Read the Docs build information
Build id: 661611
Project: icb-scanpy
Version: latest
Commit: fb9e12f36b5c600913fa6243819d1575906c384e
Date: 2021-06-23T06:31:29.217432Z
State: finished
Success: False


[rtd-command-info] start-time: 2021-06-23T06:48:59.603567Z, end-time: 2021-06-23T06:49:07.609752Z, duration: 8, exit-code: 0
git clone --no-single-branch --depth 50 https://github.com/theislab/scanpy.git .
Cloning into '.'...

[rtd-command-info] start-time: 2021-06-23T06:49:07.749323Z, end-time: 2021-06-23T06:49:08.068055Z, duration: 0, exit-code: 0
git checkout --force origin/master
Note: checking out 'origin/master'.

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 <new-branch-name>

HEAD is now at fb9e12f3 If raw was not used, use_raw should be False (#1895)

[rtd-command-info] start-time: 2021-06-23T06:49:08.205238Z, end-time: 2021-06-23T06:49:08.288931Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2021-06-23T06:49:08.406279Z, end-time: 2021-06-23T06:49:08.476011Z, duration: 0, exit-code: 0
git rev-parse HEAD
fb9e12f36b5c600913fa6243819d1575906c384e

[rtd-command-info] start-time: 2021-06-23T06:49:12.918675Z, end-time: 2021-06-23T06:49:38.676136Z, duration: 25, 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/latest/bin/python3.8
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/bin/python
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2021-06-23T06:49:38.789543Z, end-time: 2021-06-23T06:49:40.488321Z, 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/latest/lib/python3.8/site-packages (21.1.2)
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages (57.0.0)

[rtd-command-info] start-time: 2021-06-23T06:49:40.596050Z, end-time: 2021-06-23T06:50:24.366636Z, duration: 43, 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 imagesize
  Downloading imagesize-1.2.0-py2.py3-none-any.whl (4.8 kB)
Collecting six>=1.5
  Downloading six-1.16.0-py2.py3-none-any.whl (11 kB)
Collecting requests>=2.0.0
  Downloading requests-2.25.1-py2.py3-none-any.whl (61 kB)
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages (from sphinx<2) (57.0.0)
Collecting packaging
  Downloading packaging-20.9-py2.py3-none-any.whl (40 kB)
Collecting babel!=2.0,>=1.3
  Downloading Babel-2.9.1-py2.py3-none-any.whl (8.8 MB)
Collecting Pygments>=2.0
  Downloading Pygments-2.9.0-py3-none-any.whl (1.0 MB)
Collecting snowballstemmer>=1.1
  Downloading snowballstemmer-2.1.0-py2.py3-none-any.whl (93 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 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 certifi>=2017.4.17
  Downloading certifi-2021.5.30-py2.py3-none-any.whl (145 kB)
Collecting idna<3,>=2.5
  Downloading idna-2.10-py2.py3-none-any.whl (58 kB)
Collecting chardet<5,>=3.0.2
  Downloading chardet-4.0.0-py2.py3-none-any.whl (178 kB)
Collecting urllib3<1.27,>=1.21.1
  Downloading urllib3-1.26.5-py2.py3-none-any.whl (138 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=4d49888001daf923bbb27ce4239f5f991335471b23fa6d9ccd5405be8e317202
  Stored in directory: /tmp/pip-ephem-wheel-cache-pxcz0krj/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=1259999 sha256=69fd6e34106ce0982611597e436a7dc349beba97320e01c8c06bba030300de61
  Stored in directory: /tmp/pip-ephem-wheel-cache-pxcz0krj/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=829421f47cc9c5d71876ddf6ec5cf12e52043edc2ac765ab55dd8bda0cfb01b5
  Stored in directory: /tmp/pip-ephem-wheel-cache-pxcz0krj/wheels/8e/70/28/3d6ccd6e315f65f245da085482a2e1c7d14b90b30f239e2cf4
Successfully built mock pillow future
Installing collected packages: urllib3, sphinxcontrib-serializinghtml, pytz, pyparsing, MarkupSafe, idna, chardet, 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 chardet-4.0.0 commonmark-0.8.1 docutils-0.17.1 future-0.18.2 idna-2.10 imagesize-1.2.0 mock-1.0.1 packaging-20.9 pillow-5.4.1 pyparsing-2.4.7 pytz-2021.1 readthedocs-sphinx-ext-2.1.4 recommonmark-0.5.0 requests-2.25.1 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 urllib3-1.26.5

