Sat Dec 9 17:18:12 UTC 2023 I: starting to build python-cogent/bookworm/arm64 on jenkins on '2023-12-09 17:18' Sat Dec 9 17:18:12 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_1/2954/console.log Sat Dec 9 17:18:12 UTC 2023 I: Downloading source for bookworm/python-cogent=2023.2.12a1+dfsg-2+deb12u1 --2023-12-09 17:18:15-- http://cdn-fastly.deb.debian.org/debian/pool/main/p/python-cogent/python-cogent_2023.2.12a1%2bdfsg-2%2bdeb12u1.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2622 (2.6K) [text/prs.lines.tag] Saving to: ‘python-cogent_2023.2.12a1+dfsg-2+deb12u1.dsc’ 0K .. 100% 12.9M=0s 2023-12-09 17:18:15 (12.9 MB/s) - ‘python-cogent_2023.2.12a1+dfsg-2+deb12u1.dsc’ saved [2622/2622] Sat Dec 9 17:18:15 UTC 2023 I: python-cogent_2023.2.12a1+dfsg-2+deb12u1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: python-cogent Binary: python3-cogent3, python-cogent-doc Architecture: any-amd64 arm64 mips64el ppc64el s390x ia64 ppc64 riscv64 sparc64 alpha all Version: 2023.2.12a1+dfsg-2+deb12u1 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 python optional arch=any-amd64,arm64,mips64el,ppc64el,s390x,ia64,ppc64,riscv64,sparc64,alpha Checksums-Sha1: 75cfbd5007acea7e4ff14308379ed4ee57053877 3084176 python-cogent_2023.2.12a1+dfsg.orig.tar.xz 3e518e3cbbf9bf0ea3df6d2b641be2e72302e3d6 11612 python-cogent_2023.2.12a1+dfsg-2+deb12u1.debian.tar.xz Checksums-Sha256: 9c4221e7e0ed880786b624a79347f2a0b12e818e8894c9fd93c56bb6b7b5a2c0 3084176 python-cogent_2023.2.12a1+dfsg.orig.tar.xz f4e743f66d3492223f183de88808b472b033a4d87deead51bc3d104b4d69e66e 11612 python-cogent_2023.2.12a1+dfsg-2+deb12u1.debian.tar.xz Files: d044303a26f1057e2b97f9c9132009e4 3084176 python-cogent_2023.2.12a1+dfsg.orig.tar.xz 0d37e32cf9d1571deaf2aa1af27133bf 11612 python-cogent_2023.2.12a1+dfsg-2+deb12u1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQEzBAEBCgAdFiEE1Uw7+v+wQt44LaXXQc5/C58bizIFAmU+yNwACgkQQc5/C58b izK33gf/fCFY28fn8DijeH2viHGZj8m5ZzizFuHdpsYcgD3bY77T9731F4KltoCZ tj7Yb87pR5jCJDOynrZN9yMct1K9vKumSMvya4SlInJrC6zXuA8DNtg1SGfBFrTq GAGK0mMsAFPQIAeOS//RsGwxC9qzweJt2zKfET+Kb3COna8Y8w8ghAUypdByKkm0 cMn5bTTrAyAWlTCqxX79pkMwRpGELdLN/24VvIPRS3XRXtcjRDdNWflAxlcpigtF orzIa8N53nkZb1Oypi68NmToxGP58BP/sasq5IAiV/+JMEmahuux8NLpNb4pcyIn jRrWjSxDZOtJxL9//rm9i5zQ4Dv/Sw== =FyHy -----END PGP SIGNATURE----- Sat Dec 9 17:18:15 UTC 2023 I: Checking whether the package is not for us Sat Dec 9 17:18:15 UTC 2023 I: Starting 1st build on remote node codethink01-arm64.debian.net. Sat Dec 9 17:18:15 UTC 2023 I: Preparing to do remote build '1' on codethink01-arm64.debian.net. Sat Dec 9 17:25:08 UTC 2023 I: Deleting $TMPDIR on codethink01-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri Jan 10 11:41:19 -12 2025 I: pbuilder-time-stamp: 1736552479 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [python-cogent_2023.2.12a1+dfsg-2+deb12u1.dsc] I: copying [./python-cogent_2023.2.12a1+dfsg.orig.tar.xz] I: copying [./python-cogent_2023.2.12a1+dfsg-2+deb12u1.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Oct 29 21:04:28 2023 gpgv: using RSA key D54C3BFAFFB042DE382DA5D741CE7F0B9F1B8B32 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./python-cogent_2023.2.12a1+dfsg-2+deb12u1.dsc: no acceptable signature found dpkg-source: info: extracting python-cogent in python-cogent-2023.2.12a1+dfsg dpkg-source: info: unpacking python-cogent_2023.2.12a1+dfsg.orig.tar.xz dpkg-source: info: unpacking python-cogent_2023.2.12a1+dfsg-2+deb12u1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying sphinx.patch dpkg-source: info: applying fix_interpreter.patch dpkg-source: info: applying remove-jupyter-sphinx.patch dpkg-source: info: applying ignore_tests_accessing_network.patch dpkg-source: info: applying skip-parallel-tests-on-single-cpu-systems.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3131032/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='d5910a550a724b7b9be3aa740cd991ba' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='3131032' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.GxVeyJNF/pbuilderrc_AZom --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.GxVeyJNF/b1 --logfile b1/build.log python-cogent_2023.2.12a1+dfsg-2+deb12u1.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.104:3128' I: uname -a Linux codethink01-arm64 6.1.0-13-cloud-arm64 #1 SMP Debian 6.1.55-1 (2023-09-29) aarch64 GNU/Linux I: ls -l /bin total 7104 -rwxr-xr-x 1 root root 1346480 Apr 23 2023 bash -rwxr-xr-x 3 root root 67728 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 67728 Sep 19 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep -rwxr-xr-x 3 root root 67728 Sep 19 2022 bzip2 -rwxr-xr-x 1 root root 67664 Sep 19 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore -rwxr-xr-x 1 root root 68536 Sep 20 2022 cat -rwxr-xr-x 1 root root 68616 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 68552 Sep 20 2022 chmod -rwxr-xr-x 1 root root 68632 Sep 20 2022 chown -rwxr-xr-x 1 root root 200264 Sep 20 2022 cp -rwxr-xr-x 1 root root 133640 Jan 5 2023 dash -rwxr-xr-x 1 root root 134144 Sep 20 2022 date -rwxr-xr-x 1 root root 134248 Sep 20 2022 dd -rwxr-xr-x 1 root root 134888 Sep 20 2022 df -rwxr-xr-x 1 root root 200440 Sep 20 2022 dir -rwxr-xr-x 1 root root 141720 Mar 23 2023 dmesg lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname -rwxr-xr-x 1 root root 68408 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep -rwxr-xr-x 1 root root 68384 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep -rwxr-xr-x 1 root root 134584 Mar 23 2023 findmnt -rwsr-xr-x 1 root root 67744 Mar 23 2023 fusermount -rwxr-xr-x 1 root root 198880 Jan 24 2023 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 93752 Apr 10 2022 gzip -rwxr-xr-x 1 root root 67592 Dec 19 2022 hostname -rwxr-xr-x 1 root root 68664 Sep 20 2022 ln -rwxr-xr-x 1 root root 69208 Mar 23 2023 login -rwxr-xr-x 1 root root 200440 Sep 20 2022 ls -rwxr-xr-x 1 root root 264360 Mar 23 2023 lsblk -rwxr-xr-x 1 root root 134384 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 68768 Sep 20 2022 mknod -rwxr-xr-x 1 root root 68472 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 67752 Mar 23 2023 more -rwsr-xr-x 1 root root 67744 Mar 23 2023 mount -rwxr-xr-x 1 root root 67744 Mar 23 2023 mountpoint -rwxr-xr-x 1 root root 134728 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 68496 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 2023 rbash -> bash -rwxr-xr-x 1 root root 68456 Sep 20 2022 readlink -rwxr-xr-x 1 root root 68592 Sep 20 2022 rm -rwxr-xr-x 1 root root 68480 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 68392 Jul 28 2023 run-parts -rwxr-xr-x 1 root root 134536 Jan 5 2023 sed lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash -rwxr-xr-x 1 root root 68432 Sep 20 2022 sleep -rwxr-xr-x 1 root root 134088 Sep 20 2022 stty -rwsr-xr-x 1 root root 133312 Mar 23 2023 su -rwxr-xr-x 1 root root 68448 Sep 20 2022 sync -rwxr-xr-x 1 root root 539896 Apr 6 2023 tar -rwxr-xr-x 1 root root 67904 Jul 28 2023 tempfile -rwxr-xr-x 1 root root 134160 Sep 20 2022 touch -rwxr-xr-x 1 root root 68384 Sep 20 2022 true -rwxr-xr-x 1 root root 67664 Mar 23 2023 ulockmgr_server -rwsr-xr-x 1 root root 67744 Mar 23 2023 umount -rwxr-xr-x 1 root root 68416 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 200440 Sep 20 2022 vdir -rwxr-xr-x 1 root root 133312 Mar 23 2023 wdctl lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/3131032/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. 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 dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 18171 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on flit; however: Package flit is not installed. pbuilder-satisfydepends-dummy depends on cython3; however: Package cython3 is not installed. pbuilder-satisfydepends-dummy depends on pandoc; however: Package pandoc is not installed. pbuilder-satisfydepends-dummy depends on pybuild-plugin-pyproject; however: Package pybuild-plugin-pyproject is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-matplotlib; however: Package python3-matplotlib is not installed. pbuilder-satisfydepends-dummy depends on python3-numba; however: Package python3-numba is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-pandas; however: Package python3-pandas is not installed. pbuilder-satisfydepends-dummy depends on python3-scitrack; however: Package python3-scitrack is not installed. pbuilder-satisfydepends-dummy depends on python3-tqdm; however: Package python3-tqdm is not installed. pbuilder-satisfydepends-dummy depends on python3-tinydb; however: Package python3-tinydb is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx; however: Package python3-sphinx is not installed. pbuilder-satisfydepends-dummy depends on python3-numpydoc; however: Package python3-numpydoc is not installed. pbuilder-satisfydepends-dummy depends on python3-nbsphinx; however: Package python3-nbsphinx is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx-bootstrap-theme; however: Package python3-sphinx-bootstrap-theme is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx-gallery; however: Package python3-sphinx-gallery is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest-cov; however: Package python3-pytest-cov is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest-xdist; however: Package python3-pytest-xdist is not installed. pbuilder-satisfydepends-dummy depends on python3-plotly; however: Package python3-plotly is not installed. pbuilder-satisfydepends-dummy depends on python3-typing-extensions; however: Package python3-typing-extensions is not installed. pbuilder-satisfydepends-dummy depends on python3-isort; however: Package python3-isort is not installed. pbuilder-satisfydepends-dummy depends on python3-scipy; however: Package python3-scipy is not installed. pbuilder-satisfydepends-dummy depends on python3-chardet; however: Package python3-chardet is not installed. pbuilder-satisfydepends-dummy depends on python3-jupyterlab-server; however: Package python3-jupyterlab-server is not installed. pbuilder-satisfydepends-dummy depends on python3-jupyter-sphinx-theme; however: Package python3-jupyter-sphinx-theme is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} blt{a} bsdextrautils{a} ca-certificates{a} cython3{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} docutils-common{a} dwz{a} file{a} flit{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-glyphicons-halflings{a} fonts-lyx{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} jupyter-sphinx-theme-common{a} libarchive-zip-perl{a} libargon2-1{a} libblas3{a} libboost-dev{a} libboost1.74-dev{a} libbrotli1{a} libbsd0{a} libcurl3-nss{a} libdebhelper-perl{a} libdeflate0{a} libedit2{a} libelf1{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0{a} libgraphite2-3{a} libharfbuzz0b{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-bootstrap{a} libjs-bootswatch{a} libjs-jquery{a} libjs-jquery-hotkeys{a} libjs-jquery-isonscreen{a} libjs-jquery-metadata{a} libjs-jquery-tablesorter{a} libjs-jquery-throttle-debounce{a} libjs-jquery-ui{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-perl{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} libllvm14{a} liblua5.3-0{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libnorm1{a} libnspr4{a} libnss3{a} libopenblas-dev{a} libopenblas-pthread-dev{a} libopenblas0{a} libopenblas0-pthread{a} libopenjp2-7{a} libpfm4{a} libpgm-5.3-0{a} libpipeline1{a} libpng16-16{a} libpsl5{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.11{a} libpython3.11-dev{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libqhull-r8.0{a} libraqm0{a} libreadline8{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsodium23{a} libssh2-1{a} libsub-override-perl{a} libtcl8.6{a} libtiff6{a} libtk8.6{a} libtool{a} libuchardet0{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml2{a} libxrender1{a} libxsimd-dev{a} libxslt1.1{a} libxss1{a} libyaml-0-2{a} libz3-4{a} libzmq5{a} llvm-14{a} llvm-14-linker-tools{a} llvm-14-runtime{a} m4{a} man-db{a} media-types{a} nss-plugin-pem{a} openssl{a} pandoc{a} pandoc-data{a} po-debconf{a} pybuild-plugin-pyproject{a} python-babel-localedata{a} python-matplotlib-data{a} python-tinycss2-common{a} python3{a} python3-alabaster{a} python3-all{a} python3-all-dev{a} python3-anyio{a} python3-appdirs{a} python3-argon2{a} python3-attr{a} python3-babel{a} python3-beniget{a} python3-bleach{a} python3-brotli{a} python3-bs4{a} python3-build{a} python3-certifi{a} python3-cffi-backend{a} python3-chardet{a} python3-charset-normalizer{a} python3-commonmark{a} python3-contourpy{a} python3-coverage{a} python3-cycler{a} python3-dateutil{a} python3-decorator{a} python3-defusedxml{a} python3-dev{a} python3-distutils{a} python3-docutils{a} python3-entrypoints{a} python3-execnet{a} python3-fastjsonschema{a} python3-fonttools{a} python3-fs{a} python3-gast{a} python3-html5lib{a} python3-idna{a} python3-imagesize{a} python3-importlib-metadata{a} python3-iniconfig{a} python3-installer{a} python3-isort{a} python3-jinja2{a} python3-json5{a} python3-jsonschema{a} python3-jupyter-client{a} python3-jupyter-core{a} python3-jupyter-server{a} python3-jupyter-sphinx-theme{a} python3-jupyterlab-pygments{a} python3-jupyterlab-server{a} python3-kiwisolver{a} python3-lib2to3{a} python3-llvmlite{a} python3-lxml{a} python3-lz4{a} python3-markupsafe{a} python3-matplotlib{a} python3-minimal{a} python3-more-itertools{a} python3-mpmath{a} python3-nbclient{a} python3-nbconvert{a} python3-nbformat{a} python3-nbsphinx{a} python3-nest-asyncio{a} python3-numba{a} python3-numpy{a} python3-numpydoc{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-pandocfilters{a} python3-pbr{a} python3-pep517{a} python3-pil{a} python3-pil.imagetk{a} python3-pkg-resources{a} python3-plotly{a} python3-pluggy{a} python3-ply{a} python3-prometheus-client{a} python3-ptyprocess{a} python3-py{a} python3-pygments{a} python3-pyparsing{a} python3-pyrsistent{a} python3-pytest{a} python3-pytest-cov{a} python3-pytest-xdist{a} python3-pythran{a} python3-recommonmark{a} python3-requests{a} python3-roman{a} python3-scipy{a} python3-scitrack{a} python3-send2trash{a} python3-setuptools{a} python3-six{a} python3-sniffio{a} python3-snowballstemmer{a} python3-soupsieve{a} python3-sphinx{a} python3-sphinx-bootstrap-theme{a} python3-sphinx-gallery{a} python3-sympy{a} python3-tenacity{a} python3-terminado{a} python3-tinycss2{a} python3-tinydb{a} python3-tk{a} python3-toml{a} python3-tomli{a} python3-tomli-w{a} python3-tornado{a} python3-tqdm{a} python3-traitlets{a} python3-typing-extensions{a} python3-tz{a} python3-ufolib2{a} python3-urllib3{a} python3-webencodings{a} python3-websocket{a} python3-wheel{a} python3-zipp{a} python3-zmq{a} python3.11{a} python3.11-dev{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{a} tk8.6-blt2.5{a} tzdata{a} unicode-data{a} x11-common{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: binfmt-support curl isympy-common javascript-common libarchive-cpio-perl libglib2.0-data libjson-xs-perl libldap-common libltdl-dev libmail-sendmail-perl libpaper-utils libsasl2-modules llvm-14-dev lynx numba-doc optipng publicsuffix python3-bottleneck python3-gi python3-json-pointer python3-numexpr python3-odf python3-olefile python3-openpyxl python3-pip python3-rfc3987 python3-sphinxcontrib.bibtex python3-tables python3-uritemplate python3-webcolors shared-mime-info systemd wget xdg-user-dirs 0 packages upgraded, 278 newly installed, 0 to remove and 0 not upgraded. Need to get 208 MB of archives. After unpacking 1206 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 2 http://deb.debian.org/debian bookworm/main arm64 libjs-jquery-hotkeys all 0~20130707+git2d51e3a9+dfsg-2.1 [11.5 kB] Get: 3 http://deb.debian.org/debian bookworm/main arm64 libpython3.11-minimal arm64 3.11.2-6 [806 kB] Get: 4 http://deb.debian.org/debian bookworm/main arm64 libexpat1 arm64 2.5.0-1 [84.8 kB] Get: 5 http://deb.debian.org/debian bookworm/main arm64 python3.11-minimal arm64 3.11.2-6 [1858 kB] Get: 6 http://deb.debian.org/debian bookworm/main arm64 python3-minimal arm64 3.11.2-1+b1 [26.3 kB] Get: 7 http://deb.debian.org/debian bookworm/main arm64 media-types all 10.0.0 [26.1 kB] Get: 8 http://deb.debian.org/debian bookworm/main arm64 readline-common all 8.2-1.3 [69.0 kB] Get: 9 http://deb.debian.org/debian bookworm/main arm64 libreadline8 arm64 8.2-1.3 [155 kB] Get: 10 http://deb.debian.org/debian bookworm/main arm64 libpython3.11-stdlib arm64 3.11.2-6 [1747 kB] Get: 11 http://deb.debian.org/debian bookworm/main arm64 python3.11 arm64 3.11.2-6 [572 kB] Get: 12 http://deb.debian.org/debian bookworm/main arm64 libpython3-stdlib arm64 3.11.2-1+b1 [9296 B] Get: 13 http://deb.debian.org/debian bookworm/main arm64 python3 arm64 3.11.2-1+b1 [26.3 kB] Get: 14 http://deb.debian.org/debian bookworm/main arm64 sgml-base all 1.31 [15.4 kB] Get: 15 http://deb.debian.org/debian bookworm/main arm64 tzdata all 2023c-5+deb12u1 [296 kB] Get: 16 http://deb.debian.org/debian bookworm/main arm64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 17 http://deb.debian.org/debian bookworm/main arm64 openssl arm64 3.0.11-1~deb12u2 [1385 kB] Get: 18 http://deb.debian.org/debian bookworm/main arm64 ca-certificates all 20230311 [153 kB] Get: 19 http://deb.debian.org/debian bookworm/main arm64 libmagic-mgc arm64 1:5.44-3 [305 kB] Get: 20 http://deb.debian.org/debian bookworm/main arm64 libmagic1 arm64 1:5.44-3 [98.5 kB] Get: 21 http://deb.debian.org/debian bookworm/main arm64 file arm64 1:5.44-3 [42.5 kB] Get: 22 http://deb.debian.org/debian bookworm/main arm64 gettext-base arm64 0.21-12 [159 kB] Get: 23 http://deb.debian.org/debian bookworm/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 24 http://deb.debian.org/debian bookworm/main arm64 groff-base arm64 1.22.4-10 [861 kB] Get: 25 http://deb.debian.org/debian bookworm/main arm64 bsdextrautils arm64 2.38.1-5+b1 [86.9 kB] Get: 26 http://deb.debian.org/debian bookworm/main arm64 libpipeline1 arm64 1.5.7-1 [36.4 kB] Get: 27 http://deb.debian.org/debian bookworm/main arm64 man-db arm64 2.11.2-2 [1369 kB] Get: 28 http://deb.debian.org/debian bookworm/main arm64 m4 arm64 1.4.19-3 [276 kB] Get: 29 http://deb.debian.org/debian bookworm/main arm64 autoconf all 2.71-3 [332 kB] Get: 30 http://deb.debian.org/debian bookworm/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 31 http://deb.debian.org/debian bookworm/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 32 http://deb.debian.org/debian bookworm/main arm64 autopoint all 0.21-12 [495 kB] Get: 33 http://deb.debian.org/debian bookworm/main arm64 libtcl8.6 arm64 8.6.13+dfsg-2 [973 kB] Get: 34 http://deb.debian.org/debian bookworm/main arm64 libbrotli1 arm64 1.0.9-2+b6 [269 kB] Get: 35 http://deb.debian.org/debian bookworm/main arm64 libpng16-16 arm64 1.6.39-2 [269 kB] Get: 36 http://deb.debian.org/debian bookworm/main arm64 libfreetype6 arm64 2.12.1+dfsg-5 [369 kB] Get: 37 http://deb.debian.org/debian bookworm/main arm64 fonts-dejavu-core all 2.37-6 [1068 kB] Get: 38 http://deb.debian.org/debian bookworm/main arm64 fontconfig-config arm64 2.14.1-4 [315 kB] Get: 39 http://deb.debian.org/debian bookworm/main arm64 libfontconfig1 arm64 2.14.1-4 [381 kB] Get: 40 http://deb.debian.org/debian bookworm/main arm64 libxau6 arm64 1:1.0.9-1 [19.7 kB] Get: 41 http://deb.debian.org/debian bookworm/main arm64 libbsd0 arm64 0.11.7-2 [115 kB] Get: 42 http://deb.debian.org/debian bookworm/main arm64 libxdmcp6 arm64 1:1.1.2-3 [25.4 kB] Get: 43 http://deb.debian.org/debian bookworm/main arm64 libxcb1 arm64 1.15-1 [143 kB] Get: 44 http://deb.debian.org/debian bookworm/main arm64 libx11-data all 2:1.8.4-2+deb12u2 [292 kB] Get: 45 http://deb.debian.org/debian bookworm/main arm64 libx11-6 arm64 2:1.8.4-2+deb12u2 [735 kB] Get: 46 http://deb.debian.org/debian bookworm/main arm64 libxrender1 arm64 1:0.9.10-1.1 [32.0 kB] Get: 47 http://deb.debian.org/debian bookworm/main arm64 libxft2 arm64 2.3.6-1 [58.7 kB] Get: 48 http://deb.debian.org/debian bookworm/main arm64 libxext6 arm64 2:1.3.4-1+b1 [51.7 kB] Get: 49 http://deb.debian.org/debian bookworm/main arm64 x11-common all 1:7.7+23 [252 kB] Get: 50 http://deb.debian.org/debian bookworm/main arm64 libxss1 arm64 1:1.2.3-1 [17.8 kB] Get: 51 http://deb.debian.org/debian bookworm/main arm64 libtk8.6 arm64 8.6.13-2 [729 kB] Get: 52 http://deb.debian.org/debian bookworm/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-4.1 [540 kB] Get: 53 http://deb.debian.org/debian bookworm/main arm64 blt arm64 2.5.3+dfsg-4.1 [14.9 kB] Get: 54 http://deb.debian.org/debian bookworm/main arm64 cython3 arm64 0.29.32-2+b1 [1223 kB] Get: 55 http://deb.debian.org/debian bookworm/main arm64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 56 http://deb.debian.org/debian bookworm/main arm64 libtool all 2.4.7-5 [517 kB] Get: 57 http://deb.debian.org/debian bookworm/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 58 http://deb.debian.org/debian bookworm/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 59 http://deb.debian.org/debian bookworm/main arm64 libsub-override-perl all 0.09-4 [9304 B] Get: 60 http://deb.debian.org/debian bookworm/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 61 http://deb.debian.org/debian bookworm/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 62 http://deb.debian.org/debian bookworm/main arm64 libelf1 arm64 0.188-2.1 [173 kB] Get: 63 http://deb.debian.org/debian bookworm/main arm64 dwz arm64 0.15-1 [101 kB] Get: 64 http://deb.debian.org/debian bookworm/main arm64 libicu72 arm64 72.1-3 [9204 kB] Get: 65 http://deb.debian.org/debian bookworm/main arm64 libxml2 arm64 2.9.14+dfsg-1.3~deb12u1 [619 kB] Get: 66 http://deb.debian.org/debian bookworm/main arm64 gettext arm64 0.21-12 [1248 kB] Get: 67 http://deb.debian.org/debian bookworm/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 68 http://deb.debian.org/debian bookworm/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 69 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB] Get: 70 http://deb.debian.org/debian bookworm/main arm64 python3-lib2to3 all 3.11.2-3 [76.3 kB] Get: 71 http://deb.debian.org/debian bookworm/main arm64 python3-distutils all 3.11.2-3 [131 kB] Get: 72 http://deb.debian.org/debian bookworm/main arm64 dh-python all 5.20230130+deb12u1 [104 kB] Get: 73 http://deb.debian.org/debian bookworm/main arm64 xml-core all 0.18+nmu1 [23.8 kB] Get: 74 http://deb.debian.org/debian bookworm/main arm64 docutils-common all 0.19+dfsg-6 [127 kB] Get: 75 http://deb.debian.org/debian bookworm/main arm64 python3-tomli all 2.0.1-2 [17.9 kB] Get: 76 http://deb.debian.org/debian bookworm/main arm64 python3-roman all 3.3-3 [9880 B] Get: 77 http://deb.debian.org/debian bookworm/main arm64 python3-docutils all 0.19+dfsg-6 [382 kB] Get: 78 http://deb.debian.org/debian bookworm/main arm64 python3-certifi all 2022.9.24-1 [153 kB] Get: 79 http://deb.debian.org/debian bookworm/main arm64 python3-charset-normalizer all 3.0.1-2 [49.3 kB] Get: 80 http://deb.debian.org/debian bookworm/main arm64 python3-idna all 3.3-1 [39.4 kB] Get: 81 http://deb.debian.org/debian bookworm/main arm64 python3-six all 1.16.0-4 [17.5 kB] Get: 82 http://deb.debian.org/debian bookworm/main arm64 python3-urllib3 all 1.26.12-1 [117 kB] Get: 83 http://deb.debian.org/debian bookworm/main arm64 python3-pkg-resources all 66.1.1-1 [296 kB] Get: 84 http://deb.debian.org/debian bookworm/main arm64 python3-chardet all 5.1.0+dfsg-2 [110 kB] Get: 85 http://deb.debian.org/debian bookworm/main arm64 python3-requests all 2.28.1+dfsg-1 [67.9 kB] Get: 86 http://deb.debian.org/debian bookworm/main arm64 python3-tomli-w all 1.0.0-2 [8012 B] Get: 87 http://deb.debian.org/debian