Read the Docs build information Build id: 677120 Project: icb-scanpy Version: stable Commit: 9360422823fade22a625f3c7840bef132364027e Date: 2021-07-15T05:15:13.078472Z State: finished Success: False [rtd-command-info] start-time: 2021-07-15T05:15:20.494262Z, end-time: 2021-07-15T05:15:23.593454Z, duration: 3, exit-code: 0 git clone --no-single-branch --depth 50 https://github.com/theislab/scanpy.git . Cloning into '.'... [rtd-command-info] start-time: 2021-07-15T05:15:24.285834Z, end-time: 2021-07-15T05:15:24.480941Z, duration: 0, exit-code: 0 git checkout --force 9360422823fade22a625f3c7840bef132364027e Note: checking out '9360422823fade22a625f3c7840bef132364027e'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by performing another checkout. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -b with the checkout command again. Example: git checkout -b HEAD is now at 93604228 Backport PR #1937: Prep 1.8.1 (#1938) [rtd-command-info] start-time: 2021-07-15T05:15:24.907054Z, end-time: 2021-07-15T05:15:24.980814Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2021-07-15T05:15:25.092025Z, end-time: 2021-07-15T05:15:25.166040Z, duration: 0, exit-code: 0 git rev-parse HEAD 9360422823fade22a625f3c7840bef132364027e [rtd-command-info] start-time: 2021-07-15T05:15:26.127558Z, end-time: 2021-07-15T05:15:40.580587Z, duration: 14, exit-code: 0 python3.8 -mvirtualenv Using base prefix '/home/docs/.pyenv/versions/3.8.6' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/bin/python3.8 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2021-07-15T05:15:40.695280Z, end-time: 2021-07-15T05:15:42.001124Z, duration: 1, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip setuptools Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.8/site-packages (21.1.3) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.8/site-packages (57.2.0) [rtd-command-info] start-time: 2021-07-15T05:15:42.116137Z, end-time: 2021-07-15T05:16:10.075480Z, duration: 27, exit-code: 0 python -m pip install --upgrade --no-cache-dir mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.8.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<2.2 Collecting mock==1.0.1 Downloading mock-1.0.1.zip (861 kB) Collecting pillow==5.4.1 Downloading Pillow-5.4.1.tar.gz (16.0 MB) Collecting alabaster!=0.7.5,<0.8,>=0.7 Downloading alabaster-0.7.12-py2.py3-none-any.whl (14 kB) Collecting commonmark==0.8.1 Downloading commonmark-0.8.1-py2.py3-none-any.whl (47 kB) Collecting recommonmark==0.5.0 Downloading recommonmark-0.5.0-py2.py3-none-any.whl (9.8 kB) Collecting sphinx<2 Downloading Sphinx-1.8.5-py2.py3-none-any.whl (3.1 MB) Collecting sphinx-rtd-theme<0.5 Downloading sphinx_rtd_theme-0.4.3-py2.py3-none-any.whl (6.4 MB) Collecting readthedocs-sphinx-ext<2.2 Downloading readthedocs_sphinx_ext-2.1.4-py2.py3-none-any.whl (29 kB) Collecting future Downloading future-0.18.2.tar.gz (829 kB) Collecting docutils>=0.11 Downloading docutils-0.17.1-py2.py3-none-any.whl (575 kB) Collecting Pygments>=2.0 Downloading Pygments-2.9.0-py3-none-any.whl (1.0 MB) Collecting imagesize Downloading imagesize-1.2.0-py2.py3-none-any.whl (4.8 kB) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.8/site-packages (from sphinx<2) (57.2.0) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.1.0-py2.py3-none-any.whl (93 kB) Collecting babel!=2.0,>=1.3 Downloading Babel-2.9.1-py2.py3-none-any.whl (8.8 MB) Collecting requests>=2.0.0 Downloading requests-2.26.0-py2.py3-none-any.whl (62 kB) Collecting sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.2.4-py2.py3-none-any.whl (39 kB) Collecting Jinja2>=2.3 Downloading Jinja2-3.0.1-py3-none-any.whl (133 kB) Collecting six>=1.5 Downloading six-1.16.0-py2.py3-none-any.whl (11 kB) Collecting packaging Downloading packaging-21.0-py3-none-any.whl (40 kB) Collecting pytz>=2015.7 Downloading pytz-2021.1-py2.py3-none-any.whl (510 kB) Collecting MarkupSafe>=2.0 Downloading MarkupSafe-2.0.1-cp38-cp38-manylinux2010_x86_64.whl (30 kB) Collecting idna<4,>=2.5 Downloading idna-3.2-py3-none-any.whl (59 kB) Collecting certifi>=2017.4.17 Downloading certifi-2021.5.30-py2.py3-none-any.whl (145 kB) Collecting urllib3<1.27,>=1.21.1 Downloading urllib3-1.26.6-py2.py3-none-any.whl (138 kB) Collecting charset-normalizer~=2.0.0 Downloading charset_normalizer-2.0.2-py3-none-any.whl (35 kB) Collecting pyparsing>=2.0.2 Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 kB) Collecting