[rtd-command-info] start-time: 2021-06-23T06:50:24.471135Z, end-time: 2021-06-23T06:51:53.796062Z, duration: 89, 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/latest
  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 h5py>=2.10.0
  Downloading h5py-3.3.0-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (4.5 MB)
Collecting anndata>=0.7.4
  Downloading anndata-0.7.6-py3-none-any.whl (127 kB)
Collecting scipy>=1.4
  Downloading scipy-1.7.0-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.whl (28.4 MB)
Collecting joblib
  Downloading joblib-1.0.1-py3-none-any.whl (303 kB)
Collecting networkx>=2.3
  Downloading networkx-2.5.1-py3-none-any.whl (1.6 MB)
Collecting tqdm
  Downloading tqdm-4.61.1-py2.py3-none-any.whl (75 kB)
Collecting matplotlib>=3.1.2
  Downloading matplotlib-3.4.2-cp38-cp38-manylinux1_x86_64.whl (10.3 MB)
Collecting umap-learn>=0.3.10
  Downloading umap-learn-0.5.1.tar.gz (80 kB)
Collecting scikit-learn>=0.21.2
  Downloading scikit_learn-0.24.2-cp38-cp38-manylinux2010_x86_64.whl (24.9 MB)
Collecting patsy
  Downloading patsy-0.5.1-py2.py3-none-any.whl (231 kB)
Collecting statsmodels>=0.10.0rc2
  Downloading statsmodels-0.12.2-cp38-cp38-manylinux1_x86_64.whl (9.4 MB)
Collecting natsort
  Downloading natsort-7.1.1-py3-none-any.whl (35 kB)
Collecting numba>=0.41.0
  Downloading numba-0.53.1-cp38-cp38-manylinux2014_x86_64.whl (3.4 MB)
Collecting legacy-api-wrap
  Downloading legacy_api_wrap-1.2-py3-none-any.whl (37 kB)
Collecting sinfo
  Downloading sinfo-0.3.4.tar.gz (24 kB)
Collecting pandas>=0.21
  Downloading pandas-1.2.5-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.whl (9.7 MB)
Collecting tables
  Downloading tables-3.6.1-cp38-cp38-manylinux1_x86_64.whl (4.3 MB)
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 seaborn
  Downloading seaborn-0.11.1-py3-none-any.whl (285 kB)
Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages (from scanpy==1.8.0.dev104+gfb9e12f3) (20.9)
Collecting python-igraph
  Downloading python_igraph-0.9.6-cp38-cp38-manylinux2010_x86_64.whl (3.3 MB)
Collecting sphinx-autodoc-typehints
  Downloading sphinx_autodoc_typehints-1.12.0-py3-none-any.whl (9.4 kB)
Collecting scanpydoc>=0.6
  Downloading scanpydoc-0.7.1-py3-none-any.whl (29 kB)
Requirement already satisfied: sphinx-rtd-theme>=0.3.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages (from scanpy==1.8.0.dev104+gfb9e12f3) (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>=3.2
  Downloading Sphinx-4.0.2-py3-none-any.whl (2.9 MB)
Collecting xlrd<2.0
  Downloading xlrd-1.2.0-py2.py3-none-any.whl (103 kB)
Requirement already satisfied: pyparsing>=2.2.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages (from matplotlib>=3.1.2->scanpy==1.8.0.dev104+gfb9e12f3) (2.4.7)
Collecting python-dateutil>=2.7
  Downloading python_dateutil-2.8.1-py2.py3-none-any.whl (227 kB)
Collecting pillow>=6.2.0