bookworm/main arm64 flit all 3.8.0-3 [95.6 kB] Get: 88 http://deb.debian.org/debian bookworm/main arm64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [162 kB] Get: 89 http://deb.debian.org/debian bookworm/main arm64 fonts-lyx all 2.3.7-1 [186 kB] Get: 90 http://deb.debian.org/debian bookworm/main arm64 libjs-bootstrap all 3.4.1+dfsg-3 [172 kB] Get: 91 http://deb.debian.org/debian bookworm/main arm64 libjs-bootswatch all 3.3.7+dfsg2-1.1 [133 kB] Get: 92 http://deb.debian.org/debian bookworm/main arm64 python3-sphinx-bootstrap-theme all 0.8.1-1 [422 kB] Get: 93 http://deb.debian.org/debian bookworm/main arm64 jupyter-sphinx-theme-common all 0.0.6+ds1-11 [13.2 kB] Get: 94 http://deb.debian.org/debian bookworm/main arm64 libargon2-1 arm64 0~20171227-0.3+deb12u1 [18.7 kB] Get: 95 http://deb.debian.org/debian bookworm/main arm64 libblas3 arm64 3.11.0-2 [91.4 kB] Get: 96 http://deb.debian.org/debian bookworm/main arm64 libboost1.74-dev arm64 1.74.0+ds1-21 [9508 kB] Get: 97 http://deb.debian.org/debian bookworm/main arm64 libboost-dev arm64 1.74.0.3 [4548 B] Get: 98 http://deb.debian.org/debian bookworm/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg-10 [20.8 kB] Get: 99 http://deb.debian.org/debian bookworm/main arm64 libsasl2-2 arm64 2.1.28+dfsg-10 [58.0 kB] Get: 100 http://deb.debian.org/debian bookworm/main arm64 libldap-2.5-0 arm64 2.5.13+dfsg-5 [171 kB] Get: 101 http://deb.debian.org/debian bookworm/main arm64 libnghttp2-14 arm64 1.52.0-1+deb12u1 [68.3 kB] Get: 102 http://deb.debian.org/debian bookworm/main arm64 libnspr4 arm64 2:4.35-1 [105 kB] Get: 103 http://deb.debian.org/debian bookworm/main arm64 libnss3 arm64 2:3.87.1-1 [1218 kB] Get: 104 http://deb.debian.org/debian bookworm/main arm64 libpsl5 arm64 0.21.2-1 [58.6 kB] Get: 105 http://deb.debian.org/debian bookworm/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b2 [59.4 kB] Get: 106 http://deb.debian.org/debian bookworm/main arm64 libssh2-1 arm64 1.10.0-3+b1 [172 kB] Get: 107 http://deb.debian.org/debian bookworm/main arm64 nss-plugin-pem arm64 1.0.8+1-1 [50.6 kB] Get: 108 http://deb.debian.org/debian bookworm/main arm64 libcurl3-nss arm64 7.88.1-10+deb12u4 [370 kB] Get: 109 http://deb.debian.org/debian bookworm/main arm64 libdeflate0 arm64 1.14-1 [54.3 kB] Get: 110 http://deb.debian.org/debian bookworm/main arm64 libedit2 arm64 3.1-20221030-2 [88.1 kB] Get: 111 http://deb.debian.org/debian bookworm/main arm64 libexpat1-dev arm64 2.5.0-1 [135 kB] Get: 112 http://deb.debian.org/debian bookworm/main arm64 libfribidi0 arm64 1.0.8-2.1 [64.9 kB] Get: 113 http://deb.debian.org/debian bookworm/main arm64 libgfortran5 arm64 12.2.0-14 [340 kB] Get: 114 http://deb.debian.org/debian bookworm/main arm64 libglib2.0-0 arm64 2.74.6-2 [1310 kB] Get: 115 http://deb.debian.org/debian bookworm/main arm64 libgraphite2-3 arm64 1.3.14-1 [75.6 kB] Get: 116 http://deb.debian.org/debian bookworm/main arm64 libharfbuzz0b arm64 6.0.0+dfsg-3 [1914 kB] Get: 117 http://deb.debian.org/debian bookworm/main arm64 libimagequant0 arm64 2.17.0-1 [31.3 kB] Get: 118 http://deb.debian.org/debian bookworm/main arm64 libjbig0 arm64 2.1-6.1 [30.0 kB] Get: 119 http://deb.debian.org/debian bookworm/main arm64 libjpeg62-turbo arm64 1:2.1.5-2 [171 kB] Get: 120 http://deb.debian.org/debian bookworm/main arm64 libjs-jquery-isonscreen all 1.2.0-1.1 [3196 B] Get: 121 http://deb.debian.org/debian bookworm/main arm64 libjs-jquery-metadata all 12-4 [6532 B] Get: 122 http://deb.debian.org/debian bookworm/main arm64 libjs-jquery-tablesorter all 1:2.31.3+dfsg1-3 [184 kB] Get: 123 http://deb.debian.org/debian bookworm/main arm64 libjs-jquery-throttle-debounce all 1.1+dfsg.1-2 [12.2 kB] Get: 124 http://deb.debian.org/debian bookworm/main arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 125 http://deb.debian.org/debian bookworm/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 126 http://deb.debian.org/debian bookworm/main arm64 libjs-sphinxdoc all 5.3.0-4 [130 kB] Get: 127 http://deb.debian.org/debian bookworm/main arm64 libjson-perl all 4.10000-1 [87.5 kB] Get: 128 http://deb.debian.org/debian bookworm/main arm64 libopenblas0-pthread arm64 0.3.21+ds-4 [4532 kB] Get: 129 http://deb.debian.org/debian bookworm/main arm64 liblapack3 arm64 3.11.0-2 [1664 kB] Get: 130 http://deb.debian.org/debian bookworm/main arm64 liblbfgsb0 arm64 3.0+dfsg.4-1 [24.9 kB] Get: 131 http://deb.debian.org/debian bookworm/main arm64 liblcms2-2 arm64 2.14-2 [143 kB] Get: 132 http://deb.debian.org/debian bookworm/main arm64 liblerc4 arm64 4.0.0+ds-2 [138 kB] Get: 133 http://deb.debian.org/debian bookworm/main arm64 libz3-4 arm64 4.8.12-3.1 [6282 kB] Get: 134 http://deb.debian.org/debian bookworm/main arm64 libllvm14 arm64 1:14.0.6-12 [19.3 MB] Get: 135 http://deb.debian.org/debian bookworm/main arm64 liblua5.3-0 arm64 5.3.6-2 [110 kB] Get: 136 http://deb.debian.org/debian bookworm/main arm64 libnorm1 arm64 1.5.9+dfsg-2 [202 kB] Get: 137 http://deb.debian.org/debian bookworm/main arm64 libopenblas0 arm64 0.3.21+ds-4 [32.6 kB] Get: 138 http://deb.debian.org/debian bookworm/main arm64 libopenblas-pthread-dev arm64 0.3.21+ds-4 [3169 kB] Get: 139 http://deb.debian.org/debian bookworm/main arm64 libopenblas-dev arm64 0.3.21+ds-4 [44.9 kB] Get: 140 http://deb.debian.org/debian bookworm/main arm64 libopenjp2-7 arm64 2.5.0-2 [175 kB] Get: 141 http://deb.debian.org/debian bookworm/main arm64 libpfm4 arm64 4.13.0-1 [49.8 kB] Get: 142 http://deb.debian.org/debian bookworm/main arm64 libpgm-5.3-0 arm64 5.3.128~dfsg-2 [152 kB] Get: 143 http://deb.debian.org/debian bookworm/main arm64 libpython3.11 arm64 3.11.2-6 [1841 kB] Get: 144 http://deb.debian.org/debian bookworm/main arm64 zlib1g-dev arm64 1:1.2.13.dfsg-1 [913 kB] Get: 145 http://deb.debian.org/debian bookworm/main arm64 libpython3.11-dev arm64 3.11.2-6 [4395 kB] Get: 146 http://deb.debian.org/debian bookworm/main arm64 libpython3-dev arm64 3.11.2-1+b1 [9564 B] Get: 147 http://deb.debian.org/debian bookworm/main arm64 libpython3-all-dev arm64 3.11.2-1+b1 [1068 B] Get: 148 http://deb.debian.org/debian bookworm/main arm64 libqhull-r8.0 arm64 2020.2-5 [230 kB] Get: 149 http://deb.debian.org/debian bookworm/main arm64 libraqm0 arm64 0.7.0-4.1 [10.4 kB] Get: 150 http://deb.debian.org/debian bookworm/main arm64 libsodium23 arm64 1.0.18-1 [119 kB] Get: 151 http://deb.debian.org/debian bookworm/main arm64 libwebp7 arm64 1.2.4-0.2+deb12u1 [260 kB] Get: 152 http://deb.debian.org/debian bookworm/main arm64 libtiff6 arm64 4.5.0-6+deb12u1 [301 kB] Get: 153 http://deb.debian.org/debian bookworm/main arm64 libwebpdemux2 arm64 1.2.4-0.2+deb12u1 [99.3 kB] Get: 154 http://deb.debian.org/debian bookworm/main arm64 libwebpmux3 arm64 1.2.4-0.2+deb12u1 [109 kB] Get: 155 http://deb.debian.org/debian bookworm/main arm64 libxsimd-dev arm64 8.1.0-7 [88.8 kB] Get: 156 http://deb.debian.org/debian bookworm/main arm64 libxslt1.1 arm64 1.1.35-1 [231 kB] Get: 157 http://deb.debian.org/debian bookworm/main arm64 libyaml-0-2 arm64 0.2.5-1 [50.4 kB] Get: 158 http://deb.debian.org/debian bookworm/main arm64 libzmq5 arm64 4.3.4-6 [244 kB] Get: 159 http://deb.debian.org/debian bookworm/main arm64 llvm-14-runtime arm64 1:14.0.6-12 [428 kB] Get: 160 http://deb.debian.org/debian bookworm/main arm64 llvm-14-linker-tools arm64 1:14.0.6-12 [1092 kB] Get: 161 http://deb.debian.org/debian bookworm/main arm64 llvm-14 arm64 1:14.0.6-12 [10.0 MB] Get: 162 http://deb.debian.org/debian bookworm/main arm64 pandoc-data all 2.17.1.1-2~deb12u1 [418 kB] Get: 163 http://deb.debian.org/debian bookworm/main arm64 pandoc arm64 2.17.1.1-2~deb12u1 [29.0 MB] Get: 164 http://deb.debian.org/debian bookworm/main arm64 python3-typing-extensions all 4.4.0-1 [45.2 kB] Get: 165 http://deb.debian.org/debian bookworm/main arm64 python3-more-itertools all 8.10.0-2 [53.0 kB] Get: 166 http://deb.debian.org/debian bookworm/main arm64 python3-zipp all 1.0.0-6 [6696 B] Get: 167 http://deb.debian.org/debian bookworm/main arm64 python3-importlib-metadata all 4.12.0-1 [24.9 kB] Get: 168 http://deb.debian.org/debian bookworm/main arm64 python3-packaging all 23.0-1 [32.5 kB] Get: 169 http://deb.debian.org/debian bookworm/main arm64 python3-pep517 all 0.13.0-2 [17.4 kB] Get: 170 http://deb.debian.org/debian bookworm/main arm64 python3-toml all 0.10.2-1 [16.2 kB] Get: 171 http://deb.debian.org/debian bookworm/main arm64 python3-wheel all 0.38.4-2 [30.8 kB] Get: 172 http://deb.debian.org/debian bookworm/main arm64 python3-build all 0.9.0-1 [20.7 kB] Get: 173 http://deb.debian.org/debian bookworm/main arm64 python3-installer all 0.6.0+dfsg1-1 [18.1 kB] Get: 174 http://deb.debian.org/debian bookworm/main arm64 pybuild-plugin-pyproject all 5.20230130+deb12u1 [9184 B] Get: 175 http://deb.debian.org/debian bookworm/main arm64 python-babel-localedata all 2.10.3-1 [5615 kB] Get: 176 http://deb.debian.org/debian bookworm/main arm64 python-matplotlib-data all 3.6.3-1 [2744 kB] Get: 177 http://deb.debian.org/debian bookworm/main arm64 python-tinycss2-common all 1.2.1-2 [31.5 kB] Get: 178 http://deb.debian.org/debian bookworm/main arm64 python3-alabaster all 0.7.12-1 [20.8 kB] Get: 179 http://deb.debian.org/debian bookworm/main arm64 python3-all arm64 3.11.2-1+b1 [1064 B] Get: 180 http://deb.debian.org/debian bookworm/main arm64 python3.11-dev arm64 3.11.2-6 [617 kB] Get: 181 http://deb.debian.org/debian bookworm/main arm64 python3-dev arm64 3.11.2-1+b1 [26.2 kB] Get: 182 http://deb.debian.org/debian bookworm/main arm64 python3-all-dev arm64 3.11.2-1+b1 [1076 B] Get: 183 http://deb.debian.org/debian bookworm/main arm64 python3-sniffio all 1.2.0-1 [6372 B] Get: 184 http://deb.debian.org/debian bookworm/main arm64 python3-anyio all 3.6.2-1 [54.0 kB] Get: 185 http://deb.debian.org/debian bookworm/main arm64 python3-appdirs all 1.4.4-3 [13.0 kB] Get: 186 http://deb.debian.org/debian bookworm/main arm64 python3-cffi-backend arm64 1.15.1-5+b1 [84.4 kB] Get: 187 http://deb.debian.org/debian bookworm/main arm64 python3-argon2 arm64 21.1.0-2 [23.1 kB] Get: 188 http://deb.debian.org/debian bookworm/main arm64 python3-attr all 22.2.0-1 [65.4 kB] Get: 189 http://deb.debian.org/debian bookworm/main arm64 python3-tz all 2022.7.1-4 [30.1 kB] Get: 190 http://deb.debian.org/debian bookworm/main arm64 python3-babel all 2.10.3-1 [103 kB] Get: 191 http://deb.debian.org/debian bookworm/main arm64 python3-gast all 0.5.2-2 [9364 B] Get: 192 http://deb.debian.org/debian bookworm/main arm64 python3-beniget all 0.4.1-3 [9920 B] Get: 193 http://deb.debian.org/debian bookworm/main arm64 python3-webencodings all 0.5.1-5 [11.1 kB] Get: 194 http://deb.debian.org/debian bookworm/main arm64 python3-html5lib all 1.1-3 [93.0 kB] Get: 195 http://deb.debian.org/debian bookworm/main arm64 python3-bleach all 5.0.1-2 [48.5 kB] Get: 196 http://deb.debian.org/debian bookworm/main arm64 python3-brotli arm64 1.0.9-2+b6 [281 kB] Get: 197 http://deb.debian.org/debian bookworm/main arm64 python3-soupsieve all 2.3.2-1 [38.8 kB] Get: 198 http://deb.debian.org/debian bookworm/main arm64 python3-bs4 all 4.11.2-2 [121 kB] Get: 199 http://deb.debian.org/debian bookworm/main arm64 python3-commonmark all 0.9.1-4 [45.1 kB] Get: 200 http://deb.debian.org/debian bookworm/main arm64 python3-numpy arm64 1:1.24.2-1 [4751 kB] Get: 201 http://deb.debian.org/debian bookworm/main arm64 python3-contourpy arm64 1.0.7-1+b1 [154 kB] Get: 202 http://deb.debian.org/debian bookworm/main arm64 python3-coverage arm64 6.5.0+dfsg1-2+b1 [153 kB] Get: 203 http://deb.debian.org/debian bookworm/main arm64 python3-cycler all 0.11.0-1 [8020 B] Get: 204 http://deb.debian.org/debian bookworm/main arm64 python3-dateutil all 2.8.2-2 [78.3 kB] Get: 205 http://deb.debian.org/debian bookworm/main arm64 python3-decorator all 5.1.1-3 [14.9 kB] Get: 206 http://deb.debian.org/debian bookworm/main arm64 python3-defusedxml all 0.7.1-2 [43.3 kB] Get: 207 http://deb.debian.org/debian bookworm/main arm64 python3-entrypoints all 0.4-2 [7184 B] Get: 208 http://deb.debian.org/debian bookworm/main arm64 python3-execnet all 1.9.0-1 [41.5 kB] Get: 209 http://deb.debian.org/debian bookworm/main arm64 python3-fastjsonschema all 2.16.3-2 [21.6 kB] Get: 210 http://deb.debian.org/debian bookworm/main arm64 python3-ply all 3.11-5 [65.8 kB] Get: 211 http://deb.debian.org/debian bookworm/main arm64 python3-pythran arm64 0.11.0+ds-7 [427 kB] Get: 212 http://deb.debian.org/debian bookworm/main arm64 python3-scipy arm64 1.10.1-2 [14.2 MB] Get: 213 http://deb.debian.org/debian bookworm/main arm64 python3-ufolib2 all 0.14.0+dfsg1-1 [34.3 kB] Get: 214 http://deb.debian.org/debian bookworm/main arm64 python3-mpmath all 1.2.1-2 [418 kB] Get: 215 http://deb.debian.org/debian bookworm/main arm64 python3-sympy all 1.11.1-1 [4358 kB] Get: 216 http://deb.debian.org/debian bookworm/main arm64 python3-fs all 2.4.16-2 [95.2 kB] Get: 217 http://deb.debian.org/debian bookworm/main arm64 python3-lxml arm64 4.9.2-1+b1 [1074 kB] Get: 218 http://deb.debian.org/debian bookworm/main arm64 python3-lz4 arm64 4.0.2+dfsg-1+b2 [25.0 kB] Get: 219 http://deb.debian.org/debian bookworm/main arm64 unicode-data all 15.0.0-1 [7984 kB] Get: 220 http://deb.debian.org/debian bookworm/main arm64 python3-fonttools arm64 4.38.0-1+b1 [990 kB] Get: 221 http://deb.debian.org/debian bookworm/main arm64 python3-imagesize all 1.4.1-1 [6688 B] Get: 222 http://deb.debian.org/debian bookworm/main arm64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 223 http://deb.debian.org/debian bookworm/main arm64 python3-isort all 5.6.4-1 [63.2 kB] Get: 224 http://deb.debian.org/debian bookworm/main arm64 python3-markupsafe arm64 2.1.2-1+b1 [13.3 kB] Get: 225 http://deb.debian.org/debian bookworm/main arm64 python3-jinja2 all 3.1.2-1 [119 kB] Get: 226 http://deb.debian.org/debian bookworm/main arm64 python3-json5 all 0.9.10-1 [15.3 kB] Get: 227 http://deb.debian.org/debian bookworm/main arm64 python3-pyrsistent arm64 0.18.1-1+b3 [59.4 kB] Get: 228 http://deb.debian.org/debian bookworm/main arm64 python3-jsonschema all 4.10.3-1 [67.9 kB] Get: 229 http://deb.debian.org/debian bookworm/main arm64 python3-traitlets all 5.5.0-1 [92.4 kB] Get: 230 http://deb.debian.org/debian bookworm/main arm64 python3-jupyter-core all 4.12.0-1 [27.3 kB] Get: 231 http://deb.debian.org/debian bookworm/main arm64 python3-nest-asyncio all 1.5.4-1 [6248 B] Get: 232 http://deb.debian.org/debian bookworm/main arm64 python3-tornado arm64 6.2.0-3 [337 kB] Get: 233 http://deb.debian.org/debian bookworm/main arm64 python3-py all 1.11.0-1 [89.2 kB] Get: 234 http://deb.debian.org/debian bookworm/main arm64 python3-zmq arm64 24.0.1-4+b1 [249 kB] Get: 235 http://deb.debian.org/debian bookworm/main arm64 python3-jupyter-client all 7.4.9-2 [103 kB] Get: 236 http://deb.debian.org/debian bookworm/main arm64 python3-pygments all 2.14.0+dfsg-1 [783 kB] Get: 237 http://deb.debian.org/debian bookworm/main arm64 python3-jupyterlab-pygments all 0.2.2-3 [6096 B] Get: 238 http://deb.debian.org/debian bookworm/main arm64 python3-nbformat all 5.5.0-1 [43.2 kB] Get: 239 http://deb.debian.org/debian bookworm/main arm64 python3-nbclient all 0.7.2-1 [62.1 kB] Get: 240 http://deb.debian.org/debian bookworm/main arm64 python3-pandocfilters all 1.5.0-1 [23.7 kB] Get: 241 http://deb.debian.org/debian bookworm/main arm64 python3-tinycss2 all 1.2.1-2 [21.9 kB] Get: 242 http://deb.debian.org/debian bookworm/main arm64 python3-nbconvert all 6.5.3-3 [163 kB] Get: 243 http://deb.debian.org/debian bookworm/main arm64 python3-prometheus-client all 0.16.0-0.1 [45.2 kB] Get: 244 http://deb.debian.org/debian bookworm/main arm64 python3-send2trash all 1.8.1~b0-2 [16.3 kB] Get: 245 http://deb.debian.org/debian bookworm/main arm64 python3-ptyprocess all 0.7.0-5 [14.7 kB] Get: 246 http://deb.debian.org/debian bookworm/main arm64 python3-terminado all 0.17.0-1 [19.2 kB] Get: 247 http://deb.debian.org/debian bookworm/main arm64 python3-websocket all 1.2.3-1 [40.4 kB] Get: 248 http://deb.debian.org/debian bookworm/main arm64 python3-jupyter-server all 1.23.3-1 [165 kB] Get: 249 http://deb.debian.org/debian bookworm/main arm64 sphinx-common all 5.3.0-4 [653 kB] Get: 250 http://deb.debian.org/debian bookworm/main arm64 python3-snowballstemmer all 2.2.0-2 [57.8 kB] Get: 251 http://deb.debian.org/debian bookworm/main arm64 python3-sphinx all 5.3.0-4 [549 kB] Get: 252 http://deb.debian.org/debian bookworm/main arm64 python3-nbsphinx all 0.8.11+ds-1 [36.1 kB] Get: 253 http://deb.debian.org/debian bookworm/main arm64 python3-recommonmark all 0.7.1+ds-5 [17.3 kB] Get: 254 http://deb.debian.org/debian bookworm/main arm64 python3-jupyter-sphinx-theme all 0.0.6+ds1-11 [2976 B] Get: 255 http://deb.debian.org/debian bookworm/main arm64 python3-jupyterlab-server all 2.16.5-1 [48.5 kB] Get: 256 http://deb.debian.org/debian bookworm/main arm64 python3-kiwisolver arm64 1.4.4-1+b1 [55.4 kB] Get: 257 http://deb.debian.org/debian bookworm/main arm64 python3-llvmlite arm64 0.39.1-2 [136 kB] Get: 258 http://deb.debian.org/debian bookworm/main arm64 python3-pil arm64 9.4.0-1.1+b1 [452 kB] Get: 259 http://deb.debian.org/debian bookworm/main arm64 python3-tk arm64 3.11.2-3 [97.7 kB] Get: 260 http://deb.debian.org/debian bookworm/main arm64 python3-pil.imagetk arm64 9.4.0-1.1+b1 [74.4 kB] Get: 261 http://deb.debian.org/debian bookworm/main arm64 python3-pyparsing all 3.0.9-1 [138 kB] Get: 262 http://deb.debian.org/debian bookworm/main arm64 python3-matplotlib arm64 3.6.3-1+b1 [6774 kB] Get: 263 http://deb.debian.org/debian bookworm/main arm64 python3-numba arm64 0.56.4+dfsg-2 [1696 kB] Get: 264 http://deb.debian.org/debian bookworm/main arm64 python3-numpydoc all 1.5.0-1 [43.0 kB] Get: 265 http://deb.debian.org/debian bookworm/main arm64 python3-pandas-lib arm64 1.5.3+dfsg-2 [3048 kB] Get: 266 http://deb.debian.org/debian bookworm/main arm64 python3-pandas all 1.5.3+dfsg-2 [2885 kB] Get: 267 http://deb.debian.org/debian bookworm/main arm64 python3-setuptools all 66.1.1-1 [521 kB] Get: 268 http://deb.debian.org/debian bookworm/main arm64 python3-pbr all 5.10.0-2 [61.4 kB] Get: 269 http://deb.debian.org/debian bookworm/main arm64 python3-tenacity all 8.2.1-1 [43.6 kB] Get: 270 http://deb.debian.org/debian bookworm/main arm64 python3-plotly all 5.4.1+dfsg-1 [2613 kB] Get: 271 http://deb.debian.org/debian bookworm/main arm64 python3-pluggy all 1.0.0+repack-1 [19.7 kB] Get: 272 http://deb.debian.org/debian bookworm/main arm64 python3-pytest all 7.2.1-2 [236 kB] Get: 273 http://deb.debian.org/debian bookworm/main arm64 python3-pytest-cov all 4.0.0-1 [26.1 kB] Get: 274 http://deb.debian.org/debian bookworm/main arm64 python3-pytest-xdist all 3.1.0-1 [39.6 kB] Get: 275 http://deb.debian.org/debian bookworm/main arm64 python3-scitrack all 2021.5.3-3 [9272 B] Get: 276 http://deb.debian.org/debian bookworm/main arm64 python3-sphinx-gallery all 0.10.1-3 [122 kB] Get: 277 http://deb.debian.org/debian bookworm/main arm64 python3-tinydb all 3.15.2-4 [20.8 kB] Get: 278 http://deb.debian.org/debian bookworm/main arm64 python3-tqdm all 4.64.1-1 [97.7 kB] Fetched 208 MB in 5s (43.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libjs-jquery. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 18171 files and directories currently installed.) Preparing to unpack .../libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Selecting previously unselected package libjs-jquery-hotkeys. Preparing to unpack .../libjs-jquery-hotkeys_0~20130707+git2d51e3a9+dfsg-2.1_all.deb ... Unpacking libjs-jquery-hotkeys (0~20130707+git2d51e3a9+dfsg-2.1) ... Selecting previously unselected package libpython3.11-minimal:arm64. Preparing to unpack .../libpython3.11-minimal_3.11.2-6_arm64.deb ... Unpacking libpython3.11-minimal:arm64 (3.11.2-6) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.5.0-1_arm64.deb ... Unpacking libexpat1:arm64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-6_arm64.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:arm64 (3.11.2-6) ... Setting up libexpat1:arm64 (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 18513 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_arm64.deb ... Unpacking python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.0.0_all.deb ... Unpacking media-types (10.0.0) ... Selecting previously unselected package readline-common. Preparing to unpack .../2-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package libreadline8:arm64. Preparing to unpack .../3-libreadline8_8.2-1.3_arm64.deb ... Unpacking libreadline8:arm64 (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:arm64. Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_arm64.deb ... Unpacking libpython3.11-stdlib:arm64 (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../5-python3.11_3.11.2-6_arm64.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../6-libpython3-stdlib_3.11.2-1+b1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.11.2-1+b1) ... Setting up python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 18947 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.2-1+b1_arm64.deb ... Unpacking python3 (3.11.2-1+b1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package tzdata. Preparing to unpack .../002-tzdata_2023c-5+deb12u1_all.deb ... Unpacking tzdata (2023c-5+deb12u1) ... 