https://launchpad.net/ubuntu/+source/python-cogent/2023.2.12a1+dfsg-2/+build/26017742 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux lcy02-amd64-012 5.4.0-147-generic #164-Ubuntu SMP Tue Mar 21 14:23:17 UTC 2023 x86_64 Buildd toolchain package versions: launchpad-buildd_231~626~ubuntu20.04.1 python3-lpbuildd_231~626~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.10 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1. Syncing the system clock with the buildd NTP service... 2 May 02:00:55 ntpdate[1860]: adjust time server 10.131.248.1 offset 0.000192 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=mantic --arch=amd64 PACKAGEBUILD-26017742 --image-type chroot /home/buildd/filecache-default/1fc1752c0976ad9eb0e621fd063fde252dab04e3 Creating target for build PACKAGEBUILD-26017742 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=mantic --arch=amd64 PACKAGEBUILD-26017742 Starting target for build PACKAGEBUILD-26017742 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=mantic --arch=amd64 PACKAGEBUILD-26017742 'deb http://ftpmaster.internal/ubuntu mantic main universe' 'deb http://ftpmaster.internal/ubuntu mantic-security main universe' 'deb http://ftpmaster.internal/ubuntu mantic-updates main universe' 'deb http://ftpmaster.internal/ubuntu mantic-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-26017742 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=mantic --arch=amd64 PACKAGEBUILD-26017742 Updating target for build PACKAGEBUILD-26017742 Get:1 http://ftpmaster.internal/ubuntu mantic InRelease [212 kB] Get:2 http://ftpmaster.internal/ubuntu mantic-security InRelease [74.9 kB] Get:3 http://ftpmaster.internal/ubuntu mantic-updates InRelease [74.9 kB] Get:4 http://ftpmaster.internal/ubuntu mantic-proposed InRelease [74.9 kB] Get:5 http://ftpmaster.internal/ubuntu mantic/main amd64 Packages [1396 kB] Get:6 http://ftpmaster.internal/ubuntu mantic/main Translation-en [514 kB] Get:7 http://ftpmaster.internal/ubuntu mantic/universe amd64 Packages [15.0 MB] Get:8 http://ftpmaster.internal/ubuntu mantic/universe Translation-en [5906 kB] Get:9 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 Packages [81.8 kB] Get:10 http://ftpmaster.internal/ubuntu mantic-proposed/main Translation-en [37.6 kB] Get:11 http://ftpmaster.internal/ubuntu mantic-proposed/universe amd64 Packages [136 kB] Get:12 http://ftpmaster.internal/ubuntu mantic-proposed/universe Translation-en [64.2 kB] Fetched 23.6 MB in 2s (10.3 MB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: gcc-13-base libproc2-0 The following packages will be upgraded: adduser advancecomp apt base-files bash binutils binutils-common binutils-x86-64-linux-gnu ca-certificates coreutils cpp cpp-12 dash debconf diffutils dpkg dpkg-dev e2fsprogs fakeroot g++ g++-12 gcc gcc-12 gcc-12-base gpg gpg-agent gpgconf gpgv grep hostname libacl1 libapparmor1 libapt-pkg6.0 libargon2-1 libasan8 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdb5.3 libdebconfclient0 libdpkg-perl libext2fs2 libfakeroot libgcc-12-dev libgcc-s1 libgcrypt20 libgnutls30 libgomp1 libgprofng0 libitm1 libkmod2 liblsan0 liblzma5 libmpfr6 libncurses6 libncursesw6 libp11-kit0 libpcre2-8-0 libperl5.36 libquadmath0 libreadline8 libseccomp2 libselinux1 libsemanage-common libsemanage2 libsqlite3-0 libss2 libssl3 libstdc++-12-dev libstdc++6 libsystemd-shared libsystemd0 libtinfo6 libtsan2 libubsan1 libudev1 libzstd1 linux-libc-dev logsave lsb-base lto-disabled-list ncurses-base ncurses-bin openssl perl perl-base perl-modules-5.36 pkgbinarymangler procps readline-common sed sensible-utils systemd systemd-sysv sysvinit-utils tar tzdata xz-utils zlib1g 114 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 106 MB of archives. After this operation, 2339 kB disk space will be freed. Get:1 http://ftpmaster.internal/ubuntu mantic/main amd64 libcrypt-dev amd64 1:4.4.33-2 [113 kB] Get:2 http://ftpmaster.internal/ubuntu mantic/main amd64 libc6-dev amd64 2.37-0ubuntu2 [2092 kB] Get:3 http://ftpmaster.internal/ubuntu mantic/main amd64 libc-dev-bin amd64 2.37-0ubuntu2 [20.0 kB] Get:4 http://ftpmaster.internal/ubuntu mantic/main amd64 libcrypt1 amd64 1:4.4.33-2 [80.7 kB] Get:5 http://ftpmaster.internal/ubuntu mantic/main amd64 linux-libc-dev amd64 6.2.0-21.21 [1508 kB] Get:6 http://ftpmaster.internal/ubuntu mantic/main amd64 libc6 amd64 2.37-0ubuntu2 [3179 kB] Get:7 http://ftpmaster.internal/ubuntu mantic/main amd64 libc-bin amd64 2.37-0ubuntu2 [669 kB] Get:8 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 gcc-13-base amd64 13.1.0-1ubuntu1 [40.8 kB] Get:9 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libgcc-s1 amd64 13.1.0-1ubuntu1 [62.4 kB] Get:10 http://ftpmaster.internal/ubuntu mantic/main amd64 base-files amd64 12.3ubuntu3 [76.1 kB] Get:11 http://ftpmaster.internal/ubuntu mantic/main amd64 bash amd64 5.2.15-2ubuntu1 [795 kB] Get:12 http://ftpmaster.internal/ubuntu mantic/main amd64 coreutils amd64 9.1-1ubuntu2 [1407 kB] Get:13 http://ftpmaster.internal/ubuntu mantic/main amd64 liblzma5 amd64 5.4.1-0.2 [125 kB] Get:14 http://ftpmaster.internal/ubuntu mantic/main amd64 libgcrypt20 amd64 1.10.1-3ubuntu1 [529 kB] Get:15 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libstdc++6 amd64 13.1.0-1ubuntu1 [771 kB] Get:16 http://ftpmaster.internal/ubuntu mantic/main amd64 libacl1 amd64 2.3.1-3 [16.4 kB] Get:17 http://ftpmaster.internal/ubuntu mantic/main amd64 libapparmor1 amd64 3.0.8-1ubuntu2 [46.0 kB] Get:18 http://ftpmaster.internal/ubuntu mantic/main amd64 libaudit-common all 1:3.0.9-1 [5142 B] Get:19 http://ftpmaster.internal/ubuntu mantic/main amd64 libcap-ng0 amd64 0.8.3-1build2 [15.3 kB] Get:20 http://ftpmaster.internal/ubuntu mantic/main amd64 libaudit1 amd64 1:3.0.9-1 [46.0 kB] Get:21 http://ftpmaster.internal/ubuntu mantic/main amd64 libcap2 amd64 1:2.66-3ubuntu2 [28.2 kB] Get:22 http://ftpmaster.internal/ubuntu mantic/main amd64 libperl5.36 amd64 5.36.0-7 [4834 kB] Get:23 http://ftpmaster.internal/ubuntu mantic/main amd64 perl amd64 5.36.0-7 [235 kB] Get:24 http://ftpmaster.internal/ubuntu mantic/main amd64 perl-base amd64 5.36.0-7 [1779 kB] Get:25 http://ftpmaster.internal/ubuntu mantic/main amd64 perl-modules-5.36 all 5.36.0-7 [2984 kB] Get:26 http://ftpmaster.internal/ubuntu mantic/main amd64 libdb5.3 amd64 5.3.28+dfsg2-1 [742 kB] Get:27 http://ftpmaster.internal/ubuntu mantic/main amd64 zlib1g amd64 1:1.2.13.dfsg-1ubuntu4 [61.2 kB] Get:28 http://ftpmaster.internal/ubuntu mantic/main amd64 debconf all 1.5.82 [125 kB] Get:29 http://ftpmaster.internal/ubuntu mantic/main amd64 libssl3 amd64 3.0.8-1ubuntu1 [1903 kB] Get:30 http://ftpmaster.internal/ubuntu mantic/main amd64 libzstd1 amd64 1.5.4+dfsg2-4 [292 kB] Get:31 http://ftpmaster.internal/ubuntu mantic/main amd64 libkmod2 amd64 30+20221128-1ubuntu1 [49.5 kB] Get:32 http://ftpmaster.internal/ubuntu mantic/main amd64 libseccomp2 amd64 2.5.4-1ubuntu3 [49.1 kB] Get:33 http://ftpmaster.internal/ubuntu mantic/main amd64 libpcre2-8-0 amd64 10.42-1 [228 kB] Get:34 http://ftpmaster.internal/ubuntu mantic/main amd64 libselinux1 amd64 3.4-1build4 [78.1 kB] Get:35 http://ftpmaster.internal/ubuntu mantic/main amd64 systemd-sysv amd64 252.5-2ubuntu3 [11.5 kB] Get:36 http://ftpmaster.internal/ubuntu mantic/main amd64 systemd amd64 252.5-2ubuntu3 [3002 kB] Get:37 http://ftpmaster.internal/ubuntu mantic/main amd64 libsystemd-shared amd64 252.5-2ubuntu3 [1832 kB] Get:38 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libargon2-1 amd64 0~20190702+dfsg-3 [20.3 kB] Get:39 http://ftpmaster.internal/ubuntu mantic/main amd64 libcryptsetup12 amd64 2:2.6.1-1ubuntu1 [229 kB] Get:40 http://ftpmaster.internal/ubuntu mantic/main amd64 libp11-kit0 amd64 0.24.1-2ubuntu1 [248 kB] Get:41 http://ftpmaster.internal/ubuntu mantic/main amd64 libsystemd0 amd64 252.5-2ubuntu3 [389 kB] Get:42 http://ftpmaster.internal/ubuntu mantic/main amd64 libudev1 amd64 252.5-2ubuntu3 [150 kB] Get:43 http://ftpmaster.internal/ubuntu mantic/main amd64 libapt-pkg6.0 amd64 2.6.0 [919 kB] Get:44 http://ftpmaster.internal/ubuntu mantic/main amd64 tar amd64 1.34+dfsg-1.2 [293 kB] Get:45 http://ftpmaster.internal/ubuntu mantic/main amd64 dpkg amd64 1.21.21ubuntu1 [1394 kB] Get:46 http://ftpmaster.internal/ubuntu mantic/main amd64 dash amd64 0.5.12-2ubuntu1 [88.2 kB] Get:47 http://ftpmaster.internal/ubuntu mantic/main amd64 diffutils amd64 1:3.8-4 [176 kB] Get:48 http://ftpmaster.internal/ubuntu mantic/main amd64 grep amd64 3.8-5 [160 kB] Get:49 http://ftpmaster.internal/ubuntu mantic/main amd64 hostname amd64 3.23+nmu1ubuntu1 [11.0 kB] Get:50 http://ftpmaster.internal/ubuntu mantic/main amd64 ncurses-bin amd64 6.4-2 [185 kB] Get:51 http://ftpmaster.internal/ubuntu mantic/main amd64 sed amd64 4.9-1 [193 kB] Get:52 http://ftpmaster.internal/ubuntu mantic/main amd64 ncurses-base all 6.4-2 [21.3 kB] Get:53 http://ftpmaster.internal/ubuntu mantic/main amd64 sysvinit-utils amd64 3.06-2ubuntu1 [32.5 kB] Get:54 http://ftpmaster.internal/ubuntu mantic/main amd64 lsb-base all 11.6 [4606 B] Get:55 http://ftpmaster.internal/ubuntu mantic/main amd64 adduser all 3.129ubuntu1 [59.0 kB] Get:56 http://ftpmaster.internal/ubuntu mantic/main amd64 gpgv amd64 2.2.40-1.1ubuntu1 [140 kB] Get:57 http://ftpmaster.internal/ubuntu mantic/main amd64 libgnutls30 amd64 3.7.8-5ubuntu1 [985 kB] Get:58 http://ftpmaster.internal/ubuntu mantic/main amd64 apt amd64 2.6.0 [1386 kB] Get:59 http://ftpmaster.internal/ubuntu mantic/main amd64 logsave amd64 1.47.0-1ubuntu1 [14.2 kB] Get:60 http://ftpmaster.internal/ubuntu mantic/main amd64 libext2fs2 amd64 1.47.0-1ubuntu1 [212 kB] Get:61 http://ftpmaster.internal/ubuntu mantic/main amd64 e2fsprogs amd64 1.47.0-1ubuntu1 [598 kB] Get:62 http://ftpmaster.internal/ubuntu mantic/main amd64 libattr1 amd64 1:2.5.1-4 [12.4 kB] Get:63 http://ftpmaster.internal/ubuntu mantic/main amd64 libdebconfclient0 amd64 0.267ubuntu1 [7892 B] Get:64 http://ftpmaster.internal/ubuntu mantic/main amd64 libsemanage-common all 3.4-1build4 [9852 B] Get:65 http://ftpmaster.internal/ubuntu mantic/main amd64 libsemanage2 amd64 3.4-1build4 [92.7 kB] Get:66 http://ftpmaster.internal/ubuntu mantic/main amd64 libncurses6 amd64 6.4-2 [112 kB] Get:67 http://ftpmaster.internal/ubuntu mantic/main amd64 libncursesw6 amd64 6.4-2 [147 kB] Get:68 http://ftpmaster.internal/ubuntu mantic/main amd64 libtinfo6 amd64 6.4-2 [101 kB] Get:69 http://ftpmaster.internal/ubuntu mantic/main amd64 libcom-err2 amd64 1.47.0-1ubuntu1 [14.5 kB] Get:70 http://ftpmaster.internal/ubuntu mantic/main amd64 libproc2-0 amd64 2:4.0.3-1ubuntu1 [55.9 kB] Get:71 http://ftpmaster.internal/ubuntu mantic/main amd64 libss2 amd64 1.47.0-1ubuntu1 [16.8 kB] Get:72 http://ftpmaster.internal/ubuntu mantic/main amd64 procps amd64 2:4.0.3-1ubuntu1 [609 kB] Get:73 http://ftpmaster.internal/ubuntu mantic/main amd64 sensible-utils all 0.0.17+nmu1 [19.3 kB] Get:74 http://ftpmaster.internal/ubuntu mantic/main amd64 openssl amd64 3.0.8-1ubuntu1 [1180 kB] Get:75 http://ftpmaster.internal/ubuntu mantic/main amd64 ca-certificates all 20230311 [155 kB] Get:76 http://ftpmaster.internal/ubuntu mantic/main amd64 readline-common all 8.2-1.3 [55.7 kB] Get:77 http://ftpmaster.internal/ubuntu mantic/main amd64 libreadline8 amd64 8.2-1.3 [151 kB] Get:78 http://ftpmaster.internal/ubuntu mantic/main amd64 libsqlite3-0 amd64 3.40.1-1 [654 kB] Get:79 http://ftpmaster.internal/ubuntu mantic/main amd64 tzdata all 2023c-2exp1ubuntu1 [273 kB] Get:80 http://ftpmaster.internal/ubuntu mantic/main amd64 xz-utils amd64 5.4.1-0.2 [270 kB] Get:81 http://ftpmaster.internal/ubuntu mantic/main amd64 advancecomp amd64 2.5-1 [180 kB] Get:82 http://ftpmaster.internal/ubuntu mantic/main amd64 libgprofng0 amd64 2.40-2ubuntu4 [896 kB] Get:83 http://ftpmaster.internal/ubuntu mantic/main amd64 libctf0 amd64 2.40-2ubuntu4 [97.4 kB] Get:84 http://ftpmaster.internal/ubuntu mantic/main amd64 libctf-nobfd0 amd64 2.40-2ubuntu4 [101 kB] Get:85 http://ftpmaster.internal/ubuntu mantic/main amd64 binutils-x86-64-linux-gnu amd64 2.40-2ubuntu4 [2484 kB] Get:86 http://ftpmaster.internal/ubuntu mantic/main amd64 libbinutils amd64 2.40-2ubuntu4 [630 kB] Get:87 http://ftpmaster.internal/ubuntu mantic/main amd64 binutils amd64 2.40-2ubuntu4 [18.5 kB] Get:88 http://ftpmaster.internal/ubuntu mantic/main amd64 binutils-common amd64 2.40-2ubuntu4 [239 kB] Get:89 http://ftpmaster.internal/ubuntu mantic/main amd64 libmpfr6 amd64 4.2.0-1 [352 kB] Get:90 http://ftpmaster.internal/ubuntu mantic/main amd64 g++-12 amd64 12.2.0-17ubuntu1 [12.0 MB] Get:91 http://ftpmaster.internal/ubuntu mantic/main amd64 gcc-12 amd64 12.2.0-17ubuntu1 [21.4 MB] Get:92 http://ftpmaster.internal/ubuntu mantic/main amd64 cpp-12 amd64 12.2.0-17ubuntu1 [10.6 MB] Get:93 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libubsan1 amd64 13.1.0-1ubuntu1 [1105 kB] Get:94 http://ftpmaster.internal/ubuntu mantic/main amd64 libstdc++-12-dev amd64 12.2.0-17ubuntu1 [2157 kB] Get:95 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libgomp1 amd64 13.1.0-1ubuntu1 [142 kB] Get:96 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libitm1 amd64 13.1.0-1ubuntu1 [29.5 kB] Get:97 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libatomic1 amd64 13.1.0-1ubuntu1 [10.4 kB] Get:98 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libasan8 amd64 13.1.0-1ubuntu1 [2826 kB] Get:99 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 liblsan0 amd64 13.1.0-1ubuntu1 [1203 kB] Get:100 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libquadmath0 amd64 13.1.0-1ubuntu1 [153 kB] Get:101 http://ftpmaster.internal/ubuntu mantic/main amd64 libgcc-12-dev amd64 12.2.0-17ubuntu1 [2576 kB] Get:102 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libtsan2 amd64 13.1.0-1ubuntu1 [2599 kB] Get:103 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libcc1-0 amd64 13.1.0-1ubuntu1 [48.1 kB] Get:104 http://ftpmaster.internal/ubuntu mantic/main amd64 gcc-12-base amd64 12.2.0-17ubuntu1 [41.4 kB] Get:105 http://ftpmaster.internal/ubuntu mantic/main amd64 g++ amd64 4:12.2.0-3ubuntu1 [1120 B] Get:106 http://ftpmaster.internal/ubuntu mantic/main amd64 gcc amd64 4:12.2.0-3ubuntu1 [5160 B] Get:107 http://ftpmaster.internal/ubuntu mantic/main amd64 cpp amd64 4:12.2.0-3ubuntu1 [27.8 kB] Get:108 http://ftpmaster.internal/ubuntu mantic/main amd64 dpkg-dev all 1.21.21ubuntu1 [1117 kB] Get:109 http://ftpmaster.internal/ubuntu mantic/main amd64 libdpkg-perl all 1.21.21ubuntu1 [247 kB] Get:110 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 lto-disabled-list all 40 [12.4 kB] Get:111 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libfakeroot amd64 1.31-1.2 [32.0 kB] Get:112 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 fakeroot amd64 1.31-1.2 [60.1 kB] Get:113 http://ftpmaster.internal/ubuntu mantic/main amd64 gpg amd64 2.2.40-1.1ubuntu1 [523 kB] Get:114 http://ftpmaster.internal/ubuntu mantic/main amd64 gpgconf amd64 2.2.40-1.1ubuntu1 [96.3 kB] Get:115 http://ftpmaster.internal/ubuntu mantic/main amd64 gpg-agent amd64 2.2.40-1.1ubuntu1 [216 kB] Get:116 http://ftpmaster.internal/ubuntu mantic/main amd64 pkgbinarymangler all 152 [16.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 106 MB in 1s (136 MB/s) (Reading database ... 13093 files and directories currently installed.) Preparing to unpack .../libcrypt-dev_1%3a4.4.33-2_amd64.deb ... Unpacking libcrypt-dev:amd64 (1:4.4.33-2) over (1:4.4.33-1) ... Preparing to unpack .../libc6-dev_2.37-0ubuntu2_amd64.deb ... Unpacking libc6-dev:amd64 (2.37-0ubuntu2) over (2.36-0ubuntu4) ... Preparing to unpack .../libc-dev-bin_2.37-0ubuntu2_amd64.deb ... Unpacking libc-dev-bin (2.37-0ubuntu2) over (2.36-0ubuntu4) ... Preparing to unpack .../libcrypt1_1%3a4.4.33-2_amd64.deb ... Unpacking libcrypt1:amd64 (1:4.4.33-2) over (1:4.4.33-1) ... Setting up libcrypt1:amd64 (1:4.4.33-2) ... (Reading database ... 13093 files and directories currently installed.) Preparing to unpack .../linux-libc-dev_6.2.0-21.21_amd64.deb ... Unpacking linux-libc-dev:amd64 (6.2.0-21.21) over (5.19.0-21.21) ... Preparing to unpack .../libc6_2.37-0ubuntu2_amd64.deb ... Unpacking libc6:amd64 (2.37-0ubuntu2) over (2.36-0ubuntu4) ... Setting up libc6:amd64 (2.37-0ubuntu2) ... (Reading database ... 13101 files and directories currently installed.) 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Setting up libctf0:amd64 (2.40-2ubuntu4) ... Setting up cpp-12 (12.2.0-17ubuntu1) ... Setting up pkgbinarymangler (152) ... Setting up libreadline8:amd64 (8.2-1.3) ... Setting up e2fsprogs (1.47.0-1ubuntu1) ... Installing new version of config file /etc/mke2fs.conf ... Setting up ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... rehash: warning: skipping ca-certificates.crt,it does not contain exactly one certificate or CRL 22 added, 6 removed; done. Setting up perl (5.36.0-7) ... Setting up libgprofng0:amd64 (2.40-2ubuntu4) ... Setting up libgcc-12-dev:amd64 (12.2.0-17ubuntu1) ... Setting up libsystemd-shared:amd64 (252.5-2ubuntu3) ... Setting up libdpkg-perl (1.21.21ubuntu1) ... Setting up cpp (4:12.2.0-3ubuntu1) ... Setting up gpgconf (2.2.40-1.1ubuntu1) ... Setting up libc6-dev:amd64 (2.37-0ubuntu2) ... Setting up gpg (2.2.40-1.1ubuntu1) ... Setting up binutils-x86-64-linux-gnu (2.40-2ubuntu4) ... Setting up gpg-agent (2.2.40-1.1ubuntu1) ... Setting up libstdc++-12-dev:amd64 (12.2.0-17ubuntu1) ... Setting up systemd (252.5-2ubuntu3) ... Installing new version of config file /etc/systemd/logind.conf ... Installing new version of config file /etc/systemd/system.conf ... Installing new version of config file /etc/systemd/user.conf ... Initializing machine ID from random generator. Setting up binutils (2.40-2ubuntu4) ... Setting up dpkg-dev (1.21.21ubuntu1) ... Setting up gcc-12 (12.2.0-17ubuntu1) ... Setting up g++-12 (12.2.0-17ubuntu1) ... Setting up systemd-sysv (252.5-2ubuntu3) ... Setting up gcc (4:12.2.0-3ubuntu1) ... Setting up g++ (4:12.2.0-3ubuntu1) ... Processing triggers for libc-bin (2.37-0ubuntu2) ... Processing triggers for debianutils (5.7-0.4) ... Processing triggers for ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-26017742 amd64 mantic-proposed -c chroot:build-PACKAGEBUILD-26017742 --arch=amd64 --dist=mantic-proposed --nolog -A python-cogent_2023.2.12a1+dfsg-2.dsc Initiating build PACKAGEBUILD-26017742 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-147-generic #164-Ubuntu SMP Tue Mar 21 14:23:17 UTC 2023 x86_64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on lcy02-amd64-012.buildd +==============================================================================+ | python-cogent 2023.2.12a1+dfsg-2 (amd64) Tue, 02 May 2023 02:01:19 +0000 | +==============================================================================+ Package: python-cogent Version: 2023.2.12a1+dfsg-2 Source Version: 2023.2.12a1+dfsg-2 Distribution: mantic-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: binary I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-26017742/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/python-cogent-OTUds2/resolver-BYj1Tr' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- python-cogent_2023.2.12a1+dfsg-2.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/python-cogent-OTUds2/python-cogent-2023.2.12a1+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/python-cogent-OTUds2' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), dh-python, flit, cython3, pandoc, pybuild-plugin-pyproject, python3-all-dev, python3-matplotlib, python3-numba, python3-numpy, python3-pandas, python3-scitrack, python3-tqdm, python3-tinydb, python3-sphinx, python3-numpydoc, python3-nbsphinx, python3-sphinx-bootstrap-theme, python3-sphinx-gallery, python3-pytest, python3-pytest-cov, python3-pytest-xdist, python3-plotly, python3-typing-extensions, python3-isort, python3-scipy, python3-chardet, python3-jupyterlab-server, python3-jupyter-sphinx-theme, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), dh-python, flit, cython3, pandoc, pybuild-plugin-pyproject, python3-all-dev, python3-matplotlib, python3-numba, python3-numpy, python3-pandas, python3-scitrack, python3-tqdm, python3-tinydb, python3-sphinx, python3-numpydoc, python3-nbsphinx, python3-sphinx-bootstrap-theme, python3-sphinx-gallery, python3-pytest, python3-pytest-cov, python3-pytest-xdist, python3-plotly, python3-typing-extensions, python3-isort, python3-scipy, python3-chardet, python3-jupyterlab-server, python3-jupyter-sphinx-theme, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [963 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [564 B] Get:5 copy:/<>/apt_archive ./ Packages [640 B] Fetched 2167 B in 0s (0 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev blt bsdextrautils cython3 debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism docutils-common dwz file flit fontconfig-config fonts-dejavu-core fonts-glyphicons-halflings fonts-lyx gettext gettext-base groff-base intltool-debian jupyter-sphinx-theme-common libarchive-zip-perl libblas3 libboost-dev libboost1.74-dev libbrotli1 libbsd0 libcurl4 libdebhelper-perl libdeflate0 libdw1 libedit2 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0 libgraphite2-3 libharfbuzz0b libicu72 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-bootstrap libjs-bootswatch libjs-jquery libjs-jquery-hotkeys libjs-jquery-isonscreen libjs-jquery-metadata libjs-jquery-tablesorter libjs-jquery-throttle-debounce libjs-jquery-ui libjs-sphinxdoc libjs-underscore libjson-perl liblapack3 liblbfgsb0 liblcms2-2 libldap2 liblerc4 libllvm14 liblua5.3-0 libmagic-mgc libmagic1 libnghttp2-14 libnorm1 libopenblas-dev libopenblas-pthread-dev libopenblas0 libopenblas0-pthread libopenjp2-7 libpfm4 libpgm-5.3-0 libpipeline1 libpsl5 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.11 libpython3.11-dev libpython3.11-minimal libpython3.11-stdlib libqhull-r8.0 libraqm0 librtmp1 libsasl2-2 libsasl2-modules-db libsodium23 libssh-4 libsub-override-perl libtcl8.6 libtiff6 libtk8.6 libtool libuchardet0 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxsimd-dev libxslt1.1 libxss1 libyaml-0-2 libzmq5 llvm-14 llvm-14-linker-tools llvm-14-runtime m4 man-db media-types pandoc pandoc-data po-debconf pybuild-plugin-pyproject python-babel-localedata python-matplotlib-data python-tinycss2-common python3 python3-alabaster python3-all python3-all-dev python3-anyio python3-appdirs python3-argon2 python3-attr python3-babel python3-beniget python3-bleach python3-brotli python3-bs4 python3-build python3-certifi python3-cffi-backend python3-chardet python3-commonmark python3-coverage python3-cycler python3-dateutil python3-decorator python3-defusedxml python3-dev python3-distutils python3-docutils python3-entrypoints python3-execnet python3-fastjsonschema python3-fonttools python3-fs python3-gast python3-html5lib python3-idna python3-imagesize python3-importlib-metadata python3-iniconfig python3-installer python3-isort python3-jinja2 python3-json5 python3-jsonschema python3-jupyter-client python3-jupyter-core python3-jupyter-server python3-jupyter-sphinx-theme python3-jupyterlab-pygments python3-jupyterlab-server python3-kiwisolver python3-lib2to3 python3-llvmlite python3-lxml python3-lz4 python3-markupsafe python3-matplotlib python3-minimal python3-more-itertools python3-mpmath python3-nbclient python3-nbconvert python3-nbformat python3-nbsphinx python3-nest-asyncio python3-numba python3-numpy python3-numpydoc python3-packaging python3-pandas python3-pandas-lib python3-pandocfilters python3-pbr python3-pep517 python3-pil python3-pil.imagetk python3-pkg-resources python3-plotly python3-pluggy python3-ply python3-prometheus-client python3-ptyprocess python3-py python3-pygments python3-pyparsing python3-pyrsistent python3-pytest python3-pytest-cov python3-pytest-xdist python3-pythran python3-recommonmark python3-requests python3-roman python3-scipy python3-scitrack python3-send2trash python3-setuptools python3-six python3-sniffio python3-snowballstemmer python3-soupsieve python3-sphinx python3-sphinx-bootstrap-theme python3-sphinx-gallery python3-sympy python3-tenacity python3-terminado python3-tinycss2 python3-tinydb python3-tk python3-toml python3-tomli python3-tomli-w python3-tornado python3-tqdm python3-traitlets python3-typing-extensions python3-tz python3-ufolib2 python3-urllib3 python3-webencodings python3-websocket python3-wheel python3-zipp python3-zmq python3.11 python3.11-dev python3.11-minimal sgml-base sphinx-common tk8.6-blt2.5 unicode-data x11-common xml-core zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc blt-demo cython-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libboost-doc libboost1.74-doc libboost-atomic1.74-dev libboost-chrono1.74-dev libboost-container1.74-dev libboost-context1.74-dev libboost-contract1.74-dev libboost-coroutine1.74-dev libboost-date-time1.74-dev libboost-exception1.74-dev libboost-fiber1.74-dev libboost-filesystem1.74-dev libboost-graph1.74-dev libboost-graph-parallel1.74-dev libboost-iostreams1.74-dev libboost-locale1.74-dev libboost-log1.74-dev libboost-math1.74-dev libboost-mpi1.74-dev libboost-mpi-python1.74-dev libboost-numpy1.74-dev libboost-program-options1.74-dev libboost-python1.74-dev libboost-random1.74-dev libboost-regex1.74-dev libboost-serialization1.74-dev libboost-stacktrace1.74-dev libboost-system1.74-dev libboost-test1.74-dev libboost-thread1.74-dev libboost-timer1.74-dev libboost-type-erasure1.74-dev libboost-wave1.74-dev libboost1.74-tools-dev libmpfrc++-dev libntl-dev libboost-nowide1.74-dev low-memory-monitor libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 libtool-doc gfortran | fortran95-compiler gcj-jdk libxsimd-doc llvm-14-doc m4-doc apparmor less www-browser texlive-latex-recommended texlive-xetex texlive-luatex pandoc-citeproc texlive-latex-extra context wkhtmltopdf librsvg2-bin ghc nodejs php python ruby r-base-core libjs-mathjax libjs-katex citation-style-language-styles libmail-box-perl python3-doc python3-venv python-argon2-doc python-attr-doc python-bleach-doc python3-pip python-coverage-doc python-cycler-doc docutils-doc fonts-linuxlibertine | ttf-linux-libertine texlive-lang-french texlive-latex-base execnet-doc python-fastjsonschema-doc python3-genshi python-installer-doc python-jinja2-doc python-jsonschema-doc python3-json-pointer python3-rfc3987 python3-uritemplate python3-webcolors jupyter-sphinx-theme-doc llvmlite-doc python-lxml-doc cm-super-minimal dvipng ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common python3-cairocffi python3-gi python3-gi-cairo python3-gobject python3-pyqt5 python3-sip texlive-extra-utils python-mpmath-doc python3-gmpy2 python-nbconvert-doc texlive-fonts-recommended texlive-plain-generic python-nbsphinx-doc nvidia-cuda-toolkit gfortran python-pandas-doc python3-statsmodels python-pil-doc python3-ipykernel python-ply-doc subversion python-pygments-doc ttf-bitstream-vera python-pyparsing-doc python3-cryptography python3-openssl python3-socks python-requests-doc python-scipy-doc python-setuptools-doc python3-stemmer fonts-freefont-otf imagemagick-6.q16 latexmk python3-sphinx-rtd-theme sphinx-doc tex-gyre python-sphinx-gallery-doc python3-seaborn texlive-fonts-extra python-sympy-doc python-tenacity-doc python-terminado-doc python-tinycss2-doc tix python3-tk-dbg python3-pycurl python-tornado-doc python3-twisted python3.11-venv python3.11-doc binfmt-support sgml-base-doc Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs javascript-common libjson-xs-perl libldap-common publicsuffix libsasl2-modules libltdl-dev llvm-14-dev libmail-sendmail-perl libpaper-utils python3-sphinxcontrib.bibtex numba-doc python3-pip python3-bottleneck python3-numexpr python3-odf python3-openpyxl python3-tables python3-olefile python3-gi isympy-common The following NEW packages will be installed: autoconf automake autopoint