sphinxcontrib-serializinghtml Downloading sphinxcontrib_serializinghtml-1.1.5-py2.py3-none-any.whl (94 kB) Building wheels for collected packages: mock, pillow, future Building wheel for mock (setup.py): started Building wheel for mock (setup.py): finished with status 'done' Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23772 sha256=0fcd320aaf11834661708ffd45615510404cb128f82cbf6bd66e9bc3c6e8b1dc Stored in directory: /tmp/pip-ephem-wheel-cache-t5ts1meg/wheels/41/7c/21/90057f91c6ead7c77a90c52d6e85ca48bf82d8b0d3f8dfbb65 Building wheel for pillow (setup.py): started Building wheel for pillow (setup.py): finished with status 'done' Created wheel for pillow: filename=Pillow-5.4.1-cp38-cp38-linux_x86_64.whl size=1260013 sha256=050cbfb4f6aae34b0cf3e6afc2675dc16678f431c3a6400ae579ceb51c00abb2 Stored in directory: /tmp/pip-ephem-wheel-cache-t5ts1meg/wheels/5f/a8/6b/5b7b3f764d879214eb03570f74d2b086201eb514e6ffa68d6d Building wheel for future (setup.py): started Building wheel for future (setup.py): finished with status 'done' Created wheel for future: filename=future-0.18.2-py3-none-any.whl size=491070 sha256=1be01d6f0fc20c4c0ea8673f14b396fab65cdd22d72ab4b4e5679c7678e1e5e9 Stored in directory: /tmp/pip-ephem-wheel-cache-t5ts1meg/wheels/8e/70/28/3d6ccd6e315f65f245da085482a2e1c7d14b90b30f239e2cf4 Successfully built mock pillow future Installing collected packages: urllib3, sphinxcontrib-serializinghtml, pytz, pyparsing, MarkupSafe, idna, charset-normalizer, certifi, sphinxcontrib-websupport, snowballstemmer, six, requests, Pygments, packaging, Jinja2, imagesize, future, docutils, babel, alabaster, sphinx, commonmark, sphinx-rtd-theme, recommonmark, readthedocs-sphinx-ext, pillow, mock Successfully installed Jinja2-3.0.1 MarkupSafe-2.0.1 Pygments-2.9.0 alabaster-0.7.12 babel-2.9.1 certifi-2021.5.30 charset-normalizer-2.0.2 commonmark-0.8.1 docutils-0.17.1 future-0.18.2 idna-3.2 imagesize-1.2.0 mock-1.0.1 packaging-21.0 pillow-5.4.1 pyparsing-2.4.7 pytz-2021.1 readthedocs-sphinx-ext-2.1.4 recommonmark-0.5.0 requests-2.26.0 six-1.16.0 snowballstemmer-2.1.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.5 sphinxcontrib-websupport-1.2.4 urllib3-1.26.6 [rtd-command-info] start-time: 2021-07-15T05:16:10.191018Z, end-time: 2021-07-15T05:17:16.964932Z, duration: 66, exit-code: 0 python -m pip install --upgrade --upgrade-strategy eager --no-cache-dir .[doc] Processing /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable DEPRECATION: A future pip version will change local packages to be built in-place without first copying to a temporary directory. We recommend you use --use-feature=in-tree-build to test your packages with this new behavior before it becomes the default. pip 21.3 will remove support for this functionality. You can find discussion regarding this at https://github.com/pypa/pip/issues/7555. Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'done' Installing backend dependencies: started Installing backend dependencies: finished with status 'done' Preparing wheel metadata: started Preparing wheel metadata: finished with status 'done' Collecting natsort Downloading natsort-7.1.1-py3-none-any.whl (35 kB) Collecting umap-learn>=0.3.10 Downloading umap-learn-0.5.1.tar.gz (80 kB) Collecting tqdm Downloading tqdm-4.61.2-py2.py3-none-any.whl (76 kB) Collecting statsmodels>=0.10.0rc2 Downloading statsmodels-0.12.2-cp38-cp38-manylinux1_x86_64.whl (9.4 MB) Collecting joblib Downloading joblib-1.0.1-py3-none-any.whl (303 kB) Collecting numba>=0.41.0 Downloading numba-0.53.1-cp38-cp38-manylinux2014_x86_64.whl (3.4 MB) Collecting h5py>=2.10.0 Downloading h5py-3.3.0-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (4.5 MB) Collecting scikit-learn>=0.22 Downloading scikit_learn-0.24.2-cp38-cp38-manylinux2010_x86_64.whl (24.9 MB) Collecting sinfo Downloading sinfo-0.3.4.tar.gz (24 kB) Collecting patsy Downloading patsy-0.5.1-py2.py3-none-any.whl (231 kB) Collecting numpy>=1.17.0 Downloading numpy-1.21.0-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (15.7 MB) Collecting anndata>=0.7.4 Downloading anndata-0.7.6-py3-none-any.whl (127 kB) Collecting pandas>=0.21 Downloading pandas-1.3.0-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.whl (10.6 MB) Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.8/site-packages (from scanpy==1.8.1) (21.0) Collecting networkx>=2.3 Downloading networkx-2.5.1-py3-none-any.whl (1.6 MB) Collecting scipy>=1.4 Downloading scipy-1.7.0-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.whl (28.4 MB) Collecting seaborn Downloading seaborn-0.11.1-py3-none-any.whl (285 kB) Collecting matplotlib>=3.1.2 Downloading matplotlib-3.4.2-cp38-cp38-manylinux1_x86_64.whl (10.3 MB) Collecting tables Downloading tables-3.6.1-cp38-cp38-manylinux1_x86_64.whl (4.3 MB) Collecting sphinx>=3.2 Downloading Sphinx-4.1.1-py3-none-any.whl (2.9 MB) Requirement already satisfied: sphinx-rtd-theme>=0.3.