branch_lengths() print(tr) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:534: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_tree tr = make_tree("(B:3,(C:2,D:4)F:5)G;") d, tips = tr.tip_to_tip_distances() for i, t in enumerate(tips): print(t.name, d[i]) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:554: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_tree tr1 = make_tree("(B:2,(C:3,D:4)F:5)G;") tr2 = make_tree("(C:2,(B:3,D:4)F:5)G;") tr1.compare_by_tip_distances(tr2) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory cookbook/loading_tabular.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory cookbook/loading_tabular.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv") table cookbook/loading_tabular.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("https://raw.githubusercontent.com/cogent3/cogent3/develop/doc/data/stats.tsv") cookbook/loading_tabular.rst:38: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv", sep="\t") table cookbook/loading_tabular.rst:55: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import load_delimited header, rows, title, legend = load_delimited("data/CerebellumDukeDNaseSeq.pk", header=False, sep="\t") rows[:4] cookbook/loading_tabular.rst:65: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(with_header=False, sep="\t") rows = list(reader("data/CerebellumDukeDNaseSeq.pk")) rows[:4] cookbook/loading_tabular.rst:81: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv", limit=2) table cookbook/loading_tabular.rst:93: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser( lambda line: float(line[2]) <= 10, with_header=True, sep="\t" ) table = load_table("data/stats.tsv", reader=reader, digits=1) table cookbook/loading_tabular.rst:105: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: reader = FilteringParser( lambda line: float(line[2]) <= 10, with_header=True, sep="\t", negate=True ) table = load_table("data/stats.tsv", reader=reader, digits=1) table cookbook/loading_tabular.rst:118: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(columns=["Locus", "Ratio"], with_header=True, sep="\t") table = load_table("data/stats.tsv", reader=reader) table cookbook/loading_tabular.rst:128: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(columns=[0, -1], with_header=True, sep="\t") table = load_table("data/stats.tsv", reader=reader) table cookbook/loading_tabular.rst:143: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(with_header=True, sep="\t") data = list(reader("data/stats.tsv")) cookbook/loading_tabular.rst:152: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data[:2] cookbook/loading_tabular.rst:161: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table header = ["A", "B", "C"] rows = [range(3), range(3, 6), range(6, 9), range(9, 12)] table = make_table(header=["A", "B", "C"], data=rows) table cookbook/loading_tabular.rst:175: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table data = dict(A=[0, 3, 6], B=[1, 4, 7], C=[2, 5, 8]) table = make_table(data=data) table cookbook/loading_tabular.rst:186: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = make_table(header=["C", "A", "B"], data=data) table cookbook/loading_tabular.rst:196: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv", index_name="Locus") table["NP_055852"] cookbook/loading_tabular.rst:201: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table["NP_055852", "Region"] cookbook/loading_tabular.rst:210: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from pandas import DataFrame from cogent3 import make_table data = dict(a=[0, 3], b=["a", "c"]) df = DataFrame(data=data) table = make_table(data_frame=df) table cookbook/loading_tabular.rst:224: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table(header=["a", "b"], data=[[0, "a"], [3, "c"]]) table cookbook/loading_tabular.rst:236: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table data = dict(a=[0, 3], b=["a", "c"]) table = make_table(data=data) table cookbook/loading_tabular.rst:247: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table d2D = { "edge.parent": { "NineBande": "root", "edge.1": "root", "DogFaced": "root", "Human": "edge.0", }, "x": { "NineBande": 1.0, "edge.1": 1.0, "DogFaced": 1.0, "Human": 1.0, }, "length": { "NineBande": 4.0, "edge.1": 4.0, "DogFaced": 4.0, "Human": 4.0, }, } table = make_table( data=d2D, ) table cookbook/loading_tabular.rst:279: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table( header=["abcd", "data"], data=[[range(1, 6), "0"], ["x", 5.0], ["y", None]], missing_data="*", digits=1, ) table cookbook/loading_tabular.rst:294: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table() table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:21: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table() table.columns["a"] = [1, 3, 5] table.columns["b"] = [2, 4, 6] table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:35: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table data = dict(a=[0, 3], b=["a", "c"]) table = make_table(data=data, title="Sample title", legend="a legend") table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:45: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data = dict(a=[0, 3], b=["a", "c"]) table = make_table(data=data) table.title = "My title" table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:57: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv") for row in table: print(row) break /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:68: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: for row in table: print(row["Locus"]) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:78: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table data = dict(a=[0, 3, 5], b=["a", "c", "d"]) table = make_table(data=data) table.shape[0] == 3 /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:91: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.shape[1] == 2 /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:100: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv") table.columns /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:107: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.columns["Region"] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:113: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: for name in table.columns: print(name) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:121: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:128: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table[:2, "Region":] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:135: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table[:2, :1] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:145: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv") table.format_column("Ratio", "%.1e") table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:158: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv", digits=1, space=2) table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:165: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.space = " " table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:175: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table h = ["name", "A/C", "A/G", "A/T", "C/A"] rows = [["tardigrade", 0.0425, 0.1424, 0.0226, 0.0391]] wrap_table = make_table(header=h, data=rows, max_width=30) wrap_table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:184: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: wrap_table = make_table(header=h, data=rows, max_width=30, index_name="name") wrap_table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:192: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = make_table(data=dict(a=list(range(10)), b=list(range(10)))) table.head() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:199: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.head(2) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:208: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.tail() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:214: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.tail(1) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:221: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.set_repr_policy(random=3) table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:229: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.set_repr_policy(head=2, tail=3) table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:241: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") print(table.header) table = table.with_new_header("Ratio", "Stat") print(table.header) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:251: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table() table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:258: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.columns["a"] = [1, 3, 5] table.columns["b"] = [2, 4, 6] table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:269: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table = table.with_new_column( "LargeCon", lambda r_v: r_v[0] == "Con" and r_v[1] > 10.0, columns=["Region", "Ratio"], ) table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:282: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table.array /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:292: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") locus = table.to_list("Locus") locus /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:300: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.columns["Locus"].tolist() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:311: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") rows = table.to_list(["Region", "Locus"]) rows /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:324: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table.to_dict() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:334: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table.columns.to_dict() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:342: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") df = table.to_pandas() df /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:350: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: df = table.to_pandas(categories="Region") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:359: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = make_table(data={"Ts": [31, 58], "Tv": [36, 138], "": ["syn", "nsyn"]}, index_name="") table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:364: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: contingency = table.to_categorical(["Ts", "Tv"]) contingency /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:369: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: g_test = contingency.G_independence() g_test /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:376: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = make_table(data={"Ts": [31, 58], "Tv": [36, 138], "": ["syn", "nsyn"]}) contingency = table.to_categorical(["Ts", "Tv"], index_name="") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:388: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table1 = load_table("data/stats.tsv") table2 = load_table("data/stats.tsv") table = table1.appended(None, table2) table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:397: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table1.title = "Data1" table2.title = "Data2" table = table1.appended("Data#", table2, title="") table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:409: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table.summed("Ratio") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:416: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.columns["Ratio"].sum() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:425: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table all_numeric = make_table( header=["A", "B", "C"], data=[range(3), range(3, 6), range(6, 9), range(9, 12)] ) all_numeric /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:436: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: all_numeric.summed() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:442: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: all_numeric.summed(col_sum=False) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:451: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: mixed = make_table( header=["A", "B", "C"], data=[["*", 1, 2], [3, "*", 5], [6, 7, "*"]] ) mixed /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:460: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: mixed.summed(strict=False) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:466: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: mixed.summed(col_sum=False, strict=False) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:475: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") sub_table = table.filtered(lambda x: x < 10.0, columns="Ratio") sub_table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:483: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: sub_table = table.filtered("Ratio < 10.0") sub_table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:490: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: sub_table = table.filtered("Ratio < 10.0 and Region == 'NonCon'") sub_table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:500: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: big_numeric = all_numeric.filtered_by_column(lambda x: sum(x) > 20) big_numeric /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:508: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table.sorted(columns="Ratio") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:516: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.sorted(columns="Ratio", reverse="Ratio") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:523: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.sorted(columns=["Region", "Ratio"], reverse="Ratio") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:530: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") raw = table.to_list("Region") raw /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:539: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") raw = table.to_list(["Locus", "Region"]) raw /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:548: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") assert table.distinct_values("Region") == set(["NonCon", "Con"]) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:556: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") assert table.count("Region == 'NonCon' and Ratio > 1") == 1 /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:566: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table( data=dict(A=["a", "b", "b", "b", "a"], B=["c", "c", "c", "c", "d"]) ) unique = table.count_unique("A") type(unique) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:576: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: unique /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:582: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: unique = table.count_unique(["A", "B"]) unique /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:587: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: r = unique.to_table() r /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:597: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: rows = [ ["NP_004893", True], ["NP_005079", True], ["NP_005500", False], ["NP_055852", False], ] region_type = make_table(header=["Locus", "LargeCon"], data=rows) stats_table = load_table("data/stats.tsv") new = stats_table.joined(region_type, columns_self="Locus") new /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:617: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table header = ["#OTU ID", "14SK041", "14SK802"] rows = [ [-2920, "332", 294], [-1606, "302", 229], [-393, 141, 125], [-2109, 138, 120], ] table = make_table(header=header, rows=rows) table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:633: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tp = table.transposed(new_column_name="sample", select_as_header="#OTU ID") tp /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:643: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv", format="md") print(table) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:655: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv", format="tex") print(table) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:667: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") print(table.to_markdown(justify="ccr")) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:675: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table( "data/stats.tsv", title="Some stats.", legend="Derived from something." ) print(table.to_latex(justify="ccr", label="tab:table1")) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:685: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table( "data/stats.tsv", title="Some stats.", legend="Derived from something." ) print(table.to_rst(csv_table=True)) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:695: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table( "data/stats.tsv", title="Some stats.", legend="Derived from something." ) print(table.to_rst()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:707: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") print(table.to_string(format="latex")) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:717: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: rows = [ ["1", 100, 101, 1.123], ["1", 101, 102, 1.123], ["1", 102, 103, 1.123], ["1", 103, 104, 1.123], ["1", 104, 105, 1.123], ["1", 105, 106, 1.123], ["1", 106, 107, 1.123], ["1", 107, 108, 1.123], ["1", 108, 109, 1], ["1", 109, 110, 1], ["1", 110, 111, 1], ["1", 111, 112, 1], ["1", 112, 113, 1], ["1", 113, 114, 1], ["1", 114, 115, 1], ["1", 115, 116, 1], ["1", 116, 117, 1], ["1", 117, 118, 1], ["1", 118, 119, 2], ["1", 119, 120, 2], ["1", 120, 121, 2], ["1", 150, 151, 2], ["1", 151, 152, 2], ["1", 152, 153, 2], ["1", 153, 154, 2], ["1", 154, 155, 2], ["1", 155, 156, 2], ["1", 156, 157, 2], ["1", 157, 158, 2], ["1", 158, 159, 2], ["1", 159, 160, 2], ["1", 160, 161, 2], ] bgraph = make_table(header=["chrom", "start", "end", "value"], rows=rows) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:756: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: bgraph.head() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:762: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print( bgraph.to_string( format="bedgraph", name="test track", description="test of bedgraph", color=(255, 0, 0), digits=0, ) ) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:777: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv") straight_html = table.to_html() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:789: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.format.table import known_formats known_formats /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:798: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.write("stats_tab.tex", justify="ccr", label="tab:table1") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:807: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table.write("stats_tab.txt", sep="\t") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:814: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import pathlib for name in ("stats_tab.txt", "stats_tab.tex"): p = pathlib.Path(name) if p.exists(): p.unlink() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/union_dict.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.union_dict import UnionDict data = UnionDict(a=2, b={"c": 24, "d": [25]}) data.a /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/union_dict.rst:20: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data["a"] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/union_dict.rst:24: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data.b.d /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/union_dict.rst:33: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.union_dict import UnionDict data = UnionDict(a=2, b={"c": 24, "d": [25]}) data.b |= {"d": 25} data.b /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/union_dict.rst:43: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data.b.union({"d": [25]}) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/union_dict.rst:47: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data.b {"c": 24, "d": [25]} /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/union_dict.rst:55: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: KeyError from cogent3.util.union_dict import UnionDict data = UnionDict(a=2, b={"c": 24, "d": [25]}) data["k"] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/union_dict.rst:65: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: AttributeError data.k cookbook/union_dict.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.union_dict import UnionDict data = UnionDict(a=2, b={"c": 24, "d": [25]}) data.a cookbook/union_dict.rst:20: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data["a"] cookbook/union_dict.rst:24: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data.b.d cookbook/union_dict.rst:33: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.union_dict import UnionDict data = UnionDict(a=2, b={"c": 24, "d": [25]}) data.b |= {"d": 25} data.b cookbook/union_dict.rst:43: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data.b.union({"d": [25]}) cookbook/union_dict.rst:47: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data.b {"c": 24, "d": [25]} cookbook/union_dict.rst:55: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: KeyError from cogent3.util.union_dict import UnionDict data = UnionDict(a=2, b={"c": 24, "d": [25]}) data["k"] cookbook/union_dict.rst:65: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: AttributeError data.k /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:16: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: import numpy def DiffOmega(omega): def omega_from_S(S): omega_est = S / (1 - numpy.e ** (-1 * S)) return abs(omega - omega_est) ** 2 return omega_from_S omega = 0.1 f = DiffOmega(omega) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:32: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.optimisers import maximise, minimise S = minimise( f, # the function xinit=1.0, # the initial value bounds=(-100, 100), # [lower,upper] bounds for the parameter local=True, # just local optimisation, not Simulated Annealing show_progress=False, ) assert 0.0 <= f(S) < 1e-6 print("S=%.4f" % S) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:58: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: TypeError from cogent3.util.misc import iterable my_var = 10 for i in my_var: print("will not work") for i in iterable(my_var): print(i) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:75: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import curry def foo(x, y): """Some function""" return x + y bar = curry(foo, 5) print(bar.