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Selecting previously unselected package python3-pil:arm64. Preparing to unpack .../245-python3-pil_9.4.0-1.1+b1_arm64.deb ... Unpacking python3-pil:arm64 (9.4.0-1.1+b1) ... Selecting previously unselected package python3-tk:arm64. Preparing to unpack .../246-python3-tk_3.11.2-3_arm64.deb ... Unpacking python3-tk:arm64 (3.11.2-3) ... Selecting previously unselected package python3-pil.imagetk:arm64. Preparing to unpack .../247-python3-pil.imagetk_9.4.0-1.1+b1_arm64.deb ... Unpacking python3-pil.imagetk:arm64 (9.4.0-1.1+b1) ... Selecting previously unselected package python3-pyparsing. Preparing to unpack .../248-python3-pyparsing_3.0.9-1_all.deb ... Unpacking python3-pyparsing (3.0.9-1) ... Selecting previously unselected package python3-matplotlib. Preparing to unpack .../249-python3-matplotlib_3.6.3-1+b1_arm64.deb ... Unpacking python3-matplotlib (3.6.3-1+b1) ... Selecting previously unselected package python3-numba. Preparing to unpack .../250-python3-numba_0.56.4+dfsg-2_arm64.deb ... Unpacking python3-numba (0.56.4+dfsg-2) ... Selecting previously unselected package python3-numpydoc. Preparing to unpack .../251-python3-numpydoc_1.5.0-1_all.deb ... Unpacking python3-numpydoc (1.5.0-1) ... Selecting previously unselected package python3-pandas-lib:arm64. Preparing to unpack .../252-python3-pandas-lib_1.5.3+dfsg-2_arm64.deb ... Unpacking python3-pandas-lib:arm64 (1.5.3+dfsg-2) ... Selecting previously unselected package python3-pandas. Preparing to unpack .../253-python3-pandas_1.5.3+dfsg-2_all.deb ... Unpacking python3-pandas (1.5.3+dfsg-2) ... Selecting previously unselected package python3-setuptools. Preparing to unpack .../254-python3-setuptools_66.1.1-1_all.deb ... Unpacking python3-setuptools (66.1.1-1) ... Selecting previously unselected package python3-pbr. Preparing to unpack .../255-python3-pbr_5.10.0-2_all.deb ... Unpacking python3-pbr (5.10.0-2) ... Selecting previously unselected package python3-tenacity. Preparing to unpack .../256-python3-tenacity_8.2.1-1_all.deb ... Unpacking python3-tenacity (8.2.1-1) ... Selecting previously unselected package python3-plotly. Preparing to unpack .../257-python3-plotly_5.4.1+dfsg-1_all.deb ... Unpacking python3-plotly (5.4.1+dfsg-1) ... Selecting previously unselected package python3-pluggy. Preparing to unpack .../258-python3-pluggy_1.0.0+repack-1_all.deb ... Unpacking python3-pluggy (1.0.0+repack-1) ... Selecting previously unselected package python3-pytest. Preparing to unpack .../259-python3-pytest_7.2.1-2_all.deb ... Unpacking python3-pytest (7.2.1-2) ... Selecting previously unselected package python3-pytest-cov. Preparing to unpack .../260-python3-pytest-cov_4.0.0-1_all.deb ... Unpacking python3-pytest-cov (4.0.0-1) ... Selecting previously unselected package python3-pytest-xdist. Preparing to unpack .../261-python3-pytest-xdist_3.1.0-1_all.deb ... Unpacking python3-pytest-xdist (3.1.0-1) ... Selecting previously unselected package python3-scitrack. Preparing to unpack .../262-python3-scitrack_2021.5.3-3_all.deb ... Unpacking python3-scitrack (2021.5.3-3) ... Selecting previously unselected package python3-sphinx-gallery. Preparing to unpack .../263-python3-sphinx-gallery_0.10.1-3_all.deb ... Unpacking python3-sphinx-gallery (0.10.1-3) ... Selecting previously unselected package python3-tinydb. Preparing to unpack .../264-python3-tinydb_3.15.2-4_all.deb ... Unpacking python3-tinydb (3.15.2-4) ... Selecting previously unselected package python3-tqdm. Preparing to unpack .../265-python3-tqdm_4.64.1-1_all.deb ... Unpacking python3-tqdm (4.64.1-1) ... Setting up media-types (10.0.0) ... Setting up libpipeline1:arm64 (1.5.7-1) ... Setting up libgraphite2-3:arm64 (1.3.14-1) ... Setting up liblcms2-2:arm64 (2.14-2) ... Setting up libxau6:arm64 (1:1.0.9-1) ... Setting up libpsl5:arm64 (0.21.2-1) ... Setting up libboost1.74-dev:arm64 (1.74.0+ds1-21) ... Setting up libsodium23:arm64 (1.0.18-1) ... Setting up libicu72:arm64 (72.1-3) ... Setting up liblerc4:arm64 (4.0.0+ds-2) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:arm64 (0.2.5-1) ... Setting up libglib2.0-0:arm64 (2.74.6-2) ... No schema files found: doing nothing. Setting up fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... Setting up libpgm-5.3-0:arm64 (5.3.128~dfsg-2) ... Setting up fonts-lyx (2.3.7-1) ... Setting up libargon2-1:arm64 (0~20171227-0.3+deb12u1) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libbrotli1:arm64 (1.0.9-2+b6) ... Setting up libnorm1:arm64 (1.5.9+dfsg-2) ... Setting up x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libnghttp2-14:arm64 (1.52.0-1+deb12u1) ... Setting up libmagic1:arm64 (1:5.44-3) ... Setting up libdeflate0:arm64 (1.14-1) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up libqhull-r8.0:arm64 (2020.2-5) ... Setting up file (1:5.44-3) ... Setting up libjs-jquery-throttle-debounce (1.1+dfsg.1-2) ... Setting up libjbig0:arm64 (2.1-6.1) ... Setting up python-babel-localedata (2.10.3-1) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg-10) ... Setting up tzdata (2023c-5+deb12u1) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Jan 10 23:42:04 UTC 2025. Universal Time is now: Fri Jan 10 23:42:04 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up unicode-data (15.0.0-1) ... Setting up libxsimd-dev:arm64 (8.1.0-7) ... Setting up autotools-dev (20220109.1) ... Setting up libz3-4:arm64 (4.8.12-3.1) ... Setting up libblas3:arm64 (3.11.0-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libpfm4:arm64 (4.13.0-1) ... Setting up libexpat1-dev:arm64 (2.5.0-1) ... Setting up libjpeg62-turbo:arm64 (1:2.1.5-2) ... Setting up libx11-data (2:1.8.4-2+deb12u2) ... Setting up libnspr4:arm64 (2:4.35-1) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libjs-bootswatch (3.3.7+dfsg2-1.1) ... Setting up libfribidi0:arm64 (1.0.8-2.1) ... Setting up libimagequant0:arm64 (2.17.0-1) ... Setting up libpng16-16:arm64 (1.6.39-2) ... Setting up libtcl8.6:arm64 (8.6.13+dfsg-2) ... Setting up autopoint (0.21-12) ... Setting up fonts-dejavu-core (2.37-6) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg-10) ... Setting up libgfortran5:arm64 (12.2.0-14) ... Setting up autoconf (2.71-3) ... Setting up libwebp7:arm64 (1.2.4-0.2+deb12u1) ... Setting up zlib1g-dev:arm64 (1:1.2.13.dfsg-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libtiff6:arm64 (4.5.0-6+deb12u1) ... Setting up libuchardet0:arm64 (0.0.7-1) ... Setting up liblua5.3-0:arm64 (5.3.6-2) ... Setting up python-tinycss2-common (1.2.1-2) ... Setting up libjson-perl (4.10000-1) ... Setting up libopenjp2-7:arm64 (2.5.0-2) ... Setting up libsub-override-perl (0.09-4) ... Setting up libssh2-1:arm64 (1.10.0-3+b1) ... Setting up sgml-base (1.31) ... Setting up libboost-dev:arm64 (1.74.0.3) ... Setting up pandoc-data (2.17.1.1-2~deb12u1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libjs-jquery-hotkeys (0~20130707+git2d51e3a9+dfsg-2.1) ... Setting up python-matplotlib-data (3.6.3-1) ... Setting up openssl (3.0.11-1~deb12u2) ... Setting up libwebpmux3:arm64 (1.2.4-0.2+deb12u1) ... Setting up libbsd0:arm64 (0.11.7-2) ... Setting up libelf1:arm64 (0.188-2.1) ... Setting up readline-common (8.2-1.3) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.3~deb12u1) ... Setting up libjs-bootstrap (3.4.1+dfsg-3) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 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 libxdmcp6:arm64 (1:1.1.2-3) ... Setting up liblapack3:arm64 (3.11.0-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up libxcb1:arm64 (1.15-1) ... Setting up gettext (0.21-12) ... Setting up libopenblas0-pthread:arm64 (0.3.21+ds-4) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/openblas-pthread/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode update-alternatives: using /usr/lib/aarch64-linux-gnu/openblas-pthread/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode update-alternatives: using /usr/lib/aarch64-linux-gnu/openblas-pthread/libopenblas.so.0 to provide /usr/lib/aarch64-linux-gnu/libopenblas.so.0 (libopenblas.so.0-aarch64-linux-gnu) in auto mode Setting up libzmq5:arm64 (4.3.4-6) ... Setting up libtool (2.4.7-5) ... Setting up fontconfig-config (2.14.1-4) ... Setting up libwebpdemux2:arm64 (1.2.4-0.2+deb12u1) ... Setting up libedit2:arm64 (3.1-20221030-2) ... Setting up libreadline8:arm64 (8.2-1.3) ... Setting up libnss3:arm64 (2:3.87.1-1) ... Setting up libldap-2.5-0:arm64 (2.5.13+dfsg-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 140 added, 0 removed; done. Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up pandoc (2.17.1.1-2~deb12u1) ... Setting up libfreetype6:arm64 (2.12.1+dfsg-5) ... Setting up libjs-jquery-metadata (12-4) ... Setting up libjs-jquery-isonscreen (1.2.0-1.1) ... Setting up libjs-sphinxdoc (5.3.0-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libllvm14:arm64 (1:14.0.6-12) ... Setting up dwz (0.15-1) ... Setting up libjs-jquery-tablesorter (1:2.31.3+dfsg1-3) ... Setting up libopenblas0:arm64 (0.3.21+ds-4) ... Setting up groff-base (1.22.4-10) ... Setting up xml-core (0.18+nmu1) ... Setting up libxslt1.1:arm64 (1.1.35-1) ... Setting up libx11-6:arm64 (2:1.8.4-2+deb12u2) ... Setting up libharfbuzz0b:arm64 (6.0.0+dfsg-3) ... Setting up libfontconfig1:arm64 (2.14.1-4) ... Setting up llvm-14-linker-tools (1:14.0.6-12) ... Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1) ... Setting up libopenblas-pthread-dev:arm64 (0.3.21+ds-4) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/openblas-pthread/libblas.so to provide /usr/lib/aarch64-linux-gnu/libblas.so (libblas.so-aarch64-linux-gnu) in auto mode update-alternatives: using /usr/lib/aarch64-linux-gnu/openblas-pthread/liblapack.so to provide /usr/lib/aarch64-linux-gnu/liblapack.so (liblapack.so-aarch64-linux-gnu) in auto mode update-alternatives: using /usr/lib/aarch64-linux-gnu/openblas-pthread/libopenblas.so to provide /usr/lib/aarch64-linux-gnu/libopenblas.so (libopenblas.so-aarch64-linux-gnu) in auto mode Setting up libxrender1:arm64 (1:0.9.10-1.1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:arm64 (3.11.2-6) ... Setting up libxext6:arm64 (2:1.3.4-1+b1) ... Setting up nss-plugin-pem:arm64 (1.0.8+1-1) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libopenblas-dev:arm64 (0.3.21+ds-4) ... Setting up llvm-14-runtime (1:14.0.6-12) ... Setting up libraqm0:arm64 (0.7.0-4.1) ... Setting up sphinx-common (5.3.0-4) ... Setting up libcurl3-nss:arm64 (7.88.1-10+deb12u4) ... Setting up libxss1:arm64 (1:1.2.3-1) ... Setting up libpython3-stdlib:arm64 (3.11.2-1+b1) ... Setting up llvm-14 (1:14.0.6-12) ... Setting up python3.11 (3.11.2-6) ... Setting up libxft2:arm64 (2.3.6-1) ... Setting up libpython3.11:arm64 (3.11.2-6) ... Setting up libtk8.6:arm64 (8.6.13-2) ... Setting up debhelper (13.11.4) ... Setting up python3 (3.11.2-1+b1) ... Setting up python3-pandocfilters (1.5.0-1) ... Setting up python3-markupsafe (2.1.2-1+b1) ... Setting up python3-webencodings (0.5.1-5) ... Setting up python3-tz (2022.7.1-4) ... Setting up python3-six (1.16.0-4) ... Setting up python3-llvmlite (0.39.1-2) ... 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 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:arm64 (3.11.2-6) ... Setting up python3-nest-asyncio (1.5.4-1) ... Setting up python3-brotli (1.0.9-2+b6) ... Setting up python3-cycler (0.11.0-1) ... Setting up python3-kiwisolver (1.4.4-1+b1) ... Setting up python3-idna (3.3-1) ... Setting up cython3 (0.29.32-2+b1) ... 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 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 python3-fastjsonschema (2.16.3-2) ... Setting up python3-pyrsistent:arm64 (0.18.1-1+b3) ... Setting up python3-lxml:arm64 (4.9.2-1+b1) ... Setting up python3-traitlets (5.5.0-1) ... Setting up python3-scitrack (2021.5.3-3) ... Setting up python3-dateutil (2.8.2-2) ... Setting up python3-mpmath (1.2.1-2) ... Setting up python3-execnet (1.9.0-1) ... Setting up python3-lib2to3 (3.11.2-3) ... Setting up python3-tomli-w (1.0.0-2) ... Setting up python3-appdirs (1.4.4-3) ... Setting up python3-soupsieve (2.3.2-1) ... Setting up python3-websocket (1.2.3-1) ... Setting up python3-cffi-backend:arm64 (1.15.1-5+b1) ... 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 (3.11.2-3) ... Setting up dh-python (5.20230130+deb12u1) ... 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 tk8.6-blt2.5 (2.5.3+dfsg-4.1) ... Setting up python3-send2trash (1.8.1~b0-2) ... Setting up python3-tinycss2 (1.2.1-2) ... Setting up libpython3-dev:arm64 (3.11.2-1+b1) ... Setting up python3-setuptools (66.1.1-1) ... Setting up python3-tomli (2.0.1-2) ... 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-1+b2) ... Setting up python3-defusedxml (0.7.1-2) ... Setting up python3-json5 (0.9.10-1) ... Setting up python3-pbr (5.10.0-2) ... Setting up python3.11-dev (3.11.2-6) ... Setting up python3-charset-normalizer (3.0.1-2) ... Setting up python3-pytest (7.2.1-2) ... Setting up python3-alabaster (0.7.12-1) ... Setting up blt (2.5.3+dfsg-4.1) ... 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 python3-all (3.11.2-1+b1) ... Setting up python3-coverage (6.5.0+dfsg1-2+b1) ... Setting up python3-tk:arm64 (3.11.2-3) ... Setting up python3-pytest-cov (4.0.0-1) ... Setting up python3-zipp (1.0.0-6) ... Setting up python3-wheel (0.38.4-2) ... 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 python3-pygments (2.14.0+dfsg-1) ... Setting up python3-chardet (5.1.0+dfsg-2) ... Setting up python3-jsonschema (4.10.3-1) ... Setting up libpython3-all-dev:arm64 (3.11.2-1+b1) ... Setting up python3-zmq (24.0.1-4+b1) ... Setting up python3-dev (3.11.2-1+b1) ... Setting up python3-requests (2.28.1+dfsg-1) ... Setting up python3-numpy (1:1.24.2-1) ... Setting up python3-terminado (0.17.0-1) ... Setting up python3-argon2 (21.1.0-2) ... Setting up python3-contourpy (1.0.7-1+b1) ... Setting up python3-jupyter-core (4.12.0-1) ... Setting up python3-all-dev (3.11.2-1+b1) ... Setting up python3-importlib-metadata (4.12.0-1) ... Setting up python3-pytest-xdist (3.1.0-1) ... Setting up python3-pandas-lib:arm64 (1.5.3+dfsg-2) ... Setting up python3-nbformat (5.5.0-1) ... Setting up python3-jupyterlab-pygments (0.2.2-3) ... 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 python3-scipy (1.10.1-2) ... Setting up pybuild-plugin-pyproject (5.20230130+deb12u1) ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../python-cogent_2023.2.12a1+dfsg-2+deb12u1_source.changes dpkg-buildpackage: info: source package python-cogent dpkg-buildpackage: info: source version 2023.2.12a1+dfsg-2+deb12u1 dpkg-buildpackage: info: source distribution bookworm dpkg-buildpackage: info: source changed by Santiago Vila dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 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 '/build/reproducible-path/python-cogent-2023.2.12a1+dfsg' #These files are rebuilt on-the-fly for f in `find -name '*.c'` ; do \ head -n 1 "$f" | grep -q '^/\* Generated by Cython' && rm "$f" ; \ done rm -rf build build-stamp rm -rf doc/_build dh_clean make[1]: Leaving directory '/build/reproducible-path/python-cogent-2023.2.12a1+dfsg' 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 '/build/reproducible-path/python-cogent-2023.2.12a1+dfsg' 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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/.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=/build/reproducible-path/python-cogent-2023.2.12a1+dfsg http_proxy='127.0.0.1:9' /usr/bin/make html + cd doc + PYTHONPATH=/build/reproducible-path/python-cogent-2023.2.12a1+dfsg http_proxy=127.0.0.1:9 /usr/bin/make html make[2]: Entering directory '/build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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... 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[100%] pycogent /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/../src/cogent3/core/alignment.py:docstring of cogent3.core.alignment.AlignmentI.entropy_per_seq:11: CRITICAL: Unexpected section title. Notes ----- /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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. /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/../src/cogent3/core/alignment.py:docstring of cogent3.core.alignment.AlignmentI.entropy_per_seq:11: CRITICAL: Unexpected section title. Notes ----- /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/../src/cogent3/core/alignment.py:docstring of cogent3.core.alignment.ArrayAlignment:7: WARNING: Field list ends without a blank line; unexpected unindent. /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/align-codon.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/align-codon.rst:91: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aligned.info /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/align-nucleotide.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/align-nucleotide.rst:73: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aligned.info /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/align-protein.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/align-protein.rst:49: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aligned.info /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/app-help.rst:8: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import app_help app_help("omit_degenerates") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/app-overview.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/app-overview.rst:117: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: process = loader + cpos3 + writer m = process("data/primate_brca1.fasta") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/app-overview.rst:142: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: out_dstore.summary_logs /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/app-overview.rst:151: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: out_dstore.describe /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/app-overview.rst:157: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: out_dstore.summary_not_completed /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/app-overview.rst:164: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result = process.apply_to(dstore, show_progress=True) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/available-apps.rst:8: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import available_apps available_apps() /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/dstore.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/dstore.rst:38: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: m = dstore[0] m /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/dstore.rst:43: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: m.read()[:20] # truncating /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/dstore.rst:50: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: for m in dstore: print(m) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/dstore.rst:69: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore = open_data_store("data/demo-locked.sqlitedb") dstore.describe /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/dstore.rst:76: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore.unlock(force=True) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/dstore.rst:85: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore.summary_logs /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/dstore.rst:91: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore.logs /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/dstore.rst:97: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(dstore.logs[0].read()[:225]) # truncated for clarity /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/evo-ancestral-states.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/evo-ancestral-states.rst:33: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: states_result["edge.0"] /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/evo-dt-nuc-model.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/evo-dt-nuc-model.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.lf /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/evo-dt-nuc-model.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: stats["edge motif motif2 params"] /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/evo-extract-model-stats.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/evo-extract-model-stats.rst:38: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tabulated["edge params"] /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/evo-extract-model-stats.rst:49: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tabulated["global params"] /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/evo-extract-model-stats.rst:58: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tabulated["motif params"] /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/evo-hypothesis.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/evo-hypothesis.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/evo-hypothesis.rst:40: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.LR, result.df, result.pvalue /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/evo-hypothesis.rst:49: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.null /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/evo-hypothesis.rst:53: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.null.lf /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/evo-hypothesis.rst:60: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.alt.lf /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/evo-model.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/evo-model.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: gn = get_app("model", "GN") gn /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/evo-model.rst:32: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted = gn(aln) type(fitted) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/evo-model.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/evo-model.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.lf /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/evo-model.rst:56: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.lnL, fitted.nfp /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/evo-model.rst:60: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.source /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/evo-model.rst:66: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.tree, fitted.alignment /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/evo-model.rst:72: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.total_length(length_as="paralinear") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/evo-model.rst:92: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted[3] /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/evo-model-timehet.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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")], ) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/evo-model-timehet.rst:50: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.lf /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/evo-model-with-tree.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/evo-model-with-tree.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted = gn(aln) fitted /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/evo-model-with-tree.rst:51: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.lf /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/evo-natsel_neutral.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/evo-natsel_neutral.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/evo-natsel_neutral.rst:32: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.alt.lf /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/evo-natsel_sitehet.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/evo-natsel_sitehet.rst:29: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.alt.lf /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/evo-natsel_sitehet.rst:38: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: bprobs = result.alt.lf.get_bin_probs() bprobs[:, :20] /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/evo-natsel_timehet.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/evo-natsel_timehet.rst:30: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.alt.lf /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/evo-natsel_zhang.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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=' AlignedSeqsType: return val[:index] /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/app/user_function.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: first4 = up_to(index=4) first4 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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()) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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() /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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()) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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()) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:95: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(my_seq.rc()) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:101: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(my_seq.rc()) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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()) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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()) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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()) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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()) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:166: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: my_seq[1:6] /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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" /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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" /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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()) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/alignments.