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.8/site-packages (from scanpy==1.8.1) (0.4.3) Collecting sphinx-rtd-theme>=0.3.1 Downloading sphinx_rtd_theme-0.5.2-py2.py3-none-any.whl (9.1 MB) Collecting sphinx-autodoc-typehints Downloading sphinx_autodoc_typehints-1.12.0-py3-none-any.whl (9.4 kB) Collecting python-igraph Downloading python_igraph-0.9.6-cp38-cp38-manylinux2010_x86_64.whl (3.3 MB) Collecting scanpydoc==0.7.2 Downloading scanpydoc-0.7.2-py3-none-any.whl (29 kB) Collecting setuptools_scm Downloading setuptools_scm-6.0.1-py3-none-any.whl (27 kB) Collecting xlrd<2.0 Downloading xlrd-1.2.0-py2.py3-none-any.whl (103 kB) Collecting kiwisolver>=1.0.1 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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.8/site-packages (from numba>=0.41.0->scanpy==1.8.1) (57.2.0) Requirement already satisfied: pytz>=2017.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.8/site-packages (from pandas>=0.21->scanpy==1.8.1) (2021.1) Collecting threadpoolctl>=2.0.0 Downloading threadpoolctl-2.2.0-py3-none-any.whl (12 kB) Collecting sphinxcontrib-htmlhelp>=2.0.0 Downloading sphinxcontrib_htmlhelp-2.0.0-py2.py3-none-any.whl (100 kB) Requirement already satisfied: babel>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.8/site-packages (from sphinx>=3.2->scanpy==1.8.1) (2.9.1) Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.8/site-packages (from sphinx>=3.2->scanpy==1.8.1) (0.7.12) Collecting sphinxcontrib-applehelp Downloading sphinxcontrib_applehelp-1.0.2-py2.py3-none-any.whl (121 kB) Collecting sphinxcontrib-qthelp Downloading sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl (90 kB) Requirement already satisfied: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.8/site-packages (from sphinx>=3.2->scanpy==1.8.1) (2.9.0) Requirement already satisfied: requests>=2.5.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.8/site-packages (from sphinx>=3.2->scanpy==1.8.1) (2.26.0) Collecting sphinxcontrib-jsmath Downloading sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB) Collecting sphinxcontrib-devhelp Downloading sphinxcontrib_devhelp-1.0.2-py2.py3-none-any.whl (84 kB) Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.8/site-packages (from sphinx>=3.2->scanpy==1.8.1) (2.1.0) Requirement already satisfied: docutils<0.18,>=0.14 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.8/site-packages (from sphinx>=3.2->scanpy==1.8.1) (0.17.1) Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.8/site-packages (from sphinx>=3.2->scanpy==1.8.1) (1.2.0) Requirement already satisfied: sphinxcontrib-serializinghtml>=1.1.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.8/site-packages (from sphinx>=3.2->scanpy==1.8.1) (1.1.5) Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.8/site-packages (from sphinx>=3.2->scanpy==1.8.1) (3.0.1) Requirement already satisfied: MarkupSafe>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.8/site-packages (from Jinja2>=2.3->sphinx>=3.2->scanpy==1.8.1) (2.0.1) Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.8/site-packages (from requests>=2.5.0->sphinx>=3.2->scanpy==1.8.1) (2021.5.30) Requirement already satisfied: charset-normalizer~=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.8/site-packages (from requests>=2.5.0->sphinx>=3.2->scanpy==1.8.1) (2.0.2) Requirement already satisfied: urllib3<1.27,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.8/site-packages (from requests>=2.5.0->sphinx>=3.2->scanpy==1.8.1) (1.26.6) Requirement already satisfied: idna<4,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.8/site-packages (from requests>=2.5.0->sphinx>=3.2->scanpy==1.8.1) (3.2) Collecting docutils<0.18,>=0.14 Downloading docutils-0.16-py2.py3-none-any.whl (548 kB) Collecting pynndescent>=0.5 Downloading pynndescent-0.5.4.tar.gz (1.1 MB) Collecting texttable>=1.6.2 Downloading texttable-1.6.4-py2.py3-none-any.whl (10 kB) Collecting stdlib_list