  Downloading Pillow-8.2.0-cp38-cp38-manylinux1_x86_64.whl (3.0 MB)
Collecting kiwisolver>=1.0.1
  Downloading kiwisolver-1.3.1-cp38-cp38-manylinux1_x86_64.whl (1.2 MB)
Collecting cycler>=0.10
  Downloading cycler-0.10.0-py2.py3-none-any.whl (6.5 kB)
Requirement already satisfied: six in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages (from cycler>=0.10->matplotlib>=3.1.2->scanpy==1.8.0.dev104+gfb9e12f3) (1.16.0)
Collecting decorator<5,>=4.3
  Downloading decorator-4.4.2-py2.py3-none-any.whl (9.2 kB)
Collecting llvmlite<0.37,>=0.36.0rc1
  Downloading llvmlite-0.36.0-cp38-cp38-manylinux2010_x86_64.whl (25.3 MB)
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages (from numba>=0.41.0->scanpy==1.8.0.dev104+gfb9e12f3) (57.0.0)
Requirement already satisfied: pytz>=2017.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages (from pandas>=0.21->scanpy==1.8.0.dev104+gfb9e12f3) (2021.1)
Collecting get_version
  Downloading get_version-3.2-py3-none-any.whl (16 kB)
Collecting threadpoolctl>=2.0.0
  Downloading threadpoolctl-2.1.0-py3-none-any.whl (12 kB)
Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages (from sphinx>=3.2->scanpy==1.8.0.dev104+gfb9e12f3) (3.0.1)
Requirement already satisfied: requests>=2.5.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages (from sphinx>=3.2->scanpy==1.8.0.dev104+gfb9e12f3) (2.25.1)
Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages (from sphinx>=3.2->scanpy==1.8.0.dev104+gfb9e12f3) (1.2.0)
Requirement already satisfied: sphinxcontrib-serializinghtml in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages (from sphinx>=3.2->scanpy==1.8.0.dev104+gfb9e12f3) (1.1.5)
Collecting sphinxcontrib-applehelp
  Downloading sphinxcontrib_applehelp-1.0.2-py2.py3-none-any.whl (121 kB)
Collecting sphinxcontrib-jsmath
  Downloading sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB)
Collecting sphinxcontrib-qthelp
  Downloading sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl (90 kB)
Requirement already satisfied: babel>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages (from sphinx>=3.2->scanpy==1.8.0.dev104+gfb9e12f3) (2.9.1)
Requirement already satisfied: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages (from sphinx>=3.2->scanpy==1.8.0.dev104+gfb9e12f3) (2.9.0)
Requirement already satisfied: docutils<0.18,>=0.14 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages (from sphinx>=3.2->scanpy==1.8.0.dev104+gfb9e12f3) (0.17.1)
Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages (from sphinx>=3.2->scanpy==1.8.0.dev104+gfb9e12f3) (0.7.12)
Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages (from sphinx>=3.2->scanpy==1.8.0.dev104+gfb9e12f3) (2.1.0)
Collecting sphinxcontrib-devhelp
  Downloading sphinxcontrib_devhelp-1.0.2-py2.py3-none-any.whl (84 kB)
Collecting sphinxcontrib-htmlhelp
  Downloading sphinxcontrib_htmlhelp-2.0.0-py2.py3-none-any.whl (100 kB)