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/alignments.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs, make_unaligned_seqs dna = {"seq1": "ATGACC", "seq2": "ATCGCC"} seqs = make_aligned_seqs(data=dna, moltype="dna") print(type(seqs)) seqs = make_unaligned_seqs(dna, moltype="dna") print(type(seqs)) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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() /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/alignments.rst:161: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq = aln.get_gapped_seq("seq1") seq.is_gapped() print(seq) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/alignments.rst:169: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln.names aln.names /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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]) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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")) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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)) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/alignments.rst:302: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln.write("sample", format="fasta") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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() /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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]) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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]) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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] /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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] /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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", ) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/alignments.rst:500: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: nucs = aln.no_degenerates() print(nucs) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/alignments.rst:507: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: trinucs = aln.no_degenerates(motif_length=3) print(trinucs) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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]) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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]) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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]) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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]) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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"]) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/alignments.rst:576: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln.take_seqs(["Human", "Mouse"], negate=True) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/alignments.rst:605: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln.take_seqs_if(no_N_chars, negate=True) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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])) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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]) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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)) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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] /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/alignments.rst:762: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq_to_aln_map[3] seq_to_aln_map[8] /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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] /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/alignments.rst:779: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: KeyError seq_pos = aln_to_seq_map[7] /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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)) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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)) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/alignments.rst:836: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(filtered_aln.omit_gap_pos()) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/alphabet.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA, PROTEIN print(DNA.alphabet) print(PROTEIN.alphabet) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/alphabet.rst:20: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: PROTEIN.alphabet.moltype == PROTEIN /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/alphabet.rst:29: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dinuc_alphabet = DNA.alphabet.get_word_alphabet(2) print(dinuc_alphabet) trinuc_alphabet = DNA.alphabet.get_word_alphabet(3) print(trinuc_alphabet) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/alphabet.rst:39: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq = "TAGT" indices = DNA.alphabet.to_indices(seq) indices /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/alphabet.rst:48: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq = DNA.alphabet.from_indices([0, 2, 3, 0]) seq /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/annotations.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/annotations.rst:29: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: cds = seq.get_annotations_matching("CDS") print(cds) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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)]) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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)]) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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)]) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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]) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/annotations.rst:143: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: cds.get_coordinates() /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/annotations.rst:152: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: not_cds = cds.get_shadow() not_cds /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/annotations.rst:159: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: cds /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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)]) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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)] ) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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] /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/annotations.rst:209: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: s1[exon2] exon2.get_slice() /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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]) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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]) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/annotations.rst:244: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: ValueError s1[1:10, 9:15] s1[exon1, exon1] /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/annotations.rst:252: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(s1.get_region_covering_all([exon3, exon3]).get_slice()) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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]) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/annotations.rst:272: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: ValueError aln1[seq_exon] /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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() /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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]) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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] /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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] /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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]) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/annotations.rst:388: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: unified = aln_exons[0].as_one_span() print(aln3[unified]) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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]) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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]) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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="?")) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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="?")) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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)) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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() /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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)]) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/building_alignments.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/building_alignments.rst:17: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_unaligned_seqs, make_tree from cogent3.align.progressive import TreeAlign /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/building_alignments.rst:24: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seqs = load_unaligned_seqs("data/test2.fasta", moltype="dna") aln, tree = TreeAlign("HKY85", seqs, show_progress=False) aln /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/building_alignments.rst:32: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tree = make_tree( "(((NineBande:0.013,Mouse:0.185):0.023,DogFaced:0.046):0.027,Human:0.034,HowlerMon:0.019)" ) params = {"kappa": 4.0} aln, tree = TreeAlign( "HKY85", seqs, tree=tree, param_vals=params, show_progress=False ) aln /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/building_alignments.rst:48: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_unaligned_seqs, make_tree from cogent3.align.progressive import 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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/building_alignments.rst:68: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_unaligned_seqs from cogent3.align.progressive import 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) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/building_alignments.rst:88: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(unaligned_DNA.get_translation()) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/building_alignments.rst:94: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aligned_aa_seqs = [ ("hum", "KQIQESSENGSLAARQERQAQVNLT"), ("mus", "KQIQESGESGSLAARQERQAQVNLT"), ("rat", "LNKQ------PLS---------NKK"), ] aligned_aa = make_aligned_seqs(aligned_aa_seqs, moltype="protein") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/building_alignments.rst:107: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aligned_DNA = aligned_aa.replace_seqs(unaligned_DNA, aa_to_codon=True) aligned_DNA /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/building_phylogenies.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/building_phylogenies.rst:18: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna") tree = aln.quick_tree(calc="TN93", show_progress=False) tree = tree.balanced() # purely for display print(tree.ascii_art()) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/building_phylogenies.rst:29: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tree = aln.quick_tree(calc="TN93", bootstrap=100, show_progress=False) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/building_phylogenies.rst:36: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna") dists = aln.distance_matrix(calc="TN93") tree = dists.quick_tree(show_progress=False) tree = tree.balanced() # purely for display print(tree.ascii_art()) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/building_phylogenies.rst:49: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.phylo import nj aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna") dists = aln.distance_matrix(calc="TN93") tree = nj.nj(dists, show_progress=False) tree = tree.balanced() # purely for display print(tree.ascii_art()) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/building_phylogenies.rst:63: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.phylo import nj dists = {("a", "b"): 2.7, ("c", "b"): 2.33, ("c", "a"): 0.73} tree = nj.nj(dists, show_progress=False) print(tree.ascii_art()) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/building_phylogenies.rst:76: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.phylo.least_squares import WLS from cogent3.util.deserialise import deserialise_object dists = deserialise_object("data/dists_for_phylo.json") ls = WLS(dists) stat, tree = ls.trex(a=5, k=5, show_progress=False) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/building_phylogenies.rst:92: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.evolve.models import F81 from cogent3.phylo.maximum_likelihood import ML aln = load_aligned_seqs("data/primate_brca1.fasta") ml = ML(F81(), aln) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/calc_genetic_distance.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/calc_genetic_distance.rst:16: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import available_distances available_distances() /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/calc_genetic_distance.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna") dists = aln.distance_matrix(calc="tn93", show_progress=False) dists /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/calc_genetic_distance.rst:38: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_distance_calculator, load_aligned_seqs aln = load_aligned_seqs("data/primate_brca1.fasta") dist_calc = get_distance_calculator("tn93", alignment=aln) dist_calc /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/calc_genetic_distance.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dist_calc.run(show_progress=False) dists = dist_calc.get_pairwise_distances() dists /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/calc_genetic_distance.rst:54: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dist_calc.stderr /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/calc_genetic_distance.rst:65: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_model, load_aligned_seqs from cogent3.evolve import distance aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna") d = distance.EstimateDistances(aln, submodel=get_model("F81")) d.run(show_progress=False) dists = d.get_pairwise_distances() dists /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/evo_modelling.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/evo_modelling.rst:18: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import available_models available_models() /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/evo_modelling.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import get_model hky = get_model("HKY85") print(hky) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/evo_modelling.rst:44: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import get_model sub_mod = get_model("GTR", with_rate=True, distribution="gamma") print(sub_mod) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/evo_modelling.rst:56: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import get_model sub_mod = get_model("CNFGTR", with_rate=True, distribution="gamma") print(sub_mod) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/evo_modelling.rst:68: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import get_model sub_mod = get_model("JTT92", with_rate=True, distribution="gamma") print(sub_mod) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/evo_modelling.rst:80: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_tree from cogent3.evolve.models import get_model sub_mod = get_model("F81") tree = make_tree("(a,b,(c,d))") lf = sub_mod.make_likelihood_function(tree) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/evo_modelling.rst:94: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs, make_tree from cogent3.evolve.models import get_model sub_mod = get_model("F81") tree = make_tree("(a,b,(c,d))") lf = sub_mod.make_likelihood_function(tree) aln = make_aligned_seqs( [("a", "ACGT"), ("b", "AC-T"), ("c", "ACGT"), ("d", "AC-T")] ) lf.set_alignment(aln) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/evo_modelling.rst:112: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") print(tree.ascii_art()) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/evo_modelling.rst:120: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: sm = get_model("CNFGTR") lf = sm.make_likelihood_function(tree, digits=2) lf.set_param_rule( "omega", tip_names=["Human", "Orangutan"], outgroup_name="Galago", clade=True, init=0.5, ) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/evo_modelling.rst:134: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/evo_modelling.rst:145: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") sm = get_model("CNFGTR") lf = sm.make_likelihood_function(tree, digits=2) lf.set_param_rule("omega", is_constant=True) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/evo_modelling.rst:160: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") sm = get_model("CNFGTR") lf = sm.make_likelihood_function(tree, digits=2) lf.set_param_rule("omega", init=0.1) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/evo_modelling.rst:175: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") sm = get_model("CNFGTR") lf = sm.make_likelihood_function(tree, digits=2) lf.set_param_rule("omega", init=0.1, lower=1e-9, upper=20.0) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/evo_modelling.rst:190: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") sm = get_model("F81") lf = sm.make_likelihood_function(tree) lf.set_param_rule("length", upper=1.0) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/evo_modelling.rst:207: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.models import get_model sm = get_model("GTR", with_rate=True, distribution="gamma") tree = load_tree("data/primate_brca1.tree") lf = sm.make_likelihood_function(tree, bins=4, digits=2) lf.set_param_rule("bprobs", is_constant=True) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/evo_modelling.rst:222: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.models import get_model sm = get_model("GTR", with_rate=True, distribution="gamma") tree = load_tree("data/primate_brca1.tree") lf = sm.make_likelihood_function(tree, bins=4, sites_independent=False, digits=2) lf.set_param_rule("bprobs", is_constant=True) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/evo_modelling.rst:239: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") aln = load_aligned_seqs("data/primate_brca1.fasta") sm = get_model("F81") lf = sm.make_likelihood_function(tree, digits=3, space=2) lf.set_alignment(aln) lf.optimise(show_progress=False) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/evo_modelling.rst:253: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(local=True, max_restarts=5, show_progress=False) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/evo_modelling.rst:259: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(local=False, global_tolerance=1.0, show_progress=False) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/evo_modelling.rst:265: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(show_progress=False, max_restarts=5, tolerance=1e-8) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/evo_modelling.rst:276: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") aln = load_aligned_seqs("data/primate_brca1.fasta") sm = get_model("F81") lf = sm.make_likelihood_function(tree, digits=3, space=2) lf.set_alignment(aln) try: lf.optimise( show_progress=False, limit_action="raise", max_evaluations=10, return_calculator=True, ) except ArithmeticError as err: print(err) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/evo_modelling.rst:303: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model sm = get_model("GTR") tree = load_tree("data/primate_brca1.tree") lf = sm.make_likelihood_function(tree) aln = load_aligned_seqs("data/primate_brca1.fasta") lf.set_alignment(aln) lf.optimise(local=True, show_progress=False) lf /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/evo_modelling.rst:321: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lnL = lf.lnL lnL /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/evo_modelling.rst:326: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: nfp = lf.nfp nfp /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/evo_modelling.rst:338: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.get_aic() /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/evo_modelling.rst:344: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.get_aic(second_order=True) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/evo_modelling.rst:353: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.get_bic() /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/evo_modelling.rst:367: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: a_g = lf.get_param_value("A/G") a_g /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/evo_modelling.rst:372: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: human = lf.get_param_value("length", "Human") human /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/evo_modelling.rst:380: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: mprobs = lf.get_motif_probs() mprobs /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/evo_modelling.rst:388: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tables = lf.get_statistics(with_motif_probs=True, with_titles=True) tables[0] # just displaying the first /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/evo_modelling.rst:398: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") aln = load_aligned_seqs("data/primate_brca1.fasta") sm = get_model("F81") lf = sm.make_likelihood_function(tree, digits=3, space=2) lf.set_alignment(aln) lf.set_param_rule( "length", tip_names=["Human", "Chimpanzee"], outgroup_name="Galago", clade=True, is_independent=False, ) lf.set_name("Null Hypothesis") lf.optimise(local=True, show_progress=False) null_lnL = lf.lnL null_nfp = lf.nfp lf /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/evo_modelling.rst:423: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule("length", is_independent=True) lf.set_name("Alt Hypothesis") lf.optimise(local=True, show_progress=False) alt_lnL = lf.lnL alt_nfp = lf.nfp lf /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/evo_modelling.rst:434: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from scipy.stats.distributions import chi2 LR = 2 * (alt_lnL - null_lnL) # the likelihood ratio statistic df = alt_nfp - null_nfp # the test degrees of freedom p = chi2.sf(LR, df) print(f"LR={LR:.4f} ; df={df}; p={df:.4f}") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/evo_modelling.rst:450: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") aln = load_aligned_seqs("data/primate_brca1.fasta") sm = get_model("F81") lf = sm.make_likelihood_function(tree, digits=3, space=2) lf.set_alignment(aln) lf.set_param_rule( "length", tip_names=["Human", "Chimpanzee"], outgroup_name="Galago", clade=True, is_independent=False, ) lf.set_name("Null Hypothesis") lf.optimise(local=True, show_progress=False) sim_aln = lf.simulate_alignment() sim_aln[:60] /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/evo_modelling.rst:478: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") aln = load_aligned_seqs("data/primate_brca1.fasta") sm = get_model("HKY85") lf = sm.make_likelihood_function(tree) lf.set_alignment(aln) lf.optimise(local=True, show_progress=False) kappa_lo, kappa_mle, kappa_hi = lf.get_param_interval("kappa") print(f"lo={kappa_lo:.2f} ; mle={kappa_mle:.2f} ; hi={kappa_hi:.2f}") human_lo, human_mle, human_hi = lf.get_param_interval("length", "Human") print(f"lo={human_lo:.2f} ; mle={human_mle:.2f} ; hi={human_hi:.2f}") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/evo_modelling.rst:501: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model aln = make_aligned_seqs(data=dict(a="ACGG", b="ATAG", c="ATGG")) tree = make_tree(tip_names=aln.names) sm = get_model("F81") lf = sm.make_likelihood_function(tree) lf.set_alignment(aln) json = lf.to_json() json[:60] # just truncating the displayed string /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/evo_modelling.rst:516: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.deserialise import deserialise_object newlf = deserialise_object(json) newlf /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/evo_modelling.rst:528: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") aln = load_aligned_seqs("data/primate_brca1.fasta") sm = get_model("F81") lf = sm.make_likelihood_function(tree, digits=3, space=2) lf.set_alignment(aln) lf.optimise(show_progress=False) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/evo_modelling.rst:542: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: ancestors = lf.likely_ancestral_seqs() ancestors[:60] /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/evo_modelling.rst:549: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: ancestral_probs = lf.reconstruct_ancestral_seqs() ancestral_probs["root"][:5] /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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] /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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"] /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/genetic_code.rst:51: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: standard_code["A"] /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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"] /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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"] /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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()) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/genetic_code.rst:115: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from cogent3.core.alphabet import AlphabetError /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/genetic_code.rst:120: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: AlphabetError pep = my_seq.get_translation() /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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)) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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()) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/loading_sequences.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/loading_sequences.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln.info.source /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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)) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/loading_tabular.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/loading_tabular.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv") table /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/loading_tabular.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("https://raw.githubusercontent.com/cogent3/cogent3/develop/doc/data/stats.tsv") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/loading_tabular.rst:38: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv", sep="\t") table /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/loading_tabular.rst:55: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import load_delimited header, rows, title, legend = load_delimited("data/CerebellumDukeDNaseSeq.pk", header=False, sep="\t") rows[:4] /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/loading_tabular.rst:65: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(with_header=False, sep="\t") rows = list(reader("data/CerebellumDukeDNaseSeq.pk")) rows[:4] /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/loading_tabular.rst:81: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv", limit=2) table /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/loading_tabular.rst:93: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser( lambda line: float(line[2]) <= 10, with_header=True, sep="\t" ) table = load_table("data/stats.tsv", reader=reader, digits=1) table /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/loading_tabular.rst:105: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: reader = FilteringParser( lambda line: float(line[2]) <= 10, with_header=True, sep="\t", negate=True ) table = load_table("data/stats.tsv", reader=reader, digits=1) table /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/loading_tabular.rst:118: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(columns=["Locus", "Ratio"], with_header=True, sep="\t") table = load_table("data/stats.tsv", reader=reader) table /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/loading_tabular.rst:128: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(columns=[0, -1], with_header=True, sep="\t") table = load_table("data/stats.tsv", reader=reader) table /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/loading_tabular.rst:143: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(with_header=True, sep="\t") data = list(reader("data/stats.tsv")) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/loading_tabular.rst:152: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data[:2] /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/loading_tabular.rst:161: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table header = ["A", "B", "C"] rows = [range(3), range(3, 6), range(6, 9), range(9, 12)] table = make_table(header=["A", "B", "C"], data=rows) table /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/loading_tabular.rst:175: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table data = dict(A=[0, 3, 6], B=[1, 4, 7], C=[2, 5, 8]) table = make_table(data=data) table /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/loading_tabular.rst:186: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = make_table(header=["C", "A", "B"], data=data) table /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/loading_tabular.rst:196: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv", index_name="Locus") table["NP_055852"] /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/loading_tabular.rst:201: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table["NP_055852", "Region"] /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/loading_tabular.rst:210: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from pandas import DataFrame from cogent3 import make_table data = dict(a=[0, 3], b=["a", "c"]) df = DataFrame(data=data) table = make_table(data_frame=df) table /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/loading_tabular.rst:224: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table(header=["a", "b"], data=[[0, "a"], [3, "c"]]) table /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/loading_tabular.rst:236: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table data = dict(a=[0, 3], b=["a", "c"]) table = make_table(data=data) table /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/loading_tabular.rst:247: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table d2D = { "edge.parent": { "NineBande": "root", "edge.1": "root", "DogFaced": "root", "Human": "edge.0", }, "x": { "NineBande": 1.0, "edge.1": 1.0, "DogFaced": 1.0, "Human": 1.0, }, "length": { "NineBande": 4.0, "edge.1": 4.0, "DogFaced": 4.0, "Human": 4.0, }, } table = make_table( data=d2D, ) table /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/loading_tabular.rst:279: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table( header=["abcd", "data"], data=[[range(1, 6), "0"], ["x", 5.0], ["y", None]], missing_data="*", digits=1, ) table /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/loading_tabular.rst:294: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table() table /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/moltypes.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/moltypes.rst:17: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import available_moltypes available_moltypes() /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/moltypes.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs seqs = load_aligned_seqs("data/brca1-bats.fasta", moltype="dna") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/moltypes.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_moltype dna = get_moltype("dna") dna /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/moltypes.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dna.ambiguities /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/moltypes.rst:53: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dna.degenerates /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/moltypes.rst:60: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dna.complement("AGG") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/moltypes.rst:69: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq = dna.make_seq("AGGCTT", name="seq1") seq /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/moltypes.rst:77: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: rna = get_moltype("rna") rna.is_valid("ACGUACGUACGUACGU") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/moltypes.rst:87: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.core import moltype as mt DNAgapped = mt.MolType( seq_constructor=mt.DnaSequence, motifset=mt.IUPAC_DNA_chars, ambiguities=mt.IUPAC_DNA_ambiguities, complements=mt.IUPAC_DNA_ambiguities_complements, pairs=mt.DnaStandardPairs, gaps=".", ) seq = DNAgapped.make_seq("ACG.") seq /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/moltypes.rst:104: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA from cogent3.core.sequence import DnaSequence DnaSequence.moltype = DNA /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/protein_sequences.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/simple_trees.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/simple_trees.rst:14: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") print(tr.ascii_art()) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/simple_trees.rst:24: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") tr.write("data/temp.tree") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/simple_trees.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") names = tr.get_node_names() names[:4] /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/simple_trees.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: names[4:] names_nodes = tr.get_nodes_dict() names_nodes["Human"] /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/simple_trees.rst:48: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tr.get_node_matching_name("Mouse") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/simple_trees.rst:55: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") hu = tr.get_node_matching_name("Human") tr.name /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/simple_trees.rst:63: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: hu.name /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/simple_trees.rst:70: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") nodes = tr.get_nodes_dict() hu = nodes["Human"] type(hu) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/simple_trees.rst:79: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: type(tr) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/simple_trees.rst:88: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") nodes = tr.get_nodes_dict() for n in nodes.items(): print(n) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/simple_trees.rst:99: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: for n in tr.iter_tips(): print(n) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/simple_trees.rst:106: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") for n in tr.iter_nontips(): print(n.get_newick()) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/simple_trees.rst:117: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") edges = tr.get_connecting_edges("edge.1", "Human") for edge in edges: print(edge.name) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/simple_trees.rst:129: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") nodes = tr.get_nodes_dict() hu = nodes["Human"] mu = nodes["Mouse"] hu.distance(mu) hu.is_tip() /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/simple_trees.rst:143: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") nodes = tr.get_nodes_dict() hu = nodes["Human"] mu = nodes["Mouse"] lca = hu.last_common_ancestor(mu) lca /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/simple_trees.rst:154: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: type(lca) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/simple_trees.rst:161: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") hu = tr.get_node_matching_name("Human") for a in hu.ancestors(): print(a.name) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/simple_trees.rst:173: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") node = tr.get_node_matching_name("edge.1") children = list(node.iter_tips()) + list(node.iter_nontips()) for child in children: print(child.name) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/simple_trees.rst:186: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") dists = tr.get_distances() /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/simple_trees.rst:195: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: human_dists = [names for names in dists if "Human" in names] for dist in human_dists: print(dist, dists[dist]) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/simple_trees.rst:204: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") tr.max_tip_tip_distance() /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/simple_trees.rst:214: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") hu = tr.get_node_matching_name("Human") tips = hu.tips_within_distance(0.2) for t in tips: print(t) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/simple_trees.rst:230: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") print(tr.rooted_at("edge.0").ascii_art()) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/simple_trees.rst:240: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") print(tr.root_at_midpoint().ascii_art()) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/simple_trees.rst:247: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(tr.ascii_art()) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/simple_trees.rst:254: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") print(tr.ascii_art()) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/simple_trees.rst:261: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(tr.rooted_with_tip("Mouse").ascii_art()) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/simple_trees.rst:271: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") tr.get_newick() /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/simple_trees.rst:278: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tr.get_newick(with_distances=True) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/simple_trees.rst:285: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") xml = tr.get_xml() for line in xml.splitlines(): print(line) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/simple_trees.rst:299: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") print(tr.ascii_art()) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/simple_trees.rst:309: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") for t in tr.preorder(): print(t.get_newick()) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/simple_trees.rst:320: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") for t in tr.postorder(): print(t.get_newick()) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/simple_trees.rst:334: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") for tip in tr.iter_nontips(): tip_names = tip.get_tip_names() print(tip_names) sub_tree = tr.get_sub_tree(tip_names) print(sub_tree.ascii_art()) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/simple_trees.rst:348: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from cogent3.util.io import remove_files remove_files(["data/temp.tree", "data/temp.pdf"], error_on_missing=False) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/simple_trees.rst:364: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_tree simple_tree_string = "(B:0.2,(D:0.4)E:0.5)F;" simple_tree = make_tree(simple_tree_string) print(simple_tree.ascii_art()) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/simple_trees.rst:372: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: simple_tree.prune() print(simple_tree.ascii_art()) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/simple_trees.rst:377: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(simple_tree) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/simple_trees.rst:384: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr1 = load_tree("data/test.tree") print(tr1.get_newick()) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/simple_trees.rst:391: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tr2 = tr1.unrooted_deepcopy() print(tr2.get_newick()) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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()) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/simple_trees.rst:409: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(tr.bifurcating().ascii_art()) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/simple_trees.rst:422: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") print(tr.ascii_art()) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/simple_trees.rst:429: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(tr.balanced().ascii_art()) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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()) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/simple_trees.rst:475: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tr.scale_branch_lengths() print(tr) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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]) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/tables.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory cookbook/loading_tabular.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory cookbook/loading_tabular.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv") table cookbook/loading_tabular.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("https://raw.githubusercontent.com/cogent3/cogent3/develop/doc/data/stats.tsv") cookbook/loading_tabular.rst:38: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv", sep="\t") table cookbook/loading_tabular.rst:55: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import load_delimited header, rows, title, legend = load_delimited("data/CerebellumDukeDNaseSeq.pk", header=False, sep="\t") rows[:4] cookbook/loading_tabular.rst:65: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(with_header=False, sep="\t") rows = list(reader("data/CerebellumDukeDNaseSeq.pk")) rows[:4] cookbook/loading_tabular.rst:81: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv", limit=2) table cookbook/loading_tabular.rst:93: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser( lambda line: float(line[2]) <= 10, with_header=True, sep="\t" ) table = load_table("data/stats.tsv", reader=reader, digits=1) table cookbook/loading_tabular.rst:105: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: reader = FilteringParser( lambda line: float(line[2]) <= 10, with_header=True, sep="\t", negate=True ) table = load_table("data/stats.tsv", reader=reader, digits=1) table cookbook/loading_tabular.rst:118: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(columns=["Locus", "Ratio"], with_header=True, sep="\t") table = load_table("data/stats.tsv", reader=reader) table cookbook/loading_tabular.rst:128: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(columns=[0, -1], with_header=True, sep="\t") table = load_table("data/stats.tsv", reader=reader) table cookbook/loading_tabular.rst:143: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(with_header=True, sep="\t") data = list(reader("data/stats.tsv")) cookbook/loading_tabular.rst:152: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data[:2] cookbook/loading_tabular.rst:161: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table header = ["A", "B", "C"] rows = [range(3), range(3, 6), range(6, 9), range(9, 12)] table = make_table(header=["A", "B", "C"], data=rows) table cookbook/loading_tabular.rst:175: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table data = dict(A=[0, 3, 6], B=[1, 4, 7], C=[2, 5, 8]) table = make_table(data=data) table cookbook/loading_tabular.rst:186: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = make_table(header=["C", "A", "B"], data=data) table cookbook/loading_tabular.rst:196: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv", index_name="Locus") table["NP_055852"] cookbook/loading_tabular.rst:201: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table["NP_055852", "Region"] cookbook/loading_tabular.rst:210: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from pandas import DataFrame from cogent3 import make_table data = dict(a=[0, 3], b=["a", "c"]) df = DataFrame(data=data) table = make_table(data_frame=df) table cookbook/loading_tabular.rst:224: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table(header=["a", "b"], data=[[0, "a"], [3, "c"]]) table cookbook/loading_tabular.rst:236: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table data = dict(a=[0, 3], b=["a", "c"]) table = make_table(data=data) table cookbook/loading_tabular.rst:247: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table d2D = { "edge.parent": { "NineBande": "root", "edge.1": "root", "DogFaced": "root", "Human": "edge.0", }, "x": { "NineBande": 1.0, "edge.1": 1.0, "DogFaced": 1.0, "Human": 1.0, }, "length": { "NineBande": 4.0, "edge.1": 4.0, "DogFaced": 4.0, "Human": 4.0, }, } table = make_table( data=d2D, ) table cookbook/loading_tabular.rst:279: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table( header=["abcd", "data"], data=[[range(1, 