Downloading stdlib_list-0.8.0-py3-none-any.whl (63 kB) Collecting numexpr>=2.6.2 Downloading numexpr-2.7.3-cp38-cp38-manylinux2010_x86_64.whl (473 kB) Building wheels for collected packages: scanpy, umap-learn, pynndescent, sinfo Building wheel for scanpy (PEP 517): started Building wheel for scanpy (PEP 517): finished with status 'done' Created wheel for scanpy: filename=scanpy-1.8.1-py3-none-any.whl size=11382720 sha256=8ea874f1a8dd744125218daa2b949827860b2397d324b7f677ac028b136e9a99 Stored in directory: /tmp/pip-ephem-wheel-cache-dkty8x6d/wheels/88/43/1c/67f8c93dc62b29d8ac7277fadb7f9c0eb165376f3e7e3061ac Building wheel for umap-learn (setup.py): started Building wheel for umap-learn (setup.py): finished with status 'done' Created wheel for umap-learn: filename=umap_learn-0.5.1-py3-none-any.whl size=76566 sha256=220654b704074f9d9cd1c23a91a46570f1c312773dc03eaf245e1bfd4247f138 Stored in directory: /tmp/pip-ephem-wheel-cache-dkty8x6d/wheels/95/85/b7/b4b7040e49367b6d1505d7e8fb57e3e79b22fa6ac26f72520b Building wheel for pynndescent (setup.py): started Building wheel for pynndescent (setup.py): finished with status 'done' Created wheel for pynndescent: filename=pynndescent-0.5.4-py3-none-any.whl size=52372 sha256=12392cd6b73069a445d573270095feb11cf948c7f60666eb44b83cf0fa3595e9 Stored in directory: /tmp/pip-ephem-wheel-cache-dkty8x6d/wheels/c7/0d/f8/e89d09e0c7419141e444bd59072cc195df4a88785c1052834b Building wheel for sinfo (setup.py): started Building wheel for sinfo (setup.py): finished with status 'done' Created wheel for sinfo: filename=sinfo-0.3.4-py3-none-any.whl size=7899 sha256=7d4d23872841472a5b883950bcefd4d3f0a2fc2ef351baa36dab9a54521f6585 Stored in directory: /tmp/pip-ephem-wheel-cache-dkty8x6d/wheels/0e/63/be/1333921ddb5d249efe6db671c36608e46593e018994c3be11d Successfully built scanpy umap-learn pynndescent sinfo Installing collected packages: numpy, threadpoolctl, scipy, llvmlite, joblib, scikit-learn, python-dateutil, pillow, numba, kiwisolver, cycler, xlrd, stdlib-list, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, pynndescent, patsy, pandas, numexpr, natsort, matplotlib, h5py, docutils, decorator, umap-learn, tqdm, texttable, tables, statsmodels, sphinx, sinfo, setuptools-scm, seaborn, networkx, anndata, sphinx-rtd-theme, sphinx-autodoc-typehints, scanpydoc, scanpy, python-igraph Attempting uninstall: pillow Found existing installation: Pillow 5.4.1 Uninstalling Pillow-5.4.1: Successfully uninstalled Pillow-5.4.1 Attempting uninstall: docutils Found existing installation: docutils 0.17.1 Uninstalling docutils-0.17.1: Successfully uninstalled docutils-0.17.1 Attempting uninstall: sphinx Found existing installation: Sphinx 1.8.5 Uninstalling Sphinx-1.8.5: Successfully uninstalled Sphinx-1.8.5 Attempting uninstall: sphinx-rtd-theme Found existing installation: sphinx-rtd-theme 0.4.3 Uninstalling sphinx-rtd-theme-0.4.3: Successfully uninstalled sphinx-rtd-theme-0.4.3 Successfully installed anndata-0.7.6 cycler-0.10.0 decorator-4.4.2 docutils-0.16 h5py-3.3.0 joblib-1.0.1 kiwisolver-1.3.1 llvmlite-0.36.0 matplotlib-3.4.2 natsort-7.1.1 networkx-2.5.1 numba-0.53.1 numexpr-2.7.3 numpy-1.21.0 pandas-1.3.0 patsy-0.5.1 pillow-8.3.1 pynndescent-0.5.4 python-dateutil-2.8.2 python-igraph-0.9.6 scanpy-1.8.1 scanpydoc-0.7.2 scikit-learn-0.24.2 scipy-1.7.0 seaborn-0.11.1 setuptools-scm-6.0.1 sinfo-0.3.4 sphinx-4.1.1 sphinx-autodoc-typehints-1.12.0 sphinx-rtd-theme-0.5.2 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 statsmodels-0.12.2 stdlib-list-0.8.0 tables-3.6.1 texttable-1.6.4 threadpoolctl-2.2.0 tqdm-4.61.2 umap-learn-0.5.1 xlrd-1.2.0 [rtd-command-info] start-time: 2021-07-15T05:17:17.774728Z, end-time: 2021-07-15T05:17:17.850040Z, duration: 0, exit-code: 0 git rev-parse HEAD 9360422823fade22a625f3c7840bef132364027e [rtd-command-info] start-time: 2021-07-15T05:17:18.084331Z, end-time: 2021-07-15T05:17:18.158307Z, duration: 0, exit-code: 0 cat docs/conf.py import os import sys from pathlib import Path from datetime import datetime import matplotlib # noqa # Don’t use tkinter agg when importing scanpy → … → matplotlib matplotlib.use('agg') HERE = Path(__file__).parent sys.path[:0] = [str(HERE.parent), str(HERE / 'extensions')] import scanpy # noqa on_rtd = os.environ.get('READTHEDOCS') == 'True' # -- General configuration ------------------------------------------------ nitpicky = True # Warn about broken links. This is here for a reason: Do not change. needs_sphinx = '2.0' # Nicer param docs suppress_warnings = ['ref.citation'] # General information project = 'Scanpy' author = scanpy.