autotools-dev blt bsdextrautils cython3 debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism docutils-common dwz file flit fontconfig-config fonts-dejavu-core fonts-glyphicons-halflings fonts-lyx gettext gettext-base groff-base intltool-debian jupyter-sphinx-theme-common libarchive-zip-perl libblas3 libboost-dev libboost1.74-dev libbrotli1 libbsd0 libcurl4 libdebhelper-perl libdeflate0 libdw1 libedit2 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0 libgraphite2-3 libharfbuzz0b libicu72 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-bootstrap libjs-bootswatch libjs-jquery libjs-jquery-hotkeys libjs-jquery-isonscreen libjs-jquery-metadata libjs-jquery-tablesorter libjs-jquery-throttle-debounce libjs-jquery-ui libjs-sphinxdoc libjs-underscore libjson-perl liblapack3 liblbfgsb0 liblcms2-2 libldap2 liblerc4 libllvm14 liblua5.3-0 libmagic-mgc libmagic1 libnghttp2-14 libnorm1 libopenblas-dev libopenblas-pthread-dev libopenblas0 libopenblas0-pthread libopenjp2-7 libpfm4 libpgm-5.3-0 libpipeline1 libpsl5 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.11 libpython3.11-dev libpython3.11-minimal libpython3.11-stdlib libqhull-r8.0 libraqm0 librtmp1 libsasl2-2 libsasl2-modules-db libsodium23 libssh-4 libsub-override-perl libtcl8.6 libtiff6 libtk8.6 libtool libuchardet0 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxsimd-dev libxslt1.1 libxss1 libyaml-0-2 libzmq5 llvm-14 llvm-14-linker-tools llvm-14-runtime m4 man-db media-types pandoc pandoc-data po-debconf pybuild-plugin-pyproject python-babel-localedata python-matplotlib-data python-tinycss2-common python3 python3-alabaster python3-all python3-all-dev python3-anyio python3-appdirs python3-argon2 python3-attr python3-babel python3-beniget python3-bleach python3-brotli python3-bs4 python3-build python3-certifi python3-cffi-backend python3-chardet python3-commonmark python3-coverage python3-cycler python3-dateutil python3-decorator python3-defusedxml python3-dev python3-distutils python3-docutils python3-entrypoints python3-execnet python3-fastjsonschema python3-fonttools python3-fs python3-gast python3-html5lib python3-idna python3-imagesize python3-importlib-metadata python3-iniconfig python3-installer python3-isort python3-jinja2 python3-json5 python3-jsonschema python3-jupyter-client python3-jupyter-core python3-jupyter-server python3-jupyter-sphinx-theme python3-jupyterlab-pygments python3-jupyterlab-server python3-kiwisolver python3-lib2to3 python3-llvmlite python3-lxml python3-lz4 python3-markupsafe python3-matplotlib python3-minimal python3-more-itertools python3-mpmath python3-nbclient python3-nbconvert python3-nbformat python3-nbsphinx python3-nest-asyncio python3-numba python3-numpy python3-numpydoc python3-packaging python3-pandas python3-pandas-lib python3-pandocfilters python3-pbr python3-pep517 python3-pil python3-pil.imagetk python3-pkg-resources python3-plotly python3-pluggy python3-ply python3-prometheus-client python3-ptyprocess python3-py python3-pygments python3-pyparsing python3-pyrsistent python3-pytest python3-pytest-cov python3-pytest-xdist python3-pythran python3-recommonmark python3-requests python3-roman python3-scipy python3-scitrack python3-send2trash python3-setuptools python3-six python3-sniffio python3-snowballstemmer python3-soupsieve python3-sphinx python3-sphinx-bootstrap-theme python3-sphinx-gallery python3-sympy python3-tenacity python3-terminado python3-tinycss2 python3-tinydb python3-tk python3-toml python3-tomli python3-tomli-w python3-tornado python3-tqdm python3-traitlets python3-typing-extensions python3-tz python3-ufolib2 python3-urllib3 python3-webencodings python3-websocket python3-wheel python3-zipp python3-zmq python3.11 python3.11-dev python3.11-minimal sbuild-build-depends-main-dummy sgml-base sphinx-common tk8.6-blt2.5 unicode-data x11-common xml-core zlib1g-dev 0 upgraded, 268 newly installed, 0 to remove and 0 not upgraded. Need to get 208 MB of archives. After this operation, 1166 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [856 B] Get:2 http://ftpmaster.internal/ubuntu mantic/main amd64 libpython3.11-minimal amd64 3.11.2-6 [836 kB] Get:3 http://ftpmaster.internal/ubuntu mantic/main amd64 libexpat1 amd64 2.5.0-1 [84.2 kB] Get:4 http://ftpmaster.internal/ubuntu mantic/main amd64 python3.11-minimal amd64 3.11.2-6 [2245 kB] Get:5 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-minimal amd64 3.11.2-1 [24.6 kB] Get:6 http://ftpmaster.internal/ubuntu mantic/main amd64 media-types all 10.0.0 [25.8 kB] Get:7 http://ftpmaster.internal/ubuntu mantic/main amd64 libpython3.11-stdlib amd64 3.11.2-6 [1903 kB] Get:8 http://ftpmaster.internal/ubuntu mantic/main amd64 python3.11 amd64 3.11.2-6 [565 kB] Get:9 http://ftpmaster.internal/ubuntu mantic/main amd64 libpython3-stdlib amd64 3.11.2-1 [7234 B] Get:10 http://ftpmaster.internal/ubuntu mantic/main amd64 python3 amd64 3.11.2-1 [22.9 kB] Get:11 http://ftpmaster.internal/ubuntu mantic/main amd64 sgml-base all 1.31 [11.4 kB] Get:12 http://ftpmaster.internal/ubuntu mantic/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] Get:13 http://ftpmaster.internal/ubuntu mantic/universe amd64 libjs-jquery-hotkeys all 0~20130707+git2d51e3a9+dfsg-2ubuntu1 [11.4 kB] Get:14 http://ftpmaster.internal/ubuntu mantic/main amd64 libbsd0 amd64 0.11.7-4 [41.4 kB] Get:15 http://ftpmaster.internal/ubuntu mantic/main amd64 libelf1 amd64 0.188-2.1 [53.4 kB] Get:16 http://ftpmaster.internal/ubuntu mantic/main amd64 libfribidi0 amd64 1.0.8-2.1ubuntu1 [25.9 kB] Get:17 http://ftpmaster.internal/ubuntu mantic/main amd64 libglib2.0-0 amd64 2.76.1-1 [1515 kB] Get:18 http://ftpmaster.internal/ubuntu mantic/main amd64 libicu72 amd64 72.1-3ubuntu2 [10.8 MB] Get:19 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libxml2 amd64 2.9.14+dfsg-1.2 [764 kB] Get:20 http://ftpmaster.internal/ubuntu mantic/main amd64 libyaml-0-2 amd64 0.2.5-1 [52.8 kB] Get:21 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-pkg-resources all 66.1.1-1 [225 kB] Get:22 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 python3-pygments all 2.15.1+dfsg-1 [820 kB] Get:23 http://ftpmaster.internal/ubuntu mantic/main amd64 bsdextrautils amd64 2.38.1-4ubuntu1 [71.0 kB] Get:24 http://ftpmaster.internal/ubuntu mantic/main amd64 libmagic-mgc amd64 1:5.44-3 [293 kB] Get:25 http://ftpmaster.internal/ubuntu mantic/main amd64 libmagic1 amd64 1:5.44-3 [85.6 kB] Get:26 http://ftpmaster.internal/ubuntu mantic/main amd64 file amd64 1:5.44-3 [21.8 kB] Get:27 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 gettext-base amd64 0.21-12 [38.0 kB] Get:28 http://ftpmaster.internal/ubuntu mantic/main amd64 libuchardet0 amd64 0.0.7-1build2 [76.9 kB] Get:29 http://ftpmaster.internal/ubuntu mantic/main amd64 groff-base amd64 1.22.4-10 [937 kB] Get:30 http://ftpmaster.internal/ubuntu mantic/main amd64 libedit2 amd64 3.1-20221030-2 [95.2 kB] Get:31 http://ftpmaster.internal/ubuntu mantic/main amd64 libnghttp2-14 amd64 1.52.0-1 [72.0 kB] Get:32 http://ftpmaster.internal/ubuntu mantic/main amd64 libpipeline1 amd64 1.5.7-1 [23.3 kB] Get:33 http://ftpmaster.internal/ubuntu mantic/main amd64 libpsl5 amd64 0.21.2-1 [59.0 kB] Get:34 http://ftpmaster.internal/ubuntu mantic/main amd64 libxau6 amd64 1:1.0.9-1build5 [7634 B] Get:35 http://ftpmaster.internal/ubuntu mantic/main amd64 libxdmcp6 amd64 1:1.1.3-0ubuntu5 [10.9 kB] Get:36 http://ftpmaster.internal/ubuntu mantic/main amd64 libxcb1 amd64 1.15-1 [48.0 kB] Get:37 http://ftpmaster.internal/ubuntu mantic/main amd64 libx11-data all 2:1.8.4-2 [118 kB] Get:38 http://ftpmaster.internal/ubuntu mantic/main amd64 libx11-6 amd64 2:1.8.4-2 [649 kB] Get:39 http://ftpmaster.internal/ubuntu mantic/main amd64 libxext6 amd64 2:1.3.4-1build1 [31.8 kB] Get:40 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 man-db amd64 2.11.2-2 [1220 kB] Get:41 http://ftpmaster.internal/ubuntu mantic/main amd64 m4 amd64 1.4.19-3 [243 kB] Get:42 http://ftpmaster.internal/ubuntu mantic/main amd64 autoconf all 2.71-3 [339 kB] Get:43 http://ftpmaster.internal/ubuntu mantic/main amd64 autotools-dev all 20220109.1 [44.9 kB] Get:44 http://ftpmaster.internal/ubuntu mantic/main amd64 automake all 1:1.16.5-1.3 [558 kB] Get:45 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 autopoint all 0.21-12 [422 kB] Get:46 http://ftpmaster.internal/ubuntu mantic/main amd64 libtcl8.6 amd64 8.6.13+dfsg-2 [984 kB] Get:47 http://ftpmaster.internal/ubuntu mantic/main amd64 libbrotli1 amd64 1.0.9-2build8 [309 kB] Get:48 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libfreetype6 amd64 2.12.1+dfsg-5 [392 kB] Get:49 http://ftpmaster.internal/ubuntu mantic/main amd64 fonts-dejavu-core all 2.37-6 [1137 kB] Get:50 http://ftpmaster.internal/ubuntu mantic/main amd64 fontconfig-config amd64 2.14.1-3ubuntu3 [34.9 kB] Get:51 http://ftpmaster.internal/ubuntu mantic/main amd64 libfontconfig1 amd64 2.14.1-3ubuntu3 [136 kB] Get:52 http://ftpmaster.internal/ubuntu mantic/main amd64 libxrender1 amd64 1:0.9.10-1.1 [20.0 kB] Get:53 http://ftpmaster.internal/ubuntu mantic/main amd64 libxft2 amd64 2.3.6-1 [44.5 kB] Get:54 http://ftpmaster.internal/ubuntu mantic/main amd64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] Get:55 http://ftpmaster.internal/ubuntu mantic/main amd64 libxss1 amd64 1:1.2.3-1build2 [8476 B] Get:56 http://ftpmaster.internal/ubuntu mantic/main amd64 libtk8.6 amd64 8.6.13-2 [776 kB] Get:57 http://ftpmaster.internal/ubuntu mantic/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-4.1build2 [643 kB] Get:58 http://ftpmaster.internal/ubuntu mantic/main amd64 blt amd64 2.5.3+dfsg-4.1build2 [4838 B] Get:59 http://ftpmaster.internal/ubuntu mantic/universe amd64 cython3 amd64 0.29.32-2ubuntu2 [1313 kB] Get:60 http://ftpmaster.internal/ubuntu mantic/main amd64 libdebhelper-perl all 13.11.4ubuntu3 [66.1 kB] Get:61 http://ftpmaster.internal/ubuntu mantic/main amd64 libtool all 2.4.7-5 [166 kB] Get:62 http://ftpmaster.internal/ubuntu mantic/main amd64 dh-autoreconf all 20 [16.1 kB] Get:63 http://ftpmaster.internal/ubuntu mantic/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB] Get:64 http://ftpmaster.internal/ubuntu mantic/main amd64 libsub-override-perl all 0.09-4 [8706 B] Get:65 http://ftpmaster.internal/ubuntu mantic/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [18.1 kB] Get:66 http://ftpmaster.internal/ubuntu mantic/main amd64 dh-strip-nondeterminism all 1.13.1-1 [5362 B] Get:67 http://ftpmaster.internal/ubuntu mantic/main amd64 libdw1 amd64 0.188-2.1 [251 kB] Get:68 http://ftpmaster.internal/ubuntu mantic/main amd64 debugedit amd64 1:5.0-5 [46.1 kB] Get:69 http://ftpmaster.internal/ubuntu mantic/main amd64 dwz amd64 0.15-1 [112 kB] Get:70 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 gettext amd64 0.21-12 [866 kB] Get:71 http://ftpmaster.internal/ubuntu mantic/main amd64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] Get:72 http://ftpmaster.internal/ubuntu mantic/main amd64 po-debconf all 1.0.21+nmu1 [233 kB] Get:73 http://ftpmaster.internal/ubuntu mantic/main amd64 debhelper all 13.11.4ubuntu3 [925 kB] Get:74 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-lib2to3 all 3.11.2-2 [75.9 kB] Get:75 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-distutils all 3.11.2-2 [130 kB] Get:76 http://ftpmaster.internal/ubuntu mantic/universe amd64 dh-python all 5.20230130 [101 kB] Get:77 http://ftpmaster.internal/ubuntu mantic/main amd64 xml-core all 0.18+nmu1 [21.6 kB] Get:78 http://ftpmaster.internal/ubuntu mantic/main amd64 docutils-common all 0.19+dfsg-6 [129 kB] Get:79 http://ftpmaster.internal/ubuntu mantic/universe amd64 python3-tomli all 2.0.1-2 [16.5 kB] Get:80 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-roman all 3.3-3 [9632 B] Get:81 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-docutils all 0.19+dfsg-6 [386 kB] Get:82 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-certifi all 2022.9.24-1 [155 kB] Get:83 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-chardet all 5.1.0+dfsg-2 [119 kB] Get:84 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-idna all 3.3-1 [49.3 kB] Get:85 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-six all 1.16.0-4 [12.4 kB] Get:86 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-urllib3 all 1.26.12-1 [99.7 kB] Get:87 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-requests all 2.28.1+dfsg-1ubuntu1 [49.9 kB] Get:88 http://ftpmaster.internal/ubuntu mantic/universe amd64 python3-tomli-w all 1.0.0-2 [7368 B] Get:89 http://ftpmaster.internal/ubuntu mantic/universe amd64 flit all 3.8.0-3 [89.3 kB] Get:90 http://ftpmaster.internal/ubuntu mantic/universe amd64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [118 kB] Get:91 http://ftpmaster.internal/ubuntu mantic/universe amd64 fonts-lyx all 2.3.7-1 [167 kB] Get:92 http://ftpmaster.internal/ubuntu mantic/universe amd64 libjs-bootstrap all 3.4.1+dfsg-3 [129 kB] Get:93 http://ftpmaster.internal/ubuntu mantic/universe amd64 libjs-bootswatch all 3.3.7+dfsg2-1.1 [133 kB] Get:94 http://ftpmaster.internal/ubuntu mantic/universe amd64 python3-sphinx-bootstrap-theme all 0.8.1-1 [430 kB] Get:95 http://ftpmaster.internal/ubuntu mantic/universe amd64 jupyter-sphinx-theme-common all 0.0.6+ds1-11 [13.6 kB] Get:96 http://ftpmaster.internal/ubuntu mantic/main amd64 libblas3 amd64 3.11.0-2 [244 kB] Get:97 http://ftpmaster.internal/ubuntu mantic/main amd64 libboost1.74-dev amd64 1.74.0-18.1ubuntu3 [9588 kB] Get:98 http://ftpmaster.internal/ubuntu mantic/main amd64 libboost-dev amd64 1.74.0.3ubuntu7 [3490 B] Get:99 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-11 [21.1 kB] Get:100 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libsasl2-2 amd64 2.1.28+dfsg-11 [56.5 kB] Get:101 http://ftpmaster.internal/ubuntu mantic/main amd64 libldap2 amd64 2.6.3+dfsg-1~exp1ubuntu2 [184 kB] Get:102 http://ftpmaster.internal/ubuntu mantic/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2build4 [58.2 kB] Get:103 http://ftpmaster.internal/ubuntu mantic/main amd64 libssh-4 amd64 0.10.4-2 [185 kB] Get:104 http://ftpmaster.internal/ubuntu mantic/main amd64 libcurl4 amd64 7.88.1-8ubuntu1 [307 kB] Get:105 http://ftpmaster.internal/ubuntu mantic/main amd64 libdeflate0 amd64 1.15-1 [41.9 kB] Get:106 http://ftpmaster.internal/ubuntu mantic/main amd64 libexpat1-dev amd64 2.5.0-1 [137 kB] Get:107 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libgfortran5 amd64 13.1.0-1ubuntu1 [887 kB] Get:108 http://ftpmaster.internal/ubuntu mantic/main amd64 libgraphite2-3 amd64 1.3.14-1build2 [71.3 kB] Get:109 http://ftpmaster.internal/ubuntu mantic/main amd64 libharfbuzz0b amd64 6.0.0+dfsg-3build1 [411 kB] Get:110 http://ftpmaster.internal/ubuntu mantic/main amd64 libimagequant0 amd64 2.17.0-1 [34.6 kB] Get:111 http://ftpmaster.internal/ubuntu mantic/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu1 [147 kB] Get:112 http://ftpmaster.internal/ubuntu mantic/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] Get:113 http://ftpmaster.internal/ubuntu mantic/universe amd64 libjs-jquery-metadata all 12-4 [6582 B] Get:114 http://ftpmaster.internal/ubuntu mantic/universe amd64 libjs-jquery-tablesorter all 1:2.31.3+dfsg1-3 [193 kB] Get:115 http://ftpmaster.internal/ubuntu mantic/universe amd64 libjs-jquery-throttle-debounce all 1.1+dfsg.1-2 [12.5 kB] Get:116 http://ftpmaster.internal/ubuntu mantic/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] Get:117 http://ftpmaster.internal/ubuntu mantic/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] Get:118 http://ftpmaster.internal/ubuntu mantic/main amd64 libjs-sphinxdoc all 5.3.0-4 [130 kB] Get:119 http://ftpmaster.internal/ubuntu mantic/main amd64 libjson-perl all 4.10000-1 [81.9 kB] Get:120 http://ftpmaster.internal/ubuntu mantic/universe amd64 libopenblas0-pthread amd64 0.3.21+ds-4 [7228 kB] Get:121 http://ftpmaster.internal/ubuntu mantic/main amd64 liblapack3 amd64 3.11.0-2 [2659 kB] Get:122 http://ftpmaster.internal/ubuntu mantic/universe amd64 liblbfgsb0 amd64 3.0+dfsg.3-11 [29.8 kB] Get:123 http://ftpmaster.internal/ubuntu mantic/main amd64 liblcms2-2 amd64 2.14-2 [161 kB] Get:124 http://ftpmaster.internal/ubuntu mantic/main amd64 liblerc4 amd64 4.0.0+ds-2ubuntu2 [185 kB] Get:125 http://ftpmaster.internal/ubuntu mantic/universe amd64 libllvm14 amd64 1:14.0.6-12 [24.0 MB] Get:126 http://ftpmaster.internal/ubuntu mantic/main amd64 liblua5.3-0 amd64 5.3.6-2 [139 kB] Get:127 http://ftpmaster.internal/ubuntu mantic/universe amd64 libnorm1 amd64 1.5.9+dfsg-2 [221 kB] Get:128 http://ftpmaster.internal/ubuntu mantic/universe amd64 libopenblas0 amd64 0.3.21+ds-4 [6100 B] Get:129 http://ftpmaster.internal/ubuntu mantic/universe amd64 libopenblas-pthread-dev amd64 0.3.21+ds-4 [5002 kB] Get:130 http://ftpmaster.internal/ubuntu mantic/universe amd64 libopenblas-dev amd64 0.3.21+ds-4 [18.7 kB] Get:131 http://ftpmaster.internal/ubuntu mantic/universe amd64 libpgm-5.3-0 amd64 5.3.128~dfsg-2 [161 kB] Get:132 http://ftpmaster.internal/ubuntu mantic/main amd64 libpython3.11 amd64 3.11.2-6 [2213 kB] Get:133 http://ftpmaster.internal/ubuntu mantic/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1ubuntu4 [895 kB] Get:134 http://ftpmaster.internal/ubuntu mantic/main amd64 libpython3.11-dev amd64 3.11.2-6 [5338 kB] Get:135 http://ftpmaster.internal/ubuntu mantic/main amd64 libpython3-dev amd64 3.11.2-1 [7482 B] Get:136 http://ftpmaster.internal/ubuntu mantic/main amd64 libpython3-all-dev amd64 3.11.2-1 [906 B] Get:137 http://ftpmaster.internal/ubuntu mantic/universe amd64 libqhull-r8.0 amd64 2020.2-5 [194 kB] Get:138 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libraqm0 amd64 0.10.1-1 [14.6 kB] Get:139 http://ftpmaster.internal/ubuntu mantic/main amd64 libsodium23 amd64 1.0.18-1build2 [164 kB] Get:140 http://ftpmaster.internal/ubuntu mantic/main amd64 libjbig0 amd64 2.1-6ubuntu1 [29.1 kB] Get:141 http://ftpmaster.internal/ubuntu mantic/main amd64 libwebp7 amd64 1.2.4-0.1build1 [212 kB] Get:142 http://ftpmaster.internal/ubuntu mantic/main amd64 libtiff6 amd64 4.5.0-5ubuntu1 [198 kB] Get:143 http://ftpmaster.internal/ubuntu mantic/main amd64 libwebpdemux2 amd64 1.2.4-0.1build1 [9886 B] Get:144 http://ftpmaster.internal/ubuntu mantic/main amd64 libwebpmux3 amd64 1.2.4-0.1build1 [20.8 kB] Get:145 http://ftpmaster.internal/ubuntu mantic/universe amd64 libxsimd-dev amd64 8.1.0-7 [90.7 kB] Get:146 http://ftpmaster.internal/ubuntu mantic/main amd64 libxslt1.1 amd64 1.1.35-1 [164 kB] Get:147 http://ftpmaster.internal/ubuntu mantic/universe amd64 libzmq5 amd64 4.3.4-6 [255 kB] Get:148 http://ftpmaster.internal/ubuntu mantic/universe amd64 llvm-14-runtime amd64 1:14.0.6-12 [486 kB] Get:149 http://ftpmaster.internal/ubuntu mantic/universe amd64 llvm-14-linker-tools amd64 1:14.0.6-12 [1360 kB] Get:150 http://ftpmaster.internal/ubuntu mantic/universe amd64 libpfm4 amd64 4.12.1+git12-g678bca9-1 [350 kB] Get:151 http://ftpmaster.internal/ubuntu mantic/universe amd64 llvm-14 amd64 1:14.0.6-12 [12.7 MB] Get:152 http://ftpmaster.internal/ubuntu mantic/universe amd64 pandoc-data all 2.17.1.1-1.1ubuntu1 [80.7 kB] Get:153 http://ftpmaster.internal/ubuntu mantic/universe amd64 pandoc amd64 2.17.1.1-1.1ubuntu1 [23.1 MB] Get:154 http://ftpmaster.internal/ubuntu mantic/universe amd64 python3-typing-extensions all 4.4.0-1 [44.0 kB] Get:155 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-more-itertools all 8.10.0-2 [47.9 kB] Get:156 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-zipp all 1.0.0-6 [6090 B] Get:157 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-importlib-metadata all 4.12.0-1 [17.8 kB] Get:158 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-packaging all 23.0-1 [32.7 kB] Get:159 http://ftpmaster.internal/ubuntu mantic/universe amd64 python3-pep517 all 0.13.0-2 [16.8 kB] Get:160 http://ftpmaster.internal/ubuntu mantic/universe amd64 python3-toml all 0.10.2-1 [16.5 kB] Get:161 http://ftpmaster.internal/ubuntu mantic/universe amd64 python3-wheel all 0.38.4-1 [31.2 kB] Get:162 http://ftpmaster.internal/ubuntu mantic/universe amd64 python3-build all 0.9.0-1 [17.2 kB] Get:163 http://ftpmaster.internal/ubuntu mantic/universe amd64 python3-installer all 0.6.0+dfsg1-1 [17.2 kB] Get:164 http://ftpmaster.internal/ubuntu mantic/universe amd64 pybuild-plugin-pyproject all 5.20230130 [1714 B] Get:165 http://ftpmaster.internal/ubuntu mantic/main amd64 python-babel-localedata all 2.10.3-1 [6357 kB] Get:166 http://ftpmaster.internal/ubuntu mantic/universe amd64 python-matplotlib-data all 3.5.2-4ubuntu1 [2911 kB] Get:167 http://ftpmaster.internal/ubuntu mantic/universe amd64 python-tinycss2-common all 1.2.1-2 [33.9 kB] Get:168 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-all amd64 3.11.2-1 [896 B] Get:169 http://ftpmaster.internal/ubuntu mantic/main amd64 python3.11-dev amd64 3.11.2-6 [614 kB] Get:170 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-dev amd64 3.11.2-1 [26.8 kB] Get:171 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-all-dev amd64 3.11.2-1 [904 B] Get:172 http://ftpmaster.internal/ubuntu mantic/universe amd64 python3-sniffio all 1.2.0-1 [6438 B] Get:173 http://ftpmaster.internal/ubuntu mantic/universe amd64 python3-anyio all 3.6.2-1 [54.2 kB] Get:174 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-appdirs all 1.4.4-3 [10.8 kB] Get:175 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-cffi-backend amd64 1.15.1-5build1 [76.0 kB] Get:176 http://ftpmaster.internal/ubuntu mantic/universe amd64 python3-argon2 amd64 21.1.0-2 [21.1 kB] Get:177 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-attr all 22.2.0-1 [49.6 kB] Get:178 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-tz all 2022.7.1-3 [30.6 kB] Get:179 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-babel all 2.10.3-1 [87.5 kB] Get:180 http://ftpmaster.internal/ubuntu mantic/universe amd64 python3-gast all 0.5.2-2 [9394 B] Get:181 http://ftpmaster.internal/ubuntu mantic/universe amd64 python3-beniget all 0.4.1-3 [10.0 kB] Get:182 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-webencodings all 0.5.1-5 [11.5 kB] Get:183 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-html5lib all 1.1-3 [87.0 kB] Get:184 http://ftpmaster.internal/ubuntu mantic/universe amd64 python3-bleach all 5.0.1-2 [41.9 kB] Get:185 http://ftpmaster.internal/ubuntu mantic/universe amd64 python3-brotli amd64 1.0.9-2build8 [313 kB] Get:186 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-soupsieve all 2.4-1 [33.4 kB] Get:187 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-bs4 all 4.11.2-2 [98.4 kB] Get:188 http://ftpmaster.internal/ubuntu mantic/universe amd64 python3-commonmark all 0.9.1-4 [45.8 kB] Get:189 http://ftpmaster.internal/ubuntu mantic/universe amd64 python3-coverage amd64 6.5.0+dfsg1-2build1 [135 kB] Get:190 http://ftpmaster.internal/ubuntu mantic/universe amd64 python3-cycler all 0.11.0-1 [8156 B] Get:191 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 python3-dateutil all 2.8.2-2 [79.2 kB] Get:192 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-decorator all 5.1.1-3 [9938 B] Get:193 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-defusedxml all 0.7.1-2 [42.0 kB] Get:194 http://ftpmaster.internal/ubuntu mantic/universe amd64 python3-entrypoints all 0.4-2 [7146 B] Get:195 http://ftpmaster.internal/ubuntu mantic/universe amd64 python3-execnet all 1.9.0-1 [33.5 kB] Get:196 http://ftpmaster.internal/ubuntu mantic/universe amd64 python3-fastjsonschema all 2.16.2-1 [19.9 kB] Get:197 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-numpy amd64 1:1.24.2-1 [5573 kB] Get:198 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-ply all 3.11-5 [47.5 kB] Get:199 http://ftpmaster.internal/ubuntu mantic/universe amd64 python3-pythran amd64 0.11.0+ds-7 [427 kB] Get:200 http://ftpmaster.internal/ubuntu mantic/universe amd64 python3-scipy amd64 1.10.1-1 [15.4 MB] Get:201 http://ftpmaster.internal/ubuntu mantic/universe amd64 python3-ufolib2 all 0.14.0+dfsg1-1 [34.4 kB] Get:202 http://ftpmaster.internal/ubuntu mantic/universe amd64 python3-mpmath all 1.2.1-2 [419 kB] Get:203 http://ftpmaster.internal/ubuntu mantic/universe amd64 python3-sympy all 1.11.1-1 [4449 kB] Get:204 http://ftpmaster.internal/ubuntu mantic/universe amd64 python3-fs all 2.4.16-2 [91.0 kB] Get:205 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-lxml amd64 4.9.2-1build1 [1225 kB] Get:206 http://ftpmaster.internal/ubuntu mantic/universe amd64 python3-lz4 amd64 4.0.2+dfsg-1build1 [26.4 kB] Get:207 http://ftpmaster.internal/ubuntu mantic/universe amd64 unicode-data all 15.0.0-1 [8262 kB] Get:208 http://ftpmaster.internal/ubuntu mantic/universe amd64 python3-fonttools amd64 4.38.0-1build1 [1050 kB] Get:209 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-imagesize all 1.4.1-1 [6844 B] Get:210 http://ftpmaster.internal/ubuntu mantic/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] Get:211 http://ftpmaster.internal/ubuntu mantic/universe amd64 python3-isort all 5.6.4-1 [63.1 kB] Get:212 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-markupsafe amd64 2.1.2-1build1 [12.4 kB] Get:213 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-jinja2 all 3.1.2-1 [107 kB] Get:214 http://ftpmaster.internal/ubuntu mantic/universe amd64 python3-json5 all 0.9.10-1 [15.7 kB] Get:215 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-setuptools all 66.1.1-1 [453 kB] Get:216 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-pyrsistent amd64 0.18.1-1build3 [54.9 kB] Get:217 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-jsonschema all 4.6.0-3ubuntu1 [63.6 kB] Get:218 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python3-scitrack all 2021.5.3-3 [9424 B] Get:266 http://ftpmaster.internal/ubuntu mantic/universe amd64 python3-sphinx-gallery all 0.10.1-3 [94.9 kB] Get:267 http://ftpmaster.internal/ubuntu mantic/universe amd64 python3-tinydb all 3.15.2-4 [16.6 kB] Get:268 http://ftpmaster.internal/ubuntu mantic/universe amd64 python3-tqdm all 4.64.1-1 [98.9 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 208 MB in 2s (136 MB/s) Selecting previously unselected package libpython3.11-minimal:amd64. 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Setting up fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... Setting up libpgm-5.3-0:amd64 (5.3.128~dfsg-2) ... Setting up fonts-lyx (2.3.7-1) ... Setting up libpython3.11-stdlib:amd64 (3.11.2-6) ... Setting up libdebhelper-perl (13.11.4ubuntu3) ... Setting up libbrotli1:amd64 (1.0.9-2build8) ... Setting up libnorm1:amd64 (1.5.9+dfsg-2) ... Setting up x11-common (1:7.7+23ubuntu2) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up libnghttp2-14:amd64 (1.52.0-1) ... Setting up libmagic1:amd64 (1:5.44-3) ... Setting up libdeflate0:amd64 (1.15-1) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up libqhull-r8.0:amd64 (2020.2-5) ... Setting up file (1:5.44-3) ... Setting up libjs-jquery-throttle-debounce (1.1+dfsg.1-2) ... Setting up libjbig0:amd64 (2.1-6ubuntu1) ... Setting up python-babel-localedata (2.10.3-1) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg-11) ... Setting up unicode-data (15.0.0-1) ... Setting up libxsimd-dev:amd64 (8.1.0-7) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:amd64 (3.11.