6), "0"], ["x", 5.0], ["y", None]], missing_data="*", digits=1, ) table cookbook/loading_tabular.rst:294: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table() table /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/tables.rst:21: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table() table.columns["a"] = [1, 3, 5] table.columns["b"] = [2, 4, 6] table /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/tables.rst:35: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table data = dict(a=[0, 3], b=["a", "c"]) table = make_table(data=data, title="Sample title", legend="a legend") table /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/tables.rst:45: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data = dict(a=[0, 3], b=["a", "c"]) table = make_table(data=data) table.title = "My title" table /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/tables.rst:57: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv") for row in table: print(row) break /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/tables.rst:68: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: for row in table: print(row["Locus"]) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/tables.rst:78: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table data = dict(a=[0, 3, 5], b=["a", "c", "d"]) table = make_table(data=data) table.shape[0] == 3 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/tables.rst:91: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.shape[1] == 2 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/tables.rst:100: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv") table.columns /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/tables.rst:107: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.columns["Region"] /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/tables.rst:113: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: for name in table.columns: print(name) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/tables.rst:121: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/tables.rst:128: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table[:2, "Region":] /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/tables.rst:135: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table[:2, :1] /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/tables.rst:145: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv") table.format_column("Ratio", "%.1e") table /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/tables.rst:158: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv", digits=1, space=2) table /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/tables.rst:165: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.space = " " table /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/tables.rst:175: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table h = ["name", "A/C", "A/G", "A/T", "C/A"] rows = [["tardigrade", 0.0425, 0.1424, 0.0226, 0.0391]] wrap_table = make_table(header=h, data=rows, max_width=30) wrap_table /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/tables.rst:184: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: wrap_table = make_table(header=h, data=rows, max_width=30, index_name="name") wrap_table /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/tables.rst:192: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = make_table(data=dict(a=list(range(10)), b=list(range(10)))) table.head() /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/tables.rst:199: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.head(2) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/tables.rst:208: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.tail() /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/tables.rst:214: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.tail(1) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/tables.rst:221: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.set_repr_policy(random=3) table /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/tables.rst:229: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.set_repr_policy(head=2, tail=3) table /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/tables.rst:241: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") print(table.header) table = table.with_new_header("Ratio", "Stat") print(table.header) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/tables.rst:251: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table() table /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/tables.rst:258: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.columns["a"] = [1, 3, 5] table.columns["b"] = [2, 4, 6] table /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/tables.rst:269: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table = table.with_new_column( "LargeCon", lambda r_v: r_v[0] == "Con" and r_v[1] > 10.0, columns=["Region", "Ratio"], ) table /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/tables.rst:282: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table.array /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/tables.rst:292: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") locus = table.tolist("Locus") locus /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/tables.rst:300: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.columns["Locus"].tolist() /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/tables.rst:322: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table.to_dict() /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/tables.rst:332: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table.columns.to_dict() /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/tables.rst:340: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") df = table.to_dataframe() df /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/tables.rst:348: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: df = table.to_dataframe(categories="Region") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/tables.rst:362: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: contingency = table.to_categorical(["Ts", "Tv"]) contingency /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/tables.rst:367: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: g_test = contingency.G_independence() g_test /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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="") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/tables.rst:407: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table.summed("Ratio") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/tables.rst:414: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.columns["Ratio"].sum() /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/tables.rst:434: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: all_numeric.summed() /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/tables.rst:440: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: all_numeric.summed(col_sum=False) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/tables.rst:458: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: mixed.summed(strict=False) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/tables.rst:464: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: mixed.summed(col_sum=False, strict=False) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/tables.rst:481: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: sub_table = table.filtered("Ratio < 10.0") sub_table /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/tables.rst:506: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table.sorted(columns="Ratio") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/tables.rst:514: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.sorted(columns="Ratio", reverse="Ratio") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/tables.rst:521: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.sorted(columns=["Region", "Ratio"], reverse="Ratio") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/tables.rst:528: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") raw = table.tolist("Region") raw /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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"]) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/tables.rst:574: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: unique /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/tables.rst:580: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: unique = table.count_unique(["A", "B"]) unique /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/tables.rst:585: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: r = unique.to_table() r /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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")) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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")) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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)) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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()) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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")) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/tables.rst:754: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: bgraph.head() /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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, ) ) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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() /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/tables.rst:787: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.format.table import known_formats known_formats /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/tables.rst:796: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.write("stats_tab.tex", justify="ccr", label="tab:table1") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/useful_utilities.rst:16: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: import numpy def DiffOmega(omega): def omega_from_S(S): omega_est = S / (1 - numpy.e ** (-1 * S)) return abs(omega - omega_est) ** 2 return omega_from_S omega = 0.1 f = DiffOmega(omega) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/useful_utilities.rst:32: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.optimisers import maximise, minimise S = minimise( f, # the function xinit=1.0, # the initial value bounds=(-100, 100), # [lower,upper] bounds for the parameter local=True, # just local optimisation, not Simulated Annealing show_progress=False, ) assert 0.0 <= f(S) < 1e-6 print("S=%.4f" % S) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/useful_utilities.rst:58: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: TypeError from cogent3.util.misc import iterable my_var = 10 for i in my_var: print("will not work") for i in iterable(my_var): print(i) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/useful_utilities.rst:75: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import curry def foo(x, y): """Some function""" return x + y bar = curry(foo, 5) print(bar.__doc__) bar(10) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/useful_utilities.rst:92: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import is_iterable can_iter = [1, 2, 3, 4] cannot_iter = 1.234 is_iterable(can_iter) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/useful_utilities.rst:100: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: is_iterable(cannot_iter) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/useful_utilities.rst:109: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import is_char class foo: pass is_char("a") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/useful_utilities.rst:118: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: is_char("ab") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/useful_utilities.rst:122: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: is_char(foo()) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/useful_utilities.rst:131: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import recursive_flatten l = [[[[1, 2], "abcde"], [5, 6]], [7, 8], [9, 10]] /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/useful_utilities.rst:137: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: recursive_flatten(l) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/useful_utilities.rst:146: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import not_list_tuple not_list_tuple(1) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/useful_utilities.rst:152: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: not_list_tuple([1]) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/useful_utilities.rst:156: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: not_list_tuple("ab") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/useful_utilities.rst:165: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import add_lowercase d = {"A": 5, "B": 6, "C": 7, "foo": 8, 42: "life"} add_lowercase(d) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/useful_utilities.rst:177: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from numpy import array from cogent3.util.misc import DistanceFromMatrix m = array([[1, 2, 3], [4, 5, 6], [7, 8, 9]]) f = DistanceFromMatrix(m) f(0, 0) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/useful_utilities.rst:187: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: f(1, 2) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/useful_utilities.rst:196: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import ClassChecker class not_okay(object): pass no = not_okay() class okay(object): pass o = okay() class my_dict(dict): pass md = my_dict() cc = ClassChecker(str, okay, dict) o in cc /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/useful_utilities.rst:217: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: no in cc /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/useful_utilities.rst:221: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: 5 in cc /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/useful_utilities.rst:225: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: {"a": 5} in cc /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/useful_utilities.rst:229: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: "asasas" in cc /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/useful_utilities.rst:233: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: md in cc /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/useful_utilities.rst:242: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import Delegator class ListAndString(list, Delegator): def __init__(self, items, string): Delegator.__init__(self, string) for i in items: self.append(i) ls = ListAndString([1, 2, 3], "ab_cd") len(ls) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/useful_utilities.rst:255: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: ls[0] /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/useful_utilities.rst:259: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: ls.upper() /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/useful_utilities.rst:263: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: ls.split("_") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/useful_utilities.rst:272: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import FunctionWrapper f = FunctionWrapper(str) f /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/useful_utilities.rst:279: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: f(123) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/useful_utilities.rst:290: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from cogent3.util.misc import ConstraintError /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/useful_utilities.rst:295: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import ConstrainedDict d = ConstrainedDict({"a": 1, "b": 2, "c": 3}, constraint="abc") d /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/useful_utilities.rst:302: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: ConstraintError d["d"] = 5 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/what_codes.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/what_codes.rst:10: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import available_codes available_codes() /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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] /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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] /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/cookbook/what_codes.rst:39: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code gc = get_code(4) gc /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/draw/aln/plot_aln-coevolution.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/draw/aln/plot_aln-coevolution.rst:18: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/brca1.fasta", moltype="dna") aln = aln.no_degenerates(motif_length=3) aln = aln.get_translation() aln = aln[:100] # for compute speed in testing the documentation coevo = aln.coevolution(show_progress=False, drawable="heatmap") coevo.drawable.show() /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/draw/aln/plot_aln-coevolution.rst:29: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_aln-coevolution.png" coevo.drawable.write(outpath) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/draw/aln/plot_aln-coevolution.rst:39: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: coevo = aln.coevolution(show_progress=False, drawable="violin") coevo.drawable.show(width=300) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/draw/aln/plot_aln-coevolution.rst:47: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: coevo = aln.coevolution(show_progress=False, drawable="box") coevo.drawable.show(width=300) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/draw/aln/plot_aln-dotplot-1.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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() /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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() /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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() /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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() /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/draw/aln/plot_aln-dotplot-2.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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() /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/draw/aln/plot_aln-dotplot-2.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_aln-dotplot-2.png" dp.write(outpath) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/draw/aln/plot_aln-dotplot-2.rst:35: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: help(dp.remove_track) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/draw/aln/plot_aln-dotplot-2.rst:41: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dp.remove_track(left_track=True) dp.show() /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/draw/aln/plot_aln-gaps-per-seq.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/draw/aln/plot_aln-gaps-per-seq.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/brca1.fasta", moltype="dna") counts = aln.count_gaps_per_seq(unique=True) counts[10: 20] # limiting the width of the displayed output /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/draw/aln/plot_aln-gaps-per-seq.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: counts = aln.count_gaps_per_seq(unique=True, drawable="bar") counts.drawable.show(width=500) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/draw/aln/plot_aln-gaps-per-seq.rst:33: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_aln-gaps-per-seq.png" counts.drawable.write(outpath) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/draw/aln/plot_aln-gaps-per-seq.rst:43: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: counts = aln.count_gaps_per_seq(unique=True, drawable="violin") counts.drawable.show(width=300, height=500) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/draw/aln/plot_aln-gaps-per-seq.rst:51: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: counts = aln.count_gaps_per_seq(unique=True, drawable="box") counts.drawable.show(width=300, height=500) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/draw/aln/plot_aln-info-plot.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/draw/aln/plot_aln-info-plot.rst:14: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, make_aligned_seqs, make_seq s1 = make_seq("TGATGTAAGGTAGTT", name="s1", moltype="dna") s2 = make_seq("--CTGGAAGGGT---", name="s2", moltype="dna") seqs = make_aligned_seqs(data=[s1, s2], array_align=False, moltype="dna") draw = seqs.information_plot(window=2, include_gap=True) draw.show(width=500, height=400) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/draw/aln/plot_aln-info-plot.rst:30: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = load_aligned_seqs("data/brca1.fasta", moltype="protein") fig = aln.information_plot(stat="median") fig.show(width=500, height=400) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/draw/aln/plot_aln-info-plot.rst:37: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_aln-info-plot.png" fig.write(outpath) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/draw/aln/plot_aln-seqlogo.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/draw/aln/plot_aln-seqlogo.rst:16: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.parse import jaspar _, pwm = jaspar.read("data/tbp.jaspar") freqarr = pwm.to_freq_array() freqarr[:5] # illustrating the contents of the MotifFreqsArray /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/draw/aln/plot_aln-seqlogo.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: logo = freqarr.logo() logo.show(height=250, width=500) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/draw/aln/plot_aln-seqlogo.rst:30: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_aln-seqlogo.png" logo.write(outpath) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/draw/aln/plot_aln-seqlogo.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = load_aligned_seqs("data/brca1-bats.fasta", moltype="dna") l = aln[:311].seqlogo(height=300, width=500, wrap=60, vspace=0.05) l.show() /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/draw/aln/plot_aln-seqlogo.rst:53: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aa = aln.get_translation(incomplete_ok=True)[:120] logo = aa.seqlogo(width=500, height=300, wrap=50, vspace=0.1) logo.show() /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/draw/tree/plot_tree-angular.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/draw/tree/plot_tree-angular.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io reader = io.load_json() ens_tree = reader("data/GN-tree.json") fig = ens_tree.get_figure(style="angular", width=600, height=600) fig.show() /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/draw/tree/plot_tree-angular.rst:24: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fig.contemporaneous = True fig.show() /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/draw/tree/plot_tree-angular.rst:29: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_tree-angular.png" fig.write(outpath) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/draw/tree/plot_tree-circular.