Requirement already satisfied: MarkupSafe>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages (from Jinja2>=2.3->sphinx>=3.2->scanpy==1.8.0.dev104+gfb9e12f3) (2.0.1)
Requirement already satisfied: chardet<5,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages (from requests>=2.5.0->sphinx>=3.2->scanpy==1.8.0.dev104+gfb9e12f3) (4.0.0)
Requirement already satisfied: idna<3,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages (from requests>=2.5.0->sphinx>=3.2->scanpy==1.8.0.dev104+gfb9e12f3) (2.10)
Requirement already satisfied: urllib3<1.27,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages (from requests>=2.5.0->sphinx>=3.2->scanpy==1.8.0.dev104+gfb9e12f3) (1.26.5)
Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages (from requests>=2.5.0->sphinx>=3.2->scanpy==1.8.0.dev104+gfb9e12f3) (2021.5.30)
Collecting docutils<0.18,>=0.14
  Downloading docutils-0.16-py2.py3-none-any.whl (548 kB)
Collecting pynndescent>=0.5
  Downloading pynndescent-0.5.2.tar.gz (1.1 MB)
Collecting dunamai
  Downloading dunamai-1.5.5-py3-none-any.whl (16 kB)
Collecting texttable>=1.6.2
  Downloading texttable-1.6.3-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-1.8.0.dev104+gfb9e12f3-py3-none-any.whl size=11327393 sha256=442ea9f994d909b6e0438f836fae3b0eb643376e20b024e67d24877d8f152266
  Stored in directory: /tmp/pip-ephem-wheel-cache-oz7pebt0/wheels/3b/59/52/933b5c7bcaabc49289abbc1d71f859ce119211165023059b98
  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=89928d7ae6b5d40abee38f2d19b02913cce558d565ad8704d8e6a9e8e5b554e7
  Stored in directory: /tmp/pip-ephem-wheel-cache-oz7pebt0/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-0.5.2-py3-none-any.whl size=51360 sha256=5829b6d90d278cc450395b2792a95b78d5be0dae79e0f03663feeb65abe11569
  Stored in directory: /tmp/pip-ephem-wheel-cache-oz7pebt0/wheels/bb/81/5d/c78c8f15f3c815197129f91ec435d8ae0bb0a7a856d962c3ce
  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=8ce6935f0f4d79347df50ddf8f36c80c9b114a8330288eec11a95dceb109c521
  Stored in directory: /tmp/pip-ephem-wheel-cache-oz7pebt0/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, dunamai, cycler, xlrd, stdlib-list, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, pynndescent, patsy, pandas, numexpr, natsort, matplotlib, h5py, get-version, docutils, decorator, umap-learn, tqdm, texttable, tables, statsmodels, sphinx, sinfo, seaborn, networkx, legacy-api-wrap, 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 dunamai-1.5.5 get-version-3.2 h5py-3.3.0 joblib-1.0.1 kiwisolver-1.3.1 legacy-api-wrap-1.2 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-1.2.5 patsy-0.5.1 pillow-8.2.0 pynndescent-0.5.2 python-dateutil-2.8.1 python-igraph-0.9.6 scanpy-1.8.0.dev104+gfb9e12f3 scanpydoc-0.7.1 scikit-learn-0.24.2 scipy-1.7.0 seaborn-0.11.1 sinfo-0.3.4 sphinx-4.0.2 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-1.6.3 threadpoolctl-2.1.0 tqdm-4.61.1 umap-learn-0.5.1 xlrd-1.2.0