__author__ copyright = f'{datetime.now():%Y}, {author}.' version = scanpy.__version__.replace('.dirty', '') release = version # default settings templates_path = ['_templates'] source_suffix = '.rst' master_doc = 'index' default_role = 'literal' exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] pygments_style = 'sphinx' extensions = [ 'sphinx.ext.autodoc', 'sphinx.ext.intersphinx', 'sphinx.ext.doctest', 'sphinx.ext.coverage', 'sphinx.ext.mathjax', 'sphinx.ext.napoleon', 'sphinx.ext.autosummary', # 'plot_generator', 'matplotlib.sphinxext.plot_directive', 'sphinx_autodoc_typehints', # needs to be after napoleon # 'ipython_directive', # 'ipython_console_highlighting', 'scanpydoc', *[p.stem for p in (HERE / 'extensions').glob('*.py')], ] # Generate the API documentation when building autosummary_generate = True autodoc_member_order = 'bysource' # autodoc_default_flags = ['members'] napoleon_google_docstring = False napoleon_numpy_docstring = True napoleon_include_init_with_doc = False napoleon_use_rtype = True # having a separate entry generally helps readability napoleon_use_param = True napoleon_custom_sections = [('Params', 'Parameters')] todo_include_todos = False api_dir = HERE / 'api' # function_images scanpy_tutorials_url = 'https://scanpy-tutorials.readthedocs.io/en/latest/' intersphinx_mapping = dict( anndata=('https://anndata.readthedocs.io/en/stable/', None), bbknn=('https://bbknn.readthedocs.io/en/latest/', None), cycler=('https://matplotlib.org/cycler/', None), h5py=('http://docs.h5py.org/en/stable/', None), ipython=('https://ipython.readthedocs.io/en/stable/', None), leidenalg=('https://leidenalg.readthedocs.io/en/latest/', None), louvain=('https://louvain-igraph.readthedocs.io/en/latest/', None), matplotlib=('https://matplotlib.org/', None), networkx=('https://networkx.github.io/documentation/networkx-1.10/', None), numpy=('https://docs.scipy.org/doc/numpy/', None), pandas=('https://pandas.pydata.org/pandas-docs/stable/', None), pytest=('https://docs.pytest.org/en/latest/', None), python=('https://docs.python.org/3', None), scipy=('https://docs.scipy.org/doc/scipy/reference/', None), seaborn=('https://seaborn.pydata.org/', None), sklearn=('https://scikit-learn.org/stable/', None), scanpy_tutorials=(scanpy_tutorials_url, None), ) # -- Options for HTML output ---------------------------------------------- html_theme = 'scanpydoc' html_theme_options = dict( navigation_depth=4, logo_only=True, docsearch_index='scanpy', docsearch_key='fa4304eb95d2134997e3729553a674b2', ) html_context = dict( display_github=True, # Integrate GitHub github_user='theislab', # Username github_repo='scanpy', # Repo name github_version='master', # Version conf_py_path='/docs/', # Path in the checkout to the docs root ) html_static_path = ['_static'] html_show_sphinx = False html_logo = '_static/img/Scanpy_Logo_BrightFG.svg' def setup(app): app.warningiserror = on_rtd # -- Options for other output formats ------------------------------------------ htmlhelp_basename = f'{project}doc' doc_title = f'{project} Documentation' latex_documents = [(master_doc, f'{project}.tex', doc_title, author, 'manual')] man_pages = [(master_doc, project, doc_title, [author], 1)] texinfo_documents = [ ( master_doc, project, doc_title, author, project, 'One line description of project.', 'Miscellaneous', ) ] # -- Suppress link warnings ---------------------------------------------------- qualname_overrides = { "sklearn.neighbors._dist_metrics.DistanceMetric": "sklearn.neighbors.DistanceMetric", # If the docs are built with an old version of numpy, this will make it work: "numpy.random.RandomState": "numpy.random.mtrand.RandomState", "scanpy.plotting._matrixplot.MatrixPlot": "scanpy.pl.MatrixPlot", "scanpy.plotting._dotplot.DotPlot": "scanpy.pl.DotPlot", "scanpy.plotting._stacked_violin.StackedViolin": "scanpy.pl.StackedViolin", "pandas.core.series.Series": "pandas.Series", } nitpick_ignore = [ # Will probably be documented ('py:class', 'scanpy._settings.Verbosity'), # Currently undocumented: https://github.com/mwaskom/seaborn/issues/1810 ('py:class', 'seaborn.ClusterGrid'), # Won’t be documented ('py:class', 'scanpy.plotting._utils._AxesSubplot'), ('py:class', 'scanpy._utils.Empty'), ('py:class', 'numpy.random.mtrand.RandomState'), ] # Options