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libpfm4:amd64 (4.12.1+git12-g678bca9-1) ... Setting up libexpat1-dev:amd64 (2.5.0-1) ... Setting up libfreetype6:amd64 (2.12.1+dfsg-5) ... Setting up libx11-data (2:1.8.4-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2build4) ... Setting up libjs-bootswatch (3.3.7+dfsg2-1.1) ... Setting up libfribidi0:amd64 (1.0.8-2.1ubuntu1) ... Setting up libimagequant0:amd64 (2.17.0-1) ... Setting up libtcl8.6:amd64 (8.6.13+dfsg-2) ... Setting up autopoint (0.21-12) ... Setting up fonts-dejavu-core (2.37-6) ... Setting up libjpeg-turbo8:amd64 (2.1.5-2ubuntu1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg-11) ... Setting up libssh-4:amd64 (0.10.4-2) ... Setting up libgfortran5:amd64 (13.1.0-1ubuntu1) ... Setting up autoconf (2.71-3) ... Setting up libwebp7:amd64 (1.2.4-0.1build1) ... Setting up zlib1g-dev:amd64 (1:1.2.13.dfsg-1ubuntu4) ... Setting up libuchardet0:amd64 (0.0.7-1build2) ... Setting up liblua5.3-0:amd64 (5.3.6-2) ... Setting up python-tinycss2-common (1.2.1-2) ... Setting up libjson-perl (4.10000-1) ... Setting up libopenjp2-7:amd64 (2.5.0-1build1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libharfbuzz0b:amd64 (6.0.0+dfsg-3build1) ... Setting up sgml-base (1.31) ... Setting up libboost-dev:amd64 (1.74.0.3ubuntu7) ... Setting up pandoc-data (2.17.1.1-1.1ubuntu1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libjs-jquery-hotkeys (0~20130707+git2d51e3a9+dfsg-2ubuntu1) ... Setting up python-matplotlib-data (3.5.2-4ubuntu1) ... Setting up libwebpmux3:amd64 (1.2.4-0.1build1) ... Setting up libbsd0:amd64 (0.11.7-4) ... Setting up libelf1:amd64 (0.188-2.1) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.2) ... Setting up libldap2:amd64 (2.6.3+dfsg-1~exp1ubuntu2) ... Setting up libjs-bootstrap (3.4.1+dfsg-3) ... Setting up libpython3-stdlib:amd64 (3.11.2-1) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up libjpeg8:amd64 (8c-2ubuntu11) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up python3.11 (3.11.2-6) ... Setting up libdw1:amd64 (0.188-2.1) ... Setting up libxdmcp6:amd64 (1:1.1.3-0ubuntu5) ... Setting up liblapack3:amd64 (3.11.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libxcb1:amd64 (1.15-1) ... Setting up gettext (0.21-12) ... Setting up libopenblas0-pthread:amd64 (0.3.21+ds-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so.0 to provide /usr/lib/x86_64-linux-gnu/libopenblas.so.0 (libopenblas.so.0-x86_64-linux-gnu) in auto mode Setting up libzmq5:amd64 (4.3.4-6) ... Setting up libpython3.11:amd64 (3.11.2-6) ... Setting up libtool (2.4.7-5) ... Setting up fontconfig-config (2.14.1-3ubuntu3) ... Setting up libwebpdemux2:amd64 (1.2.4-0.1build1) ... Setting up libedit2:amd64 (3.1-20221030-2) ... Setting up python3 (3.11.2-1) ... Setting up python3-pandocfilters (1.5.0-1) ... Setting up python3-markupsafe (2.1.2-1build1) ... Setting up python3-webencodings (0.5.1-5) ... Setting up python3-tz (2022.7.1-3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up python3-six (1.16.0-4) ... Setting up dh-autoreconf (20) ... Setting up python3-roman (3.3-3) ... Setting up python3-decorator (5.1.1-3) ... Setting up python3-jinja2 (3.1.2-1) ... Setting up python3-packaging (23.0-1) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up pandoc (2.17.1.1-1.1ubuntu1) ... Setting up python3-pyparsing (3.0.9-1) ... Setting up python3-certifi (2022.9.24-1) ... Setting up python3-sphinx-bootstrap-theme (0.8.1-1) ... Setting up python3-snowballstemmer (2.2.0-2) ... Setting up libpython3.11-dev:amd64 (3.11.2-6) ... Setting up python3-nest-asyncio (1.5.4-1) ... Setting up python3-brotli (1.0.9-2build8) ... Setting up libjs-jquery-metadata (12-4) ... Setting up libraqm0:amd64 (0.10.1-1) ... Setting up python3-cycler (0.11.0-1) ... Setting up python3-kiwisolver (1.4.4-1build1) ... Setting up libjs-jquery-isonscreen (1.2.0-1.1) ... Setting up python3-idna (3.3-1) ... Setting up cython3 (0.29.32-2ubuntu2) ... Setting up jupyter-sphinx-theme-common (0.0.6+ds1-11) ... Setting up python3-typing-extensions (4.4.0-1) ... Setting up python3-html5lib (1.1-3) ... Setting up libjs-sphinxdoc (5.3.0-4) ... Setting up python3-toml (0.10.2-1) ... Setting up python3-installer (0.6.0+dfsg1-1) ... Setting up python3-isort (5.6.4-1) ... Setting up python3-urllib3 (1.26.12-1) ... Setting up python3-pluggy (1.0.0+repack-1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up python3-fastjsonschema (2.16.2-1) ... Setting up libllvm14:amd64 (1:14.0.6-12) ... Setting up python3-pyrsistent:amd64 (0.18.1-1build3) ... Setting up dwz (0.15-1) ... Setting up libjs-jquery-tablesorter (1:2.31.3+dfsg1-3) ... Setting up libopenblas0:amd64 (0.3.21+ds-4) ... Setting up groff-base (1.22.4-10) ... Setting up libtiff6:amd64 (4.5.0-5ubuntu1) ... Setting up xml-core (0.18+nmu1) ... Setting up python3-traitlets (5.5.0-1) ... Setting up python3-scitrack (2021.5.3-3) ... Setting up libxslt1.1:amd64 (1.1.35-1) ... Setting up debugedit (1:5.0-5) ... Setting up libcurl4:amd64 (7.88.1-8ubuntu1) ... Setting up libx11-6:amd64 (2:1.8.4-2) ... Setting up python3-dateutil (2.8.2-2) ... Setting up libfontconfig1:amd64 (2.14.1-3ubuntu3) ... Setting up python3-mpmath (1.2.1-2) ... Setting up llvm-14-linker-tools (1:14.0.6-12) ... Setting up python3-execnet (1.9.0-1) ... Setting up python3-lib2to3 (3.11.2-2) ... Setting up python3-tomli-w (1.0.0-2) ... Setting up python3-appdirs (1.4.4-3) ... Setting up python3-soupsieve (2.4-1) ... Setting up python3-websocket (1.2.3-1) ... Setting up python3-cffi-backend:amd64 (1.15.1-5build1) ... Setting up liblbfgsb0:amd64 (3.0+dfsg.3-11) ... Setting up python3-imagesize (1.4.1-1) ... Setting up python3-ptyprocess (0.7.0-5) ... Setting up python3-commonmark (0.9.1-4) ... Setting up python3-pkg-resources (66.1.1-1) ... Setting up python3-entrypoints (0.4-2) ... Setting up python3-distutils (3.11.2-2) ... Setting up libopenblas-pthread-dev:amd64 (0.3.21+ds-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so to provide /usr/lib/x86_64-linux-gnu/libopenblas.so (libopenblas.so-x86_64-linux-gnu) in auto mode Setting up dh-python (5.20230130) ... Setting up python3-more-itertools (8.10.0-2) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-sniffio (1.2.0-1) ... Setting up python3-sympy (1.11.1-1) ... Setting up python3-attr (22.2.0-1) ... Setting up python3-tornado (6.2.0-3) ... Setting up python3-send2trash (1.8.1~b0-2) ... Setting up python3-tinycss2 (1.2.1-2) ... Setting up libpython3-dev:amd64 (3.11.2-1) ... Setting up python3-setuptools (66.1.1-1) ... Setting up python3-tomli (2.0.1-2) ... Setting up libxrender1:amd64 (1:0.9.10-1.1) ... Setting up python3-py (1.11.0-1) ... Setting up python3-anyio (3.6.2-1) ... Setting up python3-babel (2.10.3-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-lz4 (4.0.2+dfsg-1build1) ... Setting up python3-defusedxml (0.7.1-2) ... Setting up python3-json5 (0.9.10-1) ... Setting up python3-pbr (5.11.1-0ubuntu1) ... Setting up python3.11-dev (3.11.2-6) ... Setting up python3-pytest (7.2.1-2) ... Setting up python3-alabaster (0.7.12-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up python3-tenacity (8.2.1-1) ... Setting up python3-ply (3.11-5) ... Setting up python3-tqdm (4.64.1-1) ... Setting up python3-tinydb (3.15.2-4) ... Setting up python3-gast (0.5.2-2) ... Setting up libxext6:amd64 (2:1.3.4-1build1) ... Setting up python3-all (3.11.2-1) ... Setting up python3-coverage (6.5.0+dfsg1-2build1) ... Setting up python3-pytest-cov (4.0.0-1) ... Setting up python3-zipp (1.0.0-6) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up python3-wheel (0.38.4-1) ... Setting up python3-bs4 (4.11.2-2) ... Setting up python3-bleach (5.0.1-2) ... Setting up python3-fs (2.4.16-2) ... Setting up python3-beniget (0.4.1-3) ... Setting up python3-prometheus-client (0.16.0-0.1) ... Setting up libopenblas-dev:amd64 (0.3.21+ds-4) ... Setting up python3-pygments (2.15.1+dfsg-1) ... Setting up python3-chardet (5.1.0+dfsg-2) ... Setting up llvm-14-runtime (1:14.0.6-12) ... Setting up python3-jsonschema (4.6.0-3ubuntu1) ... Setting up libpython3-all-dev:amd64 (3.11.2-1) ... Setting up python3-zmq (24.0.1-4build1) ... Setting up sphinx-common (5.3.0-4) ... Setting up python3-dev (3.11.2-1) ... Setting up python3-requests (2.28.1+dfsg-1ubuntu1) ... Setting up python3-numpy (1:1.24.2-1) ... Setting up python3-terminado (0.17.0-1) ... Setting up python3-lxml:amd64 (4.9.2-1build1) ... Setting up python3-argon2 (21.1.0-2) ... Setting up libxss1:amd64 (1:1.2.3-1build2) ... Setting up python3-jupyter-core (4.12.0-1) ... Setting up llvm-14 (1:14.0.6-12) ... Setting up python3-all-dev (3.11.2-1) ... Setting up libxft2:amd64 (2.3.6-1) ... Setting up python3-importlib-metadata (4.12.0-1) ... Setting up python3-pytest-xdist (3.1.0-1) ... Setting up libtk8.6:amd64 (8.6.13-2) ... Setting up python3-pandas-lib:amd64 (1.5.3+dfsg-2) ... Setting up debhelper (13.11.4ubuntu3) ... Setting up python3-nbformat (5.5.0-1) ... Setting up python3-jupyterlab-pygments (0.2.2-3) ... Setting up python3-llvmlite (0.39.1-2) ... Setting up python3-pandas (1.5.3+dfsg-2) ... Setting up python3-pep517 (0.13.0-2) ... Setting up python3-plotly (5.4.1+dfsg-1) ... Setting up python3-pythran (0.11.0+ds-7) ... Setting up python3-jupyter-client (7.4.9-2) ... Setting up python3-build (0.9.0-1) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-4.1build2) ... Setting up python3-scipy (1.10.1-1) ... Setting up pybuild-plugin-pyproject (5.20230130) ... Setting up blt (2.5.3+dfsg-4.1build2) ... Setting up python3-tk:amd64 (3.11.2-2) ... Setting up python3-numba (0.56.4+dfsg-2) ... update-alternatives: using /usr/share/python3-numba/numba to provide /usr/bin/numba (numba) in auto mode Setting up python3-nbclient (0.7.2-1) ... Setting up python3-nbconvert (6.5.3-3) ... Setting up python3-jupyter-server (1.23.3-1) ... Setting up python3-jupyterlab-server (2.16.5-1) ... Setting up python3-fonttools (4.38.0-1build1) ... Setting up python3-pil:amd64 (9.4.0-1.1build1) ... Setting up python3-pil.imagetk:amd64 (9.4.0-1.1build1) ... Setting up python3-ufolib2 (0.14.0+dfsg1-1) ... Setting up python3-matplotlib (3.5.2-4ubuntu1) ... Processing triggers for libc-bin (2.37-0ubuntu2) ... Processing triggers for systemd (252.5-2ubuntu3) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.19+dfsg-6) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.19+dfsg-6) ... Setting up flit (3.8.0-3) ... Setting up python3-sphinx (5.3.0-4) ... Setting up python3-sphinx-gallery (0.10.1-3) ... Setting up python3-nbsphinx (0.8.11+ds-1) ... Setting up python3-recommonmark (0.7.1+ds-5) ... Setting up python3-numpydoc (1.5.0-1) ... Setting up python3-jupyter-sphinx-theme (0.0.6+ds1-11) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any-amd64 arm64 mips64el ppc64el s390x ia64 ppc64 riscv64 sparc64 alpha all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-147-generic #164-Ubuntu SMP Tue Mar 21 14:23:17 UTC 2023 amd64 (x86_64) Toolchain package versions: binutils_2.40-2ubuntu4 dpkg-dev_1.21.21ubuntu1 g++-12_12.2.0-17ubuntu1 gcc-12_12.2.0-17ubuntu1 libc6-dev_2.37-0ubuntu2 libstdc++-12-dev_12.2.0-17ubuntu1 libstdc++6_13.1.0-1ubuntu1 linux-libc-dev_6.2.0-21.21 Package versions: adduser_3.129ubuntu1 advancecomp_2.5-1 apt_2.6.0 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-12 autotools-dev_20220109.1 base-files_12.3ubuntu3 base-passwd_3.6.1 bash_5.2.15-2ubuntu1 binutils_2.40-2ubuntu4 binutils-common_2.40-2ubuntu4 binutils-x86-64-linux-gnu_2.40-2ubuntu4 blt_2.5.3+dfsg-4.1build2 bsdextrautils_2.38.1-4ubuntu1 bsdutils_1:2.38.1-4ubuntu1 build-essential_12.9ubuntu3 bzip2_1.0.8-5build1 ca-certificates_20230311 coreutils_9.1-1ubuntu2 cpp_4:12.2.0-3ubuntu1 cpp-12_12.2.0-17ubuntu1 cython3_0.29.32-2ubuntu2 dash_0.5.12-2ubuntu1 debconf_1.5.82 debhelper_13.11.4ubuntu3 debianutils_5.7-0.4 debugedit_1:5.0-5 dh-autoreconf_20 dh-python_5.20230130 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.8-4 docutils-common_0.19+dfsg-6 dpkg_1.21.21ubuntu1 dpkg-dev_1.21.21ubuntu1 dwz_0.15-1 e2fsprogs_1.47.0-1ubuntu1 fakeroot_1.31-1.2 file_1:5.44-3 findutils_4.9.0-3ubuntu1 flit_3.8.0-3 fontconfig-config_2.14.1-3ubuntu3 fonts-dejavu-core_2.37-6 fonts-glyphicons-halflings_1.009~3.4.1+dfsg-3 fonts-lyx_2.3.7-1 g++_4:12.2.0-3ubuntu1 g++-12_12.2.0-17ubuntu1 gcc_4:12.2.0-3ubuntu1 gcc-12_12.2.0-17ubuntu1 gcc-12-base_12.2.0-17ubuntu1 gcc-13-base_13.1.0-1ubuntu1 gettext_0.21-12 gettext-base_0.21-12 gpg_2.2.40-1.1ubuntu1 gpg-agent_2.2.40-1.1ubuntu1 gpgconf_2.2.40-1.1ubuntu1 gpgv_2.2.40-1.1ubuntu1 grep_3.8-5 groff-base_1.22.4-10 gzip_1.12-1ubuntu1 hostname_3.23+nmu1ubuntu1 init_1.65.2 init-system-helpers_1.65.2 intltool-debian_0.35.0+20060710.6 jupyter-sphinx-theme-common_0.0.6+ds1-11 libacl1_2.3.1-3 libapparmor1_3.0.8-1ubuntu2 libapt-pkg6.0_2.6.0 libarchive-zip-perl_1.68-1 libargon2-1_0~20190702+dfsg-3 libasan8_13.1.0-1ubuntu1 libassuan0_2.5.5-5 libatomic1_13.1.0-1ubuntu1 libattr1_1:2.5.1-4 libaudit-common_1:3.0.9-1 libaudit1_1:3.0.9-1 libbinutils_2.40-2ubuntu4 libblas3_3.11.0-2 libblkid1_2.38.1-4ubuntu1 libboost-dev_1.74.0.3ubuntu7 libboost1.74-dev_1.74.0-18.1ubuntu3 libbrotli1_1.0.9-2build8 libbsd0_0.11.7-4 libbz2-1.0_1.0.8-5build1 libc-bin_2.37-0ubuntu2 libc-dev-bin_2.37-0ubuntu2 libc6_2.37-0ubuntu2 libc6-dev_2.37-0ubuntu2 libcap-ng0_0.8.3-1build2 libcap2_1:2.66-3ubuntu2 libcc1-0_13.1.0-1ubuntu1 libcom-err2_1.47.0-1ubuntu1 libcrypt-dev_1:4.4.33-2 libcrypt1_1:4.4.33-2 libcryptsetup12_2:2.6.1-1ubuntu1 libctf-nobfd0_2.40-2ubuntu4 libctf0_2.40-2ubuntu4 libcurl4_7.88.1-8ubuntu1 libdb5.3_5.3.28+dfsg2-1 libdebconfclient0_0.267ubuntu1 libdebhelper-perl_13.11.4ubuntu3 libdeflate0_1.15-1 libdevmapper1.02.1_2:1.02.185-1ubuntu1 libdpkg-perl_1.21.21ubuntu1 libdw1_0.188-2.1 libedit2_3.1-20221030-2 libelf1_0.188-2.1 libexpat1_2.5.0-1 libexpat1-dev_2.5.0-1 libext2fs2_1.47.0-1ubuntu1 libfakeroot_1.31-1.2 libfdisk1_2.38.1-4ubuntu1 libffi8_3.4.4-1 libfile-stripnondeterminism-perl_1.13.1-1 libfontconfig1_2.14.1-3ubuntu3 libfreetype6_2.12.1+dfsg-5 libfribidi0_1.0.8-2.1ubuntu1 libgcc-12-dev_12.2.0-17ubuntu1 libgcc-s1_13.1.0-1ubuntu1 libgcrypt20_1.10.1-3ubuntu1 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgfortran5_13.1.0-1ubuntu1 libglib2.0-0_2.76.1-1 libgmp10_2:6.2.1+dfsg1-1.1ubuntu1 libgnutls30_3.7.8-5ubuntu1 libgomp1_13.1.0-1ubuntu1 libgpg-error0_1.46-1 libgprofng0_2.40-2ubuntu4 libgraphite2-3_1.3.14-1build2 libgssapi-krb5-2_1.20.1-1build1 libharfbuzz0b_6.0.0+dfsg-3build1 libhogweed6_3.8.1-2 libicu72_72.1-3ubuntu2 libidn2-0_2.3.3-1build1 libimagequant0_2.17.0-1 libip4tc2_1.8.7-1ubuntu7 libisl23_0.25-1 libitm1_13.1.0-1ubuntu1 libjansson4_2.14-2 libjbig0_2.1-6ubuntu1 libjpeg-turbo8_2.1.5-2ubuntu1 libjpeg8_8c-2ubuntu11 libjs-bootstrap_3.4.1+dfsg-3 libjs-bootswatch_3.3.7+dfsg2-1.1 libjs-jquery_3.6.1+dfsg+~3.5.14-1 libjs-jquery-hotkeys_0~20130707+git2d51e3a9+dfsg-2ubuntu1 libjs-jquery-isonscreen_1.2.0-1.1 libjs-jquery-metadata_12-4 libjs-jquery-tablesorter_1:2.31.3+dfsg1-3 libjs-jquery-throttle-debounce_1.1+dfsg.1-2 libjs-jquery-ui_1.13.2+dfsg-1 libjs-sphinxdoc_5.3.0-4 libjs-underscore_1.13.4~dfsg+~1.11.4-3 libjson-c5_0.16-2 libjson-perl_4.10000-1 libk5crypto3_1.20.1-1build1 libkeyutils1_1.6.3-2 libkmod2_30+20221128-1ubuntu1 libkrb5-3_1.20.1-1build1 libkrb5support0_1.20.1-1build1 liblapack3_3.11.0-2 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2023.2.12a1+dfsg-2 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Andreas Tille Homepage: https://github.com/cogent3/cogent3 Standards-Version: 4.6.2 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: debhelper-compat (= 13), dh-python, flit, cython3, pandoc, pybuild-plugin-pyproject, python3-all-dev, python3-matplotlib, python3-numba, python3-numpy, python3-pandas, python3-scitrack, python3-tqdm, python3-tinydb, python3-sphinx, python3-numpydoc, python3-nbsphinx, python3-sphinx-bootstrap-theme, python3-sphinx-gallery, python3-pytest , python3-pytest-cov , python3-pytest-xdist , python3-plotly , python3-typing-extensions , python3-isort, python3-scipy, python3-chardet, python3-jupyterlab-server, python3-jupyter-sphinx-theme Package-List: python-cogent-doc deb doc optional arch=all python3-cogent3 deb 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dpkg-source: info: unpacking python-cogent_2023.2.12a1+dfsg.orig.tar.xz dpkg-source: info: unpacking python-cogent_2023.2.12a1+dfsg-2.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 fix-build-on-single-cpu-systems.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-26017742 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-26017742 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-26017742 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon -b -rfakeroot dpkg-buildpackage: info: source package python-cogent dpkg-buildpackage: info: source version 2023.2.12a1+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with python3 --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild dh_autoreconf_clean -O--buildsystem=pybuild debian/rules override_dh_clean make[1]: Entering directory '/<>' #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 '/<>' debian/rules binary dh binary --with python3 --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild debian/rules override_dh_auto_build make[1]: Entering directory '/<>' dh_auto_build I: pybuild plugin_pyproject:107: Building wheel for python3.11 with "build" module I: pybuild base:240: python3.11 -m build --skip-dependency-check --no-isolation --wheel --outdir /<>/.pybuild/cpython3_3.11_cogent3 * Building wheel... Successfully built cogent3-2023.2.12a1-py3-none-any.whl I: pybuild plugin_pyproject:119: Unpacking wheel built for python3.11 with "installer" module set -x; cd doc; PYTHONPATH=/<> http_proxy='127.0.0.1:9' /usr/bin/make html + cd doc + PYTHONPATH=/<> http_proxy=127.0.0.1:9 /usr/bin/make html make[2]: Entering directory '/<>/doc' sphinx-build -b html -d _build/doctrees . _build/html Running Sphinx v5.3.0 making output directory... done WARNING: html_static_path entry '_static' does not exist WARNING: The config value `today' has type `date', defaults to `str'. [autosummary] generating autosummary for: api/__init__/cogent3.__init__.available_apps.rst, api/__init__/cogent3.__init__.available_codes.rst, api/__init__/cogent3.__init__.available_models.rst, api/__init__/cogent3.__init__.available_moltypes.rst, api/__init__/cogent3.__init__.get_code.rst, api/__init__/cogent3.__init__.get_model.rst, api/__init__/cogent3.__init__.get_moltype.rst, api/__init__/cogent3.__init__.load_aligned_seqs.rst, api/__init__/cogent3.__init__.load_delimited.rst, api/__init__/cogent3.__init__.load_seq.rst, ..., examples/scope_model_params_on_trees.rst, examples/seq_features.rst, examples/simple.rst, examples/simulate_alignment.rst, examples/testing_multi_loci.rst, general.rst, index.rst, install.rst, licenses.rst, pycogent.rst building [mo]: targets for 0 po files that are out of date building [html]: targets for 125 source files that are out of date updating environment: [new config] 125 added, 0 changed, 0 removed reading sources... [ 0%] api/__init__/cogent3.__init__.available_apps reading sources... [ 1%] 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... [ 4%] 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... [ 6%] api/__init__/cogent3.__init__.load_aligned_seqs reading sources... [ 7%] api/__init__/cogent3.__init__.load_delimited reading sources... [ 8%] api/__init__/cogent3.__init__.load_seq reading sources... [ 8%] api/__init__/cogent3.__init__.load_table reading sources... [ 9%] api/__init__/cogent3.__init__.load_tree reading sources... [ 10%] api/__init__/cogent3.__init__.load_unaligned_seqs reading sources... [ 11%] api/__init__/cogent3.__init__.make_aligned_seqs reading sources... [ 12%] api/__init__/cogent3.__init__.make_seq reading sources... [ 12%] api/__init__/cogent3.__init__.make_table reading sources... [ 13%] api/__init__/cogent3.__init__.make_tree reading sources... [ 14%] api/__init__/cogent3.__init__.make_unaligned_seqs reading sources... [ 15%] api/alignment/alignment reading sources... [ 16%] api/alignment/classes/cogent3.core.alignment.Alignment reading sources... [ 16%] api/alignment/classes/cogent3.core.alignment.ArrayAlignment reading sources... [ 17%] api/alignment/classes/cogent3.core.alignment.SequenceCollection reading sources... [ 18%] api/alphabet/alphabet reading sources... [ 19%] api/alphabet/classes/cogent3.core.alphabet.Alphabet reading sources... [ 20%] api/apps/composable.define_app reading sources... [ 20%] api/genetic_code/classes/cogent3.core.genetic_code.GeneticCode reading sources... [ 21%] api/genetic_code/genetic_code reading sources... [ 22%] api/index reading sources... [ 23%] api/moltype/classes/cogent3.core.moltype.MolType reading sources... [ 24%] api/moltype/moltype reading sources... [ 24%] api/sequence/classes/cogent3.core.sequence.DnaSequence reading sources... [ 25%] api/sequence/classes/cogent3.core.sequence.ProteinSequence reading sources... [ 26%] api/sequence/classes/cogent3.core.sequence.RnaSequence reading sources... [ 27%] api/sequence/sequence reading sources... [ 28%] api/table/classes/cogent3.parse.table.FilteringParser reading sources... [ 28%] api/table/classes/cogent3.util.table.Columns reading sources... [ 29%] api/table/classes/cogent3.util.table.Table reading sources... [ 30%] api/table/table reading sources... [ 31%] api/tree/classes/cogent3.core.tree.PhyloNode reading sources... [ 32%] api/tree/tree reading sources... [ 32%] app/align-codon reading sources... [ 33%] app/align-nucleotide reading sources... [ 34%] app/align-protein reading sources... [ 35%] app/app-get reading sources... [ 36%] app/app-help reading sources... [ 36%] app/app-overview reading sources... [ 37%] app/available-apps reading sources... [ 38%] app/dstore reading sources... [ 39%] app/evo-ancestral-states reading sources... [ 40%] app/evo-dt-nuc-model reading sources... [ 40%] app/evo-extract-model-stats reading sources... [ 41%] app/evo-hypothesis reading sources... [ 42%] app/evo-model reading sources... [ 43%] app/evo-model-timehet reading sources... [ 44%] app/evo-model-with-tree reading sources... [ 44%] app/evo-natsel_neutral reading sources... [ 45%] app/evo-natsel_sitehet reading sources... [ 46%] app/evo-natsel_timehet reading sources... [ 47%] app/evo-natsel_zhang reading sources... [ 48%] app/evo-nstat-codon-model reading sources... [ 48%] app/evo-tr-codon-model reading sources... [ 49%] app/evo-tr-nuc-model reading sources... [ 50%] app/index reading sources... [ 51%] app/not-completed reading sources... [ 52%] app/user_function reading sources... [ 52%] cookbook/DNA_and_RNA_sequences reading sources... [ 53%] cookbook/alignments reading sources... [ 54%] cookbook/alphabet reading sources... [ 55%] cookbook/annotations reading sources... [ 56%] cookbook/building_alignments reading sources... [ 56%] cookbook/building_phylogenies reading sources... [ 57%] cookbook/calc_genetic_distance reading sources... [ 58%] cookbook/evo_modelling reading sources... [ 59%] cookbook/genetic_code reading sources... [ 60%] cookbook/index reading sources... [ 60%] cookbook/loading_sequences reading sources... [ 61%] cookbook/loading_tabular reading sources... [ 62%] cookbook/manipulating_biological_data reading sources... [ 63%] cookbook/moltypes reading sources... [ 64%] cookbook/protein_sequences reading sources... [ 64%] cookbook/simple_trees reading sources... [ 65%] cookbook/tables reading sources... [ 66%] cookbook/useful_utilities reading sources... [ 67%] cookbook/what_codes reading sources... [ 68%] data_file_links reading sources... [ 68%] draw/aln/plot_aln-coevolution reading sources... [ 69%] draw/aln/plot_aln-dotplot-1 reading sources... [ 70%] draw/aln/plot_aln-dotplot-2 reading sources... [ 71%] draw/aln/plot_aln-gaps-per-seq reading sources... [ 72%] draw/aln/plot_aln-info-plot reading sources... [ 72%] draw/aln/plot_aln-seqlogo reading sources... [ 73%] draw/index reading sources... [ 74%] draw/tree/plot_tree-angular reading sources... [ 75%] draw/tree/plot_tree-circular reading sources... [ 76%] draw/tree/plot_tree-radial reading sources... [ 76%] draw/tree/plot_tree-square reading sources... [ 77%] draw/tree/plot_tree-support reading sources... [ 78%] examples/align_codons_to_protein reading sources... [ 79%] examples/calculate_UPGMA_cluster reading sources... [ 80%] examples/calculate_neigbourjoining_tree reading sources... [ 80%] examples/calculate_pairwise_distances reading sources... [ 81%] examples/codon_models reading sources... [ 82%] examples/coevolution reading sources... [ 83%] examples/complete_seq_features reading sources... [ 84%] examples/empirical_protein_models reading sources... [ 84%] examples/hmm_par_heterogeneity reading sources... [ 85%] examples/index reading sources... [ 86%] examples/manipulating_tree_nodes reading sources... [ 87%] examples/neutral_test reading sources... [ 88%] examples/parallel reading sources... [ 88%] examples/parametric_bootstrap reading sources... [ 89%] examples/period_estimation reading sources... [ 90%] examples/phylo_by_ls reading sources... [ 91%] examples/rate_heterogeneity reading sources... [ 92%] examples/relative_rate reading sources... [ 92%] examples/scope_model_params_on_trees reading sources... [ 93%] examples/seq_features reading sources... [ 94%] examples/simple reading sources... [ 95%] examples/simulate_alignment reading sources... [ 96%] examples/testing_multi_loci reading sources... [ 96%] general reading sources... [ 97%] index reading sources... [ 98%] install reading sources... [ 99%] licenses reading sources... [100%] pycogent /<>/doc/../src/cogent3/core/alignment.py:docstring of cogent3.core.alignment.AlignmentI.entropy_per_seq:11: CRITICAL: Unexpected section title. Notes ----- /<>/doc/../src/cogent3/core/alignment.py:docstring of cogent3.core.annotation._Annotatable.add_feature:1: WARNING: Field list ends without a blank line; unexpected unindent. /<>/doc/../src/cogent3/core/alignment.py:docstring of cogent3.core.alignment.AlignmentI.entropy_per_seq:11: CRITICAL: Unexpected section title. Notes ----- /<>/doc/../src/cogent3/core/alignment.py:docstring of cogent3.core.alignment.ArrayAlignment:7: WARNING: Field list ends without a blank line; unexpected unindent. /<>/doc/app/align-codon.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/align-codon.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_unaligned", format="fasta") seqs = loader("data/SCA1-cds.fasta") /<>/doc/app/align-codon.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app codon_aligner = get_app("progressive_align", "codon") aligned = codon_aligner(seqs) aligned /<>/doc/app/align-codon.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: nt_aligner = get_app("progressive_align", "codon", distance="paralinear") aligned = nt_aligner(seqs) aligned /<>/doc/app/align-codon.rst:51: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: 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 /<>/doc/app/align-codon.rst:63: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: codon_aligner = get_app("progressive_align", "codon", guide_tree=tree, indel_rate=0.001, indel_length=0.01 ) aligned = codon_aligner(seqs) aligned /<>/doc/app/align-codon.rst:76: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: codon_aligner = get_app("progressive_align", "CNFHKY", guide_tree=tree, param_vals=dict(omega=0.1, kappa=3) ) aligned = codon_aligner(seqs) aligned /<>/doc/app/align-codon.rst:91: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aligned.info /<>/doc/app/align-nucleotide.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/align-nucleotide.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_unaligned", format="fasta") seqs = loader("data/SCA1-cds.fasta") /<>/doc/app/align-nucleotide.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app nt_aligner = get_app("progressive_align", "nucleotide") aligned = nt_aligner(seqs) aligned /<>/doc/app/align-nucleotide.rst:40: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: nt_aligner = get_app("progressive_align", "nucleotide", distance="TN93") aligned = nt_aligner(seqs) aligned /<>/doc/app/align-nucleotide.rst:49: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: 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 /<>/doc/app/align-nucleotide.rst:63: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: 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 /<>/doc/app/align-nucleotide.rst:73: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aligned.info /<>/doc/app/align-protein.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/align-protein.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: 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") /<>/doc/app/align-protein.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app aa_aligner = get_app("progressive_align", "protein") aligned = aa_aligner(seqs) aligned /<>/doc/app/align-protein.rst:40: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aa_aligner = get_app("progressive_align", "protein", distance="paralinear") aligned = aa_aligner(seqs) aligned /<>/doc/app/align-protein.rst:49: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aligned.info /<>/doc/app/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 /<>/doc/app/app-help.rst:8: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import app_help app_help("omit_degenerates") /<>/doc/app/app-overview.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/app-overview.rst:78: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from pathlib import Path from tempfile import TemporaryDirectory tmpdir = TemporaryDirectory(dir=".") path_to_dir = tmpdir.name /<>/doc/app/app-overview.rst:89: 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") /<>/doc/app/app-overview.rst:102: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data = loader("data/primate_brca1.fasta") just3rd = cpos3(data) m = writer(just3rd) /<>/doc/app/app-overview.rst:117: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: process = loader + cpos3 + writer m = process("data/primate_brca1.fasta") /<>/doc/app/app-overview.rst:127: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore = open_data_store("data", suffix="fasta", mode="r") result = process.apply_to(dstore) /<>/doc/app/app-overview.rst:142: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: out_dstore.summary_logs /<>/doc/app/app-overview.rst:151: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: out_dstore.describe /<>/doc/app/app-overview.rst:157: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: out_dstore.summary_not_completed /<>/doc/app/app-overview.rst:164: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result = process.apply_to(dstore, show_progress=True) /<>/doc/app/available-apps.rst:8: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import available_apps available_apps() /<>/doc/app/dstore.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/dstore.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import open_data_store dstore = open_data_store("data/raw.zip", suffix="fa*", limit=5, mode="r") /<>/doc/app/dstore.rst:38: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: m = dstore[0] m /<>/doc/app/dstore.rst:43: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: m.read()[:20] # truncating /<>/doc/app/dstore.rst:50: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: for m in dstore: print(m) /<>/doc/app/dstore.rst:69: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore = open_data_store("data/demo-locked.sqlitedb") dstore.describe /<>/doc/app/dstore.rst:76: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore.unlock(force=True) /<>/doc/app/dstore.rst:85: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore.summary_logs /<>/doc/app/dstore.rst:91: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore.logs /<>/doc/app/dstore.rst:97: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(dstore.logs[0].read()[:225]) # truncated for clarity /<>/doc/app/evo-ancestral-states.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/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) /<>/doc/app/evo-ancestral-states.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: reconstuctor = get_app("ancestral_states") states_result = reconstuctor(result) states_result /<>/doc/app/evo-ancestral-states.rst:33: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: states_result["edge.0"] /<>/doc/app/evo-ancestral-states.rst:39: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.tree.get_figure(contemporaneous=True).show(width=500, height=500) /<>/doc/app/evo-dt-nuc-model.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/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 /<>/doc/app/evo-dt-nuc-model.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.lf /<>/doc/app/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) /<>/doc/app/evo-dt-nuc-model.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tabulator = get_app("tabulate_stats") stats = tabulator(result) stats /<>/doc/app/evo-dt-nuc-model.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: stats["edge motif motif2 params"] /<>/doc/app/evo-extract-model-stats.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/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) /<>/doc/app/evo-extract-model-stats.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tabulator = get_app("tabulate_stats") tabulated = tabulator(result) tabulated /<>/doc/app/evo-extract-model-stats.rst:38: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tabulated["edge params"] /<>/doc/app/evo-extract-model-stats.rst:49: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tabulated["global params"] /<>/doc/app/evo-extract-model-stats.rst:58: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tabulated["motif params"] /<>/doc/app/evo-hypothesis.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/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) /<>/doc/app/evo-hypothesis.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result /<>/doc/app/evo-hypothesis.rst:40: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.LR, result.df, result.pvalue /<>/doc/app/evo-hypothesis.rst:49: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.null /<>/doc/app/evo-hypothesis.rst:53: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.null.lf /<>/doc/app/evo-hypothesis.rst:60: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.alt.lf /<>/doc/app/evo-model.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/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 /<>/doc/app/evo-model.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: gn = get_app("model", "GN") gn /<>/doc/app/evo-model.rst:32: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted = gn(aln) type(fitted) /<>/doc/app/evo-model.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted /<>/doc/app/evo-model.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.lf /<>/doc/app/evo-model.rst:56: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.lnL, fitted.nfp /<>/doc/app/evo-model.rst:60: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.source /<>/doc/app/evo-model.rst:66: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.tree, fitted.alignment /<>/doc/app/evo-model.rst:72: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.total_length(length_as="paralinear") /<>/doc/app/evo-model.rst:81: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: gn = get_app("model", "GN", split_codons=True) fitted = gn(aln) fitted /<>/doc/app/evo-model.rst:92: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted[3] /<>/doc/app/evo-model-timehet.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/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) /<>/doc/app/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")], ) /<>/doc/app/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) /<>/doc/app/evo-model-timehet.rst:50: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.lf /<>/doc/app/evo-model-with-tree.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/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 /<>/doc/app/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 /<>/doc/app/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 /<>/doc/app/evo-model-with-tree.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted = gn(aln) fitted /<>/doc/app/evo-model-with-tree.rst:51: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.lf /<>/doc/app/evo-natsel_neutral.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/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) /<>/doc/app/evo-natsel_neutral.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result /<>/doc/app/evo-natsel_neutral.rst:32: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.alt.lf /<>/doc/app/evo-natsel_sitehet.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/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 /<>/doc/app/evo-natsel_sitehet.rst:29: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.alt.lf /<>/doc/app/evo-natsel_sitehet.rst:38: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: bprobs = result.alt.lf.get_bin_probs() bprobs[:, :20] /<>/doc/app/evo-natsel_timehet.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/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 /<>/doc/app/evo-natsel_timehet.rst:30: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.alt.lf /<>/doc/app/evo-natsel_zhang.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/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='>/doc/app/evo-natsel_zhang.rst:31: 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") zhang_test = get_app("natsel_zhang", "GNC", tree="data/primate_brca1.tree", optimise_motif_probs=False, tip1="Human", tip2="Chimpanzee", ) result = zhang_test(aln) result /<>/doc/app/evo-natsel_zhang.rst:49: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.alt.lf /<>/doc/app/evo-natsel_zhang.rst:56: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: bprobs = result.alt.lf.get_bin_probs() bprobs[:, :20] /<>/doc/app/evo-natsel_zhang.rst:64: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tab = get_app("tabulate_stats") stats = tab(result.alt) stats /<>/doc/app/evo-natsel_zhang.rst:70: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: stats["edge bin params"][:10] # truncating the table /<>/doc/app/evo-nstat-codon-model.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/evo-nstat-codon-model.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") /<>/doc/app/evo-nstat-codon-model.rst:22: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: model = get_app("model", "GNC", tree="data/primate_brca1.tree") result = model(aln) result /<>/doc/app/evo-nstat-codon-model.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.lf /<>/doc/app/evo-nstat-codon-model.rst:37: 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) /<>/doc/app/evo-tr-codon-model.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/evo-tr-codon-model.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import available_models available_models("codon") /<>/doc/app/evo-tr-codon-model.rst:22: 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", "CNFGTR", tree="data/primate_brca1.tree", optimise_motif_probs=True, ) result = model(aln) result /<>/doc/app/evo-tr-codon-model.rst:36: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.lf /<>/doc/app/evo-tr-nuc-model.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/evo-tr-nuc-model.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import available_models available_models("nucleotide") /<>/doc/app/evo-tr-nuc-model.rst:22: 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", "GTR", tree="data/primate_brca1.tree", optimise_motif_probs=True ) result = model(aln) result /<>/doc/app/evo-tr-nuc-model.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.lf /<>/doc/app/not-completed.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/app/not-completed.rst:24: 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) result /<>/doc/app/not-completed.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result == False result.type result.message /<>/doc/app/not-completed.rst:45: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: result = reader("primate_brca1.fasta") result /<>/doc/app/not-completed.rst:54: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: process = reader + select_seqs result = process("data/primate_brca1.fasta") result /<>/doc/app/not-completed.rst:62: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: result = process("primate_brca1.fasta") result /<>/doc/app/user_function.rst:16: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app.composable import define_app from cogent3.app.typing import AlignedSeqsType @define_app def up_to(val: AlignedSeqsType, index=2) -> AlignedSeqsType: return val[:index] /<>/doc/app/user_function.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: first4 = up_to(index=4) first4 /<>/doc/app/user_function.rst:36: 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 /<>/doc/app/user_function.rst:53: 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 /<>/doc/app/user_function.rst:76: 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="percent") result = percent_dist(aln) result /<>/doc/cookbook/DNA_and_RNA_sequences.rst:20: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA my_seq = DNA.make_seq("AGTACACTGGT") my_seq print(my_seq) str(my_seq) /<>/doc/cookbook/DNA_and_RNA_sequences.rst:32: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import RNA rnaseq = RNA.make_seq("ACGUACGUACGUACGU") /<>/doc/cookbook/DNA_and_RNA_sequences.rst:41: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA my_seq = DNA.make_seq("AGTACACTGGT") print(my_seq.to_fasta()) /<>/doc/cookbook/DNA_and_RNA_sequences.rst:51: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import RNA rnaseq = RNA.make_seq("ACGUACGUACGUACGU") rnaseq.to_fasta() /<>/doc/cookbook/DNA_and_RNA_sequences.rst:63: 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) /<>/doc/cookbook/DNA_and_RNA_sequences.rst:74: 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" print(my_seq.to_fasta()) /<>/doc/cookbook/DNA_and_RNA_sequences.rst:85: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA my_seq = DNA.make_seq("AGTACACTGGT") print(my_seq.complement()) /<>/doc/cookbook/DNA_and_RNA_sequences.rst:95: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(my_seq.rc()) /<>/doc/cookbook/DNA_and_RNA_sequences.rst:101: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(my_seq.rc()) /<>/doc/cookbook/DNA_and_RNA_sequences.rst:110: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA my_seq = DNA.make_seq("GCTTGGGAAAGTCAAATGGAA", "protein-X") pep = my_seq.get_translation() type(pep) print(pep.to_fasta()) /<>/doc/cookbook/DNA_and_RNA_sequences.rst:122: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA my_seq = DNA.make_seq("ACGTACGTACGTACGT") print(my_seq.to_rna()) /<>/doc/cookbook/DNA_and_RNA_sequences.rst:132: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import RNA rnaseq = RNA.make_seq("ACGUACGUACGUACGU") print(rnaseq.to_dna()) /<>/doc/cookbook/DNA_and_RNA_sequences.rst:142: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA a = DNA.make_seq("AGTACACTGGT") a.can_pair(a.complement()) a.can_pair(a.rc()) /<>/doc/cookbook/DNA_and_RNA_sequences.rst:153: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA my_seq = DNA.make_seq("AGTACACTGGT") extra_seq = DNA.make_seq("CTGAC") long_seq = my_seq + extra_seq long_seq str(long_seq) /<>/doc/cookbook/DNA_and_RNA_sequences.rst:166: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: my_seq[1:6] /<>/doc/cookbook/DNA_and_RNA_sequences.rst:177: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA seq = DNA.make_array_seq("ATGATGATGATG") pos3 = seq[2::3] assert str(pos3) == "GGGG" /<>/doc/cookbook/DNA_and_RNA_sequences.rst:190: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA seq = DNA.make_seq("ATGATGATGATG") indices = [(i, i + 2) for i in range(len(seq))[::3]] pos12 = seq.add_feature("pos12", "pos12", indices) pos12 = pos12.get_slice() assert str(pos12) == "ATATATAT" /<>/doc/cookbook/DNA_and_RNA_sequences.rst:211: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import RNA s = RNA.make_seq("--AUUAUGCUAU-UAu--") print(s.degap()) /<>/doc/cookbook/alignments.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/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") print(type(seqs)) seqs = make_unaligned_seqs(dna, moltype="dna") print(type(seqs)) /<>/doc/cookbook/alignments.rst:41: 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)) print(seqs) /<>/doc/cookbook/alignments.rst:53: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_unaligned_seqs seqs = load_unaligned_seqs("data/test.paml") print(seqs) /<>/doc/cookbook/alignments.rst:70: 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", ) print(aln) new_seqs = make_aligned_seqs( [("seq0", "ATG-AGT-AGG"), ("seq4", "ATGCC------")], moltype="dna" ) new_aln = aln.add_seqs(new_seqs) print(new_aln) /<>/doc/cookbook/alignments.rst:92: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: new_aln = aln.add_seqs(new_seqs, before_name="seq2") print(new_aln) new_aln = aln.add_seqs(new_seqs, after_name="seq2") print(new_aln) /<>/doc/cookbook/alignments.rst:104: 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) print(new_aln) /<>/doc/cookbook/alignments.rst:126: 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") print(new_aln) /<>/doc/cookbook/alignments.rst:145: 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() /<>/doc/cookbook/alignments.rst:161: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq = aln.get_gapped_seq("seq1") seq.is_gapped() print(seq) /<>/doc/cookbook/alignments.rst:169: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln.names aln.names /<>/doc/cookbook/alignments.rst:179: 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] str(my_seq[:24]) type(my_seq) aln = load_aligned_seqs(fn, moltype="dna") aln.seqs[0][:24] print(aln.seqs[0][:24]) /<>/doc/cookbook/alignments.rst:196: 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 new = aln.take_seqs(["Human", "HowlerMon"]) new.names /<>/doc/cookbook/alignments.rst:207: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/test.paml", array_align=False, moltype="dna") seq = aln.get_seq("Human") new = aln.take_seqs(["Human", "HowlerMon"]) id(new.get_seq("Human")) == id(aln.get_seq("Human")) /<>/doc/cookbook/alignments.rst:222: 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") aln = Alignment(seq) fasta_1 = seq fasta_2 = aln assert fasta_1 == fasta_2 /<>/doc/cookbook/alignments.rst:238: 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 /<>/doc/cookbook/alignments.rst:249: 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 /<>/doc/cookbook/alignments.rst:260: 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 /<>/doc/cookbook/alignments.rst:277: 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)) /<>/doc/cookbook/alignments.rst:292: 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") /<>/doc/cookbook/alignments.rst:302: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln.write("sample", format="fasta") /<>/doc/cookbook/alignments.rst:308: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.io import remove_files remove_files(["sample", "sample.fasta"], error_on_missing=False) /<>/doc/cookbook/alignments.rst:317: 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 /<>/doc/cookbook/alignments.rst:329: 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) /<>/doc/cookbook/alignments.rst:342: 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() /<>/doc/cookbook/alignments.rst:359: 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") print(aln[:24]) /<>/doc/cookbook/alignments.rst:369: 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) print(seqs[:24]) /<>/doc/cookbook/alignments.rst:381: 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] /<>/doc/cookbook/alignments.rst:391: 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] /<>/doc/cookbook/alignments.rst:401: 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) /<>/doc/cookbook/alignments.rst:415: 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 pos3 = aln.add_feature("pos3", "pos3", indices) pos3 = pos3.get_slice() print(pos3) /<>/doc/cookbook/alignments.rst:434: 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] print(pos3) /<>/doc/cookbook/alignments.rst:454: 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() print(new) /<>/doc/cookbook/alignments.rst:467: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = make_aligned_seqs( data={ "seq1": "ACGTAA---", "seq2": "ACGAC----", # terminal codon incomplete "seq3": "ACGCAATGA", }, moltype="dna", ) new = aln.trim_stop_codons(allow_partial=True) print(new) /<>/doc/cookbook/alignments.rst:485: 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", ) /<>/doc/cookbook/alignments.rst:500: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: nucs = aln.no_degenerates() print(nucs) /<>/doc/cookbook/alignments.rst:507: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: trinucs = aln.no_degenerates(motif_length=3) print(trinucs) /<>/doc/cookbook/alignments.rst:515: 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) print(just_variable_aln[:10]) /<>/doc/cookbook/alignments.rst:527: 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) print(just_constant_aln[:10]) /<>/doc/cookbook/alignments.rst:541: 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 ) print(just_variable_aln[:9]) /<>/doc/cookbook/alignments.rst:553: 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) print(just_variable_aln[:9]) /<>/doc/cookbook/alignments.rst:567: 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"]) /<>/doc/cookbook/alignments.rst:576: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln.take_seqs(["Human", "Mouse"], negate=True) /<>/doc/cookbook/alignments.rst:585: 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) /<>/doc/cookbook/alignments.rst:605: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln.take_seqs_if(no_N_chars, negate=True) /<>/doc/cookbook/alignments.rst:617: 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() print(counts) counts = aln.counts(motif_length=3) print(counts) counts = aln.counts(include_ambiguity=True) print(counts) /<>/doc/cookbook/alignments.rst:645: 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() print(motif_probs) /<>/doc/cookbook/alignments.rst:655: 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])) /<>/doc/cookbook/alignments.rst:669: 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 /<>/doc/cookbook/alignments.rst:681: 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 /<>/doc/cookbook/alignments.rst:691: 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") /<>/doc/cookbook/alignments.rst:702: 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]) /<>/doc/cookbook/alignments.rst:717: 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)) /<>/doc/cookbook/alignments.rst:731: 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) /<>/doc/cookbook/alignments.rst:746: 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] /<>/doc/cookbook/alignments.rst:762: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq_to_aln_map[3] seq_to_aln_map[8] /<>/doc/cookbook/alignments.rst:771: 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] /<>/doc/cookbook/alignments.rst:779: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: KeyError seq_pos = aln_to_seq_map[7] /<>/doc/cookbook/alignments.rst:793: 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", ) print(aln.omit_gap_runs(2)) /<>/doc/cookbook/alignments.rst:807: 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", ) print(aln.omit_gap_pos(0.40)) /<>/doc/cookbook/alignments.rst:821: 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) print(filtered_aln) /<>/doc/cookbook/alignments.rst:836: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(filtered_aln.omit_gap_pos()) /<>/doc/cookbook/alphabet.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA, PROTEIN print(DNA.alphabet) print(PROTEIN.alphabet) /<>/doc/cookbook/alphabet.rst:20: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: PROTEIN.alphabet.moltype == PROTEIN /<>/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) /<>/doc/cookbook/alphabet.rst:39: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq = "TAGT" indices = DNA.alphabet.to_indices(seq) indices /<>/doc/cookbook/alphabet.rst:48: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq = DNA.alphabet.from_indices([0, 2, 3, 0]) seq /<>/doc/cookbook/alphabet.rst:55: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq = DNA.alphabet.from_ordinals_to_seq([0, 2, 3, 0]) seq /<>/doc/cookbook/annotations.