[rtd-command-info] start-time: 2021-06-23T06:51:54.830746Z, end-time: 2021-06-23T06:51:54.923685Z, duration: 0, exit-code: 0
git rev-parse HEAD
fb9e12f36b5c600913fa6243819d1575906c384e

[rtd-command-info] start-time: 2021-06-23T06:51:55.184572Z, end-time: 2021-06-23T06:51:55.256791Z, 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': "latest",
    'version_slug': "latest",
    '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': 'master',
    'display_github': True,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': 'master',
    'display_bitbucket': False,
    'gitlab_user': 'None',
    'gitlab_repo': 'None',
    'gitlab_version': 'master',
    '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': 'fb9e12f3',
}

# 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/661611/'

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: 2021-06-23T06:51:55.454407Z, end-time: 2021-06-23T06:52:44.137050Z, duration: 48, exit-code: 2
python -m sphinx -T -E -b html -d _build/doctrees -D language=en . _build/html
Running Sphinx v4.0.2
Matplotlib is building the font cache; this may take a moment.

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages/sphinx/config.py", line 323, in eval_config_file
    exec(code, namespace)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/conf.py", line 13, in <module>
    import scanpy  # noqa
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/__init__.py", line 17, in <module>
    from . import datasets, logging, queries, external, get, metrics
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/external/__init__.py", line 3, in <module>
    from . import pp
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/external/pp/__init__.py", line 5, in <module>
    from ._magic import magic
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/external/pp/_magic.py", line 7, in <module>
    from legacy_api_wrap import legacy_api
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages/legacy_api_wrap.py", line 18, in <module>
    from get_version import get_version
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages/get_version.py", line 183, in <module>
    __version__ = get_version(__file__)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages/get_version.py", line 172, in get_version
    or get_version_from_vcs(parent)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages/get_version.py", line 92, in get_version_from_vcs
    return version.serialize(dirty=not ON_RTD)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages/dunamai/__init__.py", line 458, in serialize
    out = serialize_pep440(
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages/dunamai/__init__.py", line 1015, in serialize_pep440
    check_version(serialized, Style.Pep440)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages/dunamai/__init__.py", line 923, in check_version
    raise ValueError(failure_message)
ValueError: Version '1.8.0dev0.post104.dev0+fb9e12f3' does not conform to the PEP 440 style

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/latest/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/latest/lib/python3.8/site-packages/sphinx/application.py", line 217, in __init__
    self.config = Config.read(self.confdir, confoverrides or {}, self.tags)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages/sphinx/config.py", line 168, in read
    namespace = eval_config_file(filename, tags)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages/sphinx/config.py", line 336, in eval_config_file
    raise ConfigError(msg % traceback.format_exc()) from exc
sphinx.errors.ConfigError: There is a programmable error in your configuration file:

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages/sphinx/config.py", line 323, in eval_config_file
    exec(code, namespace)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/conf.py", line 13, in <module>
    import scanpy  # noqa
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/__init__.py", line 17, in <module>
    from . import datasets, logging, queries, external, get, metrics
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/external/__init__.py", line 3, in <module>
    from . import pp
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/external/pp/__init__.py", line 5, in <module>
    from ._magic import magic
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/external/pp/_magic.py", line 7, in <module>
    from legacy_api_wrap import legacy_api
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages/legacy_api_wrap.py", line 18, in <module>
    from get_version import get_version
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages/get_version.py", line 183, in <module>
    __version__ = get_version(__file__)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages/get_version.py", line 172, in get_version
    or get_version_from_vcs(parent)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages/get_version.py", line 92, in get_version_from_vcs
    return version.serialize(dirty=not ON_RTD)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages/dunamai/__init__.py", line 458, in serialize
    out = serialize_pep440(
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages/dunamai/__init__.py", line 1015, in serialize_pep440
    check_version(serialized, Style.Pep440)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages/dunamai/__init__.py", line 923, in check_version
    raise ValueError(failure_message)
ValueError: Version '1.8.0dev0.post104.dev0+fb9e12f3' does not conform to the PEP 440 style


Configuration error:
There is a programmable error in your configuration file:

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages/sphinx/config.py", line 323, in eval_config_file
    exec(code, namespace)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/conf.py", line 13, in <module>
    import scanpy  # noqa
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/__init__.py", line 17, in <module>
    from . import datasets, logging, queries, external, get, metrics
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/external/__init__.py", line 3, in <module>
    from . import pp
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/external/pp/__init__.py", line 5, in <module>
    from ._magic import magic
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/external/pp/_magic.py", line 7, in <module>
    from legacy_api_wrap import legacy_api
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages/legacy_api_wrap.py", line 18, in <module>
    from get_version import get_version
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages/get_version.py", line 183, in <module>
    __version__ = get_version(__file__)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages/get_version.py", line 172, in get_version
    or get_version_from_vcs(parent)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages/get_version.py", line 92, in get_version_from_vcs
    return version.serialize(dirty=not ON_RTD)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages/dunamai/__init__.py", line 458, in serialize
    out = serialize_pep440(
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages/dunamai/__init__.py", line 1015, in serialize_pep440
    check_version(serialized, Style.Pep440)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.8/site-packages/dunamai/__init__.py", line 923, in check_version
    raise ValueError(failure_message)
ValueError: Version '1.8.0dev0.post104.dev0+fb9e12f3' does not conform to the PEP 440 style