for plot examples plot_include_source = True plot_formats = [("png", 90)] plot_html_show_formats = False plot_html_show_source_link = False plot_working_directory = HERE.parent # Project root ########################################################################### # auto-created readthedocs.org specific configuration # ########################################################################### # # The following code was added during an automated build on readthedocs.org # It is auto created and injected for every build. The result is based on the # conf.py.tmpl file found in the readthedocs.org codebase: # https://github.com/rtfd/readthedocs.org/blob/master/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl # # Note: this file should't rely on extra depencies. import importlib import sys import os.path # Borrowed from six. PY3 = sys.version_info[0] == 3 string_types = str if PY3 else basestring from sphinx import version_info # Get suffix for proper linking to GitHub # This is deprecated in Sphinx 1.3+, # as each page can have its own suffix if globals().get('source_suffix', False): if isinstance(source_suffix, string_types): SUFFIX = source_suffix elif isinstance(source_suffix, (list, tuple)): # Sphinx >= 1.3 supports list/tuple to define multiple suffixes SUFFIX = source_suffix[0] elif isinstance(source_suffix, dict): # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes SUFFIX = list(source_suffix.keys())[0] # make a ``list()`` for py2/py3 compatibility else: # default to .rst SUFFIX = '.rst' else: SUFFIX = '.rst' # Add RTD Static Path. Add to the end because it overwrites previous files. if not 'html_static_path' in globals(): html_static_path = [] if os.path.exists('_static'): html_static_path.append('_static') # Add RTD Theme only if they aren't overriding it already using_rtd_theme = ( ( 'html_theme' in globals() and html_theme in ['default'] and # Allow people to bail with a hack of having an html_style 'html_style' not in globals() ) or 'html_theme' not in globals() ) if using_rtd_theme: theme = importlib.import_module('sphinx_rtd_theme') html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} if 'html_theme_path' in globals(): html_theme_path.append(theme.get_html_theme_path()) else: html_theme_path = [theme.get_html_theme_path()] if globals().get('websupport2_base_url', False): websupport2_base_url = 'https://readthedocs.com/websupport' websupport2_static_url = 'https://assets.readthedocs.com/' #Add project information to the template context. context = { 'using_theme': using_rtd_theme, 'html_theme': html_theme, 'current_version': "stable", 'version_slug': "stable", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://assets.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ("latest", "/en/latest/"), ("stable", "/en/stable/"), ("docsearch", "/en/docsearch/"), ], 'downloads': [ ], 'subprojects': [ ], 'slug': 'icb-scanpy', 'name': u'scanpy', 'rtd_language': u'en', 'programming_language': u'py', 'canonical_url': 'https://scanpy.readthedocs.io/en/stable/', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/docs/', 'api_host': 'https://readthedocs.com', 'github_user': 'theislab', 'proxied_api_host': '/_', 'github_repo': 'scanpy', 'github_version': '9360422823fade22a625f3c7840bef132364027e', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': '9360422823fade22a625f3c7840bef132364027e', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': '9360422823fade22a625f3c7840bef132364027e', 'display_gitlab': False, 'READTHEDOCS': True, 'using_theme': (html_theme == "default"), 'new_theme': (html_theme == "sphinx_rtd_theme"), 'source_suffix': SUFFIX, 'ad_free': False, 'docsearch_disabled': False, 'user_analytics_code': '', 'global_analytics_code': 'UA-17997319-2', 'commit': '93604228', } # For sphinx >=1.8 we can use html_baseurl to set the canonical URL. # https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_baseurl if version_info >= (1, 8): if not globals().get('html_baseurl'): html_baseurl = context['canonical_url'] context['canonical_url'] = None if 'html_context' in globals(): html_context.update(context) else: html_context = context # Add custom RTD extension if 'extensions' in globals(): # Insert at the beginning because it can interfere # with other extensions. # See https://github.com/rtfd/readthedocs.org/pull/4054 extensions.insert(0, "readthedocs_ext.readthedocs") else: extensions = ["readthedocs_ext.readthedocs"] # Add External version warning banner to the external version documentation if 'branch' == 'external': extensions.insert(1, "readthedocs_ext.external_version_warning") readthedocs_vcs_url = 'None' readthedocs_build_url = 'https://readthedocs.com/projects/icb-scanpy/builds/677120/' project_language = 'en' # User's Sphinx configurations language_user = globals().get('language', None) latex_engine_user = globals().get('latex_engine', None) latex_elements_user = globals().get('latex_elements', None) # Remove this once xindy gets installed in Docker image and XINDYOPS # env variable is supported # https://github.com/rtfd/readthedocs-docker-images/pull/98 latex_use_xindy = False chinese = any([ language_user in ('zh_CN', 'zh_TW'), project_language in ('zh_CN', 'zh_TW'), ]) japanese = any([ language_user == 'ja', project_language == 'ja', ]) if chinese: latex_engine = latex_engine_user or 'xelatex' latex_elements_rtd = { 'preamble': '\\usepackage[UTF8]{ctex}\n', } latex_elements = latex_elements_user or latex_elements_rtd elif japanese: latex_engine = latex_engine_user or 'platex' # Make sure our build directory is always excluded exclude_patterns = globals().get('exclude_patterns', []) exclude_patterns.extend(['_build']) [rtd-command-info] start-time: 2021-07-15T05:17:18.271624Z, end-time: 2021-07-15T05:18:05.620997Z, duration: 47, exit-code: 2 python -m sphinx -T -b html -d _build/doctrees -D language=en . _build/html Running Sphinx v4.1.1 Matplotlib is building the font cache; this may take a moment. loading translations [en]... done making output directory... done loading intersphinx inventory from https://anndata.readthedocs.io/en/stable/objects.inv... loading intersphinx inventory from https://bbknn.readthedocs.io/en/latest/objects.inv... loading intersphinx inventory from https://matplotlib.org/cycler/objects.inv... loading intersphinx inventory from http://docs.h5py.org/en/stable/objects.inv... loading intersphinx inventory from https://ipython.readthedocs.io/en/stable/objects.inv... loading intersphinx inventory from https://leidenalg.readthedocs.io/en/latest/objects.inv... loading intersphinx inventory from https://louvain-igraph.readthedocs.io/en/latest/objects.inv... loading intersphinx inventory from https://matplotlib.org/objects.inv... loading intersphinx inventory from https://networkx.github.io/documentation/networkx-1.10/objects.inv... loading intersphinx inventory from https://docs.scipy.org/doc/numpy/objects.inv... loading intersphinx inventory from https://pandas.pydata.org/pandas-docs/stable/objects.inv... loading intersphinx inventory from https://docs.pytest.org/en/latest/objects.inv... loading intersphinx inventory from https://docs.python.org/3/objects.inv... intersphinx inventory has moved: https://networkx.github.io/documentation/networkx-1.10/objects.inv -> https://networkx.org/documentation/networkx-1.10/objects.inv loading intersphinx inventory from https://docs.scipy.org/doc/scipy/reference/objects.inv... loading intersphinx inventory from https://seaborn.pydata.org/objects.inv... intersphinx inventory has moved: http://docs.h5py.org/en/stable/objects.inv -> https://docs.h5py.org/en/stable/objects.inv loading intersphinx inventory from https://scikit-learn.org/stable/objects.inv... intersphinx inventory has moved: https://docs.scipy.org/doc/numpy/objects.inv -> https://numpy.org/doc/stable/objects.inv loading intersphinx inventory from https://scanpy-tutorials.readthedocs.io/en/latest/objects.inv... [autosummary] generating autosummary for: _key_contributors.rst, api.rst, basic_usage.rst, community.rst, contributors.rst, dev/ci.rst, dev/code.rst, dev/documentation.rst, dev/external-tools.rst, dev/getting-set-up.rst, ..., release-notes/1.6.0.rst, release-notes/1.7.0.rst, release-notes/1.7.1.rst, release-notes/1.7.2.rst, release-notes/1.8.0.rst, release-notes/1.8.1.rst, release-notes/index.rst, release-notes/release-latest.rst, tutorials.rst, usage-principles.rst [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/generated/classes/scanpy.pl.DotPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/generated/classes/scanpy.pl.MatrixPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/generated/classes/scanpy.pl.StackedViolin.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/generated/scanpy.Neighbors.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/generated/scanpy._settings.ScanpyConfig.