__doc__) bar(10) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:92: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import is_iterable can_iter = [1, 2, 3, 4] cannot_iter = 1.234 is_iterable(can_iter) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:100: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: is_iterable(cannot_iter) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:109: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import is_char class foo: pass is_char("a") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:118: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: is_char("ab") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:122: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: is_char(foo()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:131: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import recursive_flatten l = [[[[1, 2], "abcde"], [5, 6]], [7, 8], [9, 10]] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:137: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: recursive_flatten(l) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:146: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import not_list_tuple not_list_tuple(1) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:152: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: not_list_tuple([1]) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:156: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: not_list_tuple("ab") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:165: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import add_lowercase d = {"A": 5, "B": 6, "C": 7, "foo": 8, 42: "life"} add_lowercase(d) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:177: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from numpy import array from cogent3.util.misc import DistanceFromMatrix m = array([[1, 2, 3], [4, 5, 6], [7, 8, 9]]) f = DistanceFromMatrix(m) f(0, 0) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:187: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: f(1, 2) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:196: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import ClassChecker class not_okay(object): pass no = not_okay() class okay(object): pass o = okay() class my_dict(dict): pass md = my_dict() cc = ClassChecker(str, okay, dict) o in cc /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:217: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: no in cc /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:221: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: 5 in cc /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:225: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: {"a": 5} in cc /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:229: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: "asasas" in cc /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:233: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: md in cc /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:242: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import Delegator class ListAndString(list, Delegator): def __init__(self, items, string): Delegator.__init__(self, string) for i in items: self.append(i) ls = ListAndString([1, 2, 3], "ab_cd") len(ls) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:255: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: ls[0] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:259: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: ls.upper() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:263: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: ls.split("_") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:272: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import FunctionWrapper f = FunctionWrapper(str) f /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:279: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: f(123) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:290: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from cogent3.util.misc import ConstraintError /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:295: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import ConstrainedDict d = ConstrainedDict({"a": 1, "b": 2, "c": 3}, constraint="abc") d /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:302: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: ConstraintError d["d"] = 5 /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/union_dict.rst:4: WARNING: duplicate label union_dict, other instance in /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/union_dict.rst /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/what_codes.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/what_codes.rst:10: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import available_codes available_codes() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/what_codes.rst:23: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code gc = get_code(4) gc /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-coevolution.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-coevolution.rst:18: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/brca1.fasta", moltype="dna") aln = aln.no_degenerates(motif_length=3) aln = aln.get_translation() aln = aln[:100] # for compute speed in testing the documentation coevo = aln.coevolution(show_progress=False, drawable="heatmap") coevo.drawable.show() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-coevolution.rst:29: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_aln-coevolution.png" coevo.drawable.write(outpath) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-coevolution.rst:39: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: coevo = aln.coevolution(show_progress=False, drawable="violin") coevo.drawable.show(width=300) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-coevolution.rst:47: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: coevo = aln.coevolution(show_progress=False, drawable="box") coevo.drawable.show(width=300) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-coevolution.rst:11: WARNING: TODO entry found: add citation for NMI /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-1.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-1.rst:15: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_unaligned_seqs seqs = load_unaligned_seqs("data/SCA1-cds.fasta", moltype="dna") draw = seqs.dotplot() draw.show() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-1.rst:23: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_aln-dotplot-1.png" draw.write(outpath) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-1.rst:37: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: draw = seqs.dotplot(name1="Human", name2="Mouse", window=8, threshold=8) draw.show() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-1.rst:45: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: draw = seqs.dotplot(name1="Human", name2="Mouse", rc=True) draw.show() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-1.rst:57: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: draw = seqs.dotplot(name1="Human", name2="Mouse", rc=True, title="SCA1", width=400) draw.show() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-1.rst:11: WARNING: TODO entry found: Change dotplot ref to a citation /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-2.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-2.rst:16: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_json") seqs = loader("data/tp53.json") dp = seqs.dotplot(name1="Macaque", name2="Marmoset", width=600) dp.show() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-2.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_aln-dotplot-2.png" dp.write(outpath) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-2.rst:35: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: help(dp.remove_track) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-2.rst:41: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dp.remove_track(left_track=True) dp.show() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-3.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-3.rst:16: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_aligned_seqs, get_app seqs = load_aligned_seqs("data/brca1.fasta", moltype="dna").degap() seqs = seqs.take_seqs( ["LeafNose", "FalseVamp", "RoundEare", "Sloth", "Anteater", "HairyArma"] ) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-3.rst:30: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aligner = get_app("progressive_align", "nucleotide", indel_rate=1e-2, indel_length=1e-9) aln = aligner(seqs) dp = aln[2200:2500].dotplot("HairyArma", "RoundEare") dp.show() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-3.rst:38: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_aln-dotplot-3.png" dp.write(outpath) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-3.rst:49: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aln[2300:2500] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-3.rst:61: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aligner = get_app("progressive_align", "nucleotide") aln = aligner(seqs) aln[2200:2500].dotplot("HairyArma", "RoundEare").show() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-3.rst:72: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aln[2300:2500] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-gaps-per-seq.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-gaps-per-seq.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/brca1.fasta", moltype="dna") counts = aln.count_gaps_per_seq(unique=True) counts[10: 20] # limiting the width of the displayed output /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-gaps-per-seq.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: counts = aln.count_gaps_per_seq(unique=True, drawable="bar") counts.drawable.show(width=500) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-gaps-per-seq.rst:33: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_aln-gaps-per-seq.png" counts.drawable.write(outpath) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-gaps-per-seq.rst:43: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: counts = aln.count_gaps_per_seq(unique=True, drawable="violin") counts.drawable.show(width=300, height=500) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-gaps-per-seq.rst:51: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: counts = aln.count_gaps_per_seq(unique=True, drawable="box") counts.drawable.show(width=300, height=500) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-info-plot.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-info-plot.rst:14: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, make_aligned_seqs, make_seq s1 = make_seq("TGATGTAAGGTAGTT", name="s1", moltype="dna") s2 = make_seq("--CTGGAAGGGT---", name="s2", moltype="dna") seqs = make_aligned_seqs(data=[s1, s2], array_align=False, moltype="dna") draw = seqs.information_plot(window=2, include_gap=True) draw.show(width=500, height=400) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-info-plot.rst:30: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = load_aligned_seqs("data/brca1.fasta", moltype="protein") fig = aln.information_plot(stat="median") fig.show(width=500, height=400) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-info-plot.rst:37: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_aln-info-plot.png" fig.write(outpath) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-seqlogo.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-seqlogo.rst:16: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.parse import jaspar _, pwm = jaspar.read("data/tbp.jaspar") freqarr = pwm.to_freq_array() freqarr[:5] # illustrating the contents of the MotifFreqsArray /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-seqlogo.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: logo = freqarr.logo() logo.show(height=250, width=500) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-seqlogo.rst:30: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_aln-seqlogo.png" logo.write(outpath) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-seqlogo.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = load_aligned_seqs("data/brca1-bats.fasta", moltype="dna") l = aln[:311].seqlogo(height=300, width=500, wrap=60, vspace=0.05) l.show() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-seqlogo.rst:53: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aa = aln.get_translation(incomplete_ok=True)[:120] logo = aa.seqlogo(width=500, height=300, wrap=50, vspace=0.1) logo.show() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_seq-features.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_seq-features.rst:16: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_seq seq = load_seq("data/C-elegans-chromosome-I.gb", moltype="dna") seq /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_seq-features.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq = seq[25000:35000] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_seq-features.rst:31: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fig = seq.get_drawable() fig.show(height=400, width=700) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_seq-features.rst:43: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fig = seq.get_drawable(biotype=("gene", "CDS", "mRNA")) fig.show(height=300, width=650) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_seq-features.rst:48: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_seq-features.png" fig.write(outpath) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-angular.