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/draw/tree/plot_tree-circular.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io reader = io.load_json() ens_tree = reader("data/GN-tree.json") fig = ens_tree.get_figure("circular", width=600, height=600) fig.scale_bar = "top right" fig.label_pad = 0.1 fig.show() /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/draw/tree/plot_tree-circular.rst:26: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fig.style_edges( "AfricanEl", tip2="Manatee", legendgroup="Afrotheria", line=dict(color="magenta", width=2), ) fig.show(width=650, height=600) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/draw/tree/plot_tree-circular.rst:39: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fig.contemporaneous = True fig.label_pad = 0.3 fig.show(width=650, height=600) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/draw/tree/plot_tree-circular.rst:45: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_tree-circular.png" fig.write(outpath) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/draw/tree/plot_tree-radial.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/draw/tree/plot_tree-radial.rst:9: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io reader = io.load_json() ens_tree = reader("data/GN-tree.json") fig = ens_tree.get_figure("radial", width=600, height=600) fig.show() /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/draw/tree/plot_tree-radial.rst:19: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_tree-radial.png" fig.write(outpath) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/draw/tree/plot_tree-radial.rst:29: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fig.contemporaneous = True fig.label_pad = 0.23 fig.show() /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/draw/tree/plot_tree-square.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/draw/tree/plot_tree-square.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io reader = io.load_json() ens_tree = reader("data/GN-tree.json") fig = ens_tree.get_figure(width=600, height=600) fig.scale_bar = "top right" fig.show() /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/draw/tree/plot_tree-square.rst:24: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_tree-square.png" fig.write(outpath) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/draw/tree/plot_tree-square.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fig.style_edges( "AfricanEl", tip2="Manatee", legendgroup="Afrotheria", line=dict(color="magenta"), ) fig.show() /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/draw/tree/plot_tree-square.rst:47: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fig.contemporaneous = True fig.show() /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/draw/tree/plot_tree-support.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/draw/tree/plot_tree-support.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io reader = io.load_json() tree = reader("data/tree-with-support.json") fig = tree.get_figure(show_support=True, threshold=0.8) fig.scale_bar = None fig.show(width=500, height=400) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/draw/tree/plot_tree-support.rst:29: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fig.support_xshift = 15 fig.support_yshift = 0 fig.show(width=500, height=400) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/draw/tree/plot_tree-support.rst:35: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_tree-support.png" fig.write(outpath) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/align_codons_to_protein.rst:8: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs, make_unaligned_seqs /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/align_codons_to_protein.rst:14: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seqs = { "hum": "AAGCAGATCCAGGAAAGCAGCGAGAATGGCAGCCTGGCCGCGCGCCAGGAGAGGCAGGCCCAGGTCAACCTCACT", "mus": "AAGCAGATCCAGGAGAGCGGCGAGAGCGGCAGCCTGGCCGCGCGGCAGGAGAGGCAGGCCCAAGTCAACCTCACG", "rat": "CTGAACAAGCAGCCACTTTCAAACAAGAAA", } unaligned_DNA = make_unaligned_seqs(seqs, moltype="dna") print(unaligned_DNA.to_fasta()) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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()) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/align_codons_to_protein.rst:33: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aligned_aa_seqs = { "hum": "KQIQESSENGSLAARQERQAQVNLT", "mus": "KQIQESGESGSLAARQERQAQVNLT", "rat": "LNKQ------PLS---------NKK", } aligned_aa = make_aligned_seqs(aligned_aa_seqs, moltype="protein") aligned_DNA = aligned_aa.replace_seqs(unaligned_DNA) aligned_DNA /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/calculate_UPGMA_cluster.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/calculate_UPGMA_cluster.rst:15: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.cluster.UPGMA import upgma from cogent3.evolve import distance /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/calculate_UPGMA_cluster.rst:23: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import HKY85 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/calculate_UPGMA_cluster.rst:29: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: al = load_aligned_seqs("data/test.paml") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/calculate_UPGMA_cluster.rst:35: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: d = distance.EstimateDistances(al, submodel=HKY85()) d.run(show_progress=False) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/calculate_UPGMA_cluster.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: mycluster = upgma(d.get_pairwise_distances()) print(mycluster.ascii_art()) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/calculate_UPGMA_cluster.rst:49: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: mycluster.write("test_upgma.tree") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/calculate_UPGMA_cluster.rst:55: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import os os.remove("test_upgma.tree") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/calculate_neigbourjoining_tree.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/calculate_neigbourjoining_tree.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.evolve import distance from cogent3.phylo import nj /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/calculate_neigbourjoining_tree.rst:21: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import get_model /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/calculate_neigbourjoining_tree.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: al = load_aligned_seqs("data/long_testseqs.fasta") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/calculate_neigbourjoining_tree.rst:33: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: d = distance.EstimateDistances(al, submodel=get_model("HKY85")) d.run(show_progress=False) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/calculate_neigbourjoining_tree.rst:40: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: mytree = nj.nj(d.get_pairwise_distances(), show_progress=False) print(mytree.ascii_art()) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/calculate_neigbourjoining_tree.rst:47: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: mytree.write("test_nj.tree") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/calculate_neigbourjoining_tree.rst:53: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import os os.remove("test_nj.tree") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/calculate_pairwise_distances.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/calculate_pairwise_distances.rst:15: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.evolve import distance /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/calculate_pairwise_distances.rst:22: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import HKY85 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/calculate_pairwise_distances.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: al = load_aligned_seqs("data/long_testseqs.fasta") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/calculate_pairwise_distances.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: d = distance.EstimateDistances(al, submodel=HKY85()) d.run(show_progress=False) d.get_pairwise_distances() /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/calculate_pairwise_distances.rst:44: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: d.write("dists_for_phylo.phylip", format="phylip") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/calculate_pairwise_distances.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: import pickle with open("dists_for_phylo.pickle", "wb") as f: pickle.dump(d.get_pairwise_distances(), f) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/calculate_pairwise_distances.rst:61: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import os for file_name in "dists_for_phylo.phylip", "dists_for_phylo.pickle": os.remove(file_name) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/codon_models.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/codon_models.rst:36: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import get_model /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/codon_models.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tf = get_model("GY94") nf = get_model("MG94GTR") cnf = get_model("CNFGTR") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/codon_models.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna") tree = load_tree("data/primate_brca1.tree") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/codon_models.rst:64: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf = cnf.make_likelihood_function(tree, digits=2, space=3) lf.set_param_rule("omega", is_constant=True, value=1.0) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/codon_models.rst:73: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: optimiser_args = dict( local=True, max_restarts=5, tolerance=1e-8, show_progress=False ) lf.set_alignment(aln) lf.optimise(**optimiser_args) lf /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/codon_models.rst:92: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: neutral_lnL = lf.get_log_likelihood() neutral_nfp = lf.get_num_free_params() lf.set_param_rule("omega", is_constant=False) lf.optimise(**optimiser_args) non_neutral_lnL = lf.get_log_likelihood() non_neutral_nfp = lf.get_num_free_params() lf /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/codon_models.rst:104: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from scipy.stats.distributions import chi2 LR = 2 * (non_neutral_lnL - neutral_lnL) df = non_neutral_nfp - neutral_nfp print(chi2.sf(LR, df)) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/codon_models.rst:114: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule( "omega", tip_names=["Chimpanzee", "Human"], outgroup_name="Galago", clade=True ) lf.optimise(**optimiser_args) lf chimp_human_clade_lnL = lf.get_log_likelihood() chimp_human_clade_nfp = lf.get_num_free_params() /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/codon_models.rst:124: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: LR = 2 * (chimp_human_clade_lnL - non_neutral_lnL) df = chimp_human_clade_nfp - non_neutral_nfp print(chi2.sf(LR, df)) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/codon_models.rst:137: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf = cnf.make_likelihood_function(tree, digits=2, space=3) lf.set_alignment(aln) lf.optimise(**optimiser_args) non_neutral_lnL = lf.get_log_likelihood() non_neutral_nfp = lf.get_num_free_params() /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/codon_models.rst:149: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: annot_tree = lf.get_annotated_tree() omega_mle = lf.get_param_value("omega") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/codon_models.rst:156: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: rate_lf = cnf.make_likelihood_function( annot_tree, bins=["neutral", "adaptive"], digits=2, space=3 ) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/codon_models.rst:164: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: epsilon = 1e-6 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/codon_models.rst:170: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: rate_lf.set_param_rule("omega", bin="neutral", upper=1, init=omega_mle) rate_lf.set_param_rule( "omega", bin="adaptive", lower=1 + epsilon, upper=100, init=1 + 2 * epsilon ) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/codon_models.rst:179: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: rate_lf.set_param_rule("bprobs", init=[1 - epsilon, epsilon]) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/codon_models.rst:185: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: rate_lf.set_alignment(aln) rate_lf.optimise(**optimiser_args) rate_lnL = rate_lf.get_log_likelihood() rate_nfp = rate_lf.get_num_free_params() LR = 2 * (rate_lnL - non_neutral_lnL) df = rate_nfp - non_neutral_nfp rate_lf /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/codon_models.rst:195: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(chi2.sf(LR, df)) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/codon_models.rst:201: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: pp = rate_lf.get_bin_probs() /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/codon_models.rst:212: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from IPython.core.display import HTML from numpy import array from cogent3 import make_table header = ['Site Class', 'Proportion', 'Background Edges', 'Foreground Edges'] data = {'Site Class': array(['0', '1', '2a', '2b'], dtype=' 1', '0 < omega0 < 1'], dtype=' 1.8: tips_to_delete.append(n) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/manipulating_tree_nodes.rst:121: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: for n in tips_to_delete: n.parent.remove(n) complex_tree.prune() /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/manipulating_tree_nodes.rst:129: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(complex_tree.ascii_art(show_internal=False)) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/neutral_test.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/neutral_test.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model from scipy.stats.distributions import chi2 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/neutral_test.rst:21: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: al = load_aligned_seqs("data/long_testseqs.fasta") t = load_tree("data/test.tree") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/neutral_test.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: sm = get_model("MG94GTR") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/neutral_test.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf = sm.make_likelihood_function(t, digits=2, space=2) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/neutral_test.rst:40: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_alignment(al) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/neutral_test.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(global_tolerance=1.0, show_progress=False) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/neutral_test.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/neutral_test.rst:58: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: null_lnL = lf.get_log_likelihood() null_nfp = lf.get_num_free_params() /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/neutral_test.rst:65: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule("omega", is_independent=True) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/neutral_test.rst:71: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(local=True, show_progress=False) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/neutral_test.rst:77: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/neutral_test.rst:83: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: at = lf.get_annotated_tree() /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/neutral_test.rst:89: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: LR = 2 * (lf.get_log_likelihood() - null_lnL) df = lf.get_num_free_params() - null_nfp P = chi2.sf(LR, df) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/neutral_test.rst:97: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(f"Likelihood ratio statistic = {LR}") print(f"degrees-of-freedom = {df}") print(f"probability = {P}") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/parametric_bootstrap.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/parametric_bootstrap.rst:17: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve import bootstrap from cogent3.evolve.models import HKY85 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/parametric_bootstrap.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: def create_alt_function(): t = load_tree("data/test.tree") sm = HKY85() return sm.make_likelihood_function(t) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/parametric_bootstrap.rst:36: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: def create_null_function(): lf = create_alt_function() # set the local clock for humans & howler monkey lf.set_local_clock("Human", "HowlerMon") return lf /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/parametric_bootstrap.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = load_aligned_seqs("data/long_testseqs.fasta") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/parametric_bootstrap.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: estimateP = bootstrap.EstimateProbability( create_null_function(), create_alt_function(), aln ) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/parametric_bootstrap.rst:60: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: estimateP.set_num_replicates(5) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/parametric_bootstrap.rst:66: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: estimateP.run(show_progress=False) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/parametric_bootstrap.rst:72: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: p = estimateP.get_estimated_prob() /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/parametric_bootstrap.rst:78: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print("%.2f, %.2f" % estimateP.get_observed_lnL()) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/period_estimation.rst:26: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import numpy numpy.random.seed(11) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/period_estimation.rst:33: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: import numpy t = numpy.arange(0, 10, 0.1) n = numpy.random.randn(len(t)) nse = numpy.convolve(n, numpy.exp(-t / 0.05)) * 0.1 nse = nse[: len(t)] sig = numpy.sin(2 * numpy.pi * t) + nse /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/period_estimation.rst:48: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import dft pwr, period = dft(sig) print(period) print(pwr) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/period_estimation.rst:58: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: pwr = abs(pwr) max_pwr, max_period = sorted(zip(pwr, period))[-1] print(max_pwr, max_period) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/period_estimation.rst:69: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import auto_corr pwr, period = auto_corr(sig) print(period) print(pwr) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/period_estimation.rst:79: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: max_pwr, max_period = sorted(zip(pwr, period))[-1] print(max_pwr, max_period) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/period_estimation.rst:89: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: s = ( "ATCGTTGGGACCGGTTCAAGTTTTGGAACTCGCAAGGGGTGAATGGTCTTCGTCTAACGCTGG" "GGAACCCTGAATCGTTGTAACGCTGGGGTCTTTAACCGTTCTAATTTAACGCTGGGGGGTTCT" "AATTTTTAACCGCGGAATTGCGTC" ) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/period_estimation.rst:99: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.stats.period import SeqToSymbols seq_to_symbols = SeqToSymbols(["AA", "TT", "AT"]) symbols = seq_to_symbols(s) len(symbols) == len(s) symbols /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/period_estimation.rst:110: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import ipdft powers, periods = ipdft(symbols) powers /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/period_estimation.rst:117: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: periods /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/period_estimation.rst:123: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import auto_corr, hybrid powers, periods = auto_corr(symbols) powers /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/period_estimation.rst:130: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: periods /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/period_estimation.rst:134: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: powers, periods = hybrid(symbols) powers /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/period_estimation.rst:139: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: periods /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/period_estimation.rst:151: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import goertzel pwr = goertzel(sig, 10) print(pwr) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/period_estimation.rst:165: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: powers, periods = auto_corr(symbols) llim = 2 period5 = 5 - llim periods[period5] /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/period_estimation.rst:172: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: powers[period5] /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/period_estimation.rst:178: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import goertzel period = 4 power = goertzel(symbols, period) ipdft_powers, periods = ipdft(symbols) ipdft_power = abs(ipdft_powers[period - llim]) round(power, 6) == round(ipdft_power, 6) power /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/period_estimation.rst:191: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: power = hybrid(symbols, period=period) power /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/period_estimation.rst:204: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import Goertzel goertzel_calc = Goertzel(len(sig), period=10) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/period_estimation.rst:212: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.stats.period import blockwise_bootstrap obs_stat, p = blockwise_bootstrap( sig, calc=goertzel_calc, block_size=10, num_reps=1000 ) print(obs_stat) print(p) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/period_estimation.rst:230: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import Hybrid hybrid_calculator = Hybrid(len(s), period=4) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/period_estimation.rst:240: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.stats.period import SeqToSymbols seq_to_symbols = SeqToSymbols(["AA", "TT", "AT"], length=len(s)) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/period_estimation.rst:248: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.stats.period import blockwise_bootstrap stat, p = blockwise_bootstrap( s, calc=hybrid_calculator, block_size=10, num_reps=1000, seq_to_symbols=seq_to_symbols, ) print(stat) p < 0.1 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/phylo_by_ls.