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/generated/scanpy.datasets.blobs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/generated/scanpy.datasets.ebi_expression_atlas.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/generated/scanpy.datasets.krumsiek11.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/generated/scanpy.datasets.moignard15.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/generated/scanpy.datasets.paul15.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/generated/scanpy.tl.louvain.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/generated/scanpy.tl.marker_gene_overlap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/generated/scanpy.tl.paga.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/generated/scanpy.tl.pca.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/generated/scanpy.tl.rank_genes_groups.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/generated/scanpy.tl.score_genes.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/generated/scanpy.tl.score_genes_cell_cycle.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/generated/scanpy.tl.sim.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/generated/scanpy.tl.tsne.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/generated/scanpy.tl.umap.rst Error in github_url('scanpy._settings.ScanpyConfig.N_PCS'): Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.8/site-packages/sphinx/events.py", line 101, in emit results.append(listener.handler(self.app, *args)) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.8/site-packages/sphinx/ext/autosummary/__init__.py", line 771, in process_generate_options generate_autosummary_docs(genfiles, suffix=suffix, base_path=app.srcdir, File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.8/site-packages/sphinx/ext/autosummary/generate.py", line 454, in generate_autosummary_docs generate_autosummary_docs(new_files, output_dir=output_dir, File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.8/site-packages/sphinx/ext/autosummary/generate.py", line 432, in generate_autosummary_docs content = generate_autosummary_content(name, obj, parent, template, entry.template, File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.8/site-packages/sphinx/ext/autosummary/generate.py", line 365, in generate_autosummary_content return template.render(doc.objtype, ns) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.8/site-packages/sphinx/ext/autosummary/generate.py", line 169, in render return template.render(context) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.8/site-packages/jinja2/environment.py", line 1304, in render self.environment.handle_exception() File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.8/site-packages/jinja2/environment.py", line 925, in handle_exception raise rewrite_traceback_stack(source=source) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/_templates/autosummary/base.rst", line 1, in top-level template code :github_url: {{ fullname | github_url }} File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.8/site-packages/scanpydoc/rtd_github_links.py", line 109, in github_url obj, module = _get_obj_module(qualname) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.8/site-packages/scanpydoc/rtd_github_links.py", line 77, in _get_obj_module thing = getattr(mod if obj is None else obj, attr_name) AttributeError: type object 'ScanpyConfig' has no attribute 'N_PCS' The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.8/site-packages/sphinx/cmd/build.py", line 276, in build_main app = Sphinx(args.sourcedir, args.confdir, args.outputdir, File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.8/site-packages/sphinx/application.py", line 270, in __init__ self._init_builder() File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.8/site-packages/sphinx/application.py", line 328, in _init_builder self.events.emit('builder-inited') File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.8/site-packages/sphinx/events.py", line 109, in emit raise ExtensionError(__("Handler %r for event %r threw an exception") % sphinx.errors.ExtensionError: Handler for event 'builder-inited' threw an exception (exception: type object 'ScanpyConfig' has no attribute 'N_PCS') Extension error (sphinx.ext.autosummary): Handler for event 'builder-inited' threw an exception (exception: type object 'ScanpyConfig' has no attribute 'N_PCS')