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-angular.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io reader = io.load_json() ens_tree = reader("data/GN-tree.json") fig = ens_tree.get_figure(style="angular", width=600, height=600) fig.show() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-angular.rst:24: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fig.contemporaneous = True fig.show() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-angular.rst:29: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_tree-angular.png" fig.write(outpath) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-circular.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-circular.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io reader = io.load_json() ens_tree = reader("data/GN-tree.json") fig = ens_tree.get_figure("circular", width=600, height=600) fig.scale_bar = "top right" fig.label_pad = 0.1 fig.show() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-circular.rst:26: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fig.style_edges( "AfricanEl", tip2="Manatee", legendgroup="Afrotheria", line=dict(color="magenta", width=2), ) fig.show(width=650, height=600) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-circular.rst:39: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fig.contemporaneous = True fig.label_pad = 0.3 fig.show(width=650, height=600) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-circular.rst:45: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_tree-circular.png" fig.write(outpath) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-radial.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-radial.rst:9: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io reader = io.load_json() ens_tree = reader("data/GN-tree.json") fig = ens_tree.get_figure("radial", width=600, height=600) fig.show() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-radial.rst:19: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_tree-radial.png" fig.write(outpath) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-radial.rst:29: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fig.contemporaneous = True fig.label_pad = 0.23 fig.show() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-square.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-square.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io reader = io.load_json() ens_tree = reader("data/GN-tree.json") fig = ens_tree.get_figure(width=600, height=600) fig.scale_bar = "top right" fig.show() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-square.rst:24: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_tree-square.png" fig.write(outpath) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-square.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fig.style_edges( "AfricanEl", tip2="Manatee", legendgroup="Afrotheria", line=dict(color="magenta"), ) fig.show() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-square.rst:47: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fig.contemporaneous = True fig.show() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-support.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-support.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io reader = io.load_json() tree = reader("data/tree-with-support.json") fig = tree.get_figure(show_support=True, threshold=0.8) fig.scale_bar = None fig.show(width=500, height=400) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-support.rst:29: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fig.support_xshift = 15 fig.support_yshift = 0 fig.show(width=500, height=400) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-support.rst:35: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_tree-support.png" fig.write(outpath) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/align_codons_to_protein.rst:8: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs, make_unaligned_seqs /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/align_codons_to_protein.rst:14: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seqs = { "hum": "AAGCAGATCCAGGAAAGCAGCGAGAATGGCAGCCTGGCCGCGCGCCAGGAGAGGCAGGCCCAGGTCAACCTCACT", "mus": "AAGCAGATCCAGGAGAGCGGCGAGAGCGGCAGCCTGGCCGCGCGGCAGGAGAGGCAGGCCCAAGTCAACCTCACG", "rat": "CTGAACAAGCAGCCACTTTCAAACAAGAAA", } unaligned_DNA = make_unaligned_seqs(seqs, moltype="dna") unaligned_DNA /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/align_codons_to_protein.rst:26: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: unaligned_aa = unaligned_DNA.get_translation() unaligned_aa /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/align_codons_to_protein.rst:33: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aligned_aa_seqs = { "hum": "KQIQESSENGSLAARQERQAQVNLT", "mus": "KQIQESGESGSLAARQERQAQVNLT", "rat": "LNKQ------PLS---------NKK", } aligned_aa = make_aligned_seqs(aligned_aa_seqs, moltype="protein") aligned_DNA = aligned_aa.replace_seqs(unaligned_DNA) aligned_DNA /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_UPGMA_cluster.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_UPGMA_cluster.rst:15: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.cluster.UPGMA import upgma from cogent3.evolve import distance /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_UPGMA_cluster.rst:23: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import HKY85 /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_UPGMA_cluster.rst:29: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: al = load_aligned_seqs("data/test.paml") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_UPGMA_cluster.rst:35: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: d = distance.EstimateDistances(al, submodel=HKY85()) d.run(show_progress=False) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_UPGMA_cluster.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: mycluster = upgma(d.get_pairwise_distances()) print(mycluster.ascii_art()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_UPGMA_cluster.rst:49: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: mycluster.write("test_upgma.tree") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_UPGMA_cluster.rst:55: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import os os.remove("test_upgma.tree") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_neigbourjoining_tree.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_neigbourjoining_tree.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.evolve import distance from cogent3.phylo import nj /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_neigbourjoining_tree.rst:21: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import get_model /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_neigbourjoining_tree.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: al = load_aligned_seqs("data/long_testseqs.fasta") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_neigbourjoining_tree.rst:33: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: d = distance.EstimateDistances(al, submodel=get_model("HKY85")) d.run(show_progress=False) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_neigbourjoining_tree.rst:40: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: mytree = nj.nj(d.get_pairwise_distances(), show_progress=False) print(mytree.ascii_art()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_neigbourjoining_tree.rst:47: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: mytree.write("test_nj.tree") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_neigbourjoining_tree.rst:53: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import os os.remove("test_nj.tree") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_pairwise_distances.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_pairwise_distances.rst:15: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.evolve import distance /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_pairwise_distances.rst:22: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import HKY85 /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_pairwise_distances.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: al = load_aligned_seqs("data/long_testseqs.fasta") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_pairwise_distances.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: d = distance.EstimateDistances(al, submodel=HKY85()) d.run(show_progress=False) d.get_pairwise_distances() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_pairwise_distances.rst:44: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: d.write("dists_for_phylo.phylip", format="phylip") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_pairwise_distances.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: import pickle with open("dists_for_phylo.pickle", "wb") as f: pickle.dump(d.get_pairwise_distances(), f) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_pairwise_distances.rst:61: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import os for file_name in "dists_for_phylo.phylip", "dists_for_phylo.pickle": os.remove(file_name) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_pairwise_distances.rst:48: WARNING: TODO entry found: write out in json format /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:36: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import get_model /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tf = get_model("GY94") nf = get_model("MG94GTR") cnf = get_model("CNFGTR") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna") tree = load_tree("data/primate_brca1.tree") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:64: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf = cnf.make_likelihood_function(tree, digits=2, space=3) lf.set_param_rule("omega", is_constant=True, value=1.0) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:73: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: optimiser_args = dict( local=True, max_restarts=5, tolerance=1e-8, show_progress=False ) lf.set_alignment(aln) lf.optimise(**optimiser_args) lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:92: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: neutral_lnL = lf.get_log_likelihood() neutral_nfp = lf.get_num_free_params() lf.set_param_rule("omega", is_constant=False) lf.optimise(**optimiser_args) non_neutral_lnL = lf.get_log_likelihood() non_neutral_nfp = lf.get_num_free_params() lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:104: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from scipy.stats.distributions import chi2 LR = 2 * (non_neutral_lnL - neutral_lnL) df = non_neutral_nfp - neutral_nfp print(chi2.sf(LR, df)) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:114: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule( "omega", tip_names=["Chimpanzee", "Human"], outgroup_name="Galago", clade=True ) lf.optimise(**optimiser_args) lf chimp_human_clade_lnL = lf.get_log_likelihood() chimp_human_clade_nfp = lf.get_num_free_params() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:124: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: LR = 2 * (chimp_human_clade_lnL - non_neutral_lnL) df = chimp_human_clade_nfp - non_neutral_nfp print(chi2.sf(LR, df)) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:137: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf = cnf.make_likelihood_function(tree, digits=2, space=3) lf.set_alignment(aln) lf.optimise(**optimiser_args) non_neutral_lnL = lf.get_log_likelihood() non_neutral_nfp = lf.get_num_free_params() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:149: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: annot_tree = lf.get_annotated_tree() omega_mle = lf.get_param_value("omega") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:156: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: rate_lf = cnf.make_likelihood_function( annot_tree, bins=["neutral", "adaptive"], digits=2, space=3 ) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:164: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: epsilon = 1e-6 /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:170: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: rate_lf.set_param_rule("omega", bin="neutral", upper=1, init=omega_mle) rate_lf.set_param_rule( "omega", bin="adaptive", lower=1 + epsilon, upper=100, init=1 + 2 * epsilon ) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:179: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: rate_lf.set_param_rule("bprobs", init=[1 - epsilon, epsilon]) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:185: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: rate_lf.set_alignment(aln) rate_lf.optimise(**optimiser_args) rate_lnL = rate_lf.get_log_likelihood() rate_nfp = rate_lf.get_num_free_params() LR = 2 * (rate_lnL - non_neutral_lnL) df = rate_nfp - non_neutral_nfp rate_lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:195: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(chi2.sf(LR, df)) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:201: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: pp = rate_lf.get_bin_probs() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:212: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from IPython.core.display import HTML from numpy import array from cogent3 import make_table header = ["Site Class", "Proportion", "Background Edges", "Foreground Edges"] data = { "Site Class": array(["0", "1", "2a", "2b"], dtype=" 1", "0 < omega0 < 1"], dtype=" 1.8: tips_to_delete.append(n) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/manipulating_tree_nodes.rst:121: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: for n in tips_to_delete: n.parent.remove(n) complex_tree.prune() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/manipulating_tree_nodes.rst:129: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(complex_tree.ascii_art(show_internal=False)) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model from scipy.stats.distributions import chi2 /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:21: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: al = load_aligned_seqs("data/long_testseqs.fasta") t = load_tree("data/test.tree") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: sm = get_model("MG94GTR") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf = sm.make_likelihood_function(t, digits=2, space=2) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:40: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_alignment(al) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(global_tolerance=1.0, show_progress=False) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:58: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: null_lnL = lf.get_log_likelihood() null_nfp = lf.get_num_free_params() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:65: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule("omega", is_independent=True) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:71: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(local=True, show_progress=False) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:77: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:83: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: at = lf.get_annotated_tree() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:89: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: LR = 2 * (lf.get_log_likelihood() - null_lnL) df = lf.get_num_free_params() - null_nfp P = chi2.sf(LR, df) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:97: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(f"Likelihood ratio statistic = {LR}") print(f"degrees-of-freedom = {df}") print(f"probability = {P}") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/parametric_bootstrap.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/parametric_bootstrap.rst:17: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve import bootstrap from cogent3.evolve.models import HKY85 /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/parametric_bootstrap.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: def create_alt_function(): t = load_tree("data/test.tree") sm = HKY85() return sm.make_likelihood_function(t) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/parametric_bootstrap.rst:36: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: def create_null_function(): lf = create_alt_function() # set the local clock for humans & howler monkey lf.set_local_clock("Human", "HowlerMon") return lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/parametric_bootstrap.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = load_aligned_seqs("data/long_testseqs.fasta") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/parametric_bootstrap.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: estimateP = bootstrap.EstimateProbability( create_null_function(), create_alt_function(), aln ) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/parametric_bootstrap.rst:60: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: estimateP.set_num_replicates(5) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/parametric_bootstrap.rst:66: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: estimateP.run(show_progress=False) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/parametric_bootstrap.rst:72: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: p = estimateP.get_estimated_prob() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/parametric_bootstrap.rst:78: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print("%.2f, %.2f" % estimateP.get_observed_lnL()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:26: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import numpy numpy.random.seed(11) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:33: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: import numpy t = numpy.arange(0, 10, 0.1) n = numpy.random.randn(len(t)) nse = numpy.convolve(n, numpy.exp(-t / 0.05)) * 0.1 nse = nse[: len(t)] sig = numpy.sin(2 * numpy.pi * t) + nse /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:48: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import dft pwr, period = dft(sig) print(period) print(pwr) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:58: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: pwr = abs(pwr) max_pwr, max_period = sorted(zip(pwr, period))[-1] print(max_pwr, max_period) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:69: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import auto_corr pwr, period = auto_corr(sig) print(period) print(pwr) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:79: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: max_pwr, max_period = sorted(zip(pwr, period))[-1] print(max_pwr, max_period) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:89: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: s = ( "ATCGTTGGGACCGGTTCAAGTTTTGGAACTCGCAAGGGGTGAATGGTCTTCGTCTAACGCTGG" "GGAACCCTGAATCGTTGTAACGCTGGGGTCTTTAACCGTTCTAATTTAACGCTGGGGGGTTCT" "AATTTTTAACCGCGGAATTGCGTC" ) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:99: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.stats.period import SeqToSymbols seq_to_symbols = SeqToSymbols(["AA", "TT", "AT"]) symbols = seq_to_symbols(s) len(symbols) == len(s) symbols /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:110: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import ipdft powers, periods = ipdft(symbols) powers /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:117: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: periods /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:123: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import auto_corr, hybrid powers, periods = auto_corr(symbols) powers /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:130: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: periods /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:134: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: powers, periods = hybrid(symbols) powers /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:139: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: periods /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:151: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import goertzel pwr = goertzel(sig, 10) print(pwr) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:165: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: powers, periods = auto_corr(symbols) llim = 2 period5 = 5 - llim periods[period5] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:172: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: powers[period5] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:178: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import goertzel period = 4 power = goertzel(symbols, period) ipdft_powers, periods = ipdft(symbols) ipdft_power = abs(ipdft_powers[period - llim]) round(power, 6) == round(ipdft_power, 6) power /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:191: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: power = hybrid(symbols, period=period) power /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:204: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import Goertzel goertzel_calc = Goertzel(len(sig), period=10) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:212: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.stats.period import blockwise_bootstrap obs_stat, p = blockwise_bootstrap( sig, calc=goertzel_calc, block_size=10, num_reps=1000 ) print(obs_stat) print(p) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:230: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import Hybrid hybrid_calculator = Hybrid(len(s), period=4) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:240: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.stats.period import SeqToSymbols seq_to_symbols = SeqToSymbols(["AA", "TT", "AT"], length=len(s)) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:248: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.stats.period import blockwise_bootstrap stat, p = blockwise_bootstrap( s, calc=hybrid_calculator, block_size=10, num_reps=1000, seq_to_symbols=seq_to_symbols, ) print(stat) p < 0.1 /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:15: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import pickle from cogent3 import load_aligned_seqs from cogent3.evolve import distance from cogent3.evolve.fast_distance import DistanceMatrix from cogent3.evolve.models import HKY85 al = load_aligned_seqs("data/long_testseqs.fasta") d = distance.EstimateDistances(al, submodel=HKY85()) d.run(show_progress=False) with open("dists_for_phylo.pickle", "wb") as f: pickle.dump(d.get_pairwise_distances(), f) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:32: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: import pickle from cogent3.phylo import least_squares /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:40: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: with open("dists_for_phylo.pickle", "rb") as f: dists = pickle.load(f) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:49: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: ls = least_squares.WLS(dists) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:55: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: ls_distance_matrix = least_squares.WLS(DistanceMatrix(dists)) ls_pairwise_matrix = least_squares.WLS(dists.to_dict()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:67: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: score, tree = ls.trex(a=5, k=1, show_progress=False) assert score < 1e-4 /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:79: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: trees = ls.trex(a=5, k=5, return_all=True, show_progress=False) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:85: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(len(trees)) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:91: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: wls_stats = [tree[0] for tree in trees] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:103: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: t1 = trees[0][1].balanced() t2 = trees[1][1].balanced() print(t1.ascii_art()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:109: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(t2.ascii_art()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:120: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_tree query_tree = make_tree( "((Human:.2,DogFaced:.2):.3,(NineBande:.1, Mouse:.5):.2,HowlerMon:.1)" ) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:130: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: ls.evaluate_tree(query_tree) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:136: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: wls, t = ls.evaluate_topology(query_tree) assert "%.4f" % wls == "0.0084" /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:148: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import os os.remove("dists_for_phylo.pickle") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/rate_heterogeneity.