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/cookbook/annotations.rst:21: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.genbank import RichGenbankParser parser = RichGenbankParser(open("data/ST_genome_part.gb")) for accession, seq in parser: print(accession) /<>/doc/cookbook/annotations.rst:29: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: cds = seq.get_annotations_matching("CDS") print(cds) /<>/doc/cookbook/annotations.rst:39: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.core.annotation import Feature def add_annotation(seq, feature, spans): type_ = feature["type"] if type_ != "CDS": return name = feature.get("locus_tag", None) if name and not isinstance(name, str): name = " ".join(name) seq.add_annotation(Feature, type_, name, spans) parser = RichGenbankParser( open("data/ST_genome_part.gb"), add_annotation=add_annotation ) for accession, seq in parser: # just reading one accession,sequence break genes = seq.get_annotations_matching("CDS") print(genes) /<>/doc/cookbook/annotations.rst:63: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA from cogent3.core.annotation import Feature s1 = DNA.make_seq( "AAGAAGAAGACCCCCAAAAAAAAAA" "TTTTTTTTTTAAAAAGGGAACCCT", name="seq1" ) print(s1[10:15]) # this will be exon 1 print(s1[30:40]) # this will be exon 2 print(s1[45:48]) # this will be exon 3 s2 = DNA.make_seq("CGAAACGTTT", name="seq2") s3 = DNA.make_seq("CGAAACGTTT", name="seq3") /<>/doc/cookbook/annotations.rst:83: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA from cogent3.core.annotation import Feature s1 = DNA.make_seq( "AAGAAGAAGACCCCCAAAAAAAAAA" "TTTTTTTTTTAAAAAGGGAACCCT", name="seq1" ) exon1 = s1.add_annotation(Feature, "exon", "A", [(10, 15)]) exon2 = s1.add_annotation(Feature, "exon", "B", [(30, 40)]) /<>/doc/cookbook/annotations.rst:97: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA s1 = DNA.make_seq( "AAGAAGAAGACCCCCAAAAAAAAAA" "TTTTTTTTTTAAAAAGGGAACCCT", name="seq1" ) exon3 = s1.add_feature("exon", "C", [(45, 48)]) /<>/doc/cookbook/annotations.rst:111: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA s2 = DNA.make_seq("CGAAACGTTT", name="seq2") cpgs_series = s2.add_feature("cpgsite", "cpg", [(0, 2), (5, 7)]) s3 = DNA.make_seq("CGAAACGTTT", name="seq3") cpg1 = s3.add_feature("cpgsite", "cpg", [(0, 2)]) cpg2 = s3.add_feature("cpgsite", "cpg", [(5, 7)]) /<>/doc/cookbook/annotations.rst:126: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA s1 = DNA.make_seq( "AAGAAGAAGACCCCCAAAAAAAAAA" "TTTTTTTTTTAAAAAGGGAACCCT", name="seq1" ) exon1 = s1.add_feature("exon", "A", [(10, 15)]) exon2 = s1.add_feature("exon", "B", [(30, 40)]) exon3 = s1.add_feature("exon", "C", [(45, 48)]) cds = s1.get_region_covering_all([exon1, exon2, exon3]) /<>/doc/cookbook/annotations.rst:143: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: cds.get_coordinates() /<>/doc/cookbook/annotations.rst:152: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: not_cds = cds.get_shadow() not_cds /<>/doc/cookbook/annotations.rst:159: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: cds /<>/doc/cookbook/annotations.rst:168: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln1 = make_aligned_seqs( data=[["x", "-AAACCCCCA"], ["y", "TTTT--TTTT"]], array_align=False ) seq_exon = aln1.get_seq("x").add_feature("exon", "A", [(3, 8)]) /<>/doc/cookbook/annotations.rst:182: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.core.annotation import Variable red_data = aln1.add_annotation( Variable, "redline", "align", [((0, 15), 1), ((15, 30), 2), ((30, 45), 3)] ) /<>/doc/cookbook/annotations.rst:195: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA s1 = DNA.make_seq( "AAGAAGAAGACCCCCAAAAAAAAAA" "TTTTTTTTTTAAAAAGGGAACCCT", name="seq1" ) exon1 = s1.add_feature("exon", "A", [(10, 15)]) exon2 = s1.add_feature("exon", "B", [(30, 40)]) s1[exon1] s1[10:15] /<>/doc/cookbook/annotations.rst:209: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: s1[exon2] exon2.get_slice() /<>/doc/cookbook/annotations.rst:217: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA s1 = DNA.make_seq( "AAGAAGAAGACCCCCAAAAAAAAAA" "TTTTTTTTTTAAAAAGGGAACCCT", name="seq1" ) exon1 = s1.add_feature("exon", "A", [(10, 15)]) exon2 = s1.add_feature("exon", "B", [(30, 40)]) exon3 = s1.add_feature("exon", "C", [(45, 48)]) cds = s1.get_region_covering_all([exon1, exon2, exon3]) print(s1[cds]) print(s1[exon1, exon2, exon3]) /<>/doc/cookbook/annotations.rst:233: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(s1) print(s1[exon1, exon2, exon3]) print(s1[exon2]) print(s1[exon3]) print(s1[exon1, exon3, exon2]) /<>/doc/cookbook/annotations.rst:244: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: ValueError s1[1:10, 9:15] s1[exon1, exon1] /<>/doc/cookbook/annotations.rst:252: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(s1.get_region_covering_all([exon3, exon3]).get_slice()) /<>/doc/cookbook/annotations.rst:259: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(s1[exon2]) ex2_start = exon2[0:3] print(s1[ex2_start]) ex2_end = exon2[-3:] print(s1[ex2_end]) /<>/doc/cookbook/annotations.rst:272: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: ValueError aln1[seq_exon] /<>/doc/cookbook/annotations.rst:282: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln2 = make_aligned_seqs( data=[["x", "-AAAAAAAAA"], ["y", "TTTT--TTTT"]], array_align=False ) seq = DNA.make_seq("CCCCCCCCCCCCCCCCCCCC", "x") match_exon = seq.add_feature("exon", "A", [(3, 8)]) aln2.get_seq("x").copy_annotations(seq) copied = list(aln2.get_annotations_from_seq("x", "exon")) copied /<>/doc/cookbook/annotations.rst:295: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln2 = make_aligned_seqs(data=[["x", "-AAAA"], ["y", "TTTTT"]], array_align=False) seq = DNA.make_seq("CCCCCCCCCCCCCCCCCCCC", "x") match_exon = seq.add_feature("exon", "A", [(5, 8)]) aln2.get_seq("x").copy_annotations(seq) copied = list(aln2.get_annotations_from_seq("x", "exon")) copied copied[0].get_slice() /<>/doc/cookbook/annotations.rst:307: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: # new test aln2 = make_aligned_seqs( data=[["x", "-AAAAAAAAA"], ["y", "TTTT--TTTT"]], array_align=False ) seq = DNA.make_seq("CCCCCCCCCCCCCCCCCCCC", "x") match_exon = seq.add_feature("exon", "A", [(5, 8)]) aln2.get_seq("y").copy_annotations(seq) copied = list(aln2.get_annotations_from_seq("y", "exon")) copied /<>/doc/cookbook/annotations.rst:321: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln2 = make_aligned_seqs( data=[["x", "-AAAAAAAAA"], ["y", "TTTT--TTTT"]], array_align=False ) diff_len_seq = DNA.make_seq("CCCCCCCCCCCCCCCCCCCCCCCCCCCC", "x") nonmatch = diff_len_seq.add_feature("repeat", "A", [(12, 14)]) aln2.get_seq("y").copy_annotations(diff_len_seq) copied = list(aln2.get_annotations_from_seq("y", "repeat")) copied /<>/doc/cookbook/annotations.rst:337: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln_exon = aln1.get_annotations_from_any_seq("exon") print(aln1[aln_exon]) /<>/doc/cookbook/annotations.rst:345: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: ValueError cpgsite2 = s2.get_annotations_matching("cpgsite") print(s2[cpgsite2]) cpgsite3 = s3.get_annotations_matching("cpgsite") s2[cpgsite3] /<>/doc/cookbook/annotations.rst:358: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: # this test is new dont_exist = s2.get_annotations_matching("dont_exist") dont_exist s2[dont_exist] /<>/doc/cookbook/annotations.rst:370: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln3 = make_aligned_seqs( data=[["x", "C-CCCAAAAA"], ["y", "-T----TTTT"]], array_align=False ) exon = aln3.get_seq("x").add_feature("exon", "ex1", [(0, 4)]) print(exon.get_slice()) aln_exons = list(aln3.get_annotations_from_seq("x", "exon")) print(aln_exons) print(aln3[aln_exons]) /<>/doc/cookbook/annotations.rst:388: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: unified = aln_exons[0].as_one_span() print(aln3[unified]) /<>/doc/cookbook/annotations.rst:398: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: plus = DNA.make_seq("CCCCCAAAAAAAAAATTTTTTTTTTAAAGG") plus_rpt = plus.add_feature("blah", "a", [(5, 15), (25, 28)]) print(plus[plus_rpt]) minus = plus.rc() print(minus) minus_rpt = minus.get_annotations_matching("blah") print(minus[minus_rpt]) /<>/doc/cookbook/annotations.rst:413: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.genbank import RichGenbankParser parser = RichGenbankParser(open("data/ST_genome_part.gb")) seq = [seq for accession, seq in parser][0] no_cds = seq.with_masked_annotations("CDS") print(no_cds[150:400]) /<>/doc/cookbook/annotations.rst:429: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: 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.get_seq("x").add_feature("exon", "norwegian", [(0, 4)]) print(aln.with_masked_annotations("exon", mask_char="?")) /<>/doc/cookbook/annotations.rst:443: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: rc = aln.rc() print(rc) print(rc.with_masked_annotations("exon", mask_char="?")) /<>/doc/cookbook/annotations.rst:452: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA s = DNA.make_seq("CCCCAAAAAGGGAA", "x") exon = s.add_feature("exon", "norwegian", [(0, 4)]) rpt = s.add_feature("repeat", "norwegian", [(9, 12)]) rc = s.rc() print(s.with_masked_annotations("exon", shadow=True)) print(rc.with_masked_annotations("exon", shadow=True)) print(s.with_masked_annotations(["exon", "repeat"], shadow=True)) print(rc.with_masked_annotations(["exon", "repeat"], shadow=True)) /<>/doc/cookbook/annotations.rst:468: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA s = DNA.make_seq("ATGACCCTGTAAAAAATGTGTTAACCC", name="a") cds1 = s.add_feature("cds", "cds1", [(0, 12)]) cds2 = s.add_feature("cds", "cds2", [(15, 24)]) all_cds = s.get_annotations_matching("cds") all_cds /<>/doc/cookbook/annotations.rst:483: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.genbank import RichGenbankParser parser = RichGenbankParser(open("data/ST_genome_part.gb")) seq = [seq for accession, seq in parser][0] all_cds = seq.get_annotations_matching("CDS") coding_seqs = seq.get_region_covering_all(all_cds) coding_seqs coding_seqs.get_slice() noncoding_seqs = coding_seqs.get_shadow() noncoding_seqs noncoding_seqs.get_slice() /<>/doc/cookbook/annotations.rst:502: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data=[["x", "-AAAAAAAAA"], ["y", "TTTT--TTTT"]], array_align=False ) print(aln) exon = aln.get_seq("x").add_feature("exon", "1", [(3, 8)]) aln_exons = aln.get_annotations_from_seq("x", "exon") aln_exons = aln.get_annotations_from_any_seq("exon") aln_exons /<>/doc/cookbook/annotations.rst:522: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA seq = DNA.make_seq("aaaccggttt" * 10) v = seq.add_feature("exon", "exon", [(20, 35)]) v = seq.add_feature("repeat_unit", "repeat_unit", [(39, 49)]) v = seq.add_feature("repeat_unit", "rep2", [(49, 60)]) /<>/doc/cookbook/annotations.rst:536: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from cogent3.util.io import remove_files remove_files(["annotated_%d.png" % i for i in range(1, 4)], error_on_missing=False) /<>/doc/cookbook/building_alignments.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/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 TreeAlign /<>/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 = TreeAlign("HKY85", seqs, show_progress=False) aln /<>/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 = TreeAlign( "HKY85", seqs, tree=tree, param_vals=params, show_progress=False ) aln /<>/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 TreeAlign 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 = TreeAlign( "MG94HKY", seqs, tree=tree, param_vals=params, show_progress=False ) aln /<>/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 TreeAlign from cogent3.evolve.models import get_model seqs = [ ( "hum", "AAGCAGATCCAGGAAAGCAGCGAGAATGGCAGCCTGGCCGCGCGCCAGGAGAGGCAGGCCCAGGTCAACCTCACT", ), ( "mus", "AAGCAGATCCAGGAGAGCGGCGAGAGCGGCAGCCTGGCCGCGCGGCAGGAGAGGCAGGCCCAAGTCAACCTCACG", ), ("rat", "CTGAACAAGCAGCCACTTTCAAACAAGAAA"), ] unaligned_DNA = make_unaligned_seqs(seqs, moltype="dna") print(unaligned_DNA) /<>/doc/cookbook/building_alignments.rst:88: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(unaligned_DNA.get_translation()) /<>/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") /<>/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 /<>/doc/cookbook/building_phylogenies.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/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()) /<>/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) /<>/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()) /<>/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()) /<>/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()) /<>/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) /<>/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) /<>/doc/cookbook/calc_genetic_distance.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/cookbook/calc_genetic_distance.rst:16: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import available_distances available_distances() /<>/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 /<>/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 /<>/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 /<>/doc/cookbook/calc_genetic_distance.rst:54: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dist_calc.stderr /<>/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 /<>/doc/cookbook/evo_modelling.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/cookbook/evo_modelling.rst:18: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import available_models available_models() /<>/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) /<>/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) /<>/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) /<>/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) /<>/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) /<>/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) /<>/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()) /<>/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, ) /<>/doc/cookbook/evo_modelling.rst:134: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf /<>/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) /<>/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) /<>/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) /<>/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) /<>/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) /<>/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) /<>/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) /<>/doc/cookbook/evo_modelling.rst:253: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(local=True, max_restarts=5, show_progress=False) /<>/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) /<>/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) /<>/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) /<>/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 /<>/doc/cookbook/evo_modelling.rst:321: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lnL = lf.lnL lnL /<>/doc/cookbook/evo_modelling.rst:326: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: nfp = lf.nfp nfp /<>/doc/cookbook/evo_modelling.rst:338: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.get_aic() /<>/doc/cookbook/evo_modelling.rst:344: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.get_aic(second_order=True) /<>/doc/cookbook/evo_modelling.rst:353: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.get_bic() /<>/doc/cookbook/evo_modelling.rst:367: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: a_g = lf.get_param_value("A/G") a_g /<>/doc/cookbook/evo_modelling.rst:372: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: human = lf.get_param_value("length", "Human") human /<>/doc/cookbook/evo_modelling.rst:380: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: mprobs = lf.get_motif_probs() mprobs /<>/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 /<>/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 /<>/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 /<>/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}") /<>/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] /<>/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}") /<>/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 /<>/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 /<>/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) /<>/doc/cookbook/evo_modelling.rst:542: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: ancestors = lf.likely_ancestral_seqs() ancestors[:60] /<>/doc/cookbook/evo_modelling.rst:549: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: ancestral_probs = lf.reconstruct_ancestral_seqs() ancestral_probs["root"][:5] /<>/doc/cookbook/genetic_code.rst:4: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code standard_code = get_code(1) standard_code.translate("TTTGCAAAC") /<>/doc/cookbook/genetic_code.rst:16: 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) /<>/doc/cookbook/genetic_code.rst:28: 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 stop_index = stops_frame1[0] seq[stop_index : stop_index + 3] /<>/doc/cookbook/genetic_code.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code, make_seq standard_code = get_code(1) standard_code["TTT"] /<>/doc/cookbook/genetic_code.rst:51: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: standard_code["A"] /<>/doc/cookbook/genetic_code.rst:58: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code standard_code = get_code(1) standard_code["TTT"] /<>/doc/cookbook/genetic_code.rst:68: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code standard_code = get_code(1) standard_code["A"] /<>/doc/cookbook/genetic_code.rst:78: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: targets = ["A", "C"] codons = [standard_code[aa] for aa in targets] codons flat_list = sum(codons, []) flat_list /<>/doc/cookbook/genetic_code.rst:89: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("AGTACACTGGTT", moltype="dna") sorted(my_seq.codon_alphabet()) len(my_seq.codon_alphabet()) /<>/doc/cookbook/genetic_code.rst:102: 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) print(codons) /<>/doc/cookbook/genetic_code.rst:115: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from cogent3.core.alphabet import AlphabetError /<>/doc/cookbook/genetic_code.rst:120: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: AlphabetError pep = my_seq.get_translation() /<>/doc/cookbook/genetic_code.rst:128: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("ATGCACTGGTAA", name="my_gene", moltype="dna") seq = my_seq.trim_stop_codon() pep = seq.get_translation() print(pep.to_fasta()) print(type(pep)) /<>/doc/cookbook/genetic_code.rst:141: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("CAAATGTATTAA", name="my_gene", moltype="dna") pep = my_seq[:-3].get_translation() print(pep.to_fasta()) /<>/doc/cookbook/loading_sequences.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/cookbook/loading_sequences.rst:16: 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) /<>/doc/cookbook/loading_sequences.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln.info.source /<>/doc/cookbook/loading_sequences.rst:38: 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) /<>/doc/cookbook/loading_sequences.rst:51: 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") /<>/doc/cookbook/loading_sequences.rst:63: 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 /<>/doc/cookbook/loading_sequences.rst:75: 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 print(proteins_loaded) proteins_loaded = make_aligned_seqs(protein_seqs, moltype="protein") print(proteins_loaded) /<>/doc/cookbook/loading_sequences.rst:94: 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) /<>/doc/cookbook/loading_sequences.rst:104: 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) print(seqs_loaded) /<>/doc/cookbook/loading_sequences.rst:117: 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 /<>/doc/cookbook/loading_sequences.rst:137: 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 /<>/doc/cookbook/loading_sequences.rst:157: 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 /<>/doc/cookbook/loading_sequences.rst:170: 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)) /<>/doc/cookbook/loading_sequences.rst:186: 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) /<>/doc/cookbook/loading_tabular.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/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 /<>/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") /<>/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 /<>/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] /<>/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] /<>/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 /<>/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 /<>/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 /<>/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 /<>/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 /<>/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")) /<>/doc/cookbook/loading_tabular.rst:152: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data[:2] /<>/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 /<>/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 /<>/doc/cookbook/loading_tabular.rst:186: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = make_table(header=["C", "A", "B"], data=data) table /<>/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"] /<>/doc/cookbook/loading_tabular.rst:201: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table["NP_055852", "Region"] /<>/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 /<>/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 /<>/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 /<>/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 /<>/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 /<>/doc/cookbook/loading_tabular.rst:294: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table() table /<>/doc/cookbook/moltypes.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/cookbook/moltypes.rst:17: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import available_moltypes available_moltypes() /<>/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") /<>/doc/cookbook/moltypes.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_moltype dna = get_moltype("dna") dna /<>/doc/cookbook/moltypes.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dna.ambiguities /<>/doc/cookbook/moltypes.rst:53: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dna.degenerates /<>/doc/cookbook/moltypes.rst:60: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dna.complement("AGG") /<>/doc/cookbook/moltypes.rst:69: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq = dna.make_seq("AGGCTT", name="seq1") seq /<>/doc/cookbook/moltypes.rst:77: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: rna = get_moltype("rna") rna.is_valid("ACGUACGUACGUACGU") /<>/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 /<>/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 /<>/doc/cookbook/protein_sequences.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/cookbook/protein_sequences.rst:14: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import PROTEIN p = PROTEIN.make_seq("THISISAPRQTEIN", "myProtein") type(p) str(p) /<>/doc/cookbook/protein_sequences.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.core.genetic_code import DEFAULT as standard_code standard_code.translate("TTTGCAAAC") /<>/doc/cookbook/protein_sequences.rst:36: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs seq = load_aligned_seqs("data/abglobin_aa.phylip", moltype="protein") /<>/doc/cookbook/simple_trees.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/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()) /<>/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") /<>/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] /<>/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"] /<>/doc/cookbook/simple_trees.rst:48: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tr.get_node_matching_name("Mouse") /<>/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 /<>/doc/cookbook/simple_trees.rst:63: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: hu.name /<>/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) /<>/doc/cookbook/simple_trees.rst:79: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: type(tr) /<>/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) /<>/doc/cookbook/simple_trees.rst:99: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: for n in tr.iter_tips(): print(n) /<>/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()) /<>/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) /<>/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() /<>/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 /<>/doc/cookbook/simple_trees.rst:154: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: type(lca) /<>/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) /<>/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) /<>/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() /<>/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]) /<>/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() /<>/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) /<>/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()) /<>/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()) /<>/doc/cookbook/simple_trees.rst:247: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(tr.ascii_art()) /<>/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()) /<>/doc/cookbook/simple_trees.rst:261: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(tr.rooted_with_tip("Mouse").ascii_art()) /<>/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() /<>/doc/cookbook/simple_trees.rst:278: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tr.get_newick(with_distances=True) /<>/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) /<>/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()) /<>/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()) /<>/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()) /<>/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()) /<>/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) /<>/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()) /<>/doc/cookbook/simple_trees.rst:372: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: simple_tree.prune() print(simple_tree.ascii_art()) /<>/doc/cookbook/simple_trees.rst:377: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(simple_tree) /<>/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()) /<>/doc/cookbook/simple_trees.rst:391: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tr2 = tr1.unrooted_deepcopy() print(tr2.get_newick()) /<>/doc/cookbook/simple_trees.rst:401: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_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()) /<>/doc/cookbook/simple_trees.rst:409: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(tr.bifurcating().ascii_art()) /<>/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()) /<>/doc/cookbook/simple_trees.rst:429: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(tr.balanced().ascii_art()) /<>/doc/cookbook/simple_trees.rst:438: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_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) /<>/doc/cookbook/simple_trees.rst:452: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = make_tree("(B:0.2,(C:0.3,D:0.4)F:0.5)G;") print(tr.ascii_art()) /<>/doc/cookbook/simple_trees.rst:459: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tr.set_tip_distances() for t in tr.preorder(): print(t.name, t.TipDistance) /<>/doc/cookbook/simple_trees.rst:468: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = make_tree("(B:0.2,(C:0.3,D:0.4)F:0.5)G;") print(tr) /<>/doc/cookbook/simple_trees.rst:475: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tr.scale_branch_lengths() print(tr) /<>/doc/cookbook/simple_trees.rst:485: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_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]) /<>/doc/cookbook/simple_trees.rst:505: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_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) /<>/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 /<>/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 /<>/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 /<>/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 /<>/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 /<>/doc/cookbook/tables.rst:68: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: for row in table: print(row["Locus"]) /<>/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 /<>/doc/cookbook/tables.rst:91: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.shape[1] == 2 /<>/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 /<>/doc/cookbook/tables.rst:107: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.columns["Region"] /<>/doc/cookbook/tables.rst:113: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: for name in table.columns: print(name) /<>/doc/cookbook/tables.rst:121: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table /<>/doc/cookbook/tables.rst:128: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table[:2, "Region":] /<>/doc/cookbook/tables.rst:135: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table[:2, :1] /<>/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 /<>/doc/cookbook/tables.rst:158: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv", digits=1, space=2) table /<>/doc/cookbook/tables.rst:165: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.space = " " table /<>/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 /<>/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 /<>/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() /<>/doc/cookbook/tables.rst:199: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.head(2) /<>/doc/cookbook/tables.rst:208: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.tail() /<>/doc/cookbook/tables.rst:214: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.tail(1) /<>/doc/cookbook/tables.rst:221: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.set_repr_policy(random=3) table /<>/doc/cookbook/tables.rst:229: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.set_repr_policy(head=2, tail=3) table /<>/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) /<>/doc/cookbook/tables.rst:251: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table() table /<>/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 /<>/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 /<>/doc/cookbook/tables.rst:282: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table.array /<>/doc/cookbook/tables.rst:292: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") locus = table.tolist("Locus") locus /<>/doc/cookbook/tables.rst:300: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.columns["Locus"].tolist() /<>/doc/cookbook/tables.rst:309: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") rows = table.tolist(["Region", "Locus"]) rows /<>/doc/cookbook/tables.rst:322: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table.to_dict() /<>/doc/cookbook/tables.rst:332: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table.columns.to_dict() /<>/doc/cookbook/tables.rst:340: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") df = table.to_dataframe() df /<>/doc/cookbook/tables.rst:348: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: df = table.to_dataframe(categories="Region") /<>/doc/cookbook/tables.rst:357: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = make_table(data={"Ts": [31, 58], "Tv": [36, 138], "": ["syn", "nsyn"]}, index_name="") table /<>/doc/cookbook/tables.rst:362: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: contingency = table.to_categorical(["Ts", "Tv"]) contingency /<>/doc/cookbook/tables.rst:367: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: g_test = contingency.G_independence() g_test /<>/doc/cookbook/tables.rst:374: 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="") /<>/doc/cookbook/tables.rst:386: 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 /<>/doc/cookbook/tables.rst:395: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table1.title = "Data1" table2.title = "Data2" table = table1.appended("Data#", table2, title="") table /<>/doc/cookbook/tables.rst:407: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table.summed("Ratio") /<>/doc/cookbook/tables.rst:414: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.columns["Ratio"].sum() /<>/doc/cookbook/tables.rst:423: 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 /<>/doc/cookbook/tables.rst:434: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: all_numeric.summed() /<>/doc/cookbook/tables.rst:440: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: all_numeric.summed(col_sum=False) /<>/doc/cookbook/tables.rst:449: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: mixed = make_table( header=["A", "B", "C"], data=[["*", 1, 2], [3, "*", 5], [6, 7, "*"]] ) mixed /<>/doc/cookbook/tables.rst:458: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: mixed.summed(strict=False) /<>/doc/cookbook/tables.rst:464: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: mixed.summed(col_sum=False, strict=False) /<>/doc/cookbook/tables.rst:473: 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 /<>/doc/cookbook/tables.rst:481: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: sub_table = table.filtered("Ratio < 10.0") sub_table /<>/doc/cookbook/tables.rst:488: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: sub_table = table.filtered("Ratio < 10.0 and Region == 'NonCon'") sub_table /<>/doc/cookbook/tables.rst:498: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: big_numeric = all_numeric.filtered_by_column(lambda x: sum(x) > 20) big_numeric /<>/doc/cookbook/tables.rst:506: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table.sorted(columns="Ratio") /<>/doc/cookbook/tables.rst:514: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.sorted(columns="Ratio", reverse="Ratio") /<>/doc/cookbook/tables.rst:521: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.sorted(columns=["Region", "Ratio"], reverse="Ratio") /<>/doc/cookbook/tables.rst:528: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") raw = table.tolist("Region") raw /<>/doc/cookbook/tables.rst:537: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") raw = table.tolist(["Locus", "Region"]) raw /<>/doc/cookbook/tables.rst:546: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") assert table.distinct_values("Region") == set(["NonCon", "Con"]) /<>/doc/cookbook/tables.rst:554: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") assert table.count("Region == 'NonCon' and Ratio > 1") == 1 /<>/doc/cookbook/tables.rst:564: 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) /<>/doc/cookbook/tables.rst:574: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: unique /<>/doc/cookbook/tables.rst:580: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: unique = table.count_unique(["A", "B"]) unique /<>/doc/cookbook/tables.rst:585: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: r = unique.to_table() r /<>/doc/cookbook/tables.rst:595: 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 /<>/doc/cookbook/tables.rst:615: 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 /<>/doc/cookbook/tables.rst:631: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tp = table.transposed(new_column_name="sample", select_as_header="#OTU ID") tp /<>/doc/cookbook/tables.rst:641: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv", format="md") print(table) /<>/doc/cookbook/tables.rst:653: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv", format="tex") print(table) /<>/doc/cookbook/tables.rst:665: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") print(table.to_markdown(justify="ccr")) /<>/doc/cookbook/tables.rst:673: 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")) /<>/doc/cookbook/tables.rst:683: 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)) /<>/doc/cookbook/tables.rst:693: 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()) /<>/doc/cookbook/tables.rst:705: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") print(table.to_string(format="latex")) /<>/doc/cookbook/tables.rst:715: 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) /<>/doc/cookbook/tables.rst:754: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: bgraph.head() /<>/doc/cookbook/tables.rst:760: 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, ) ) /<>/doc/cookbook/tables.rst:775: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv") straight_html = table.to_html() /<>/doc/cookbook/tables.rst:787: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.format.table import known_formats known_formats /<>/doc/cookbook/tables.rst:796: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.write("stats_tab.tex", justify="ccr", label="tab:table1") /<>/doc/cookbook/tables.rst:805: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table.write("stats_tab.txt", sep="\t") /<>/doc/cookbook/tables.rst:812: 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() 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 /<>/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) /<>/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) /<>/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) /<>/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) /<>/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) /<>/doc/cookbook/useful_utilities.rst:100: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: is_iterable(cannot_iter) /<>/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") /<>/doc/cookbook/useful_utilities.rst:118: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: is_char("ab") /<>/doc/cookbook/useful_utilities.rst:122: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: is_char(foo()) /<>/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]] /<>/doc/cookbook/useful_utilities.rst:137: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: recursive_flatten(l) /<>/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) /<>/doc/cookbook/useful_utilities.rst:152: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: not_list_tuple([1]) /<>/doc/cookbook/useful_utilities.rst:156: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: not_list_tuple("ab") /<>/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) /<>/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) /<>/doc/cookbook/useful_utilities.rst:187: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: f(1, 2) /<>/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 /<>/doc/cookbook/useful_utilities.rst:217: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: no in cc /<>/doc/cookbook/useful_utilities.rst:221: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: 5 in cc /<>/doc/cookbook/useful_utilities.rst:225: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: {"a": 5} in cc /<>/doc/cookbook/useful_utilities.rst:229: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: "asasas" in cc /<>/doc/cookbook/useful_utilities.rst:233: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: md in cc /<>/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) /<>/doc/cookbook/useful_utilities.rst:255: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: ls[0] /<>/doc/cookbook/useful_utilities.rst:259: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: ls.upper() /<>/doc/cookbook/useful_utilities.rst:263: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: ls.split("_") /<>/doc/cookbook/useful_utilities.rst:272: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import FunctionWrapper f = FunctionWrapper(str) f /<>/doc/cookbook/useful_utilities.rst:279: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: f(123) /<>/doc/cookbook/useful_utilities.rst:290: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from cogent3.util.misc import ConstraintError /<>/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 /<>/doc/cookbook/useful_utilities.rst:302: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: ConstraintError d["d"] = 5 /<>/doc/cookbook/what_codes.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/cookbook/what_codes.rst:10: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import available_codes available_codes() /<>/doc/cookbook/what_codes.rst:20: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs nt_seqs = load_aligned_seqs("data/brca1-bats.fasta", moltype="dna") nt_seqs[:21] /<>/doc/cookbook/what_codes.rst:29: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aa_seqs = nt_seqs.get_translation(gc=1, incomplete_ok=True) aa_seqs[:20] /<>/doc/cookbook/what_codes.rst:39: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code gc = get_code(4) gc /<>/doc/draw/aln/plot_aln-coevolution.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/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() /<>/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) /<>/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) /<>/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) /<>/doc/draw/aln/plot_aln-dotplot-1.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/draw/aln/plot_aln-dotplot-1.rst:15: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: import os from cogent3 import load_unaligned_seqs seqs = load_unaligned_seqs("data/SCA1-cds.fasta", moltype="dna") draw = seqs.dotplot() draw.show() /<>/doc/draw/aln/plot_aln-dotplot-1.rst:25: 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) /<>/doc/draw/aln/plot_aln-dotplot-1.rst:39: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: draw = seqs.dotplot(name1="Human", name2="Mouse", window=8, threshold=8) draw.show() /<>/doc/draw/aln/plot_aln-dotplot-1.rst:47: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: draw = seqs.dotplot(name1="Human", name2="Mouse", rc=True) draw.show() /<>/doc/draw/aln/plot_aln-dotplot-1.rst:59: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: draw = seqs.dotplot(name1="Human", name2="Mouse", rc=True, title="SCA1", width=400) draw.show() /<>/doc/draw/aln/plot_aln-dotplot-2.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/draw/aln/plot_aln-dotplot-2.rst:16: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app.io import get_data_store, load_json loader = load_json() seqs = loader("data/tp53.json") dp = seqs.dotplot(name1="Macaque", name2="Marmoset", width=600) dp.show() /<>/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) /<>/doc/draw/aln/plot_aln-dotplot-2.rst:35: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: help(dp.remove_track) /<>/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() /<>/doc/draw/aln/plot_aln-gaps-per-seq.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/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 /<>/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) /<>/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) /<>/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) /<>/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) /<>/doc/draw/aln/plot_aln-info-plot.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/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) /<>/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) /<>/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) /<>/doc/draw/aln/plot_aln-seqlogo.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/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 /<>/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) /<>/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) /<>/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() /<>/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() /<>/doc/draw/tree/plot_tree-angular.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/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() /<>/doc/draw/tree/plot_tree-angular.rst:24: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fig.contemporaneous = True fig.show() /<>/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) /<>/doc/draw/tree/plot_tree-circular.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/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() /<>/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) /<>/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) /<>/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) /<>/doc/draw/tree/plot_tree-radial.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/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() /<>/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) /<>/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() /<>/doc/draw/tree/plot_tree-square.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/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() /<>/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) /<>/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() /<>/doc/draw/tree/plot_tree-square.rst:47: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fig.contemporaneous = True fig.show() /<>/doc/draw/tree/plot_tree-support.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/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) /<>/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) /<>/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) /<>/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 /<>/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") print(unaligned_DNA.to_fasta()) /<>/doc/examples/align_codons_to_protein.rst:26: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: unaligned_aa = unaligned_DNA.get_translation() print(unaligned_aa.to_fasta()) /<>/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 /<>/doc/examples/calculate_UPGMA_cluster.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/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 /<>/doc/examples/calculate_UPGMA_cluster.rst:23: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import HKY85 /<>/doc/examples/calculate_UPGMA_cluster.rst:29: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: al = load_aligned_seqs("data/test.paml") /<>/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) /<>/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()) /<>/doc/examples/calculate_UPGMA_cluster.rst:49: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: mycluster.write("test_upgma.tree") /<>/doc/examples/calculate_UPGMA_cluster.rst:55: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import os os.remove("test_upgma.tree") /<>/doc/examples/calculate_neigbourjoining_tree.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/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 /<>/doc/examples/calculate_neigbourjoining_tree.rst:21: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import get_model /<>/doc/examples/calculate_neigbourjoining_tree.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: al = load_aligned_seqs("data/long_testseqs.fasta") /<>/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) /<>/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()) /<>/doc/examples/calculate_neigbourjoining_tree.rst:47: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: mytree.write("test_nj.tree") /<>/doc/examples/calculate_neigbourjoining_tree.rst:53: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import os os.remove("test_nj.tree") /<>/doc/examples/calculate_pairwise_distances.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/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 /<>/doc/examples/calculate_pairwise_distances.rst:22: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import HKY85 /<>/doc/examples/calculate_pairwise_distances.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: al = load_aligned_seqs("data/long_testseqs.fasta") /<>/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() /<>/doc/examples/calculate_pairwise_distances.rst:44: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: d.write("dists_for_phylo.phylip", format="phylip") /<>/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) /<>/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) /<>/doc/examples/codon_models.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/examples/codon_models.rst:36: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import get_model /<>/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") /<>/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") /<>/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) /<>/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 /<>/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 /<>/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)) /<>/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() /<>/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)) /<>/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() /<>/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") /<>/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 ) /<>/doc/examples/codon_models.rst:164: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: epsilon = 1e-6 /<>/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 ) /<>/doc/examples/codon_models.rst:179: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: rate_lf.set_param_rule("bprobs", init=[1 - epsilon, epsilon]) /<>/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 /<>/doc/examples/codon_models.rst:195: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(chi2.sf(LR, df)) /<>/doc/examples/codon_models.rst:201: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: pp = rate_lf.get_bin_probs() /<>/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='>/doc/examples/codon_models.rst:232: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: rate_lf = cnf.make_likelihood_function(tree, bins=["0", "1"], digits=2, space=3) rate_lf.set_param_rule("omega", bin="0", upper=1.0 - epsilon, init=1 - epsilon) rate_lf.set_param_rule("omega", bins="1", is_constant=True, value=1.0) rate_lf.set_alignment(aln) rate_lf.optimise(**optimiser_args) tables = rate_lf.get_statistics(with_titles=True) for table in tables: if "bin" in table.title: print(table) /<>/doc/examples/codon_models.rst:246: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: globals = [t for t in tables if "global" in t.title][0] globals = dict(zip(globals.header, globals.tolist()[0])) bin_params = [t for t in tables if "bin" in t.title][0] rate_class_omegas = dict(bin_params.tolist(["bin", "omega"])) rate_class_probs = dict(bin_params.tolist(["bin", "bprobs"])) lengths = [t for t in tables if "edge" in t.title][0] lengths = dict(lengths.tolist(["edge", "length"])) /<>/doc/examples/codon_models.rst:258: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: rate_branch_lf = cnf.make_likelihood_function( tree, bins=["0", "1", "2a", "2b"], digits=2, space=3 ) /<>/doc/examples/codon_models.rst:266: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: for branch, length in lengths.items(): rate_branch_lf.set_param_rule("length", edge=branch, init=length) /<>/doc/examples/codon_models.rst:273: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: for param, mle in globals.items(): rate_branch_lf.set_param_rule(param, init=mle) /<>/doc/examples/codon_models.rst:280: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: rate_branch_lf.set_param_rule( "omega", bins=["0", "2a"], upper=1.0, init=rate_class_omegas["0"] ) rate_branch_lf.set_param_rule( "omega", bins=["1", "2b"], is_constant=True, value=1.0 ) rate_branch_lf.set_param_rule( "omega", bins=["2a", "2b"], edges=["Chimpanzee", "Human"], init=99, lower=1.0, upper=100.0, is_constant=False, ) /<>/doc/examples/codon_models.rst:300: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: rate_branch_lf.set_param_rule( "bprobs", init=[ rate_class_probs["0"] - epsilon, rate_class_probs["1"] - epsilon, epsilon, epsilon, ], ) /<>/doc/examples/codon_models.rst:314: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: rate_branch_lf.set_alignment(aln) /<>/doc/examples/coevolution.rst:10: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs from cogent3.core.alignment import ArrayAlignment from cogent3.evolve.coevolution import validate_alignment aln = make_aligned_seqs( {"1": "GAA", "2": "CTA", "3": "CTC", "4": "-TC"}, moltype="protein", array_align=True, ) validate_alignment(aln) /<>/doc/examples/coevolution.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs from cogent3.core.alignment import ArrayAlignment aln = make_aligned_seqs( {"1": "AAA", "2": "CTA", "3": "CTC", "4": "-TC"}, moltype="protein", array_align=True, ) /<>/doc/examples/coevolution.rst:38: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.coevolution import ( coevolve_pair, coevolve_pair_functions, ) coevolve_pair(coevolve_pair_functions["mi"], aln, pos1=1, pos2=2) /<>/doc/examples/coevolution.rst:49: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.coevolution import ( coevolve_pair, coevolve_pair_functions, ) coevolve_pair(coevolve_pair_functions["sca"], aln, pos1=1, pos2=2, cutoff=0.5) /<>/doc/examples/coevolution.rst:60: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.coevolution import ( coevolve_position, coevolve_position_functions, ) coevolve_position(coevolve_position_functions["mi"], aln, position=1) /<>/doc/examples/coevolution.rst:71: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.coevolution import ( coevolve_alignment, coevolve_alignment_functions, ) coevolve_alignment(coevolve_alignment_functions["mi"], aln) /<>/doc/examples/coevolution.rst:82: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(coevolve_pair_functions.keys()) /<>/doc/examples/coevolution.rst:88: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.coevolution import ( coevolve_alignment_functions, coevolve_alignments, ) aln1 = make_aligned_seqs( { "human+protein1": "AAA", "pig+protein1": "CTA", "chicken+protein1": "CTC", "echidna+weird_db_identifier": "-TC", }, moltype="protein", array_align=True, ) aln2 = make_aligned_seqs( { "pig+protein2": "AAAY", "chicken+protein2": "CTAY", "echidna+protein2": "CTCF", "human+protein2": "-TCF", }, moltype="protein", array_align=True, ) coevolve_alignments(coevolve_alignment_functions["mi"], aln1, aln2) /<>/doc/examples/complete_seq_features.rst:8: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA from cogent3.core.annotation import Feature s = DNA.make_seq("AAGAAGAAGACCCCCAAAAAAAAAATTTTTTTTTTAAAAAAAAAAAAA", name="Orig") exon1 = s.add_annotation(Feature, "exon", "fred", [(10, 15)]) exon2 = s.add_annotation(Feature, "exon", "trev", [(30, 40)]) /<>/doc/examples/complete_seq_features.rst:19: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: s[exon1] exon1.get_slice() /<>/doc/examples/complete_seq_features.rst:26: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: exons = s.get_annotations_matching("exon") print(exons) /<>/doc/examples/complete_seq_features.rst:33: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dont_exist = s.get_annotations_matching("dont_exist") dont_exist s[dont_exist] /<>/doc/examples/complete_seq_features.rst:41: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(s.get_region_covering_all(exons)) print(s.get_region_covering_all(exons).get_shadow()) /<>/doc/examples/complete_seq_features.rst:48: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: s.get_region_covering_all(exons).get_slice() /<>/doc/examples/complete_seq_features.rst:54: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: s[exon1, exon2] /<>/doc/examples/complete_seq_features.rst:60: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: ValueError print(s.get_region_covering_all(exons + exons)) s[exon1, exon1, exon1, exon1, exon1] /<>/doc/examples/complete_seq_features.rst:68: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: ValueError s[15:20, 5:16] /<>/doc/examples/complete_seq_features.rst:75: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: exon1[0:3].get_slice() /<>/doc/examples/complete_seq_features.rst:81: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: c = s[exon1[4:]] + s print(len(c)) for feat in c.annotations: print(feat) /<>/doc/examples/complete_seq_features.rst:90: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: ValueError print(c[exon1]) /<>/doc/examples/complete_seq_features.rst:97: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: len(s.annotations) region = s.get_region_covering_all(exons) len(s.annotations) region.attach() len(s.annotations) region.detach() len(s.annotations) /<>/doc/examples/complete_seq_features.rst:109: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: plus = DNA.make_seq("AAGGGGAAAACCCCCAAAAAAAAAATTTTTTTTTTAAA", name="plus") plus_cds = plus.add_annotation(Feature, "CDS", "gene", [(2, 6), (10, 15), (25, 35)]) print(plus_cds.get_slice()) minus = plus.rc() minus_cds = minus.get_annotations_matching("CDS")[0] print(minus_cds.get_slice()) /<>/doc/examples/complete_seq_features.rst:120: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( [["x", "-AAAAAAAAA"], ["y", "TTTT--TTTT"]], array_align=False ) print(aln) exon = aln.get_seq("x").add_annotation(Feature, "exon", "fred", [(3, 8)]) aln_exons = aln.get_annotations_from_seq("x", "exon") aln_exons = aln.get_annotations_from_any_seq("exon") /<>/doc/examples/complete_seq_features.rst:134: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(exon) print(aln_exons[0]) print(aln_exons[0].get_slice()) aln_exons[0].attach() len(aln.annotations) /<>/doc/examples/complete_seq_features.rst:144: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: exons = aln.get_projected_annotations("y", "exon") print(exons) print(aln.get_seq("y")[exons[0].map.without_gaps()]) /<>/doc/examples/complete_seq_features.rst:152: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = make_aligned_seqs( [["x", "-AAAAAAAAA"], ["y", "TTTT--CCCC"]], array_align=False ) s = DNA.make_seq("AAAAAAAAA", name="x") exon = s.add_annotation(Feature, "exon", "fred", [(3, 8)]) exon = aln.get_seq("x").copy_annotations(s) aln_exons = list(aln.get_annotations_from_seq("x", "exon")) print(aln_exons) /<>/doc/examples/complete_seq_features.rst:165: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: exon = aln.get_seq("y").copy_annotations(s) aln_exons = list(aln.get_annotations_from_seq("y", "exon")) print(aln_exons) print(aln[aln_exons]) /<>/doc/examples/complete_seq_features.rst:174: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = make_aligned_seqs([["x", "-AAAA"], ["y", "TTTTT"]], array_align=False) seq = DNA.make_seq("CCCCCCCCCCCCCCCCCCCC", "x") exon = seq.add_feature("exon", "A", [(5, 8)]) aln.get_seq("x").copy_annotations(seq) copied = list(aln.get_annotations_from_seq("x", "exon")) copied copied[0].get_slice() /<>/doc/examples/complete_seq_features.rst:186: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = make_aligned_seqs( [["x", "-AAAAAAAAA"], ["y", "TTTT--TTTT"]], array_align=False ) seq = DNA.make_seq("CCCCCCCCCCCCCCCCCCCC", "x") match_exon = seq.add_feature("exon", "A", [(5, 8)]) aln.get_seq("y").copy_annotations(seq) copied = list(aln.get_annotations_from_seq("y", "exon")) copied /<>/doc/examples/complete_seq_features.rst:199: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = make_aligned_seqs( [["x", "-AAAAAAAAA"], ["y", "TTTT--TTTT"]], array_align=False ) diff_len_seq = DNA.make_seq("CCCCCCCCCCCCCCCCCCCCCCCCCCCC", "x") nonmatch = diff_len_seq.add_feature("repeat", "A", [(12, 14)]) aln.get_seq("y").copy_annotations(diff_len_seq) copied = list(aln.get_annotations_from_seq("y", "repeat")) copied /<>/doc/examples/complete_seq_features.rst:212: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = make_aligned_seqs( [["x", "-AAAAAAAAA"], ["y", "------TTTT"]], array_align=False ) exon = aln.get_seq("x").add_feature("exon", "fred", [(3, 8)]) aln_exons = list(aln.get_annotations_from_seq("x", "exon")) print(aln_exons) print(aln_exons[0].get_slice()) aln = make_aligned_seqs( [["x", "-AAAAAAAAA"], ["y", "TTTT--T---"]], array_align=False ) exon = aln.get_seq("x").add_feature("exon", "fred", [(3, 8)]) aln_exons = list(aln.get_annotations_from_seq("x", "exon")) print(aln_exons[0].get_slice()) /<>/doc/examples/complete_seq_features.rst:230: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = make_aligned_seqs( [["x", "C-CCCAAAAA"], ["y", "-T----TTTT"]], moltype="dna", array_align=False ) print(aln) exon = aln.get_seq("x").add_feature("exon", "ex1", [(0, 4)]) print(exon) print(exon.get_slice()) aln_exons = list(aln.get_annotations_from_seq("x", "exon")) print(aln_exons) print(aln_exons[0].get_slice()) /<>/doc/examples/complete_seq_features.rst:245: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(aln_exons[0].as_one_span().get_slice()) /<>/doc/examples/complete_seq_features.rst:251: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln_rc = aln.rc() rc_exons = list(aln_rc.get_annotations_from_any_seq("exon")) print(aln_rc[rc_exons]) # not using as_one_span, so gap removed from x print(aln_rc[rc_exons[0].as_one_span()]) /<>/doc/examples/complete_seq_features.rst:260: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: all_exons = aln.get_region_covering_all(aln_exons) coords = all_exons.get_coordinates() assert coords == [(0, 1), (2, 5)] /<>/doc/examples/complete_seq_features.rst:270: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = make_aligned_seqs( [["x", "C-CCCAAAAAGGGAA"], ["y", "-T----TTTTG-GTT"]], array_align=False ) print(aln) exon = aln.get_seq("x").add_feature("exon", "norwegian", [(0, 4)]) print(exon.get_slice()) repeat = aln.get_seq("x").add_feature("repeat", "blue", [(9, 12)]) print(repeat.get_slice()) repeat = aln.get_seq("y").add_feature("repeat", "frog", [(5, 7)]) print(repeat.get_slice()) /<>/doc/examples/complete_seq_features.rst:285: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(aln.get_seq("x").with_masked_annotations("exon", mask_char="?")) print(aln.get_seq("x").with_masked_annotations("exon", mask_char="?", shadow=True)) print(aln.get_seq("x").with_masked_annotations(["exon", "repeat"], mask_char="?")) print( aln.get_seq("x").with_masked_annotations( ["exon", "repeat"], mask_char="?", shadow=True ) ) print(aln.get_seq("y").with_masked_annotations("exon", mask_char="?")) print(aln.get_seq("y").with_masked_annotations("repeat", mask_char="?")) print( aln.get_seq("y").with_masked_annotations("repeat", mask_char="?", shadow=True) ) /<>/doc/examples/complete_seq_features.rst:303: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(aln.with_masked_annotations("exon", mask_char="?")) print(aln.with_masked_annotations("exon", mask_char="?", shadow=True)) print(aln.with_masked_annotations("repeat", mask_char="?")) print(aln.with_masked_annotations("repeat", mask_char="?", shadow=True)) print(aln.with_masked_annotations(["repeat", "exon"], mask_char="?")) print(aln.with_masked_annotations(["repeat", "exon"], shadow=True)) /<>/doc/examples/complete_seq_features.rst:314: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data = [["human", "CGAAACGTTT"], ["mouse", "CTAAACGTCG"]] as_series = make_aligned_seqs(data, array_align=False) as_items = make_aligned_seqs(data, array_align=False) /<>/doc/examples/complete_seq_features.rst:322: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: as_series.get_seq("human").add_feature("cpgsite", "cpg", [(0, 2), (5, 7)]) as_series.get_seq("mouse").add_feature("cpgsite", "cpg", [(5, 7), (8, 10)]) /<>/doc/examples/complete_seq_features.rst:329: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: as_items.get_seq("human").add_feature("cpgsite", "cpg", [(0, 2)]) as_items.get_seq("human").add_feature("cpgsite", "cpg", [(5, 7)]) as_items.get_seq("mouse").add_feature("cpgsite", "cpg", [(5, 7)]) as_items.get_seq("mouse").add_feature("cpgsite", "cpg", [(8, 10)]) /<>/doc/examples/complete_seq_features.rst:338: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: serial = as_series.with_masked_annotations(["cpgsite"]) print(serial) itemwise = as_items.with_masked_annotations(["cpgsite"]) print(itemwise) /<>/doc/examples/complete_seq_features.rst:347: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(plus.with_masked_annotations("CDS")) print(minus.with_masked_annotations("CDS")) /<>/doc/examples/empirical_protein_models.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/examples/empirical_protein_models.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, make_tree from cogent3.evolve.substitution_model import EmpiricalProteinMatrix from cogent3.parse.paml_matrix import PamlMatrixParser /<>/doc/examples/empirical_protein_models.rst:21: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: treestring = "(((rabbit,rat),human),goat-cow,marsupial);" t = make_tree(treestring) /<>/doc/examples/empirical_protein_models.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: al = load_aligned_seqs("data/abglobin_aa.phylip", moltype="protein") /<>/doc/examples/empirical_protein_models.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: matrix_file = open("data/dayhoff.dat") /<>/doc/examples/empirical_protein_models.rst:40: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: empirical_matrix, empirical_frequencies = PamlMatrixParser(matrix_file) /<>/doc/examples/empirical_protein_models.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: sm = EmpiricalProteinMatrix(empirical_matrix, empirical_frequencies) /<>/doc/examples/empirical_protein_models.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf = sm.make_likelihood_function(t) lf.set_alignment(al) lf.optimise(show_progress=False) lf /<>/doc/examples/hmm_par_heterogeneity.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/doc/examples/hmm_par_heterogeneity.rst:21: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.substitution_model import ( TimeReversibleNucleotide, predicate, ) from scipy.stats.distributions import chi2 /<>/doc/examples/hmm_par_heterogeneity.rst:32: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = load_aligned_seqs("data/long_testseqs.fasta") tree = load_tree("data/test.tree") /<>/doc/examples/hmm_par_heterogeneity.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: MotifChange = predicate.MotifChange treat_gap = dict(recode_gaps=True, model_gaps=False) kappa = (~MotifChange("R", "Y")).aliased("kappa") model = TimeReversibleNucleotide(predicates=[kappa], **treat_gap) /<>/doc/examples/hmm_par_heterogeneity.rst:51: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf_one = model.make_likelihood_function(tree, digits=2, space=3) lf_one.set_alignment(aln) lf_one.optimise(show_progress=False) lnL_one = lf_one.get_log_likelihood() df_one = lf_one.get_num_free_params() lf_one /<>/doc/examples/hmm_par_heterogeneity.rst:65: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: bin_submod = TimeReversibleNucleotide( predicates=[kappa], ordered_param="rate", distribution="gamma", **treat_gap ) lf_bins = bin_submod.make_likelihood_function( tree, bins=2, sites_independent=True, digits=2, space=3 ) lf_bins.set_param_rule("bprobs", is_constant=True) lf_bins.set_alignment(aln) lf_bins.optimise(local=True, show_progress=False) lnL_bins = lf_bins.get_log_likelihood() df_bins = lf_bins.get_num_free_params() assert df_bins == 9 lf_bins /<>/doc/examples/hmm_par_heterogeneity.rst:86: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf_patches = bin_submod.make_likelihood_function( tree, bins=2, sites_independent=False, digits=2, space=3 ) lf_patches.set_param_rule("bprobs", is_constant=True) lf_patches.set_alignment(aln) lf_patches.optimise(local=True, show_progress=False) lnL_patches = lf_patches.get_log_likelihood() df_patches = lf_patches.get_num_free_params() lf_patches /<>/doc/examples/hmm_par_heterogeneity.rst:100: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: LR = lambda alt, null: 2 * (alt - null) /<>/doc/examples/hmm_par_heterogeneity.rst:106: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lr = LR(lnL_bins, lnL_one) lr /<>/doc/examples/hmm_par_heterogeneity.rst:111: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print("%.4f" % chi2.sf(lr, df_patches - df_bins)) /<>/doc/examples/hmm_par_heterogeneity.rst:117: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: bprobs = lf_patches.get_param_value("bprobs") print("%.1f : %.1f" % tuple(bprobs)) /<>/doc/examples/hmm_par_heterogeneity.rst:124: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: pp = lf_patches.get_bin_probs() /<>/doc/examples/hmm_par_heterogeneity.rst:130: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(pp["bin0"][20]) /<>/doc/examples/hmm_par_heterogeneity.rst:143: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from numpy import array single_kappa = lf_one.get_param_value("kappa") /<>/doc/examples/hmm_par_heterogeneity.rst:151: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: kappa_bin_submod = TimeReversibleNucleotide(predicates=[kappa], **treat_gap) lf_kappa = kappa_bin_submod.make_likelihood_function( tree, bins=["slow", "fast"], sites_independent=False, digits=1, space=3 ) /<>/doc/examples/hmm_par_heterogeneity.rst:160: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: epsilon = 1e-6 lf_kappa.set_param_rule( kappa, init=single_kappa - epsilon, upper=single_kappa, bin="slow" ) lf_kappa.set_param_rule( kappa, init=single_kappa + epsilon, lower=single_kappa, bin="fast" ) /<>/doc/examples/hmm_par_heterogeneity.rst:172: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf_kappa.set_param_rule("bprobs", init=array([1.0 - epsilon, 0.0 + epsilon])) lf_kappa.set_alignment(aln) lf_kappa.optimise(local=True, show_progress=False) lf_kappa /<>/doc/examples/manipulating_tree_nodes.rst:8: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree, make_tree from cogent3.core.tree import PhyloNode from cogent3.parse.tree import DndParser /<>/doc/examples/manipulating_tree_nodes.rst:24: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: simple_tree_string = "(B:0.2,(C:0.3,D:0.4)E:0.5)F;" complex_tree_string = "(((363564 AB294167.1 Alkalibacterium putridalgicola:0.0028006,55874 AB083411.1 Marinilactibacillus psychrotolerans:0.0022089):0.40998,(15050 Y10772.1 Facklamia hominis:0.32304,(132509 AY707780.1 Aerococcus viridans:0.58815,((143063 AY879307.1 Abiotrophia defectiva:0.5807,83619 AB042060.1 Bacillus schlegelii:0.23569):0.03586,169722 AB275483.1 Fibrobacter succinogenes:0.38272):0.06516):0.03492):0.14265):0.63594,(3589 M62687.1 Fibrobacter intestinalis:0.65866,314063 CP001146.1 Dictyoglomus thermophilum:0.38791):0.32147,276579 EU652053.1 Thermus scotoductus:0.57336);" simple_tree = make_tree(simple_tree_string) complex_tree = DndParser(complex_tree_string, PhyloNode) /<>/doc/examples/manipulating_tree_nodes.rst:35: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(simple_tree.ascii_art()) /<>/doc/examples/manipulating_tree_nodes.rst:41: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: A_node = PhyloNode(name="A", Length=0.1) /<>/doc/examples/manipulating_tree_nodes.rst:47: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(simple_tree.children) /<>/doc/examples/manipulating_tree_nodes.rst:53: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: simple_tree.children[1].remove("C") /<>/doc/examples/manipulating_tree_nodes.rst:59: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: simple_tree.children[1].insert(0, A_node) /<>/doc/examples/manipulating_tree_nodes.rst:65: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(simple_tree.ascii_art()) /<>/doc/examples/manipulating_tree_nodes.rst:71: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: simple_tree.children[1].remove("A") print(simple_tree.ascii_art()) /<>/doc/examples/manipulating_tree_nodes.rst:78: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: simple_tree.prune() print(simple_tree.ascii_art()) /<>/doc/examples/manipulating_tree_nodes.rst:90: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: for n in complex_tree.iter_tips(): n.name = n.name.split()[2] + " " + n.name.split()[3] /<>/doc/examples/manipulating_tree_nodes.rst:97: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(complex_tree.ascii_art(show_internal=False)) /<>/doc/examples/manipulating_tree_nodes.rst:105: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tips = complex_tree.tips() /<>/doc/examples/manipulating_tree_nodes.rst:111: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tips_to_delete = [] AEROCOCCUS_INDEX = 3 for n in tips: if tips[AEROCOCCUS_INDEX].distance(n) > 1.8: tips_to_delete.append(n) /<>/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() /<>/doc/examples/manipulating_tree_nodes.rst:129: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(complex_tree.ascii_art(show_internal=False)) /<>/doc/examples/neutral_test.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/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 /<>/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") /<>/doc/examples/neutral_test.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: sm = get_model("MG94GTR") /<>/doc/examples/neutral_test.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf = sm.make_likelihood_function(t, digits=2, space=2) /<>/doc/examples/neutral_test.rst:40: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_alignment(al) /<>/doc/examples/neutral_test.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(global_tolerance=1.0, show_progress=False) /<>/doc/examples/neutral_test.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf /<>/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() /<>/doc/examples/neutral_test.rst:65: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule("omega", is_independent=True) /<>/doc/examples/neutral_test.rst:71: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(local=True, show_progress=False) /<>/doc/examples/neutral_test.rst:77: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf /<>/doc/examples/neutral_test.rst:83: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: at = lf.get_annotated_tree() /<>/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) /<>/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}") /<>/doc/examples/parametric_bootstrap.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/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 /<>/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) /<>/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 /<>/doc/examples/parametric_bootstrap.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = load_aligned_seqs("data/long_testseqs.fasta") /<>/doc/examples/parametric_bootstrap.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: estimateP = bootstrap.EstimateProbability( create_null_function(), create_alt_function(), aln ) /<>/doc/examples/parametric_bootstrap.rst:60: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: estimateP.set_num_replicates(5) /<>/doc/examples/parametric_bootstrap.rst:66: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: estimateP.run(show_progress=False) /<>/doc/examples/parametric_bootstrap.rst:72: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: p = estimateP.get_estimated_prob() /<>/doc/examples/parametric_bootstrap.rst:78: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print("%.2f, %.2f" % estimateP.get_observed_lnL()) /<>/doc/examples/period_estimation.rst:26: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import numpy numpy.random.seed(11) /<>/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 /<>/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) /<>/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) /<>/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) /<>/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) /<>/doc/examples/period_estimation.rst:89: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: s = ( "ATCGTTGGGACCGGTTCAAGTTTTGGAACTCGCAAGGGGTGAATGGTCTTCGTCTAACGCTGG" "GGAACCCTGAATCGTTGTAACGCTGGGGTCTTTAACCGTTCTAATTTAACGCTGGGGGGTTCT" "AATTTTTAACCGCGGAATTGCGTC" ) /<>/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 /<>/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 /<>/doc/examples/period_estimation.rst:117: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: periods /<>/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 /<>/doc/examples/period_estimation.rst:130: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: periods /<>/doc/examples/period_estimation.rst:134: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: powers, periods = hybrid(symbols) powers /<>/doc/examples/period_estimation.rst:139: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: periods /<>/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) /<>/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] /<>/doc/examples/period_estimation.rst:172: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: powers[period5] /<>/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 /<>/doc/examples/period_estimation.rst:191: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: power = hybrid(symbols, period=period) power /<>/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) /<>/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) /<>/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) /<>/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)) /<>/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 /<>/doc/examples/phylo_by_ls.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/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) /<>/doc/examples/phylo_by_ls.rst:32: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: import pickle from cogent3.phylo import least_squares /<>/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) /<>/doc/examples/phylo_by_ls.rst:49: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: ls = least_squares.WLS(dists) /<>/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()) /<>/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 /<>/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) /<>/doc/examples/phylo_by_ls.rst:85: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(len(trees)) /<>/doc/examples/phylo_by_ls.rst:91: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: wls_stats = [tree[0] for tree in trees] /<>/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()) /<>/doc/examples/phylo_by_ls.rst:109: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(t2.ascii_art()) /<>/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)" ) /<>/doc/examples/phylo_by_ls.rst:130: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: ls.evaluate_tree(query_tree) /<>/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" /<>/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") /<>/doc/examples/rate_heterogeneity.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/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 /<>/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 /<>/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) /<>/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 /<>/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) /<>/doc/examples/relative_rate.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/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 /<>/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") /<>/doc/examples/relative_rate.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: sm = get_model("HKY85") /<>/doc/examples/relative_rate.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf = sm.make_likelihood_function(t, digits=2, space=3) /<>/doc/examples/relative_rate.rst:40: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_local_clock("Human", "HowlerMon") /<>/doc/examples/relative_rate.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_alignment(aln) /<>/doc/examples/relative_rate.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(show_progress=False) /<>/doc/examples/relative_rate.rst:58: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_name("clock") lf /<>/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() /<>/doc/examples/relative_rate.rst:72: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule("length", is_independent=True) /<>/doc/examples/relative_rate.rst:78: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(show_progress=False) /<>/doc/examples/relative_rate.rst:84: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_name("non clock") lf /<>/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) /<>/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) /<>/doc/examples/scope_model_params_on_trees.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/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") /<>/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) /<>/doc/examples/scope_model_params_on_trees.rst:35: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(tree.ascii_art()) /<>/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 /<>/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 /<>/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) /<>/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 /<>/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) /<>/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 /<>/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 /<>/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 /<>/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 /<>/doc/examples/seq_features.rst:14: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA s = DNA.make_seq("aagaagaagacccccaaaaaaaaaattttttttttaaaaaaaaaaaaa", name="Orig") exon1 = s.add_feature("exon", "exon1", [(10, 15)]) exon2 = s.add_feature("exon", "exon2", [(30, 40)]) /<>/doc/examples/seq_features.rst:26: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.core.annotation import Feature s2 = DNA.make_seq("aagaagaagacccccaaaaaaaaaattttttttttaaaaaaaaaaaaa", name="Orig2") exon3 = s2.add_annotation(Feature, "exon", "exon1", [(35, 40)]) /<>/doc/examples/seq_features.rst:35: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: s[exon1] /<>/doc/examples/seq_features.rst:41: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: exons = s.get_annotations_matching("exon") print(exons) /<>/doc/examples/seq_features.rst:48: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(s.get_region_covering_all(exons)) s.get_region_covering_all(exons).get_slice() /<>/doc/examples/seq_features.rst:55: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(s.get_region_covering_all(exons).get_shadow().get_slice()) /<>/doc/examples/seq_features.rst:63: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: exon1[0:3].get_slice() /<>/doc/examples/simple.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/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 /<>/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 /<>/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);") /<>/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 /<>/doc/examples/simulate_alignment.rst:33: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: simulated = lf.simulate_alignment(sequence_length=1000) simulated /<>/doc/examples/testing_multi_loci.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /<>/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:] /<>/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() /<>/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 /<>/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 /<>/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 /<>/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, ) /<>/doc/index.rst:8: ERROR: Unknown directive type "dropdown". .. dropdown:: Click to see an animation showing testing a hypothesis involving a non-stationary nucleotide process. .. raw:: html /<>/doc/index.rst:16: ERROR: Unknown directive type "dropdown". .. dropdown:: Click to see an animation showing defining and using sequence annotations. .. raw:: html /<>/doc/index.rst:22: ERROR: Unknown directive type "panels". .. panels:: :header: bg-primary :footer: text-right --- ``cogent3`` apps ^^^^^^^^^^^^^^^^ ``cogent3`` comes with pre-defined "apps" that simplify otherwise complex tasks. They provide capabilities that can be used by themselves, or added together to define a pipeline. They also simplify parallel execution of pipelines. +++++++++++ .. link-button:: app/index :type: ref :text: … :classes: stretched-link --- Cookbook ^^^^^^^^ The cookbook presents short code recipes targeted at specific problems. +++++++++++ .. link-button:: cookbook/index :type: ref :text: … :classes: stretched-link --- Tutorials ^^^^^^^^^ The tutorials present code for solving more extensive problems. +++++++++++ .. link-button:: examples/index :type: ref :text: … :classes: stretched-link --- API ^^^ The API for major ``cogent3`` objects +++++++++++ .. link-button:: api/index :type: ref :text: … :classes: stretched-link looking for now-outdated files... none found pickling environment... done checking consistency... /<>/doc/data_file_links.rst: WARNING: document isn't included in any toctree /<>/doc/draw/index.rst: WARNING: document isn't included in any toctree /<>/doc/general.rst: WARNING: document isn't included in any toctree /<>/doc/install.rst: WARNING: document isn't included in any toctree /<>/doc/licenses.rst: WARNING: document isn't included in any toctree /<>/doc/pycogent.rst: WARNING: document isn't included in any toctree done preparing documents... done writing output... 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[100%] pycogent generating indices... genindex done writing additional pages... search done copying downloadable files... [ 4%] data/abglobin_aa.phylip copying downloadable files... [ 8%] data/dists_for_phylo.json copying downloadable files... [ 12%] data/long_testseqs.fasta copying downloadable files... [ 16%] data/primate_brca1.fasta copying downloadable files... [ 20%] data/primate_brca1.tree copying downloadable files... [ 24%] data/primate_cdx2_promoter.fasta copying downloadable files... [ 28%] data/test.paml copying downloadable files... [ 32%] data/test.tree copying downloadable files... [ 36%] data/test2.fasta copying downloadable files... [ 40%] data/trna_profile.fasta copying downloadable files... [ 44%] data/refseqs.fasta copying downloadable files... [ 48%] data/refseqs_protein.fasta copying downloadable files... [ 52%] data/inseqs.fasta copying downloadable files... [ 56%] data/inseqs_protein.fasta copying downloadable files... 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The HTML pages are in _build/html. make[2]: Leaving directory '/<>/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 '/<>' dh_auto_test -O--buildsystem=pybuild I: pybuild pybuild:307: cp -r /<>/tests/data /<>/.pybuild/cpython3_3.11_cogent3/build I: pybuild base:240: cd /<>/.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 3.11.2, pytest-7.2.1, pluggy-1.0.0+repack rootdir: /<>, configfile: pyproject.toml plugins: cov-4.0.0, anyio-3.6.2, xdist-3.1.0 collected 2873 items / 4 deselected / 2869 selected tests/test_phylo.py ................ [ 0%] tests/test_recalculation.py . [ 0%] tests/test_align/test_align.py ............................... [ 1%] tests/test_align/test_compare.py ....................................... [ 3%] .... [ 3%] tests/test_app/test_align.py ....................... [ 3%] tests/test_app/test_app_mpi.py s [ 4%] tests/test_app/test_composable.py .............xX....................... [ 5%] ........................................... [ 6%] tests/test_app/test_data_store_new.py .................................. [ 8%] ....................... [ 8%] tests/test_app/test_dist.py ....... [ 9%] tests/test_app/test_evo.py ........................................s [ 10%] tests/test_app/test_init.py ............. [ 10%] tests/test_app/test_io_new.py .......................................... [ 12%] ...... [ 12%] tests/test_app/test_result.py ............................ [ 13%] tests/test_app/test_sample.py ................. [ 14%] tests/test_app/test_sqlite_data_store.py ............................... [ 15%] .................. 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[ 54%] tests/test_data/test_molecular_weight.py . [ 54%] tests/test_draw/test_dendrogram.py .......... [ 54%] tests/test_draw/test_dotplot.py ........... [ 54%] tests/test_draw/test_draw_integration.py ........................ [ 55%] tests/test_draw/test_logo.py ..... [ 55%] tests/test_draw/test_shapes.py ... [ 56%] tests/test_evolve/test_best_likelihood.py ....... [ 56%] tests/test_evolve/test_bootstrap.py .. [ 56%] tests/test_evolve/test_coevolution.py .................................. [ 57%] ........................................................................ [ 60%] .............. [ 60%] tests/test_evolve/test_distance.py ..................................... [ 61%] ..... [ 62%] tests/test_evolve/test_likelihood_function.py .......................... [ 62%] .............................................. [ 64%] tests/test_evolve/test_models.py ........... [ 64%] tests/test_evolve/test_motifchange.py ............. [ 65%] tests/test_evolve/test_newq.py ............. [ 65%] tests/test_evolve/test_ns_substitution_model.py .............. [ 66%] tests/test_evolve/test_parameter_controller.py .......... [ 66%] tests/test_evolve/test_scale_rules.py .... [ 66%] tests/test_evolve/test_substitution_model.py ...................... [ 67%] tests/test_format/test_bedgraph.py ........ [ 67%] tests/test_format/test_clustal.py ... [ 67%] tests/test_format/test_fasta.py . [ 68%] tests/test_maths/test_distance_transform.py ............................ [ 68%] ....... [ 69%] tests/test_maths/test_geometry.py .......... [ 69%] tests/test_maths/test_matrix_exponential_integration.py .... [ 69%] tests/test_maths/test_matrix_logarithm.py ... [ 69%] tests/test_maths/test_measure.py ........ [ 70%] tests/test_maths/test_optimisers.py ...... [ 70%] tests/test_maths/test_period.py ....... [ 70%] tests/test_maths/test_util.py ....... [ 70%] tests/test_maths/test_stats/test_contingency.py .................... [ 71%] tests/test_maths/test_stats/test_distribution.py ....................... [ 72%] . [ 72%] tests/test_maths/test_stats/test_information_criteria.py ... [ 72%] tests/test_maths/test_stats/test_jackknife.py .... [ 72%] tests/test_maths/test_stats/test_ks.py ...... [ 72%] tests/test_maths/test_stats/test_number.py ...................... [ 73%] tests/test_maths/test_stats/test_period.py .......... [ 73%] tests/test_maths/test_stats/test_special.py ....................... [ 74%] tests/test_maths/test_stats/test_test.py ............................... [ 75%] ...................................................................... [ 78%] tests/test_parse/test_blast.py .............. [ 78%] tests/test_parse/test_blast_xml.py ............... [ 79%] tests/test_parse/test_cigar.py ..... [ 79%] tests/test_parse/test_clustal.py ......... [ 79%] tests/test_parse/test_dialign.py ... [ 79%] tests/test_parse/test_ebi.py ........................................... [ 81%] ............ [ 81%] tests/test_parse/test_fasta.py ..................... [ 82%] tests/test_parse/test_gbseq.py . [ 82%] tests/test_parse/test_genbank.py ................ [ 83%] tests/test_parse/test_gff.py ...... [ 83%] tests/test_parse/test_greengenes.py .... [ 83%] tests/test_parse/test_locuslink.py ............. [ 83%] tests/test_parse/test_ncbi_taxonomy.py .................. [ 84%] tests/test_parse/test_nexus.py ............... [ 85%] tests/test_parse/test_pamlmatrix.py . [ 85%] tests/test_parse/test_phylip.py ... [ 85%] tests/test_parse/test_psl.py ... [ 85%] tests/test_parse/test_pwm_parsers.py .. [ 85%] tests/test_parse/test_rdb.py .................. [ 85%] tests/test_parse/test_record.py ........................................ [ 87%] .. [ 87%] tests/test_parse/test_record_finder.py ................. [ 88%] tests/test_parse/test_tinyseq.py . [ 88%] tests/test_parse/test_tree.py ............... [ 88%] tests/test_parse/test_unigene.py .... [ 88%] tests/test_util/test_deserialise.py ............................ [ 89%] tests/test_util/test_dictarray.py ............................... [ 90%] tests/test_util/test_io.py ...................................ssss.sss [ 92%] tests/test_util/test_misc.py ........................................... [ 93%] .......................................... [ 95%] tests/test_util/test_parallel.py sss [ 95%] tests/test_util/test_recode_alignment.py ............... [ 95%] tests/test_util/test_table.py .......................................... [ 97%] ............................................................. [ 99%] tests/test_util/test_transform.py ..... [ 99%] tests/test_util/test_union_dict.py ........... [100%] =============================== warnings summary =============================== ../../../../../../usr/lib/python3/dist-packages/llvmlite/binding/ffi.py:159 /usr/lib/python3/dist-packages/llvmlite/binding/ffi.py:159: DeprecationWarning: path is deprecated. Use files() instead. Refer to https://importlib-resources.readthedocs.io/en/latest/using.html#migrating-from-legacy for migration advice. _lib_handle = importlib.resources.path(pkgname, _lib_name) .pybuild/cpython3_3.11_cogent3/build/tests/test_app/test_evo.py::TestHypothesisResult::test_alt_hyp_fail_error /<>/.pybuild/cpython3_3.11_cogent3/build/cogent3/core/sequence.py:1123: UserWarning: Dropped remainder "GA" from end of sequence warnings.warn( .pybuild/cpython3_3.11_cogent3/build/tests/test_core/test_alignment.py::SequenceCollectionTests::test_set_repr_policy_valid_input /usr/lib/python3.11/unittest/case.py:678: DeprecationWarning: It is deprecated to return a value that is not None from a test case (>) return self.run(*args, **kwds) .pybuild/cpython3_3.11_cogent3/build/tests/test_core/test_alignment.py::SequenceCollectionTests::test_set_wrap_affects_repr_html /usr/lib/python3.11/unittest/case.py:678: DeprecationWarning: It is deprecated to return a value that is not None from a test case (>) return self.run(*args, **kwds) .pybuild/cpython3_3.11_cogent3/build/tests/test_core/test_core_standalone.py::TestConstructorFunctions::test_load_seq /<>/.pybuild/cpython3_3.11_cogent3/build/cogent3/core/info.py:208: UserWarning: Keys overwritten by other sequence: source warn("Keys overwritten by other sequence: " + "".join(overwrites)) .pybuild/cpython3_3.11_cogent3/build/tests/test_evolve/test_likelihood_function.py::LikelihoodFunctionTests::test_get_param_rules_multilocus .pybuild/cpython3_3.11_cogent3/build/tests/test_util/test_deserialise.py::TestDeserialising::test_deserialise_likelihood_function_multilocus /<>/.pybuild/cpython3_3.11_cogent3/build/cogent3/evolve/parameter_controller.py:414: UserWarning: Used mean of 12 mprobs values .pybuild/cpython3_3.11_cogent3/build/tests/test_evolve/test_likelihood_function.py::LikelihoodFunctionTests::test_make_discrete_markov /<>/.pybuild/cpython3_3.11_cogent3/build/tests/test_evolve/test_likelihood_function.py:808: UserWarning: Ignoring tree edge lengths .pybuild/cpython3_3.11_cogent3/build/tests/test_evolve/test_likelihood_function.py::LikelihoodFunctionTests::test_set_param_rule_adjust_bounds /<>/.pybuild/cpython3_3.11_cogent3/build/cogent3/evolve/parameter_controller.py:414: UserWarning: Used mean of 7 beta values .pybuild/cpython3_3.11_cogent3/build/tests/test_evolve/test_ns_substitution_model.py::NonStatMarkov::test_general_vs_constructed_general /<>/.pybuild/cpython3_3.11_cogent3/build/cogent3/maths/optimisers.py:189: UserWarning: Unused arg for local alignment: results .pybuild/cpython3_3.11_cogent3/build/tests/test_maths/test_stats/test_test.py::StatTests::test_t_two_sample_switch /usr/lib/python3/dist-packages/numpy/core/_methods.py:269: RuntimeWarning: Degrees of freedom <= 0 for slice .pybuild/cpython3_3.11_cogent3/build/tests/test_util/test_misc.py::UtilsTests::test_get_setting_from_environ /<>/.pybuild/cpython3_3.11_cogent3/build/cogent3/util/misc.py:1034: UserWarning: could not cast name=blah to type , skipping -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html =========================== short test summary info ============================ SKIPPED [1] tests/test_app/test_app_mpi.py:26: Not using MPI SKIPPED [1] tests/test_app/test_evo.py:857: Does not work on single-cpu systems SKIPPED [4] tests/test_util/test_io.py:320: Do not test in Debian since offline SKIPPED [1] tests/test_util/test_io.py:361: Do not test in Debian since offline SKIPPED [1] tests/test_util/test_io.py:378: Do not test in Debian since offline SKIPPED [1] tests/test_util/test_io.py:388: Do not test in Debian since offline SKIPPED [1] tests/test_util/test_parallel.py:38: Does not work on single-cpu systems SKIPPED [1] tests/test_util/test_parallel.py:61: Does not work on single-cpu systems SKIPPED [1] tests/test_util/test_parallel.py:49: Does not work on single-cpu systems XFAIL tests/test_app/test_composable.py::test_as_completed_progress[True] - passes except when run in full test suite XPASS tests/test_app/test_composable.py::test_as_completed_progress[False] passes except when run in full test suite = 2855 passed, 12 skipped, 4 deselected, 1 xfailed, 1 xpassed, 12 warnings in 116.00s (0:01:56) = create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild plugin_pyproject:161: Copying package built for python3.11 to destdir dh_install -O--buildsystem=pybuild debian/rules override_dh_installdocs make[1]: Entering directory '/<>' dh_installdocs 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 '/<>' dh_installchangelogs -O--buildsystem=pybuild debian/rules override_dh_python3 make[1]: Entering directory '/<>' dh_python3 --shebang=/usr/bin/python3 make[1]: Leaving directory '/<>' dh_installsystemduser -O--buildsystem=pybuild dh_lintian -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild debian/rules override_dh_compress make[1]: Entering directory '/<>' dh_compress --exclude=.js --exclude=.fasta --exclude=.txt --exclude=.pdb make[1]: Leaving directory '/<>' dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild debian/rules override_dh_shlibdeps make[1]: Entering directory '/<>' dh_shlibdeps dh_numpy3 make[1]: Leaving directory '/<>' dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dpkg-gencontrol: warning: Depends field of package python3-cogent3: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package python-cogent-doc: substitution variable ${python3:Depends} unused, but is defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild INFO: pkgstriptranslations version 152 INFO: pkgstriptranslations version 152 pkgstriptranslations: processing python3-cogent3 (in debian/python3-cogent3); do_strip: , oemstrip: pkgstriptranslations: processing python-cogent-doc (in debian/python-cogent-doc); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/python3-cogent3/DEBIAN/control, package python3-cogent3, directory debian/python3-cogent3 pkgstripfiles: processing control file: debian/python-cogent-doc/DEBIAN/control, package python-cogent-doc, directory debian/python-cogent-doc pkgstripfiles: Running PNG optimization (using 4 cpus) for package python3-cogent3 ... pkgstripfiles: No PNG files. INFO: pkgstripfiles: waiting for lock (python-cogent-doc) ... dpkg-deb: building package 'python3-cogent3' in '../python3-cogent3_2023.2.12a1+dfsg-2_amd64.deb'. pkgstripfiles: Disabled PNG optimization for -doc package python-cogent-doc (to save build time) dpkg-deb: building package 'python-cogent-doc' in '../python-cogent-doc_2023.2.12a1+dfsg-2_all.deb'. dpkg-genbuildinfo --build=binary -O../python-cogent_2023.2.12a1+dfsg-2_amd64.buildinfo dpkg-genchanges --build=binary -mLaunchpad Build Daemon -O../python-cogent_2023.2.12a1+dfsg-2_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) -------------------------------------------------------------------------------- Build finished at 2023-05-02T02:05:10Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | 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merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.71-3), automake (= 1:1.16.5-1.3), autopoint (= 0.21-12), autotools-dev (= 20220109.1), base-files (= 12.3ubuntu3), base-passwd (= 3.6.1), bash (= 5.2.15-2ubuntu1), binutils (= 2.40-2ubuntu4), binutils-common (= 2.40-2ubuntu4), binutils-x86-64-linux-gnu (= 2.40-2ubuntu4), blt (= 2.5.3+dfsg-4.1build2), bsdextrautils (= 2.38.1-4ubuntu1), bsdutils (= 1:2.38.1-4ubuntu1), build-essential (= 12.9ubuntu3), bzip2 (= 1.0.8-5build1), ca-certificates (= 20230311), coreutils (= 9.1-1ubuntu2), cpp (= 4:12.2.0-3ubuntu1), cpp-12 (= 12.2.0-17ubuntu1), cython3 (= 0.29.32-2ubuntu2), dash (= 0.5.12-2ubuntu1), debconf (= 1.5.82), debhelper (= 13.11.4ubuntu3), debianutils (= 5.7-0.4), debugedit (= 1:5.0-5), dh-autoreconf (= 20), dh-python (= 5.20230130), dh-strip-nondeterminism (= 1.13.1-1), diffutils (= 1:3.8-4), docutils-common (= 0.19+dfsg-6), dpkg (= 1.21.21ubuntu1), dpkg-dev (= 1.21.21ubuntu1), dwz (= 0.15-1), file (= 1:5.44-3), findutils (= 4.9.0-3ubuntu1), flit (= 3.8.0-3), fontconfig-config (= 2.14.1-3ubuntu3), fonts-dejavu-core (= 2.37-6), fonts-glyphicons-halflings (= 1.009~3.4.1+dfsg-3), fonts-lyx (= 2.3.7-1), g++ (= 4:12.2.0-3ubuntu1), g++-12 (= 12.2.0-17ubuntu1), gcc (= 4:12.2.0-3ubuntu1), gcc-12 (= 12.2.0-17ubuntu1), gcc-12-base (= 12.2.0-17ubuntu1), gcc-13-base (= 13.1.0-1ubuntu1), gettext (= 0.21-12), gettext-base (= 0.21-12), grep (= 3.8-5), groff-base (= 1.22.4-10), gzip (= 1.12-1ubuntu1), hostname (= 3.23+nmu1ubuntu1), init-system-helpers (= 1.65.2), intltool-debian (= 0.35.0+20060710.6), jupyter-sphinx-theme-common (= 0.0.6+ds1-11), libacl1 (= 2.3.1-3), libarchive-zip-perl (= 1.68-1), libargon2-1 (= 0~20190702+dfsg-3), libasan8 (= 13.1.0-1ubuntu1), libatomic1 (= 13.1.0-1ubuntu1), libattr1 (= 1:2.5.1-4), libaudit-common (= 1:3.0.9-1), libaudit1 (= 1:3.0.9-1), libbinutils (= 2.40-2ubuntu4), libblas3 (= 3.11.0-2), libblkid1 (= 2.38.1-4ubuntu1), libboost-dev (= 1.74.0.3ubuntu7), libboost1.74-dev (= 1.74.0-18.1ubuntu3), libbrotli1 (= 1.0.9-2build8), libbsd0 (= 0.11.7-4), libbz2-1.0 (= 1.0.8-5build1), libc-bin (= 2.37-0ubuntu2), libc-dev-bin (= 2.37-0ubuntu2), libc6 (= 2.37-0ubuntu2), libc6-dev (= 2.37-0ubuntu2), libcap-ng0 (= 0.8.3-1build2), libcap2 (= 1:2.66-3ubuntu2), libcc1-0 (= 13.1.0-1ubuntu1), libcom-err2 (= 1.47.0-1ubuntu1), libcrypt-dev (= 1:4.4.33-2), libcrypt1 (= 1:4.4.33-2), libctf-nobfd0 (= 2.40-2ubuntu4), libctf0 (= 2.40-2ubuntu4), libcurl4 (= 7.88.1-8ubuntu1), libdb5.3 (= 5.3.28+dfsg2-1), libdebconfclient0 (= 0.267ubuntu1), libdebhelper-perl (= 13.11.4ubuntu3), libdeflate0 (= 1.15-1), libdpkg-perl (= 1.21.21ubuntu1), libdw1 (= 0.188-2.1), libedit2 (= 3.1-20221030-2), libelf1 (= 0.188-2.1), libexpat1 (= 2.5.0-1), libexpat1-dev (= 2.5.0-1), libffi8 (= 3.4.4-1), libfile-stripnondeterminism-perl (= 1.13.1-1), libfontconfig1 (= 2.14.1-3ubuntu3), libfreetype6 (= 2.12.1+dfsg-5), libfribidi0 (= 1.0.8-2.1ubuntu1), libgcc-12-dev (= 12.2.0-17ubuntu1), libgcc-s1 (= 13.1.0-1ubuntu1), libgcrypt20 (= 1.10.1-3ubuntu1), libgdbm-compat4 (= 1.23-3), libgdbm6 (= 1.23-3), libgfortran5 (= 13.1.0-1ubuntu1), libglib2.0-0 (= 2.76.1-1), libgmp10 (= 2:6.2.1+dfsg1-1.1ubuntu1), libgnutls30 (= 3.7.8-5ubuntu1), libgomp1 (= 13.1.0-1ubuntu1), libgpg-error0 (= 1.46-1), libgprofng0 (= 2.40-2ubuntu4), libgraphite2-3 (= 1.3.14-1build2), libgssapi-krb5-2 (= 1.20.1-1build1), libharfbuzz0b (= 6.0.0+dfsg-3build1), libhogweed6 (= 3.8.1-2), libicu72 (= 72.1-3ubuntu2), libidn2-0 (= 2.3.3-1build1), libimagequant0 (= 2.17.0-1), libisl23 (= 0.25-1), libitm1 (= 13.1.0-1ubuntu1), libjansson4 (= 2.14-2), libjbig0 (= 2.1-6ubuntu1), libjpeg-turbo8 (= 2.1.5-2ubuntu1), libjpeg8 (= 8c-2ubuntu11), libjs-bootstrap (= 3.4.1+dfsg-3), libjs-bootswatch (= 3.3.7+dfsg2-1.1), libjs-jquery (= 3.6.1+dfsg+~3.5.14-1), libjs-jquery-hotkeys (= 0~20130707+git2d51e3a9+dfsg-2ubuntu1), libjs-jquery-isonscreen (= 1.2.0-1.1), libjs-jquery-metadata (= 12-4), libjs-jquery-tablesorter (= 1:2.31.3+dfsg1-3), libjs-jquery-throttle-debounce (= 1.1+dfsg.1-2), libjs-jquery-ui (= 1.13.2+dfsg-1), libjs-sphinxdoc (= 5.3.0-4), libjs-underscore (= 1.13.4~dfsg+~1.11.4-3), libjson-perl (= 4.10000-1), libk5crypto3 (= 1.20.1-1build1), libkeyutils1 (= 1.6.3-2), libkrb5-3 (= 1.20.1-1build1), libkrb5support0 (= 1.20.1-1build1), liblapack3 (= 3.11.0-2), liblbfgsb0 (= 3.0+dfsg.3-11), liblcms2-2 (= 2.14-2), libldap2 (= 2.6.3+dfsg-1~exp1ubuntu2), liblerc4 (= 4.0.0+ds-2ubuntu2), libllvm14 (= 1:14.0.6-12), liblsan0 (= 13.1.0-1ubuntu1), liblua5.3-0 (= 5.3.6-2), liblz4-1 (= 1.9.4-1), liblzma5 (= 5.4.1-0.2), libmagic-mgc (= 1:5.44-3), libmagic1 (= 1:5.44-3), libmd0 (= 1.0.4-2), libmount1 (= 2.38.1-4ubuntu1), libmpc3 (= 1.3.1-1), libmpfr6 (= 4.2.0-1), libncursesw6 (= 6.4-2), libnettle8 (= 3.8.1-2), libnghttp2-14 (= 1.52.0-1), libnorm1 (= 1.5.9+dfsg-2), libnsl-dev (= 1.3.0-2build2), libnsl2 (= 1.3.0-2build2), libopenblas-dev (= 0.3.21+ds-4), libopenblas-pthread-dev (= 0.3.21+ds-4), libopenblas0 (= 0.3.21+ds-4), libopenblas0-pthread (= 0.3.21+ds-4), libopenjp2-7 (= 2.5.0-1build1), libp11-kit0 (= 0.24.1-2ubuntu1), libpam-modules (= 1.5.2-5ubuntu1), libpam-modules-bin (= 1.5.2-5ubuntu1), libpam-runtime (= 1.5.2-5ubuntu1), libpam0g (= 1.5.2-5ubuntu1), libpcre2-8-0 (= 10.42-1), libperl5.36 (= 5.36.0-7), libpfm4 (= 4.12.1+git12-g678bca9-1), libpgm-5.3-0 (= 5.3.128~dfsg-2), libpipeline1 (= 1.5.7-1), libpng16-16 (= 1.6.39-2), libpsl5 (= 0.21.2-1), libpython3-all-dev (= 3.11.2-1), libpython3-dev (= 3.11.2-1), libpython3-stdlib (= 3.11.2-1), libpython3.11 (= 3.11.2-6), libpython3.11-dev (= 3.11.2-6), libpython3.11-minimal (= 3.11.2-6), libpython3.11-stdlib (= 3.11.2-6), libqhull-r8.0 (= 2020.2-5), libquadmath0 (= 13.1.0-1ubuntu1), libraqm0 (= 0.10.1-1), libreadline8 (= 8.2-1.3), librtmp1 (= 2.4+20151223.gitfa8646d.1-2build4), libsasl2-2 (= 2.1.28+dfsg-11), libsasl2-modules-db (= 2.1.28+dfsg-11), libseccomp2 (= 2.5.4-1ubuntu3), libselinux1 (= 3.4-1build4), libsmartcols1 (= 2.38.1-4ubuntu1), libsodium23 (= 1.0.18-1build2), libsqlite3-0 (= 3.40.1-1), libssh-4 (= 0.10.4-2), libssl3 (= 3.0.8-1ubuntu1), libstdc++-12-dev (= 12.2.0-17ubuntu1), libstdc++6 (= 13.1.0-1ubuntu1), libsub-override-perl (= 0.09-4), libsystemd0 (= 252.5-2ubuntu3), libtasn1-6 (= 4.19.0-2), libtcl8.6 (= 8.6.13+dfsg-2), libtiff6 (= 4.5.0-5ubuntu1), libtinfo6 (= 6.4-2), libtirpc-common (= 1.3.3+ds-1), libtirpc-dev (= 1.3.3+ds-1), libtirpc3 (= 1.3.3+ds-1), libtk8.6 (= 8.6.13-2), libtool (= 2.4.7-5), libtsan2 (= 13.1.0-1ubuntu1), libubsan1 (= 13.1.0-1ubuntu1), libuchardet0 (= 0.0.7-1build2), libudev1 (= 252.5-2ubuntu3), libunistring2 (= 1.0-2), libuuid1 (= 2.38.1-4ubuntu1), libwebp7 (= 1.2.4-0.1build1), libwebpdemux2 (= 1.2.4-0.1build1), libwebpmux3 (= 1.2.4-0.1build1), libx11-6 (= 2:1.8.4-2), libx11-data (= 2:1.8.4-2), libxau6 (= 1:1.0.9-1build5), libxcb1 (= 1.15-1), libxdmcp6 (= 1:1.1.3-0ubuntu5), libxext6 (= 2:1.3.4-1build1), libxft2 (= 2.3.6-1), libxml2 (= 2.9.14+dfsg-1.2), libxrender1 (= 1:0.9.10-1.1), libxsimd-dev (= 8.1.0-7), libxslt1.1 (= 1.1.35-1), libxss1 (= 1:1.2.3-1build2), libyaml-0-2 (= 0.2.5-1), libzmq5 (= 4.3.4-6), libzstd1 (= 1.5.4+dfsg2-4), linux-libc-dev (= 6.2.0-21.21), llvm-14 (= 1:14.0.6-12), llvm-14-linker-tools (= 1:14.0.6-12), llvm-14-runtime (= 1:14.0.6-12), login (= 1:4.13+dfsg1-1ubuntu1), lsb-base (= 11.6), lto-disabled-list (= 40), m4 (= 1.4.19-3), make (= 4.3-4.1build1), man-db (= 2.11.2-2), mawk (= 1.3.4.20200120-3.1), media-types (= 10.0.0), ncurses-base (= 6.4-2), ncurses-bin (= 6.4-2), openssl (= 3.0.8-1ubuntu1), pandoc (= 2.17.1.1-1.1ubuntu1), pandoc-data (= 2.17.1.1-1.1ubuntu1), patch (= 2.7.6-7build2), perl (= 5.36.0-7), perl-base (= 5.36.0-7), perl-modules-5.36 (= 5.36.0-7), po-debconf (= 1.0.21+nmu1), pybuild-plugin-pyproject (= 5.20230130), python-babel-localedata (= 2.10.3-1), python-matplotlib-data (= 3.5.2-4ubuntu1), python-tinycss2-common (= 1.2.1-2), python3 (= 3.11.2-1), python3-alabaster (= 0.7.12-1), python3-all (= 3.11.2-1), python3-all-dev (= 3.11.2-1), python3-anyio (= 3.6.2-1), python3-appdirs (= 1.4.4-3), python3-argon2 (= 21.1.0-2), python3-attr (= 22.2.0-1), python3-babel (= 2.10.3-1), python3-beniget (= 0.4.1-3), python3-bleach (= 5.0.1-2), python3-brotli (= 1.0.9-2build8), python3-bs4 (= 4.11.2-2), python3-build (= 0.9.0-1), python3-certifi (= 2022.9.24-1), python3-cffi-backend (= 1.15.1-5build1), python3-chardet (= 5.1.0+dfsg-2), python3-commonmark (= 0.9.1-4), python3-coverage (= 6.5.0+dfsg1-2build1), python3-cycler (= 0.11.0-1), python3-dateutil (= 2.8.2-2), python3-decorator (= 5.1.1-3), python3-defusedxml (= 0.7.1-2), python3-dev (= 3.11.2-1), python3-distutils (= 3.11.2-2), python3-docutils (= 0.19+dfsg-6), python3-entrypoints (= 0.4-2), python3-execnet (= 1.9.0-1), python3-fastjsonschema (= 2.16.2-1), python3-fonttools (= 4.38.0-1build1), python3-fs (= 2.4.16-2), python3-gast (= 0.5.2-2), python3-html5lib (= 1.1-3), python3-idna (= 3.3-1), python3-imagesize (= 1.4.1-1), python3-importlib-metadata (= 4.12.0-1), python3-iniconfig (= 1.1.1-2), python3-installer (= 0.6.0+dfsg1-1), python3-isort (= 5.6.4-1), python3-jinja2 (= 3.1.2-1), python3-json5 (= 0.9.10-1), python3-jsonschema (= 4.6.0-3ubuntu1), python3-jupyter-client (= 7.4.9-2), python3-jupyter-core (= 4.12.0-1), python3-jupyter-server (= 1.23.3-1), python3-jupyter-sphinx-theme (= 0.0.6+ds1-11), python3-jupyterlab-pygments (= 0.2.2-3), python3-jupyterlab-server (= 2.16.5-1), python3-kiwisolver (= 1.4.4-1build1), python3-lib2to3 (= 3.11.2-2), python3-llvmlite (= 0.39.1-2), python3-lxml (= 4.9.2-1build1), python3-lz4 (= 4.0.2+dfsg-1build1), python3-markupsafe (= 2.1.2-1build1), python3-matplotlib (= 3.5.2-4ubuntu1), python3-minimal (= 3.11.2-1), python3-more-itertools (= 8.10.0-2), python3-mpmath (= 1.2.1-2), python3-nbclient (= 0.7.2-1), python3-nbconvert (= 6.5.3-3), python3-nbformat (= 5.5.0-1), python3-nbsphinx (= 0.8.11+ds-1), python3-nest-asyncio (= 1.5.4-1), python3-numba (= 0.56.4+dfsg-2), python3-numpy (= 1:1.24.2-1), python3-numpydoc (= 1.5.0-1), python3-packaging (= 23.0-1), python3-pandas (= 1.5.3+dfsg-2), python3-pandas-lib (= 1.5.3+dfsg-2), python3-pandocfilters (= 1.5.0-1), python3-pbr (= 5.11.1-0ubuntu1), python3-pep517 (= 0.13.0-2), python3-pil (= 9.4.0-1.1build1), python3-pil.imagetk (= 9.4.0-1.1build1), python3-pkg-resources (= 66.1.1-1), python3-plotly (= 5.4.1+dfsg-1), python3-pluggy (= 1.0.0+repack-1), python3-ply (= 3.11-5), python3-prometheus-client (= 0.16.0-0.1), python3-ptyprocess (= 0.7.0-5), python3-py (= 1.11.0-1), python3-pygments (= 2.15.1+dfsg-1), python3-pyparsing (= 3.0.9-1), python3-pyrsistent (= 0.18.1-1build3), python3-pytest (= 7.2.1-2), python3-pytest-cov (= 4.0.0-1), python3-pytest-xdist (= 3.1.0-1), python3-pythran (= 0.11.0+ds-7), python3-recommonmark (= 0.7.1+ds-5), python3-requests (= 2.28.1+dfsg-1ubuntu1), python3-roman (= 3.3-3), python3-scipy (= 1.10.1-1), python3-scitrack (= 2021.5.3-3), python3-send2trash (= 1.8.1~b0-2), python3-setuptools (= 66.1.1-1), python3-six (= 1.16.0-4), python3-sniffio (= 1.2.0-1), python3-snowballstemmer (= 2.2.0-2), python3-soupsieve (= 2.4-1), python3-sphinx (= 5.3.0-4), python3-sphinx-bootstrap-theme (= 0.8.1-1), python3-sphinx-gallery (= 0.10.1-3), python3-sympy (= 1.11.1-1), python3-tenacity (= 8.2.1-1), python3-terminado (= 0.17.0-1), python3-tinycss2 (= 1.2.1-2), python3-tinydb (= 3.15.2-4), python3-tk (= 3.11.2-2), python3-toml (= 0.10.2-1), python3-tomli (= 2.0.1-2), python3-tomli-w (= 1.0.0-2), python3-tornado (= 6.2.0-3), python3-tqdm (= 4.64.1-1), python3-traitlets (= 5.5.0-1), python3-typing-extensions (= 4.4.0-1), python3-tz (= 2022.7.1-3), python3-ufolib2 (= 0.14.0+dfsg1-1), python3-urllib3 (= 1.26.12-1), python3-webencodings (= 0.5.1-5), python3-websocket (= 1.2.3-1), python3-wheel (= 0.38.4-1), python3-zipp (= 1.0.0-6), python3-zmq (= 24.0.1-4build1), python3.11 (= 3.11.2-6), python3.11-dev (= 3.11.2-6), python3.11-minimal (= 3.11.2-6), readline-common (= 8.2-1.3), rpcsvc-proto (= 1.4.2-0ubuntu6), sed (= 4.9-1), sensible-utils (= 0.0.17+nmu1), sgml-base (= 1.31), sphinx-common (= 5.3.0-4), sysvinit-utils (= 3.06-2ubuntu1), tar (= 1.34+dfsg-1.2), tk8.6-blt2.5 (= 2.5.3+dfsg-4.1build2), tzdata (= 2023c-2exp1ubuntu1), unicode-data (= 15.0.0-1), usrmerge (= 33ubuntu1), util-linux (= 2.38.1-4ubuntu1), util-linux-extra (= 2.38.1-4ubuntu1), x11-common (= 1:7.7+23ubuntu2), xml-core (= 0.18+nmu1), xz-utils (= 5.4.1-0.2), zlib1g (= 1:1.2.13.dfsg-1ubuntu4), zlib1g-dev (= 1:1.2.13.dfsg-1ubuntu4) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1677244681" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ python-cogent-doc_2023.2.12a1+dfsg-2_all.deb -------------------------------------------- new Debian package, version 2.0. size 743514 bytes: control archive=10428 bytes. 789 bytes, 21 lines control 40644 bytes, 359 lines md5sums Package: python-cogent-doc Source: python-cogent Version: 2023.2.12a1+dfsg-2 Architecture: all Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 9244 Depends: libjs-jquery, libjs-underscore Suggests: python3-cogent3 (= 2023.2.12a1+dfsg-2) 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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1:1.22.0), python3-numpy-abi9, python3-scipy, python3-scitrack, python3-tinydb, python3-tqdm, python3-typing-extensions, python3:any, python3-matplotlib, python3-pandas, python3-plotly Recommends: ncbi-blast+-legacy, dialign Suggests: python-cogent-doc Breaks: python-cogent Replaces: python-cogent Provides: python-cogent Section: python Priority: optional Homepage: https://github.com/cogent3/cogent3 Description: framework for genomic biology PyCogent is a software library for genomic biology. It is a fully integrated and thoroughly tested framework for: * controlling third-party applications, * devising workflows; querying databases, * conducting novel probabilistic analyses of biological sequence evolution, and * generating publication quality graphics. 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Job: python-cogent_2023.2.12a1+dfsg-2.dsc Machine Architecture: amd64 Package: python-cogent Package-Time: 231 Source-Version: 2023.2.12a1+dfsg-2 Space: 58636 Status: successful Version: 2023.2.12a1+dfsg-2 -------------------------------------------------------------------------------- Finished at 2023-05-02T02:05:10Z Build needed 00:03:51, 58636k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=mantic --arch=amd64 PACKAGEBUILD-26017742 Scanning for processes to kill in build PACKAGEBUILD-26017742