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/phylo_by_ls.rst:15: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import pickle from cogent3 import load_aligned_seqs from cogent3.evolve import distance from cogent3.evolve.fast_distance import DistanceMatrix from cogent3.evolve.models import HKY85 al = load_aligned_seqs("data/long_testseqs.fasta") d = distance.EstimateDistances(al, submodel=HKY85()) d.run(show_progress=False) with open("dists_for_phylo.pickle", "wb") as f: pickle.dump(d.get_pairwise_distances(), f) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/phylo_by_ls.rst:32: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: import pickle from cogent3.phylo import least_squares /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/phylo_by_ls.rst:40: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: with open("dists_for_phylo.pickle", "rb") as f: dists = pickle.load(f) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/phylo_by_ls.rst:49: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: ls = least_squares.WLS(dists) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/phylo_by_ls.rst:55: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: ls_distance_matrix = least_squares.WLS(DistanceMatrix(dists)) ls_pairwise_matrix = least_squares.WLS(dists.to_dict()) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/phylo_by_ls.rst:67: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: score, tree = ls.trex(a=5, k=1, show_progress=False) assert score < 1e-4 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/phylo_by_ls.rst:79: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: trees = ls.trex(a=5, k=5, return_all=True, show_progress=False) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/phylo_by_ls.rst:85: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(len(trees)) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/phylo_by_ls.rst:91: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: wls_stats = [tree[0] for tree in trees] /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/phylo_by_ls.rst:103: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: t1 = trees[0][1].balanced() t2 = trees[1][1].balanced() print(t1.ascii_art()) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/phylo_by_ls.rst:109: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(t2.ascii_art()) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/phylo_by_ls.rst:120: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_tree query_tree = make_tree( "((Human:.2,DogFaced:.2):.3,(NineBande:.1, Mouse:.5):.2,HowlerMon:.1)" ) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/phylo_by_ls.rst:130: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: ls.evaluate_tree(query_tree) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/phylo_by_ls.rst:136: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: wls, t = ls.evaluate_topology(query_tree) assert "%.4f" % wls == "0.0084" /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/phylo_by_ls.rst:148: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import os os.remove("dists_for_phylo.pickle") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/rate_heterogeneity.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/rate_heterogeneity.rst:15: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.substitution_model import TimeReversibleNucleotide /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/rate_heterogeneity.rst:22: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: model = TimeReversibleNucleotide(equal_motif_probs=True) tree = load_tree("data/test.tree") lf = model.make_likelihood_function(tree) lf.set_param_rule("length", value=0.6, is_constant=True) aln1 = lf.simulate_alignment(sequence_length=10000) lf.set_param_rule("length", value=0.2, is_constant=True) aln2 = lf.simulate_alignment(sequence_length=10000) aln3 = aln1 + aln2 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/rate_heterogeneity.rst:35: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: model = TimeReversibleNucleotide( equal_motif_probs=True, ordered_param="rate", distribution="free" ) lf = model.make_likelihood_function(tree, bins=2, digits=2, space=3) lf.set_alignment(aln3) lf.optimise(local=True, max_restarts=2, show_progress=False) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/rate_heterogeneity.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: bprobs = [t for t in lf.get_statistics() if "bin" in t.title][0] bprobs /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/rate_heterogeneity.rst:53: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: model = TimeReversibleNucleotide( equal_motif_probs=True, ordered_param="rate", distribution="gamma" ) lf = model.make_likelihood_function(tree, bins=4) lf.set_param_rule("bprobs", is_constant=True) lf.set_alignment(aln3) lf.optimise(local=True, max_restarts=2, show_progress=False) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/relative_rate.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/relative_rate.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model from scipy.stats.distributions import chi2 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/relative_rate.rst:21: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = load_aligned_seqs("data/long_testseqs.fasta") t = load_tree(filename="data/test.tree") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/relative_rate.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: sm = get_model("HKY85") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/relative_rate.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf = sm.make_likelihood_function(t, digits=2, space=3) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/relative_rate.rst:40: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_local_clock("Human", "HowlerMon") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/relative_rate.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_alignment(aln) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/relative_rate.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(show_progress=False) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/relative_rate.rst:58: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_name("clock") lf /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/relative_rate.rst:65: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: null_lnL = lf.get_log_likelihood() null_nfp = lf.get_num_free_params() /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/relative_rate.rst:72: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule("length", is_independent=True) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/relative_rate.rst:78: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(show_progress=False) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/relative_rate.rst:84: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_name("non clock") lf /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/relative_rate.rst:91: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: LR = 2 * (lf.get_log_likelihood() - null_lnL) df = lf.get_num_free_params() - null_nfp P = chi2.sf(LR, df) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/relative_rate.rst:99: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print("Likelihood ratio statistic = ", LR) print("degrees-of-freedom = ", df) print("probability = ", P) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/scope_model_params_on_trees.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/scope_model_params_on_trees.rst:17: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import MG94HKY aln = load_aligned_seqs("data/long_testseqs.fasta") tree = load_tree("data/test.tree") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/scope_model_params_on_trees.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: sm = MG94HKY() lf = sm.make_likelihood_function(tree, digits=2, space=3) lf.set_alignment(aln) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/scope_model_params_on_trees.rst:35: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(tree.ascii_art()) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/scope_model_params_on_trees.rst:53: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule( "omega", tip_names=["DogFaced", "Mouse"], outgroup_name="Human", init=2.0, clade=True, ) lf /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/scope_model_params_on_trees.rst:73: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule("omega", init=1.0) lf.set_param_rule( "omega", tip_names=["Human", "HowlerMon"], outgroup_name="Mouse", init=2.0, stem=True, clade=False, ) lf /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/scope_model_params_on_trees.rst:91: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: lf.set_param_rule("omega", init=1.0) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/scope_model_params_on_trees.rst:96: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule( "omega", tip_names=["Human", "HowlerMon"], outgroup_name="Mouse", init=2.0, stem=True, clade=True, ) lf /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/scope_model_params_on_trees.rst:160: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: lf.set_param_rule("omega", init=1.0) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/scope_model_params_on_trees.rst:165: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule( "omega", tip_names=["Human", "HowlerMon"], outgroup_name="Mouse", clade=True, value=1.0, is_constant=True, ) lf.optimise(local=True, show_progress=False) lf /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/scope_model_params_on_trees.rst:180: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule( "omega", tip_names=["Human", "HowlerMon"], outgroup_name="Mouse", clade=True, is_constant=False, ) lf.optimise(local=True, show_progress=False) lf /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/scope_model_params_on_trees.rst:194: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule( "omega", tip_names=["Human", "HowlerMon"], outgroup_name="Mouse", clade=True, is_independent=True, ) lf.optimise(local=True, show_progress=False) lf /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/scope_model_params_on_trees.rst:208: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule("omega", is_independent=True) lf.optimise(local=True, show_progress=False) lf /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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)]) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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)]) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/seq_features.rst:35: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: s[exon1] /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/seq_features.rst:41: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: exons = s.get_annotations_matching("exon") print(exons) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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() /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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()) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/seq_features.rst:63: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: exon1[0:3].get_slice() /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/simple.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/simple.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, make_tree from cogent3.evolve.models import get_model model = get_model("HKY85") aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta") tree = make_tree(tip_names=aln.names) lf = model.make_likelihood_function(tree) lf.set_alignment(aln) lf.optimise(show_progress=False) lf /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/simulate_alignment.rst:8: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: import sys from cogent3 import make_tree from cogent3.evolve.models import get_model /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/simulate_alignment.rst:17: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: t = make_tree("(a:0.4,b:0.3,(c:0.15,d:0.2)edge.0:0.1);") /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/simulate_alignment.rst:23: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: sm = get_model("F81") lf = sm.make_likelihood_function(t) lf.set_constant_lengths() lf.set_motif_probs(dict(A=0.1, C=0.2, G=0.3, T=0.4)) lf /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/simulate_alignment.rst:33: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: simulated = lf.simulate_alignment(sequence_length=1000) simulated /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/testing_multi_loci.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/testing_multi_loci.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, make_table, make_tree from cogent3.evolve.models import HKY85 from scipy.stats.distributions import chi2 from cogent3.recalculation.scope import ALL, EACH aln = load_aligned_seqs("data/long_testseqs.fasta") half = len(aln) // 2 aln1 = aln[:half] aln2 = aln[half:] /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/testing_multi_loci.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: loci_names = ["1st-half", "2nd-half"] loci = [aln1, aln2] tree = make_tree(tip_names=aln.names) mod = HKY85() /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/testing_multi_loci.rst:36: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf = mod.make_likelihood_function(tree, loci=loci_names, digits=2, space=3) lf.set_param_rule("length", is_independent=False) lf.set_param_rule("kappa", loci=ALL) lf.set_alignment(loci) lf.optimise(show_progress=False) lf /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/testing_multi_loci.rst:45: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: all_lnL = lf.lnL all_nfp = lf.nfp lf.set_param_rule("kappa", loci=EACH) lf.optimise(show_progress=False) lf /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/testing_multi_loci.rst:53: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: each_lnL = lf.lnL each_nfp = lf.nfp LR = 2 * (each_lnL - all_lnL) df = each_nfp - all_nfp /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/examples/testing_multi_loci.rst:62: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: make_table( header=["LR", "df", "p"], rows=[[LR, df, chi2.sf(LR, df)]], digits=2, space=3, ) /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/index.rst:16: ERROR: Unknown directive type "dropdown". .. dropdown:: Click to see an animation showing defining and using sequence annotations. .. raw:: html /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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... /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/data_file_links.rst: WARNING: document isn't included in any toctree /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/draw/index.rst: WARNING: document isn't included in any toctree /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/general.rst: WARNING: document isn't included in any toctree /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/install.rst: WARNING: document isn't included in any toctree /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc/licenses.rst: WARNING: document isn't included in any toctree /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/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 '/build/reproducible-path/python-cogent-2023.2.12a1+dfsg/doc' # remove superfluous files and dirs find doc/_build -name "*.doctree*" -delete rm -f doc/_build/html/_sources/COGENT_LICENSE.txt rm -f doc/_build/html/_static/jquery.js rm -f doc/_build/html/_static/underscore.js rm -rf doc/_build/html/_images/math/ make[1]: Leaving directory '/build/reproducible-path/python-cogent-2023.2.12a1+dfsg' dh_auto_test -O--buildsystem=pybuild I: pybuild pybuild:307: cp -r /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/tests/data /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/.pybuild/cpython3_3.11_cogent3/build I: pybuild base:240: cd /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/.pybuild/cpython3_3.11_cogent3/build; python3.11 -m pytest -k 'not test_pickleable_member_roundtrip and not test_pickleable_roundtrip' ============================= test session starts ============================== platform linux -- Python 3.11.2, pytest-7.2.1, pluggy-1.0.0+repack rootdir: /build/reproducible-path/python-cogent-2023.2.12a1+dfsg, configfile: pyproject.toml plugins: xdist-3.1.0, cov-4.0.0, anyio-3.6.2 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 ......................................... [ 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 ............................... 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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 ............. 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[ 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 ... [ 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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/.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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/.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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/.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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/.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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/.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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/.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 /build/reproducible-path/python-cogent-2023.2.12a1+dfsg/.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 [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 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 = 2859 passed, 8 skipped, 4 deselected, 1 xfailed, 1 xpassed, 12 warnings in 226.55s (0:03:46) = 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 '/build/reproducible-path/python-cogent-2023.2.12a1+dfsg' 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 '/build/reproducible-path/python-cogent-2023.2.12a1+dfsg' dh_installchangelogs -O--buildsystem=pybuild debian/rules override_dh_python3 make[1]: Entering directory '/build/reproducible-path/python-cogent-2023.2.12a1+dfsg' dh_python3 --shebang=/usr/bin/python3 make[1]: Leaving directory '/build/reproducible-path/python-cogent-2023.2.12a1+dfsg' 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 '/build/reproducible-path/python-cogent-2023.2.12a1+dfsg' dh_compress --exclude=.js --exclude=.fasta --exclude=.txt --exclude=.pdb make[1]: Leaving directory '/build/reproducible-path/python-cogent-2023.2.12a1+dfsg' 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 '/build/reproducible-path/python-cogent-2023.2.12a1+dfsg' dh_shlibdeps dh_numpy3 make[1]: Leaving directory '/build/reproducible-path/python-cogent-2023.2.12a1+dfsg' dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dpkg-gencontrol: warning: package python-cogent-doc: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: Depends field of package python3-cogent3: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'python-cogent-doc' in '../python-cogent-doc_2023.2.12a1+dfsg-2+deb12u1_all.deb'. dpkg-deb: building package 'python3-cogent3' in '../python3-cogent3_2023.2.12a1+dfsg-2+deb12u1_arm64.deb'. dpkg-genbuildinfo --build=binary -O../python-cogent_2023.2.12a1+dfsg-2+deb12u1_arm64.buildinfo dpkg-genchanges --build=binary -O../python-cogent_2023.2.12a1+dfsg-2+deb12u1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3131032 and its subdirectories I: Current time: Fri Jan 10 11:48:08 -12 2025 I: pbuilder-time-stamp: 1736552888 Sat Dec 9 17:25:09 UTC 2023 I: 1st build successful. Starting 2nd build on remote node codethink02-arm64.debian.net. Sat Dec 9 17:25:09 UTC 2023 I: Preparing to do remote build '2' on codethink02-arm64.debian.net. Sat Dec 9 17:38:47 UTC 2023 I: Deleting $TMPDIR on codethink02-arm64.debian.net. Sat Dec 9 17:38:48 UTC 2023 I: python-cogent_2023.2.12a1+dfsg-2+deb12u1_arm64.changes: Format: 1.8 Date: Sun, 29 Oct 2023 21:45:00 +0100 Source: python-cogent Binary: python-cogent-doc python3-cogent3 Architecture: all arm64 Version: 2023.2.12a1+dfsg-2+deb12u1 Distribution: bookworm Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Santiago Vila Description: python-cogent-doc - docs for python3-cogent3 python3-cogent3 - framework for genomic biology Closes: 1030885 Changes: python-cogent (2023.2.12a1+dfsg-2+deb12u1) bookworm; urgency=medium . * Team upload. * Drop old patch fix-build-on-single-cpu-systems.patch, as it was disabling the affected tests for everybody. * Add new patch skip-parallel-tests-on-single-cpu-systems.patch, where the tests are only skipped when the system has a single CPU. Closes: #1030885. Checksums-Sha1: 6fd15726b72eac6d08d3215617dba32f5d0ee70b 733512 python-cogent-doc_2023.2.12a1+dfsg-2+deb12u1_all.deb ced3e34bc61e6bffa2ea5fa2b56d7ad617909ed9 13562 python-cogent_2023.2.12a1+dfsg-2+deb12u1_arm64.buildinfo 7627d4889093352d18a81f476807777d6b4ee90c 1895936 python3-cogent3_2023.2.12a1+dfsg-2+deb12u1_arm64.deb Checksums-Sha256: 2a103de9ae22c318418b9831a0ca64e8517a04c757312f31497b16cbdbc6fcc0 733512 python-cogent-doc_2023.2.12a1+dfsg-2+deb12u1_all.deb fc3aa4c6f712947bd808e1bf565febd9cd9b5982a3347f3b185731c5371191d0 13562 python-cogent_2023.2.12a1+dfsg-2+deb12u1_arm64.buildinfo 9ae86b4e30b166201e4ec816849c647433a3d6d1c6b410594c720cca84085c65 1895936 python3-cogent3_2023.2.12a1+dfsg-2+deb12u1_arm64.deb Files: bc01ad0efc868e8398e19dffb56bb423 733512 doc optional python-cogent-doc_2023.2.12a1+dfsg-2+deb12u1_all.deb 75356ceed41389a17d0f8f2b0c191d6c 13562 python optional python-cogent_2023.2.12a1+dfsg-2+deb12u1_arm64.buildinfo 4b2566712ee6b14cdb6553484276e11c 1895936 python optional python3-cogent3_2023.2.12a1+dfsg-2+deb12u1_arm64.deb Sat Dec 9 17:38:49 UTC 2023 I: diffoscope 240 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.GxVeyJNF/python-cogent_2023.2.12a1+dfsg-2+deb12u1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.GxVeyJNF/python-cogent_2023.2.12a1+dfsg-2+deb12u1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.GxVeyJNF/python-cogent_2023.2.12a1+dfsg-2+deb12u1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.GxVeyJNF/b1/python-cogent_2023.2.12a1+dfsg-2+deb12u1_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.GxVeyJNF/b2/python-cogent_2023.2.12a1+dfsg-2+deb12u1_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.364s) 0.364s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.106s) 0.106s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Sat Dec 9 17:38:49 UTC 2023 I: diffoscope 240 found no differences in the changes files, and a .buildinfo file also exists. Sat Dec 9 17:38:49 UTC 2023 I: python-cogent from bookworm built successfully and reproducibly on arm64. Sat Dec 9 17:38:53 UTC 2023 I: Submitting .buildinfo files to external archives: Sat Dec 9 17:38:53 UTC 2023 I: Submitting 16K b1/python-cogent_2023.2.12a1+dfsg-2+deb12u1_arm64.buildinfo.asc Sat Dec 9 17:38:54 UTC 2023 I: Submitting 16K b2/python-cogent_2023.2.12a1+dfsg-2+deb12u1_arm64.buildinfo.asc Sat Dec 9 17:38:55 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sat Dec 9 17:38:55 UTC 2023 I: Done submitting .buildinfo files. Sat Dec 9 17:38:55 UTC 2023 I: Removing signed python-cogent_2023.2.12a1+dfsg-2+deb12u1_arm64.buildinfo.asc files: removed './b1/python-cogent_2023.2.12a1+dfsg-2+deb12u1_arm64.buildinfo.asc' removed './b2/python-cogent_2023.2.12a1+dfsg-2+deb12u1_arm64.buildinfo.asc'