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/rate_heterogeneity.rst:15: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.substitution_model import TimeReversibleNucleotide /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/rate_heterogeneity.rst:22: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: model = TimeReversibleNucleotide(equal_motif_probs=True) tree = load_tree("data/test.tree") lf = model.make_likelihood_function(tree) lf.set_param_rule("length", value=0.6, is_constant=True) aln1 = lf.simulate_alignment(sequence_length=10000) lf.set_param_rule("length", value=0.2, is_constant=True) aln2 = lf.simulate_alignment(sequence_length=10000) aln3 = aln1 + aln2 /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/rate_heterogeneity.rst:35: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: model = TimeReversibleNucleotide( equal_motif_probs=True, ordered_param="rate", distribution="free" ) lf = model.make_likelihood_function(tree, bins=2, digits=2, space=3) lf.set_alignment(aln3) lf.optimise(local=True, max_restarts=2, show_progress=False) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/rate_heterogeneity.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: bprobs = [t for t in lf.get_statistics() if "bin" in t.title][0] bprobs /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/rate_heterogeneity.rst:53: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: model = TimeReversibleNucleotide( equal_motif_probs=True, ordered_param="rate", distribution="gamma" ) lf = model.make_likelihood_function(tree, bins=4) lf.set_param_rule("bprobs", is_constant=True) lf.set_alignment(aln3) lf.optimise(local=True, max_restarts=2, show_progress=False) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model from scipy.stats.distributions import chi2 /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:21: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = load_aligned_seqs("data/long_testseqs.fasta") t = load_tree(filename="data/test.tree") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: sm = get_model("HKY85") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf = sm.make_likelihood_function(t, digits=2, space=3) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:40: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_local_clock("Human", "HowlerMon") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_alignment(aln) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(show_progress=False) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:58: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_name("clock") lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:65: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: null_lnL = lf.get_log_likelihood() null_nfp = lf.get_num_free_params() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:72: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule("length", is_independent=True) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:78: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(show_progress=False) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:84: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_name("non clock") lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:91: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: LR = 2 * (lf.get_log_likelihood() - null_lnL) df = lf.get_num_free_params() - null_nfp P = chi2.sf(LR, df) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:99: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print("Likelihood ratio statistic = ", LR) print("degrees-of-freedom = ", df) print("probability = ", P) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/scope_model_params_on_trees.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/scope_model_params_on_trees.rst:17: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import MG94HKY aln = load_aligned_seqs("data/long_testseqs.fasta") tree = load_tree("data/test.tree") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/scope_model_params_on_trees.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: sm = MG94HKY() lf = sm.make_likelihood_function(tree, digits=2, space=3) lf.set_alignment(aln) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/scope_model_params_on_trees.rst:35: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(tree.ascii_art()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/scope_model_params_on_trees.rst:53: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule( "omega", tip_names=["DogFaced", "Mouse"], outgroup_name="Human", init=2.0, clade=True, ) lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/scope_model_params_on_trees.rst:73: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule("omega", init=1.0) lf.set_param_rule( "omega", tip_names=["Human", "HowlerMon"], outgroup_name="Mouse", init=2.0, stem=True, clade=False, ) lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/scope_model_params_on_trees.rst:91: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: lf.set_param_rule("omega", init=1.0) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/scope_model_params_on_trees.rst:96: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule( "omega", tip_names=["Human", "HowlerMon"], outgroup_name="Mouse", init=2.0, stem=True, clade=True, ) lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/scope_model_params_on_trees.rst:160: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: lf.set_param_rule("omega", init=1.0) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/scope_model_params_on_trees.rst:165: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule( "omega", tip_names=["Human", "HowlerMon"], outgroup_name="Mouse", clade=True, value=1.0, is_constant=True, ) lf.optimise(local=True, show_progress=False) lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/scope_model_params_on_trees.rst:180: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule( "omega", tip_names=["Human", "HowlerMon"], outgroup_name="Mouse", clade=True, is_constant=False, ) lf.optimise(local=True, show_progress=False) lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/scope_model_params_on_trees.rst:194: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule( "omega", tip_names=["Human", "HowlerMon"], outgroup_name="Mouse", clade=True, is_independent=True, ) lf.optimise(local=True, show_progress=False) lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/scope_model_params_on_trees.rst:208: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule("omega", is_independent=True) lf.optimise(local=True, show_progress=False) lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/simple.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/simple.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, make_tree from cogent3.evolve.models import get_model model = get_model("HKY85") aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta") tree = make_tree(tip_names=aln.names) lf = model.make_likelihood_function(tree) lf.set_alignment(aln) lf.optimise(show_progress=False) lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/simulate_alignment.rst:8: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: import sys from cogent3 import make_tree from cogent3.evolve.models import get_model /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/simulate_alignment.rst:17: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: t = make_tree("(a:0.4,b:0.3,(c:0.15,d:0.2)edge.0:0.1);") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/simulate_alignment.rst:23: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: sm = get_model("F81") lf = sm.make_likelihood_function(t) lf.set_constant_lengths() lf.set_motif_probs(dict(A=0.1, C=0.2, G=0.3, T=0.4)) lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/simulate_alignment.rst:33: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: simulated = lf.simulate_alignment(sequence_length=1000) simulated /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/testing_multi_loci.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/testing_multi_loci.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, make_table, make_tree from cogent3.evolve.models import HKY85 from scipy.stats.distributions import chi2 from cogent3.recalculation.scope import ALL, EACH aln = load_aligned_seqs("data/long_testseqs.fasta") half = len(aln) // 2 aln1 = aln[:half] aln2 = aln[half:] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/testing_multi_loci.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: loci_names = ["1st-half", "2nd-half"] loci = [aln1, aln2] tree = make_tree(tip_names=aln.names) mod = HKY85() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/testing_multi_loci.rst:36: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf = mod.make_likelihood_function(tree, loci=loci_names, digits=2, space=3) lf.set_param_rule("length", is_independent=False) lf.set_param_rule("kappa", loci=ALL) lf.set_alignment(loci) lf.optimise(show_progress=False) lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/testing_multi_loci.rst:45: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: all_lnL = lf.lnL all_nfp = lf.nfp lf.set_param_rule("kappa", loci=EACH) lf.optimise(show_progress=False) lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/testing_multi_loci.rst:53: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: each_lnL = lf.lnL each_nfp = lf.nfp LR = 2 * (each_lnL - all_lnL) df = each_nfp - all_nfp /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/testing_multi_loci.rst:62: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: make_table( header=["LR", "df", "p"], rows=[[LR, df, chi2.sf(LR, df)]], digits=2, space=3, ) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/templates/class.rst:3: ERROR: Error in "currentmodule" directive: maximum 1 argument(s) allowed, 3 supplied. .. currentmodule:: {{ module }} WARNING: invalid signature for autoclass ('{{ name }}') WARNING: don't know which module to import for autodocumenting '{{ name }}' (try placing a "module" or "currentmodule" directive in the document, or giving an explicit module name) looking for now-outdated files... none found pickling environment... done checking consistency... /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/alignment/classes/cogent3.core.alignment.Alignment.rst: WARNING: document isn't included in any toctree /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/alignment/classes/cogent3.core.alignment.ArrayAlignment.rst: WARNING: document isn't included in any toctree /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/alignment/classes/cogent3.core.alignment.SequenceCollection.rst: WARNING: document isn't included in any toctree /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/alphabet/classes/cogent3.core.alphabet.Alphabet.rst: WARNING: document isn't included in any toctree /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/annotation/classes/cogent3.core.annotation.Feature.rst: WARNING: document isn't included in any toctree /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/annotation_db/classes/cogent3.core.annotation_db.BasicAnnotationDb.rst: WARNING: document isn't included in any toctree /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/annotation_db/classes/cogent3.core.annotation_db.GenbankAnnotationDb.rst: WARNING: document isn't included in any toctree /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/annotation_db/classes/cogent3.core.annotation_db.GffAnnotationDb.rst: WARNING: document isn't included in any toctree /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/genetic_code/classes/cogent3.core.genetic_code.GeneticCode.rst: WARNING: document isn't included in any toctree /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/moltype/classes/cogent3.core.moltype.MolType.rst: WARNING: document isn't included in any toctree /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/sequence/classes/cogent3.core.sequence.DnaSequence.rst: WARNING: document isn't included in any toctree /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/sequence/classes/cogent3.core.sequence.ProteinSequence.rst: WARNING: document isn't included in any toctree /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/sequence/classes/cogent3.core.sequence.RnaSequence.rst: WARNING: document isn't included in any toctree /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/table/classes/cogent3.parse.table.FilteringParser.rst: WARNING: document isn't included in any toctree /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/table/classes/cogent3.util.table.Columns.rst: WARNING: document isn't included in any toctree /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/table/classes/cogent3.util.table.Table.rst: WARNING: document isn't included in any toctree /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/tree/classes/cogent3.core.tree.PhyloNode.rst: WARNING: document isn't included in any toctree /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-trim-stops.rst: WARNING: document isn't included in any toctree /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/index-help.rst: WARNING: document isn't included in any toctree 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WARNING: unsupported theme option 'show_nav_level' given WARNING: unsupported theme option 'logo' given done copying assets... copying downloadable files... [ 3%] data/abglobin_aa.phylip copying downloadable files... [ 6%] data/dists_for_phylo.json copying downloadable files... [ 9%] data/long_testseqs.fasta copying downloadable files... [ 12%] data/mycoplasma-genitalium.fa copying downloadable files... [ 15%] data/mycoplasma-genitalium.gb copying downloadable files... [ 18%] data/mycoplasma-genitalium.gff copying downloadable files... [ 21%] data/C-elegans-chromosome-I.fa copying downloadable files... [ 24%] data/C-elegans-chromosome-I.gb copying downloadable files... [ 27%] data/C-elegans-chromosome-I.gff copying downloadable files... [ 30%] data/primate_brca1.fasta copying downloadable files... [ 33%] data/primate_brca1.tree copying downloadable files... [ 36%] data/brca1_hsa_shortened.gff copying downloadable files... 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[100%] templates/class generating indices... genindex done copying linked files... copying notebooks ... writing additional pages... search done dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 1171 warnings. The HTML pages are in _build/html. Build finished. The HTML pages are in _build/html. make[2]: Leaving directory '/build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc' # remove superfluous files and dirs find doc/_build -name "*.doctree*" -delete rm -f doc/_build/html/_sources/COGENT_LICENSE.txt rm -f doc/_build/html/_static/jquery.js rm -f doc/_build/html/_static/underscore.js rm -rf doc/_build/html/_images/math/ make[1]: Leaving directory '/build/reproducible-path/python-cogent-2024.5.7a1+dfsg' dh_auto_test -i -O--buildsystem=pybuild I: pybuild pybuild:308: cp -r /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/tests/data /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/.pybuild/cpython3_3.11_cogent3/build I: pybuild base:311: cd /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/.pybuild/cpython3_3.11_cogent3/build; python3.11 -m pytest -k 'not test_pickleable_member_roundtrip and not test_pickleable_roundtrip' ============================= test session starts ============================== platform linux -- Python 3.11.9, pytest-8.2.2, pluggy-1.5.0 rootdir: /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/.pybuild/cpython3_3.11_cogent3/build configfile: pyproject.toml plugins: anyio-4.4.0, xdist-3.6.1, cov-5.0.0 collected 11030 items / 4 deselected / 11026 selected tests/test_align/test_align.py ...............................X... 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[ 95%] tests/test_parse/test_pwm_parsers.py .. [ 95%] tests/test_parse/test_rdb.py .................. [ 95%] tests/test_parse/test_record.py ........................................ [ 95%] .. [ 95%] tests/test_parse/test_record_finder.py ................. [ 96%] tests/test_parse/test_tinyseq.py . [ 96%] tests/test_parse/test_tree.py ................... [ 96%] tests/test_parse/test_unigene.py .... [ 96%] tests/test_phylo.py .................. [ 96%] tests/test_recalculation.py . [ 96%] tests/test_tree_distance.py ............................... [ 96%] tests/test_util/test_deserialise.py .................................... [ 97%] .. [ 97%] tests/test_util/test_dictarray.py ............................... [ 97%] tests/test_util/test_io.py ...................................ssss.sss [ 97%] tests/test_util/test_misc.py ........................................... [ 98%] ............................................ [ 98%] tests/test_util/test_parallel.py ... [ 98%] tests/test_util/test_recode_alignment.py ............... [ 98%] tests/test_util/test_table.py .......................................... [ 99%] ............................................................... [ 99%] tests/test_util/test_transform.py ..... [ 99%] tests/test_util/test_union_dict.py ........... [ 99%] tests/test_util/test_warning.py ......................... [100%] =============================== warnings summary =============================== ../../../../../../usr/lib/python3/dist-packages/_pytest/config/__init__.py:1507 /usr/lib/python3/dist-packages/_pytest/config/__init__.py:1507: PytestConfigWarning: No files were found in testpaths; consider removing or adjusting your testpaths configuration. Searching recursively from the current directory instead. self.args, self.args_source = self._decide_args( tests/test_maths/test_stats/test_test.py::StatTests::test_t_two_sample_switch /usr/lib/python3/dist-packages/numpy/core/_methods.py:206: RuntimeWarning: Degrees of freedom <= 0 for slice tests/test_util/test_deserialise.py::test_convert_annotation_to_annotation_db tests/test_util/test_deserialise.py::test_deserialise_old_style_annotated tests/test_util/test_deserialise.py::test_deserialise_old_style_annotated tests/test_util/test_deserialise.py::test_deserialise_old_style_annotated tests/test_util/test_deserialise.py::test_deserialise_old_style_annotated tests/test_util/test_deserialise.py::test_deser_annotated_aln /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/.pybuild/cpython3_3.11_cogent3/build/cogent3/util/warning.py:226: DeprecationWarning: class Map is discontinued and will be removed in version 2024.6 reason='Replaced by IndelMap and FeatureMap' -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html = 11014 passed, 9 skipped, 4 deselected, 1 xfailed, 2 xpassed, 8 warnings in 257.81s (0:04:17) = I: pybuild pybuild:308: cp -r /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/tests/data /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/.pybuild/cpython3_3.12_cogent3/build I: pybuild base:311: cd /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/.pybuild/cpython3_3.12_cogent3/build; python3.12 -m pytest -k 'not test_pickleable_member_roundtrip and not test_pickleable_roundtrip' ============================= test session starts ============================== platform linux -- Python 3.12.4, pytest-8.2.2, pluggy-1.5.0 rootdir: /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/.pybuild/cpython3_3.12_cogent3/build configfile: pyproject.toml plugins: anyio-4.4.0, xdist-3.6.1, cov-5.0.0 collected 11030 items / 4 deselected / 11026 selected tests/test_align/test_align.py ...............................X... 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[ 95%] tests/test_parse/test_pwm_parsers.py .. [ 95%] tests/test_parse/test_rdb.py .................. [ 95%] tests/test_parse/test_record.py ........................................ [ 95%] .. [ 95%] tests/test_parse/test_record_finder.py ................. [ 96%] tests/test_parse/test_tinyseq.py . [ 96%] tests/test_parse/test_tree.py ................... [ 96%] tests/test_parse/test_unigene.py .... [ 96%] tests/test_phylo.py .................. [ 96%] tests/test_recalculation.py . [ 96%] tests/test_tree_distance.py ............................... [ 96%] tests/test_util/test_deserialise.py .................................... [ 97%] .. [ 97%] tests/test_util/test_dictarray.py ............................... [ 97%] tests/test_util/test_io.py ...................................ssss.sss [ 97%] tests/test_util/test_misc.py ........................................... [ 98%] ............................................ [ 98%] tests/test_util/test_parallel.py ... [ 98%] tests/test_util/test_recode_alignment.py ............... [ 98%] tests/test_util/test_table.py .......................................... [ 99%] ............................................................... [ 99%] tests/test_util/test_transform.py ..... [ 99%] tests/test_util/test_union_dict.py ........... [ 99%] tests/test_util/test_warning.py ......................... [100%] =============================== warnings summary =============================== ../../../../../../usr/lib/python3/dist-packages/_pytest/config/__init__.py:1507 /usr/lib/python3/dist-packages/_pytest/config/__init__.py:1507: PytestConfigWarning: No files were found in testpaths; consider removing or adjusting your testpaths configuration. Searching recursively from the current directory instead. self.args, self.args_source = self._decide_args( tests/test_maths/test_stats/test_test.py::StatTests::test_t_two_sample_switch /usr/lib/python3/dist-packages/numpy/core/_methods.py:206: RuntimeWarning: Degrees of freedom <= 0 for slice tests/test_util/test_deserialise.py::test_convert_annotation_to_annotation_db tests/test_util/test_deserialise.py::test_deserialise_old_style_annotated tests/test_util/test_deserialise.py::test_deserialise_old_style_annotated tests/test_util/test_deserialise.py::test_deserialise_old_style_annotated tests/test_util/test_deserialise.py::test_deserialise_old_style_annotated tests/test_util/test_deserialise.py::test_deser_annotated_aln /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/.pybuild/cpython3_3.12_cogent3/build/cogent3/util/warning.py:226: DeprecationWarning: class Map is discontinued and will be removed in version 2024.6 reason='Replaced by IndelMap and FeatureMap' -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html = 11014 passed, 9 skipped, 4 deselected, 1 xfailed, 2 xpassed, 8 warnings in 259.93s (0:04:19) = create-stamp debian/debhelper-build-stamp dh_testroot -i -O--buildsystem=pybuild dh_prep -i -O--buildsystem=pybuild dh_auto_install -i -O--buildsystem=pybuild I: pybuild plugin_pyproject:178: Copying package built for python3.11 to destdir I: pybuild plugin_pyproject:178: Copying package built for python3.12 to destdir dh_install -i -O--buildsystem=pybuild dh_installdocs -i -O--buildsystem=pybuild debian/rules execute_after_dh_installdocs make[1]: Entering directory '/build/reproducible-path/python-cogent-2024.5.7a1+dfsg' rm -rf debian/python-cogent/usr/share/doc/python-cogent/html/_sources find debian -name doctrees -type d | xargs rm -rf make[1]: Leaving directory '/build/reproducible-path/python-cogent-2024.5.7a1+dfsg' debian/rules override_dh_sphinxdoc-indep make[1]: Entering directory '/build/reproducible-path/python-cogent-2024.5.7a1+dfsg' dh_sphinxdoc -i dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/python-cogent-doc/usr/share/doc/python-cogent-doc/html/_static/js/index.be7d3bbb2ef33a8344ce.js dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/python-cogent-doc/usr/share/doc/python-cogent-doc/html/_static/design-tabs.js sed -i 's%https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js%file:///usr/share/javascript/requirejs/require.min.js%' `find /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/debian/python-cogent-doc/usr/share/doc/python-cogent-doc/html/ -type f -name "*.html"` make[1]: Leaving directory '/build/reproducible-path/python-cogent-2024.5.7a1+dfsg' dh_installchangelogs -i -O--buildsystem=pybuild debian/rules override_dh_python3 make[1]: Entering directory '/build/reproducible-path/python-cogent-2024.5.7a1+dfsg' dh_python3 --shebang=/usr/bin/python3 W: dh_python3 fs:122: Paths differ: debian/python3-cogent3/usr/lib/python3.12/dist-packages/.pytest_cache/v/cache/nodeids and debian/python3-cogent3/usr/lib/python3/dist-packages/.pytest_cache/v/cache/nodeids I: dh_python3 pydist:325: Ignoring complex environment marker: numba>0.53; python_version>='3.9' and python_version <'3.12' I: dh_python3 pydist:325: Ignoring complex environment marker: numba>0.54; python_version>='3.10' and python_version <'3.12' make[1]: Leaving directory '/build/reproducible-path/python-cogent-2024.5.7a1+dfsg' dh_installsystemduser -i -O--buildsystem=pybuild dh_perl -i -O--buildsystem=pybuild dh_link -i -O--buildsystem=pybuild dh_strip_nondeterminism -i -O--buildsystem=pybuild debian/rules override_dh_compress make[1]: Entering directory '/build/reproducible-path/python-cogent-2024.5.7a1+dfsg' dh_compress --exclude=.js --exclude=.fasta --exclude=.txt --exclude=.pdb make[1]: Leaving directory '/build/reproducible-path/python-cogent-2024.5.7a1+dfsg' dh_fixperms -i -O--buildsystem=pybuild dh_missing -i -O--buildsystem=pybuild dh_installdeb -i -O--buildsystem=pybuild dh_gencontrol -i -O--buildsystem=pybuild dpkg-gencontrol: warning: package python-cogent-doc: substitution variable ${sphinxdoc:Built-Using} unused, but is defined dh_md5sums -i -O--buildsystem=pybuild dh_builddeb -i -O--buildsystem=pybuild dpkg-deb: building package 'python-cogent-doc' in '../python-cogent-doc_2024.5.7a1+dfsg-3_all.deb'. dpkg-genbuildinfo --build=all -O../python-cogent_2024.5.7a1+dfsg-3_all.buildinfo dpkg-genchanges --build=all -O../python-cogent_2024.5.7a1+dfsg-3_all.changes dpkg-genchanges: info: binary-only arch-indep upload (source code and arch-specific packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2025-10-04T11:17:21Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Sat, 04 Oct 2025 11:17:22 +0000 | +------------------------------------------------------------------------------+ python-cogent_2024.5.7a1+dfsg-3_all.changes: -------------------------------------------- Format: 1.8 Date: Fri, 05 Jul 2024 18:45:00 +0200 Source: python-cogent Binary: python-cogent-doc Architecture: all Version: 2024.5.7a1+dfsg-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Santiago Vila Description: python-cogent-doc - docs for python3-cogent3 Closes: 1030885 Changes: python-cogent (2024.5.7a1+dfsg-3) unstable; urgency=medium . * Team upload. * Update skip-parallel-tests-on-single-cpu-systems.patch to skip "test_write_db_parallel" again. Closes: #1030885. Checksums-Sha1: acc79566109ab354bf57aa3d2aea8094b5d83b4d 17355900 python-cogent-doc_2024.5.7a1+dfsg-3_all.deb 9014a1568de314ac3c757d1d3c45eda2a19e5ca0 13674 python-cogent_2024.5.7a1+dfsg-3_all.buildinfo Checksums-Sha256: 975389ee813a980fda7224081d1fa4dad80518f9d82de61bde94c82eaa2c822f 17355900 python-cogent-doc_2024.5.7a1+dfsg-3_all.deb 3bdc4e08f9451b3e43a9438cd80b31a3327e722bdb7294ef3ef09c0d4477f94a 13674 python-cogent_2024.5.7a1+dfsg-3_all.buildinfo Files: 1960dfb7cced664aea4158f1340f626b 17355900 doc optional python-cogent-doc_2024.5.7a1+dfsg-3_all.deb b7ed67920b84dab80f550b125a53c3e0 13674 python optional python-cogent_2024.5.7a1+dfsg-3_all.buildinfo +------------------------------------------------------------------------------+ | Buildinfo Sat, 04 Oct 2025 11:17:23 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 Source: python-cogent Binary: python-cogent-doc Architecture: all Version: 2024.5.7a1+dfsg-3 Checksums-Md5: 1960dfb7cced664aea4158f1340f626b 17355900 python-cogent-doc_2024.5.7a1+dfsg-3_all.deb Checksums-Sha1: acc79566109ab354bf57aa3d2aea8094b5d83b4d 17355900 python-cogent-doc_2024.5.7a1+dfsg-3_all.deb Checksums-Sha256: 975389ee813a980fda7224081d1fa4dad80518f9d82de61bde94c82eaa2c822f 17355900 python-cogent-doc_2024.5.7a1+dfsg-3_all.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Sat, 04 Oct 2025 11:17:21 +0000 Build-Path: /build/reproducible-path/python-cogent-2024.5.7a1+dfsg Build-Tainted-By: merged-usr-via-aliased-dirs Installed-Build-Depends: architecture-properties (= 0.1.1+b1), autoconf (= 2.71-3), automake (= 1:1.16.5-1.3), autopoint (= 0.22.5-1), autotools-dev (= 20220109.1), base-files (= 13.3), base-passwd (= 3.6.4), bash (= 5.2.21-2.1), binutils (= 2.42.50.20240625-1), binutils-common (= 2.42.50.20240625-1), binutils-x86-64-linux-gnu (= 2.42.50.20240625-1), blt (= 2.5.3+dfsg-7), bsdextrautils (= 2.40.1-9), bsdutils (= 1:2.40.1-9), build-essential (= 12.10), bzip2 (= 1.0.8-5.1), ca-certificates (= 20240203), coreutils (= 9.4-3.1), cpp (= 4:13.2.0-7), cpp-13 (= 13.3.0-1), cpp-13-x86-64-linux-gnu (= 13.3.0-1), cpp-x86-64-linux-gnu (= 4:13.2.0-7), cython3 (= 3.0.10+dfsg-5), dash (= 0.5.12-9), debconf (= 1.5.86), debhelper (= 13.16), debianutils (= 5.19), dh-autoreconf (= 20), dh-python (= 6.20240603), dh-strip-nondeterminism (= 1.14.0-1), diffutils (= 1:3.10-1), docutils-common (= 0.20.1+dfsg-3), dpkg (= 1.22.6), dpkg-dev (= 1.22.6), dwz (= 0.15-1+b1), file (= 1:5.45-3), findutils (= 4.10.0-2), flit (= 3.9.0-2), fontconfig-config (= 2.15.0-1.1), fonts-dejavu-core (= 2.37-8), fonts-dejavu-mono (= 2.37-8), fonts-glyphicons-halflings (= 1.009~3.4.1+dfsg-3), fonts-lyx (= 2.4.1-1), g++ (= 4:13.2.0-7), g++-13 (= 13.3.0-1), g++-13-x86-64-linux-gnu (= 13.3.0-1), g++-x86-64-linux-gnu (= 4:13.2.0-7), gcc (= 4:13.2.0-7), gcc-13 (= 13.3.0-1), gcc-13-base (= 13.3.0-1), gcc-13-x86-64-linux-gnu (= 13.3.0-1), gcc-14-base (= 14.1.0-3), gcc-x86-64-linux-gnu (= 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python-matplotlib-data (= 3.6.3-2), python-tinycss2-common (= 1.3.0-1), python3 (= 3.12.2-1), python3-alabaster (= 0.7.16-0.1), python3-all (= 3.12.2-1), python3-all-dev (= 3.12.2-1), python3-anyio (= 4.4.0-1), python3-appdirs (= 1.4.4-4), python3-argon2 (= 21.1.0-2), python3-attr (= 23.2.0-2), python3-babel (= 2.14.0-1), python3-bleach (= 6.1.0-2), python3-brotli (= 1.1.0-2+b3), python3-bs4 (= 4.12.3-1), python3-build (= 1.2.1-1), python3-certifi (= 2024.6.2-1), python3-cffi-backend (= 1.16.0-2+b2), python3-chardet (= 5.2.0+dfsg-1), python3-charset-normalizer (= 3.3.2-1), python3-commonmark (= 0.9.1-6), python3-contourpy (= 1.0.7-3), python3-coverage (= 7.2.7+dfsg1-1+b1), python3-cycler (= 0.12.1-1), python3-dateutil (= 2.9.0-2), python3-decorator (= 5.1.1-5), python3-defusedxml (= 0.7.1-2), python3-dev (= 3.12.2-1), python3-distutils (= 3.12.3-3.1), python3-docutils (= 0.20.1+dfsg-3), python3-entrypoints (= 0.4-2), python3-execnet (= 2.1.1-1), python3-fastjsonschema (= 2.20.0-1), 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python3-pytest (= 8.2.2-2), python3-pytest-cov (= 5.0.0-1), python3-pytest-xdist (= 3.6.1-1), python3-recommonmark (= 0.7.1+ds-5), python3-referencing (= 0.31.0-1), python3-requests (= 2.32.3+dfsg-1), python3-roman (= 3.3-3), python3-rpds-py (= 0.12.0-3), python3-scipy (= 1.12.0-2), python3-scitrack (= 2021.5.3-3), python3-send2trash (= 1.8.2-1), python3-setuptools (= 68.1.2-2), python3-setuptools-scm (= 8.1.0-1), python3-six (= 1.16.0-6), python3-sniffio (= 1.3.1-1), python3-snowballstemmer (= 2.2.0-4), python3-soupsieve (= 2.5-1), python3-sphinx (= 7.3.7-3), python3-sphinx-bootstrap-theme (= 0.8.1-5), python3-sphinx-design (= 0.6.0-2), python3-sphinx-gallery (= 0.16.0-1), python3-sphinxcontrib.bibtex (= 2.6.2-1), python3-stevedore (= 5.2.0-2), python3-sympy (= 1.12.1-1), python3-tabulate (= 0.9.0-1), python3-tenacity (= 8.4.2-1), python3-terminado (= 0.18.1-1), python3-tinycss2 (= 1.3.0-1), python3-tinydb (= 3.15.2-4), python3-tk (= 3.12.3-3.1), python3-toml (= 0.10.2-1), python3-tomli-w (= 1.0.0-2), python3-tornado (= 6.4.1-1), python3-tqdm (= 4.66.4-1), python3-traitlets (= 5.14.3-1), python3-trove-classifiers (= 2024.4.10-1), python3-typing-extensions (= 4.12.2-1), python3-tz (= 2024.1-2), python3-ufolib2 (= 0.16.0+dfsg1-1), python3-urllib3 (= 2.0.7-2), python3-webencodings (= 0.5.1-5), python3-websocket (= 1.7.0-1), python3-wheel (= 0.43.0-1), python3-yaml (= 6.0.1-2), python3-zmq (= 24.0.1-5+b1), python3.11 (= 3.11.9-1), python3.11-dev (= 3.11.9-1), python3.11-minimal (= 3.11.9-1), python3.12 (= 3.12.4-1), python3.12-dev (= 3.12.4-1), python3.12-minimal (= 3.12.4-1), readline-common (= 8.2-4), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-2), sensible-utils (= 0.0.24), sgml-base (= 1.31), sphinx-common (= 7.3.7-3), sysvinit-utils (= 3.09-2), tar (= 1.35+dfsg-3), tk8.6-blt2.5 (= 2.5.3+dfsg-7), tzdata (= 2024a-4), unicode-data (= 15.1.0-1), usr-is-merged (= 39), util-linux (= 2.40.1-9), x11-common (= 1:7.7+23), xml-core (= 0.19), xz-utils (= 5.6.2-1), zlib1g (= 1:1.3.dfsg+really1.3.1-1), zlib1g-dev (= 1:1.3.dfsg+really1.3.1-1) Environment: DEB_BUILD_OPTIONS="parallel=6" LANG="C.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1720197900" +------------------------------------------------------------------------------+ | Package contents Sat, 04 Oct 2025 11:17:23 +0000 | +------------------------------------------------------------------------------+ python-cogent-doc_2024.5.7a1+dfsg-3_all.deb ------------------------------------------- new Debian package, version 2.0. size 17355900 bytes: control archive=12452 bytes. 752 bytes, 20 lines control 49888 bytes, 430 lines md5sums Package: python-cogent-doc Source: python-cogent Version: 2024.5.7a1+dfsg-3 Architecture: all Maintainer: Debian Med Packaging Team Installed-Size: 22615 Depends: libjs-jquery, libjs-requirejs, libjs-underscore, libjs-sphinxdoc (>= 7.3) Suggests: python3-cogent3 (= 2024.5.7a1+dfsg-3) Section: doc Priority: optional Multi-Arch: foreign Homepage: https://github.com/cogent3/cogent3 Description: docs for python3-cogent3 PyCogent is a software library for genomic biology. . It is distinguished by many unique built-in capabilities (such as true codon alignment) and the frequent addition of entirely new methods for the analysis of genomic data. . 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2024-07-05 16:45 ./usr/share/doc/python-cogent-doc/html/templates/ -rw-r--r-- root/root 6074 2024-07-05 16:45 ./usr/share/doc/python-cogent-doc/html/templates/class.html +------------------------------------------------------------------------------+ | Post Build Sat, 04 Oct 2025 11:17:24 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Sat, 04 Oct 2025 11:17:24 +0000 | +------------------------------------------------------------------------------+ Purging /build/reproducible-path Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Sat, 04 Oct 2025 11:17:26 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: all Build-Space: 220088 Build-Time: 601 Distribution: unstable Host Architecture: amd64 Install-Time: 4 Job: /srv/rebuilderd/tmp/rebuilderdkS7JpC/inputs/python-cogent_2024.5.7a1+dfsg-3.dsc Machine Architecture: amd64 Package: python-cogent Package-Time: 624 Source-Version: 2024.5.7a1+dfsg-3 Space: 220088 Status: successful Version: 2024.5.7a1+dfsg-3 -------------------------------------------------------------------------------- Finished at 2025-10-04T11:17:21Z Build needed 00:10:24, 220088k disk space build artifacts stored in /srv/rebuilderd/tmp/rebuilderdkS7JpC/out size differs for python-cogent-doc_2024.5.7a1+dfsg-3_all.deb checking python-cogent-doc_2024.5.7a1+dfsg-3_all.deb: