Read the Docs build information
Build id: 780096
Project: icb-scanpy
Version: 2055
Commit: 0814c85a755c3a990e047f9d88d8a77ebaa4704b
Date: 2021-11-22T17:20:38.337751Z
State: finished
Success: False


[rtd-command-info] start-time: 2021-11-22T17:24:22.993819Z, end-time: 2021-11-22T17:24:31.674181Z, 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: 2021-11-22T17:24:31.810371Z, end-time: 2021-11-22T17:24:32.475666Z, duration: 0, exit-code: 0
git fetch origin --force --tags --prune --prune-tags --depth 50 pull/2055/head:external-2055
From https://github.com/theislab/scanpy
 * [new ref]           refs/pull/2055/head -> external-2055

[rtd-command-info] start-time: 2021-11-22T17:24:32.637457Z, end-time: 2021-11-22T17:24:32.826532Z, duration: 0, exit-code: 0
git checkout --force 0814c85a755c3a990e047f9d88d8a77ebaa4704b
Note: checking out '0814c85a755c3a990e047f9d88d8a77ebaa4704b'.

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 0814c85a - added doc and example for dotplot groupby_expand = True

[rtd-command-info] start-time: 2021-11-22T17:24:32.962773Z, end-time: 2021-11-22T17:24:33.042433Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2021-11-22T17:24:35.048249Z, end-time: 2021-11-22T17:24:47.600641Z, duration: 12, 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/2055/bin/python3.8
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2055/bin/python
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2021-11-22T17:24:47.749088Z, end-time: 2021-11-22T17:24:49.075351Z, 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/2055/lib/python3.8/site-packages (21.3.1)
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2055/lib/python3.8/site-packages (59.2.0)

[rtd-command-info] start-time: 2021-11-22T17:24:49.196868Z, end-time: 2021-11-22T17:25:21.142004Z, duration: 31, 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)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting pillow==5.4.1
  Downloading Pillow-5.4.1.tar.gz (16.0 MB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
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-1.8.6-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)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting docutils>=0.11
  Downloading docutils-0.18-py2.py3-none-any.whl (569 kB)
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2055/lib/python3.8/site-packages (from sphinx<2) (59.2.0)
Collecting six>=1.5
  Downloading six-1.16.0-py2.py3-none-any.whl (11 kB)
Collecting snowballstemmer>=1.1
  Downloading snowballstemmer-2.2.0-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 docutils>=0.11
  Downloading docutils-0.17.1-py2.py3-none-any.whl (575 kB)
Collecting imagesize
  Downloading imagesize-1.3.0-py2.py3-none-any.whl (5.2 kB)
Collecting Pygments>=2.0
  Downloading Pygments-2.10.0-py3-none-any.whl (1.0 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 packaging
  Downloading packaging-21.3-py3-none-any.whl (40 kB)
Collecting Jinja2>=2.3
  Downloading Jinja2-3.0.3-py3-none-any.whl (133 kB)
Collecting pytz>=2015.7
  Downloading pytz-2021.3-py2.py3-none-any.whl (503 kB)
Collecting MarkupSafe>=2.0
  Downloading MarkupSafe-2.0.1-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (30 kB)
Collecting urllib3<1.27,>=1.21.1
  Downloading urllib3-1.26.7-py2.py3-none-any.whl (138 kB)
Collecting idna<4,>=2.5
  Downloading idna-3.3-py3-none-any.whl (61 kB)
Collecting certifi>=2017.4.17
  Downloading certifi-2021.10.8-py2.py3-none-any.whl (149 kB)
Collecting charset-normalizer~=2.0.0
  Downloading charset_normalizer-2.0.7-py3-none-any.whl (38 kB)
Collecting pyparsing!=3.0.5,>=2.0.2
  Downloading pyparsing-3.0.6-py3-none-any.whl (97 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=3450cdc579f3365f42a1c73663f167f928e0a69b0c7dfff89dd515be8b9a6c28
  Stored in directory: /tmp/pip-ephem-wheel-cache-d0irpc9t/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=1260112 sha256=18e7af564a168b58dbf8bf23c6b3956eb208d073373002b2515bba673cda5843
  Stored in directory: /tmp/pip-ephem-wheel-cache-d0irpc9t/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=6b51ba7d8c4804b3263a28e4dda66ba76862b1ed0e35632044a65d74eac3cec4
  Stored in directory: /tmp/pip-ephem-wheel-cache-d0irpc9t/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 Jinja2-3.0.3 MarkupSafe-2.0.1 Pygments-2.10.0 alabaster-0.7.12 babel-2.9.1 certifi-2021.10.8 charset-normalizer-2.0.7 commonmark-0.8.1 docutils-0.17.1 future-0.18.2 idna-3.3 imagesize-1.3.0 mock-1.0.1 packaging-21.3 pillow-5.4.1 pyparsing-3.0.6 pytz-2021.3 readthedocs-sphinx-ext-2.1.4 recommonmark-0.5.0 requests-2.26.0 six-1.16.0 snowballstemmer-2.2.0 sphinx-1.8.6 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.5 sphinxcontrib-websupport-1.2.4 urllib3-1.26.7

[rtd-command-info] start-time: 2021-11-22T17:25:21.248146Z, end-time: 2021-11-22T17:26:46.193116Z, duration: 84, 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/2055
  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 metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): finished with status 'done'
Collecting matplotlib>=3.1.2
  Downloading matplotlib-3.5.0-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.whl (11.3 MB)
Collecting patsy
  Downloading patsy-0.5.2-py2.py3-none-any.whl (233 kB)
Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2055/lib/python3.8/site-packages (from scanpy==1.9.0.dev37+g0814c85a) (21.3)
Collecting pandas>=0.21
  Downloading pandas-1.3.4-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.5 MB)
Collecting joblib
  Downloading joblib-1.1.0-py2.py3-none-any.whl (306 kB)
Collecting scipy>=1.4
  Downloading scipy-1.7.2-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (39.3 MB)
Collecting h5py>=2.10.0
  Downloading h5py-3.6.0-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (4.5 MB)
Collecting statsmodels>=0.10.0rc2
  Downloading statsmodels-0.13.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (9.9 MB)
Collecting networkx>=2.3
  Downloading networkx-2.6.3-py3-none-any.whl (1.9 MB)
Collecting umap-learn>=0.3.10
  Downloading umap-learn-0.5.2.tar.gz (86 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting seaborn
  Downloading seaborn-0.11.2-py3-none-any.whl (292 kB)
Collecting natsort
  Downloading natsort-8.0.0-py3-none-any.whl (37 kB)
Collecting numba>=0.41.0
  Downloading numba-0.54.1-cp38-cp38-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (3.3 MB)
Collecting tqdm
  Downloading tqdm-4.62.3-py2.py3-none-any.whl (76 kB)
Collecting tables
  Downloading tables-3.6.1-cp38-cp38-manylinux1_x86_64.whl (4.3 MB)
Collecting numpy>=1.17.0
  Downloading numpy-1.21.4-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (15.7 MB)
Collecting anndata>=0.7.4
  Downloading anndata-0.7.8-py3-none-any.whl (91 kB)
Collecting sinfo
  Downloading sinfo-0.3.4.tar.gz (24 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting scikit-learn>=0.22
  Downloading scikit_learn-1.0.1-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (25.9 MB)
Collecting python-igraph
  Downloading python-igraph-0.9.8.tar.gz (9.5 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting scanpydoc>=0.7.3
  Downloading scanpydoc-0.7.3-py3-none-any.whl (29 kB)
Collecting sphinx-autodoc-typehints
  Downloading sphinx_autodoc_typehints-1.12.0-py3-none-any.whl (9.4 kB)
Collecting sphinx<4.2,>=4.1
  Downloading Sphinx-4.1.2-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/2055/lib/python3.8/site-packages (from scanpy==1.9.0.dev37+g0814c85a) (0.4.3)
Collecting sphinx-rtd-theme>=0.3.1
  Downloading sphinx_rtd_theme-1.0.0-py2.py3-none-any.whl (2.8 MB)
Collecting xlrd<2.0
  Downloading xlrd-1.2.0-py2.py3-none-any.whl (103 kB)
Collecting python-dateutil>=2.7
  Downloading python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
Requirement already satisfied: pyparsing>=2.2.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2055/lib/python3.8/site-packages (from matplotlib>=3.1.2->scanpy==1.9.0.dev37+g0814c85a) (3.0.6)
Collecting setuptools-scm>=4
  Downloading setuptools_scm-6.3.2-py3-none-any.whl (33 kB)
Collecting cycler>=0.10
  Downloading cycler-0.11.0-py3-none-any.whl (6.4 kB)
Collecting pillow>=6.2.0
  Downloading Pillow-8.4.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.1 MB)
Collecting kiwisolver>=1.0.1
  Downloading kiwisolver-1.3.2-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.whl (1.2 MB)
Collecting fonttools>=4.22.0
  Downloading fonttools-4.28.2-py3-none-any.whl (880 kB)
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2055/lib/python3.8/site-packages (from numba>=0.41.0->scanpy==1.9.0.dev37+g0814c85a) (59.2.0)
Collecting numpy>=1.17.0
  Downloading numpy-1.20.3-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (15.4 MB)
Collecting llvmlite<0.38,>=0.37.0rc1
  Downloading llvmlite-0.37.0-cp38-cp38-manylinux2014_x86_64.whl (26.3 MB)
Requirement already satisfied: pytz>=2017.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2055/lib/python3.8/site-packages (from pandas>=0.21->scanpy==1.9.0.dev37+g0814c85a) (2021.3)
Collecting get_version
  Downloading get_version-3.5.3-py3-none-any.whl (18 kB)
Collecting threadpoolctl>=2.0.0
  Downloading threadpoolctl-3.0.0-py3-none-any.whl (14 kB)
Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2055/lib/python3.8/site-packages (from sphinx<4.2,>=4.1->scanpy==1.9.0.dev37+g0814c85a) (0.7.12)
Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2055/lib/python3.8/site-packages (from sphinx<4.2,>=4.1->scanpy==1.9.0.dev37+g0814c85a) (3.0.3)
Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2055/lib/python3.8/site-packages (from sphinx<4.2,>=4.1->scanpy==1.9.0.dev37+g0814c85a) (1.3.0)
Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2055/lib/python3.8/site-packages (from sphinx<4.2,>=4.1->scanpy==1.9.0.dev37+g0814c85a) (2.2.0)
Collecting sphinxcontrib-applehelp
  Downloading sphinxcontrib_applehelp-1.0.2-py2.py3-none-any.whl (121 kB)
Requirement already satisfied: docutils<0.18,>=0.14 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2055/lib/python3.8/site-packages (from sphinx<4.2,>=4.1->scanpy==1.9.0.dev37+g0814c85a) (0.17.1)
Collecting sphinxcontrib-devhelp
  Downloading sphinxcontrib_devhelp-1.0.2-py2.py3-none-any.whl (84 kB)
Collecting sphinxcontrib-htmlhelp>=2.0.0
  Downloading sphinxcontrib_htmlhelp-2.0.0-py2.py3-none-any.whl (100 kB)
Requirement already satisfied: sphinxcontrib-serializinghtml>=1.1.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2055/lib/python3.8/site-packages (from sphinx<4.2,>=4.1->scanpy==1.9.0.dev37+g0814c85a) (1.1.5)
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/2055/lib/python3.8/site-packages (from sphinx<4.2,>=4.1->scanpy==1.9.0.dev37+g0814c85a) (2.9.1)
Requirement already satisfied: requests>=2.5.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2055/lib/python3.8/site-packages (from sphinx<4.2,>=4.1->scanpy==1.9.0.dev37+g0814c85a) (2.26.0)
Collecting sphinxcontrib-jsmath
  Downloading sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB)
Requirement already satisfied: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2055/lib/python3.8/site-packages (from sphinx<4.2,>=4.1->scanpy==1.9.0.dev37+g0814c85a) (2.10.0)
Requirement already satisfied: six in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2055/lib/python3.8/site-packages (from patsy->scanpy==1.9.0.dev37+g0814c85a) (1.16.0)
Collecting pynndescent>=0.5
  Downloading pynndescent-0.5.5.tar.gz (1.1 MB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting igraph==0.9.8
  Downloading igraph-0.9.8-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (3.3 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)
Requirement already satisfied: MarkupSafe>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2055/lib/python3.8/site-packages (from Jinja2>=2.3->sphinx<4.2,>=4.1->scanpy==1.9.0.dev37+g0814c85a) (2.0.1)
Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2055/lib/python3.8/site-packages (from requests>=2.5.0->sphinx<4.2,>=4.1->scanpy==1.9.0.dev37+g0814c85a) (2021.10.8)
Requirement already satisfied: charset-normalizer~=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2055/lib/python3.8/site-packages (from requests>=2.5.0->sphinx<4.2,>=4.1->scanpy==1.9.0.dev37+g0814c85a) (2.0.7)
Requirement already satisfied: idna<4,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2055/lib/python3.8/site-packages (from requests>=2.5.0->sphinx<4.2,>=4.1->scanpy==1.9.0.dev37+g0814c85a) (3.3)
Requirement already satisfied: urllib3<1.27,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2055/lib/python3.8/site-packages (from requests>=2.5.0->sphinx<4.2,>=4.1->scanpy==1.9.0.dev37+g0814c85a) (1.26.7)
Collecting tomli>=1.0.0
  Downloading tomli-1.2.2-py3-none-any.whl (12 kB)
Collecting dunamai
  Downloading dunamai-1.7.0-py3-none-any.whl (16 kB)
Building wheels for collected packages: umap-learn, python-igraph, scanpy, sinfo, pynndescent
  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-0.5.2-py3-none-any.whl size=82709 sha256=1ab4d8829a3df759ffe07370a1ef3aab0b0fb23f7d1d542e5d5948f4e1916383
  Stored in directory: /tmp/pip-ephem-wheel-cache-qahefb7p/wheels/f2/64/75/df601da9514261c8cb0830b9515d2b94b5a51f09ddeae92b9e
  Building wheel for python-igraph (setup.py): started
  Building wheel for python-igraph (setup.py): finished with status 'done'
  Created wheel for python-igraph: filename=python_igraph-0.9.8-py3-none-any.whl size=9070 sha256=03137543fa4761524720b5747cf7a1aa7ec03409ca6241ffd9ace9323f8f1c1b
  Stored in directory: /tmp/pip-ephem-wheel-cache-qahefb7p/wheels/f9/14/00/acd6e2e744895a9833123220e47f6f947a423f26e66fc9e4fd
  Building wheel for scanpy (pyproject.toml): started
  Building wheel for scanpy (pyproject.toml): finished with status 'done'
  Created wheel for scanpy: filename=scanpy-1.9.0.dev37+g0814c85a-py3-none-any.whl size=11405690 sha256=735f555d084081e382aee6c9c2ec1c9f5f7b33e3c333e4a1df61cf2b0c448e03
  Stored in directory: /tmp/pip-ephem-wheel-cache-qahefb7p/wheels/96/4b/d1/247c8fe9bb0c0a9c8aa2150d32f486bca7b13a856b3fbeecd8
  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=6da1e311e701381bcd1903c31f5bd8c46c174aa0a8cd45e29075a024b88610de
  Stored in directory: /tmp/pip-ephem-wheel-cache-qahefb7p/wheels/0e/63/be/1333921ddb5d249efe6db671c36608e46593e018994c3be11d
  Building wheel for pynndescent (setup.py): started
  Building wheel for pynndescent (setup.py): finished with status 'done'
  Created wheel for pynndescent: filename=pynndescent-0.5.5-py3-none-any.whl size=52603 sha256=1565f540e8ae8478374260710f929c8d465cd291d3ea9f789e1082ebae1cc1e8
  Stored in directory: /tmp/pip-ephem-wheel-cache-qahefb7p/wheels/e4/0e/b5/07c0c231aacb04e5d1046fe7459bb27ea79f95b5edbe88e435
Successfully built umap-learn python-igraph scanpy sinfo pynndescent
Installing collected packages: numpy, tomli, threadpoolctl, scipy, llvmlite, joblib, setuptools-scm, scikit-learn, python-dateutil, pillow, numba, kiwisolver, fonttools, cycler, xlrd, tqdm, texttable, stdlib-list, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, pynndescent, patsy, pandas, numexpr, natsort, matplotlib, h5py, dunamai, umap-learn, tables, statsmodels, sphinx, sinfo, seaborn, networkx, igraph, get-version, 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: sphinx
    Found existing installation: Sphinx 1.8.6
    Uninstalling Sphinx-1.8.6:
      Successfully uninstalled Sphinx-1.8.6
  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-0.7.8 cycler-0.11.0 dunamai-1.7.0 fonttools-4.28.2 get-version-3.5.3 h5py-3.6.0 igraph-0.9.8 joblib-1.1.0 kiwisolver-1.3.2 llvmlite-0.37.0 matplotlib-3.5.0 natsort-8.0.0 networkx-2.6.3 numba-0.54.1 numexpr-2.7.3 numpy-1.20.3 pandas-1.3.4 patsy-0.5.2 pillow-8.4.0 pynndescent-0.5.5 python-dateutil-2.8.2 python-igraph-0.9.8 scanpy-1.9.0.dev37+g0814c85a scanpydoc-0.7.3 scikit-learn-1.0.1 scipy-1.7.2 seaborn-0.11.2 setuptools-scm-6.3.2 sinfo-0.3.4 sphinx-4.1.2 sphinx-autodoc-typehints-1.12.0 sphinx-rtd-theme-1.0.0 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-0.13.1 stdlib-list-0.8.0 tables-3.6.1 texttable-1.6.4 threadpoolctl-3.0.0 tomli-1.2.2 tqdm-4.62.3 umap-learn-0.5.2 xlrd-1.2.0

[rtd-command-info] start-time: 2021-11-22T17:26:47.385928Z, end-time: 2021-11-22T17:26:47.451998Z, 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'),
    # Will work once scipy 1.8 is released
    ('py:class', 'scipy.sparse.base.spmatrix'),
    ('py:class', 'scipy.sparse.csr.csr_matrix'),
]

# 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 shouldn't rely on extra dependencies.

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': "2055",
    'version_slug': "2055",
    'MEDIA_URL': "https://media.readthedocs.com/media/",
    'STATIC_URL': "https://assets.readthedocs.com/",
    'PRODUCTION_DOMAIN': "readthedocs.com",
    'versions': [
    ("latest", "/en/latest/"),
    ("stable", "/en/stable/"),
    ],
    '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': '0814c85a755c3a990e047f9d88d8a77ebaa4704b',
    'display_github': True,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': '0814c85a755c3a990e047f9d88d8a77ebaa4704b',
    'display_bitbucket': False,
    'gitlab_user': 'None',
    'gitlab_repo': 'None',
    'gitlab_version': '0814c85a755c3a990e047f9d88d8a77ebaa4704b',
    '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': '0814c85a',
}

# 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 'external' == 'external':
    extensions.insert(1, "readthedocs_ext.external_version_warning")
    readthedocs_vcs_url = 'https://github.com/theislab/scanpy/pull/2055'
    readthedocs_build_url = 'https://readthedocs.com/projects/icb-scanpy/builds/780096/'

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: 2021-11-22T17:26:47.616837Z, end-time: 2021-11-22T17:30:08.645408Z, duration: 201, exit-code: 2
python -m sphinx -T -E -b html -d _build/doctrees -D language=en . _build/html
Running Sphinx v4.1.2
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: http://docs.h5py.org/en/stable/objects.inv -> https://docs.h5py.org/en/stable/objects.inv
loading intersphinx inventory from https://docs.scipy.org/doc/scipy/reference/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://seaborn.pydata.org/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/1.7.2.rst, release-notes/1.8.0.rst, release-notes/1.8.1.rst, release-notes/1.8.2.rst, release-notes/1.8.3.rst, release-notes/1.9.0.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/2055/docs/generated/classes/scanpy.pl.DotPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2055/docs/generated/classes/scanpy.pl.MatrixPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2055/docs/generated/classes/scanpy.pl.StackedViolin.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2055/docs/generated/scanpy.Neighbors.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2055/docs/generated/scanpy._settings.ScanpyConfig.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2055/docs/generated/scanpy.datasets.blobs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2055/docs/generated/scanpy.datasets.ebi_expression_atlas.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2055/docs/generated/scanpy.datasets.krumsiek11.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2055/docs/generated/scanpy.datasets.moignard15.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2055/docs/generated/scanpy.datasets.paul15.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2055/docs/generated/scanpy.tl.louvain.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2055/docs/generated/scanpy.tl.marker_gene_overlap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2055/docs/generated/scanpy.tl.paga.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2055/docs/generated/scanpy.tl.pca.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2055/docs/generated/scanpy.tl.rank_genes_groups.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2055/docs/generated/scanpy.tl.score_genes.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2055/docs/generated/scanpy.tl.score_genes_cell_cycle.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2055/docs/generated/scanpy.tl.sim.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2055/docs/generated/scanpy.tl.tsne.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2055/docs/generated/scanpy.tl.umap.rst
[autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2055/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_HEIGHT.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2055/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_WIDTH.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2055/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLORMAP.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2055/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_LEGEND_TITLE.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2055/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_ON.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2055/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGECOLOR.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2055/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGELW.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2055/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MAX.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2055/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MIN.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2055/docs/generated/classes/scanpy.pl.DotPlot.DEFAULT_LARGEST_DOT.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2055/docs/generated/scanpy._settings.ScanpyConfig.file_format_data.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2055/docs/generated/scanpy._settings.ScanpyConfig.file_format_figs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2055/docs/generated/scanpy._settings.ScanpyConfig.logfile.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2055/docs/generated/scanpy._settings.ScanpyConfig.logpath.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2055/docs/generated/scanpy._settings.ScanpyConfig.max_memory.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2055/docs/generated/scanpy._settings.ScanpyConfig.n_jobs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2055/docs/generated/scanpy._settings.ScanpyConfig.plot_suffix.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2055/docs/generated/scanpy._settings.ScanpyConfig.set_figure_params.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2055/docs/generated/scanpy._settings.ScanpyConfig.verbosity.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2055/docs/generated/scanpy._settings.ScanpyConfig.writedir.rst
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 61 source files that are out of date
updating environment: [new config] 312 added, 0 changed, 0 removed
reading sources... [  0%] _key_contributors
reading sources... [  0%] api
reading sources... [  0%] basic_usage
reading sources... [  1%] community
reading sources... [  1%] contributors
reading sources... [  1%] dev/ci
reading sources... [  2%] dev/code
reading sources... [  2%] dev/documentation
reading sources... [  2%] dev/external-tools
reading sources... [  3%] dev/getting-set-up
reading sources... [  3%] dev/index
reading sources... [  3%] dev/release
reading sources... [  4%] dev/testing
reading sources... [  4%] dev/versioning
reading sources... [  4%] ecosystem
reading sources... [  5%] external
reading sources... [  5%] generated/classes/scanpy.pl.DotPlot
reading sources... [  5%] generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_HEIGHT
reading sources... [  6%] generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_WIDTH
reading sources... [  6%] generated/classes/scanpy.pl.DotPlot.DEFAULT_COLORMAP
reading sources... [  6%] generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_LEGEND_TITLE
reading sources... [  7%] generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_ON
reading sources... [  7%] generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGECOLOR
reading sources... [  7%] generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGELW
reading sources... [  8%] generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MAX
reading sources... [  8%] generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MIN
reading sources... [  8%] generated/classes/scanpy.pl.DotPlot.DEFAULT_LARGEST_DOT
reading sources... [  8%] generated/classes/scanpy.pl.DotPlot.DEFAULT_LEGENDS_WIDTH
reading sources... [  9%] generated/classes/scanpy.pl.DotPlot.DEFAULT_PLOT_X_PADDING
reading sources... [  9%] generated/classes/scanpy.pl.DotPlot.DEFAULT_PLOT_Y_PADDING
reading sources... [  9%] generated/classes/scanpy.pl.DotPlot.DEFAULT_SAVE_PREFIX
reading sources... [ 10%] generated/classes/scanpy.pl.DotPlot.DEFAULT_SIZE_EXPONENT
reading sources... [ 10%] generated/classes/scanpy.pl.DotPlot.DEFAULT_SIZE_LEGEND_TITLE
reading sources... [ 10%] generated/classes/scanpy.pl.DotPlot.DEFAULT_SMALLEST_DOT
reading sources... [ 11%] generated/classes/scanpy.pl.DotPlot.DEFAULT_WSPACE
reading sources... [ 11%] generated/classes/scanpy.pl.DotPlot.MAX_NUM_CATEGORIES
reading sources... [ 11%] generated/classes/scanpy.pl.DotPlot.MIN_FIGURE_HEIGHT
reading sources... [ 12%] generated/classes/scanpy.pl.DotPlot.add_dendrogram
reading sources... [ 12%] generated/classes/scanpy.pl.DotPlot.add_totals
reading sources... [ 12%] generated/classes/scanpy.pl.DotPlot.get_axes
reading sources... [ 13%] generated/classes/scanpy.pl.DotPlot.getdoc
reading sources... [ 13%] generated/classes/scanpy.pl.DotPlot.legend
reading sources... [ 13%] generated/classes/scanpy.pl.DotPlot.make_figure
reading sources... [ 14%] generated/classes/scanpy.pl.DotPlot.savefig
reading sources... [ 14%] generated/classes/scanpy.pl.DotPlot.show
reading sources... [ 14%] generated/classes/scanpy.pl.DotPlot.style
reading sources... [ 15%] generated/classes/scanpy.pl.DotPlot.swap_axes
reading sources... [ 15%] generated/classes/scanpy.pl.MatrixPlot
reading sources... [ 15%] generated/classes/scanpy.pl.MatrixPlot.DEFAULT_CATEGORY_HEIGHT
reading sources... [ 16%] generated/classes/scanpy.pl.MatrixPlot.DEFAULT_CATEGORY_WIDTH
reading sources... [ 16%] generated/classes/scanpy.pl.MatrixPlot.DEFAULT_COLORMAP
reading sources... [ 16%] generated/classes/scanpy.pl.MatrixPlot.DEFAULT_COLOR_LEGEND_TITLE
reading sources... [ 16%] generated/classes/scanpy.pl.MatrixPlot.DEFAULT_EDGE_COLOR
reading sources... [ 17%] generated/classes/scanpy.pl.MatrixPlot.DEFAULT_EDGE_LW
reading sources... [ 17%] generated/classes/scanpy.pl.MatrixPlot.DEFAULT_LEGENDS_WIDTH
reading sources... [ 17%] generated/classes/scanpy.pl.MatrixPlot.DEFAULT_SAVE_PREFIX
reading sources... [ 18%] generated/classes/scanpy.pl.MatrixPlot.DEFAULT_WSPACE
reading sources... [ 18%] generated/classes/scanpy.pl.MatrixPlot.MAX_NUM_CATEGORIES
reading sources... [ 18%] generated/classes/scanpy.pl.MatrixPlot.MIN_FIGURE_HEIGHT
reading sources... [ 19%] generated/classes/scanpy.pl.MatrixPlot.add_dendrogram
reading sources... [ 19%] generated/classes/scanpy.pl.MatrixPlot.add_totals
reading sources... [ 19%] generated/classes/scanpy.pl.MatrixPlot.get_axes
reading sources... [ 20%] generated/classes/scanpy.pl.MatrixPlot.getdoc
reading sources... [ 20%] generated/classes/scanpy.pl.MatrixPlot.legend
reading sources... [ 20%] generated/classes/scanpy.pl.MatrixPlot.make_figure
reading sources... [ 21%] generated/classes/scanpy.pl.MatrixPlot.savefig
reading sources... [ 21%] generated/classes/scanpy.pl.MatrixPlot.show
reading sources... [ 21%] generated/classes/scanpy.pl.MatrixPlot.style
reading sources... [ 22%] generated/classes/scanpy.pl.MatrixPlot.swap_axes
reading sources... [ 22%] generated/classes/scanpy.pl.StackedViolin
reading sources... [ 22%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_CATEGORY_HEIGHT
reading sources... [ 23%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_CATEGORY_WIDTH
reading sources... [ 23%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_COLORMAP
reading sources... [ 23%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_COLOR_LEGEND_TITLE
reading sources... [ 24%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_CUT
reading sources... [ 24%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_INNER
reading sources... [ 24%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_JITTER
reading sources... [ 25%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_JITTER_SIZE
reading sources... [ 25%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_LEGENDS_WIDTH
reading sources... [ 25%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_LINE_WIDTH
reading sources... [ 25%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_PLOT_X_PADDING
reading sources... [ 26%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_PLOT_YTICKLABELS
reading sources... [ 26%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_PLOT_Y_PADDING
reading sources... [ 26%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_ROW_PALETTE
reading sources... [ 27%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_SAVE_PREFIX
reading sources... [ 27%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_SCALE
reading sources... [ 27%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_STRIPPLOT
reading sources... [ 28%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_WSPACE
reading sources... [ 28%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_YLIM
reading sources... [ 28%] generated/classes/scanpy.pl.StackedViolin.MAX_NUM_CATEGORIES
reading sources... [ 29%] generated/classes/scanpy.pl.StackedViolin.MIN_FIGURE_HEIGHT
reading sources... [ 29%] generated/classes/scanpy.pl.StackedViolin.add_dendrogram
reading sources... [ 29%] generated/classes/scanpy.pl.StackedViolin.add_totals
reading sources... [ 30%] generated/classes/scanpy.pl.StackedViolin.get_axes
reading sources... [ 30%] generated/classes/scanpy.pl.StackedViolin.getdoc
reading sources... [ 30%] generated/classes/scanpy.pl.StackedViolin.legend
reading sources... [ 31%] generated/classes/scanpy.pl.StackedViolin.make_figure
reading sources... [ 31%] generated/classes/scanpy.pl.StackedViolin.savefig
reading sources... [ 31%] generated/classes/scanpy.pl.StackedViolin.show
reading sources... [ 32%] generated/classes/scanpy.pl.StackedViolin.style
reading sources... [ 32%] generated/classes/scanpy.pl.StackedViolin.swap_axes
reading sources... [ 32%] generated/scanpy.Neighbors
reading sources... [ 33%] generated/scanpy.Neighbors.compute_eigen
reading sources... [ 33%] generated/scanpy.Neighbors.compute_neighbors
reading sources... [ 33%] generated/scanpy.Neighbors.compute_transitions
reading sources... [ 33%] generated/scanpy.Neighbors.connectivities
reading sources... [ 34%] generated/scanpy.Neighbors.distances
reading sources... [ 34%] generated/scanpy.Neighbors.distances_dpt
reading sources... [ 34%] generated/scanpy.Neighbors.eigen_basis
reading sources... [ 35%] generated/scanpy.Neighbors.eigen_values
reading sources... [ 35%] generated/scanpy.Neighbors.getdoc
reading sources... [ 35%] generated/scanpy.Neighbors.rp_forest
reading sources... [ 36%] generated/scanpy.Neighbors.to_igraph
reading sources... [ 36%] generated/scanpy.Neighbors.transitions
reading sources... [ 36%] generated/scanpy.Neighbors.transitions_sym
reading sources... [ 37%] generated/scanpy._settings.ScanpyConfig
reading sources... [ 37%] generated/scanpy._settings.ScanpyConfig.autosave
reading sources... [ 37%] generated/scanpy._settings.ScanpyConfig.autoshow
reading sources... [ 38%] generated/scanpy._settings.ScanpyConfig.cache_compression
reading sources... [ 38%] generated/scanpy._settings.ScanpyConfig.cachedir
reading sources... [ 38%] generated/scanpy._settings.ScanpyConfig.categories_to_ignore
reading sources... [ 39%] generated/scanpy._settings.ScanpyConfig.datasetdir
reading sources... [ 39%] generated/scanpy._settings.ScanpyConfig.figdir
reading sources... [ 39%] generated/scanpy._settings.ScanpyConfig.file_format_data
reading sources... [ 40%] generated/scanpy._settings.ScanpyConfig.file_format_figs
reading sources... [ 40%] generated/scanpy._settings.ScanpyConfig.logfile
reading sources... [ 40%] generated/scanpy._settings.ScanpyConfig.logpath
reading sources... [ 41%] generated/scanpy._settings.ScanpyConfig.max_memory
reading sources... [ 41%] generated/scanpy._settings.ScanpyConfig.n_jobs
reading sources... [ 41%] generated/scanpy._settings.ScanpyConfig.plot_suffix
reading sources... [ 41%] generated/scanpy._settings.ScanpyConfig.set_figure_params
reading sources... [ 42%] generated/scanpy._settings.ScanpyConfig.verbosity
reading sources... [ 42%] generated/scanpy._settings.ScanpyConfig.writedir
reading sources... [ 42%] generated/scanpy.datasets.blobs
reading sources... [ 43%] generated/scanpy.datasets.ebi_expression_atlas
reading sources... [ 43%] generated/scanpy.datasets.krumsiek11
reading sources... [ 43%] generated/scanpy.datasets.moignard15
reading sources... [ 44%] generated/scanpy.datasets.paul15
reading sources... [ 44%] generated/scanpy.datasets.pbmc3k
reading sources... [ 44%] generated/scanpy.datasets.pbmc3k_processed
reading sources... [ 45%] generated/scanpy.datasets.pbmc68k_reduced
reading sources... [ 45%] generated/scanpy.datasets.toggleswitch
reading sources... [ 45%] generated/scanpy.datasets.visium_sge
reading sources... [ 46%] generated/scanpy.external.exporting.cellbrowser
reading sources... [ 46%] generated/scanpy.external.exporting.spring_project
reading sources... [ 46%] generated/scanpy.external.pl.phate
reading sources... [ 47%] generated/scanpy.external.pl.sam
reading sources... [ 47%] generated/scanpy.external.pl.scrublet_score_distribution
reading sources... [ 47%] generated/scanpy.external.pl.trimap
reading sources... [ 48%] generated/scanpy.external.pl.wishbone_marker_trajectory
reading sources... [ 48%] generated/scanpy.external.pp.bbknn
reading sources... [ 48%] generated/scanpy.external.pp.dca
reading sources... [ 49%] generated/scanpy.external.pp.harmony_integrate
reading sources... [ 49%] generated/scanpy.external.pp.hashsolo
reading sources... [ 49%] generated/scanpy.external.pp.magic
reading sources... [ 50%] generated/scanpy.external.pp.mnn_correct
reading sources... [ 50%] generated/scanpy.external.pp.scanorama_integrate
reading sources... [ 50%] generated/scanpy.external.pp.scrublet
reading sources... [ 50%] generated/scanpy.external.pp.scrublet_simulate_doublets
reading sources... [ 51%] generated/scanpy.external.tl.cyclone
reading sources... [ 51%] generated/scanpy.external.tl.harmony_timeseries
reading sources... [ 51%] generated/scanpy.external.tl.palantir
reading sources... [ 52%] generated/scanpy.external.tl.palantir_results
reading sources... [ 52%] generated/scanpy.external.tl.phate
reading sources... [ 52%] generated/scanpy.external.tl.phenograph
reading sources... [ 53%] generated/scanpy.external.tl.sam
reading sources... [ 53%] generated/scanpy.external.tl.sandbag
reading sources... [ 53%] generated/scanpy.external.tl.trimap
reading sources... [ 54%] generated/scanpy.external.tl.wishbone
reading sources... [ 54%] generated/scanpy.get.obs_df
reading sources... [ 54%] generated/scanpy.get.rank_genes_groups_df
reading sources... [ 55%] generated/scanpy.get.var_df
reading sources... [ 55%] generated/scanpy.logging.print_header
reading sources... [ 55%] generated/scanpy.logging.print_versions
reading sources... [ 56%] generated/scanpy.metrics.confusion_matrix
reading sources... [ 56%] generated/scanpy.metrics.gearys_c
reading sources... [ 56%] generated/scanpy.metrics.morans_i
reading sources... [ 57%] generated/scanpy.pl.clustermap
reading sources... [ 57%] generated/scanpy.pl.dendrogram
reading sources... [ 57%] generated/scanpy.pl.diffmap
reading sources... [ 58%] generated/scanpy.pl.dotplot
WARNING: dendrogram data not found (using key=dendrogram_bulk_labels). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.
WARNING: Groups are not reordered because the `groupby` categories and the `var_group_labels` are different.
categories: CD4+/CD25 T Reg, CD4+/CD45RA+/CD25- Naive T, CD4+/CD45RO+ Memory, etc.
var_group_labels: T-cell, B-cell, myeloid
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2055/lib/python3.8/site-packages/anndata/_core/anndata.py:1228: FutureWarning: The `inplace` parameter in pandas.Categorical.reorder_categories is deprecated and will be removed in a future version. Reordering categories will always return a new Categorical object.
  c.reorder_categories(natsorted(c.categories), inplace=True)
... storing 'sampleid' as categorical
reading sources... [ 58%] generated/scanpy.pl.dpt_groups_pseudotime
reading sources... [ 58%] generated/scanpy.pl.dpt_timeseries
reading sources... [ 58%] generated/scanpy.pl.draw_graph
WARNING: Package 'fa2' is not installed, falling back to layout 'fr'.To use the faster and better ForceAtlas2 layout, install package 'fa2' (`pip install fa2`).
reading sources... [ 59%] generated/scanpy.pl.embedding
reading sources... [ 59%] generated/scanpy.pl.embedding_density
reading sources... [ 59%] generated/scanpy.pl.filter_genes_dispersion
reading sources... [ 60%] generated/scanpy.pl.heatmap
reading sources... [ 60%] generated/scanpy.pl.highest_expr_genes
reading sources... [ 60%] generated/scanpy.pl.highly_variable_genes
reading sources... [ 61%] generated/scanpy.pl.matrixplot
WARNING: dendrogram data not found (using key=dendrogram_bulk_labels). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.
WARNING: Groups are not reordered because the `groupby` categories and the `var_group_labels` are different.
categories: CD4+/CD25 T Reg, CD4+/CD45RA+/CD25- Naive T, CD4+/CD45RO+ Memory, etc.
var_group_labels: T-cell, B-cell, myeloid
reading sources... [ 61%] generated/scanpy.pl.paga

  0%|          | 0.00/23.5M [00:00<?, ?B/s]
 53%|█████▎    | 12.6M/23.5M [00:00<00:00, 132MB/s]
100%|██████████| 23.5M/23.5M [00:00<00:00, 158MB/s]reading sources... [ 61%] generated/scanpy.pl.paga_compare
reading sources... [ 62%] generated/scanpy.pl.paga_path
reading sources... [ 62%] generated/scanpy.pl.pca
reading sources... [ 62%] generated/scanpy.pl.pca_loadings
reading sources... [ 63%] generated/scanpy.pl.pca_overview
reading sources... [ 63%] generated/scanpy.pl.pca_variance_ratio
reading sources... [ 63%] generated/scanpy.pl.rank_genes_groups
reading sources... [ 64%] generated/scanpy.pl.rank_genes_groups_dotplot

WARNING: Default of the method has been changed to 't-test' from 't-test_overestim_var'
WARNING: dendrogram data not found (using key=dendrogram_bulk_labels). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.
WARNING: Groups are not reordered because the `groupby` categories and the `var_group_labels` are different.
categories: CD4+/CD25 T Reg, CD4+/CD45RA+/CD25- Naive T, CD4+/CD45RO+ Memory, etc.
var_group_labels: T-cell, B-cell, myeloid
reading sources... [ 64%] generated/scanpy.pl.rank_genes_groups_heatmap
WARNING: Default of the method has been changed to 't-test' from 't-test_overestim_var'
WARNING: dendrogram data not found (using key=dendrogram_bulk_labels). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.
WARNING: Gene labels are not shown when more than 50 genes are visualized. To show gene labels set `show_gene_labels=True`
reading sources... [ 64%] generated/scanpy.pl.rank_genes_groups_matrixplot
WARNING: Default of the method has been changed to 't-test' from 't-test_overestim_var'
WARNING: dendrogram data not found (using key=dendrogram_bulk_labels). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.
WARNING: Groups are not reordered because the `groupby` categories and the `var_group_labels` are different.
categories: CD4+/CD25 T Reg, CD4+/CD45RA+/CD25- Naive T, CD4+/CD45RO+ Memory, etc.
var_group_labels: T-cell, B-cell, myeloid
reading sources... [ 65%] generated/scanpy.pl.rank_genes_groups_stacked_violin
reading sources... [ 65%] generated/scanpy.pl.rank_genes_groups_tracksplot
WARNING: Default of the method has been changed to 't-test' from 't-test_overestim_var'
WARNING: dendrogram data not found (using key=dendrogram_bulk_labels). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.
reading sources... [ 65%] generated/scanpy.pl.rank_genes_groups_violin
reading sources... [ 66%] generated/scanpy.pl.ranking
reading sources... [ 66%] generated/scanpy.pl.scatter
reading sources... [ 66%] generated/scanpy.pl.sim
reading sources... [ 66%] generated/scanpy.pl.spatial
reading sources... [ 67%] generated/scanpy.pl.stacked_violin
reading sources... [ 67%] generated/scanpy.pl.tracksplot
reading sources... [ 67%] generated/scanpy.pl.tsne
reading sources... [ 68%] generated/scanpy.pl.umap
reading sources... [ 68%] generated/scanpy.pl.violin
reading sources... [ 68%] generated/scanpy.pp.calculate_qc_metrics
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2055/lib/python3.8/site-packages/sklearn/manifold/_t_sne.py:780: FutureWarning: The default initialization in TSNE will change from 'random' to 'pca' in 1.2.
  warnings.warn(

  0%|          | 0.00/5.58M [00:00<?, ?B/s]
  0%|          | 16.0k/5.58M [00:00<01:06, 87.2kB/s]
  1%|          | 48.0k/5.58M [00:00<00:42, 138kB/s] 
  2%|▏         | 104k/5.58M [00:00<00:26, 214kB/s] 
  4%|▍         | 216k/5.58M [00:00<00:15, 370kB/s]
  8%|▊         | 440k/5.58M [00:00<00:07, 676kB/s]
 16%|█▌        | 896k/5.58M [00:01<00:03, 1.29MB/s]
 31%|███▏      | 1.76M/5.58M [00:01<00:01, 2.47MB/s]
 49%|████▉     | 2.75M/5.58M [00:01<00:00, 3.39MB/s]
 65%|██████▌   | 3.65M/5.58M [00:01<00:00, 3.88MB/s]
 81%|████████▏ | 4.55M/5.58M [00:01<00:00, 4.22MB/s]
 97%|█████████▋| 5.44M/5.58M [00:02<00:00, 4.44MB/s]
100%|██████████| 5.58M/5.58M [00:02<00:00, 2.79MB/s]reading sources... [ 69%] generated/scanpy.pp.combat
reading sources... [ 69%] generated/scanpy.pp.downsample_counts
reading sources... [ 69%] generated/scanpy.pp.filter_cells
reading sources... [ 70%] generated/scanpy.pp.filter_genes
reading sources... [ 70%] generated/scanpy.pp.filter_genes_dispersion
reading sources... [ 70%] generated/scanpy.pp.highly_variable_genes
reading sources... [ 71%] generated/scanpy.pp.log1p
reading sources... [ 71%] generated/scanpy.pp.neighbors
reading sources... [ 71%] generated/scanpy.pp.normalize_per_cell
reading sources... [ 72%] generated/scanpy.pp.normalize_total
reading sources... [ 72%] generated/scanpy.pp.pca
reading sources... [ 72%] generated/scanpy.pp.recipe_seurat
reading sources... [ 73%] generated/scanpy.pp.recipe_weinreb17
reading sources... [ 73%] generated/scanpy.pp.recipe_zheng17
reading sources... [ 73%] generated/scanpy.pp.regress_out
reading sources... [ 74%] generated/scanpy.pp.scale
reading sources... [ 74%] generated/scanpy.pp.subsample
reading sources... [ 74%] generated/scanpy.queries.biomart_annotations
reading sources... [ 75%] generated/scanpy.queries.enrich
reading sources... [ 75%] generated/scanpy.queries.gene_coordinates
reading sources... [ 75%] generated/scanpy.queries.mitochondrial_genes
reading sources... [ 75%] generated/scanpy.read
reading sources... [ 76%] generated/scanpy.read_10x_h5
reading sources... [ 76%] generated/scanpy.read_10x_mtx
reading sources... [ 76%] generated/scanpy.read_csv
reading sources... [ 77%] generated/scanpy.read_excel
reading sources... [ 77%] generated/scanpy.read_h5ad
reading sources... [ 77%] generated/scanpy.read_hdf
reading sources... [ 78%] generated/scanpy.read_loom
reading sources... [ 78%] generated/scanpy.read_mtx
reading sources... [ 78%] generated/scanpy.read_text
reading sources... [ 79%] generated/scanpy.read_umi_tools
reading sources... [ 79%] generated/scanpy.read_visium
reading sources... [ 79%] generated/scanpy.set_figure_params
reading sources... [ 80%] generated/scanpy.tl.dendrogram
reading sources... [ 80%] generated/scanpy.tl.diffmap
reading sources... [ 80%] generated/scanpy.tl.dpt
reading sources... [ 81%] generated/scanpy.tl.draw_graph
reading sources... [ 81%] generated/scanpy.tl.embedding_density
reading sources... [ 81%] generated/scanpy.tl.filter_rank_genes_groups
reading sources... [ 82%] generated/scanpy.tl.ingest
reading sources... [ 82%] generated/scanpy.tl.leiden
reading sources... [ 82%] generated/scanpy.tl.louvain
reading sources... [ 83%] generated/scanpy.tl.marker_gene_overlap
reading sources... [ 83%] generated/scanpy.tl.paga
reading sources... [ 83%] generated/scanpy.tl.pca
reading sources... [ 83%] generated/scanpy.tl.rank_genes_groups
reading sources... [ 84%] generated/scanpy.tl.score_genes
reading sources... [ 84%] generated/scanpy.tl.score_genes_cell_cycle
reading sources... [ 84%] generated/scanpy.tl.sim
reading sources... [ 85%] generated/scanpy.tl.tsne
reading sources... [ 85%] generated/scanpy.tl.umap
reading sources... [ 85%] index
reading sources... [ 86%] installation
reading sources... [ 86%] news
reading sources... [ 86%] references
reading sources... [ 87%] release-notes/0.1.0
reading sources... [ 87%] release-notes/0.2.1
reading sources... [ 87%] release-notes/0.2.9
reading sources... [ 88%] release-notes/0.3.0
reading sources... [ 88%] release-notes/0.3.2
reading sources... [ 88%] release-notes/0.4.0
reading sources... [ 89%] release-notes/0.4.2
reading sources... [ 89%] release-notes/0.4.3
reading sources... [ 89%] release-notes/0.4.4
reading sources... [ 90%] release-notes/1.0.0
reading sources... [ 90%] release-notes/1.1.0
reading sources... [ 90%] release-notes/1.2.0
reading sources... [ 91%] release-notes/1.2.1
reading sources... [ 91%] release-notes/1.3.1
reading sources... [ 91%] release-notes/1.3.3
reading sources... [ 91%] release-notes/1.3.4
reading sources... [ 92%] release-notes/1.3.5
reading sources... [ 92%] release-notes/1.3.6
reading sources... [ 92%] release-notes/1.3.7
reading sources... [ 93%] release-notes/1.3.8
reading sources... [ 93%] release-notes/1.4.1
reading sources... [ 93%] release-notes/1.4.2
reading sources... [ 94%] release-notes/1.4.3
reading sources... [ 94%] release-notes/1.4.4
reading sources... [ 94%] release-notes/1.4.5
reading sources... [ 95%] release-notes/1.4.6
reading sources... [ 95%] release-notes/1.5.0
reading sources... [ 95%] release-notes/1.5.1
reading sources... [ 96%] release-notes/1.6.0
reading sources... [ 96%] release-notes/1.7.0
reading sources... [ 96%] release-notes/1.7.1
reading sources... [ 97%] release-notes/1.7.2
reading sources... [ 97%] release-notes/1.8.0
reading sources... [ 97%] release-notes/1.8.1
reading sources... [ 98%] release-notes/1.8.2
reading sources... [ 98%] release-notes/1.8.3
reading sources... [ 98%] release-notes/1.9.0
reading sources... [ 99%] release-notes/index
reading sources... [ 99%] release-notes/release-latest
reading sources... [ 99%] tutorials
reading sources... [100%] usage-principles

looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
writing output... [  0%] _key_contributors
writing output... [  0%] api
writing output... [  0%] basic_usage
writing output... [  1%] community
writing output... [  1%] contributors
writing output... [  1%] dev/ci
writing output... [  2%] dev/code
writing output... [  2%] dev/documentation
writing output... [  2%] dev/external-tools
writing output... [  3%] dev/getting-set-up
writing output... [  3%] dev/index
writing output... [  3%] dev/release
writing output... [  4%] dev/testing
writing output... [  4%] dev/versioning
writing output... [  4%] ecosystem
writing output... [  5%] external
writing output... [  5%] generated/classes/scanpy.pl.DotPlot
writing output... [  5%] generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_HEIGHT
writing output... [  6%] generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_WIDTH
writing output... [  6%] generated/classes/scanpy.pl.DotPlot.DEFAULT_COLORMAP
writing output... [  6%] generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_LEGEND_TITLE
writing output... [  7%] generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_ON
writing output... [  7%] generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGECOLOR
writing output... [  7%] generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGELW
writing output... [  8%] generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MAX
writing output... [  8%] generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MIN
writing output... [  8%] generated/classes/scanpy.pl.DotPlot.DEFAULT_LARGEST_DOT
writing output... [  8%] generated/classes/scanpy.pl.DotPlot.DEFAULT_LEGENDS_WIDTH
writing output... [  9%] generated/classes/scanpy.pl.DotPlot.DEFAULT_PLOT_X_PADDING
writing output... [  9%] generated/classes/scanpy.pl.DotPlot.DEFAULT_PLOT_Y_PADDING
writing output... [  9%] generated/classes/scanpy.pl.DotPlot.DEFAULT_SAVE_PREFIX
writing output... [ 10%] generated/classes/scanpy.pl.DotPlot.DEFAULT_SIZE_EXPONENT
writing output... [ 10%] generated/classes/scanpy.pl.DotPlot.DEFAULT_SIZE_LEGEND_TITLE
writing output... [ 10%] generated/classes/scanpy.pl.DotPlot.DEFAULT_SMALLEST_DOT
writing output... [ 11%] generated/classes/scanpy.pl.DotPlot.DEFAULT_WSPACE
writing output... [ 11%] generated/classes/scanpy.pl.DotPlot.MAX_NUM_CATEGORIES
writing output... [ 11%] generated/classes/scanpy.pl.DotPlot.MIN_FIGURE_HEIGHT
writing output... [ 12%] generated/classes/scanpy.pl.DotPlot.add_dendrogram
writing output... [ 12%] generated/classes/scanpy.pl.DotPlot.add_totals
writing output... [ 12%] generated/classes/scanpy.pl.DotPlot.get_axes
writing output... [ 13%] generated/classes/scanpy.pl.DotPlot.getdoc
writing output... [ 13%] generated/classes/scanpy.pl.DotPlot.legend
writing output... [ 13%] generated/classes/scanpy.pl.DotPlot.make_figure
writing output... [ 14%] generated/classes/scanpy.pl.DotPlot.savefig
writing output... [ 14%] generated/classes/scanpy.pl.DotPlot.show
writing output... [ 14%] generated/classes/scanpy.pl.DotPlot.style
writing output... [ 15%] generated/classes/scanpy.pl.DotPlot.swap_axes
writing output... [ 15%] generated/classes/scanpy.pl.MatrixPlot
writing output... [ 15%] generated/classes/scanpy.pl.MatrixPlot.DEFAULT_CATEGORY_HEIGHT
writing output... [ 16%] generated/classes/scanpy.pl.MatrixPlot.DEFAULT_CATEGORY_WIDTH
writing output... [ 16%] generated/classes/scanpy.pl.MatrixPlot.DEFAULT_COLORMAP
writing output... [ 16%] generated/classes/scanpy.pl.MatrixPlot.DEFAULT_COLOR_LEGEND_TITLE
writing output... [ 16%] generated/classes/scanpy.pl.MatrixPlot.DEFAULT_EDGE_COLOR
writing output... [ 17%] generated/classes/scanpy.pl.MatrixPlot.DEFAULT_EDGE_LW
writing output... [ 17%] generated/classes/scanpy.pl.MatrixPlot.DEFAULT_LEGENDS_WIDTH
writing output... [ 17%] generated/classes/scanpy.pl.MatrixPlot.DEFAULT_SAVE_PREFIX
writing output... [ 18%] generated/classes/scanpy.pl.MatrixPlot.DEFAULT_WSPACE
writing output... [ 18%] generated/classes/scanpy.pl.MatrixPlot.MAX_NUM_CATEGORIES
writing output... [ 18%] generated/classes/scanpy.pl.MatrixPlot.MIN_FIGURE_HEIGHT
writing output... [ 19%] generated/classes/scanpy.pl.MatrixPlot.add_dendrogram
writing output... [ 19%] generated/classes/scanpy.pl.MatrixPlot.add_totals
writing output... [ 19%] generated/classes/scanpy.pl.MatrixPlot.get_axes
writing output... [ 20%] generated/classes/scanpy.pl.MatrixPlot.getdoc
writing output... [ 20%] generated/classes/scanpy.pl.MatrixPlot.legend
writing output... [ 20%] generated/classes/scanpy.pl.MatrixPlot.make_figure
writing output... [ 21%] generated/classes/scanpy.pl.MatrixPlot.savefig
writing output... [ 21%] generated/classes/scanpy.pl.MatrixPlot.show
writing output... [ 21%] generated/classes/scanpy.pl.MatrixPlot.style
writing output... [ 22%] generated/classes/scanpy.pl.MatrixPlot.swap_axes
writing output... [ 22%] generated/classes/scanpy.pl.StackedViolin
writing output... [ 22%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_CATEGORY_HEIGHT
writing output... [ 23%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_CATEGORY_WIDTH
writing output... [ 23%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_COLORMAP
writing output... [ 23%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_COLOR_LEGEND_TITLE
writing output... [ 24%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_CUT
writing output... [ 24%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_INNER
writing output... [ 24%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_JITTER
writing output... [ 25%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_JITTER_SIZE
writing output... [ 25%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_LEGENDS_WIDTH
writing output... [ 25%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_LINE_WIDTH
writing output... [ 25%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_PLOT_X_PADDING
writing output... [ 26%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_PLOT_YTICKLABELS
writing output... [ 26%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_PLOT_Y_PADDING
writing output... [ 26%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_ROW_PALETTE
writing output... [ 27%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_SAVE_PREFIX
writing output... [ 27%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_SCALE
writing output... [ 27%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_STRIPPLOT
writing output... [ 28%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_WSPACE
writing output... [ 28%] generated/classes/scanpy.pl.StackedViolin.DEFAULT_YLIM
writing output... [ 28%] generated/classes/scanpy.pl.StackedViolin.MAX_NUM_CATEGORIES
writing output... [ 29%] generated/classes/scanpy.pl.StackedViolin.MIN_FIGURE_HEIGHT
writing output... [ 29%] generated/classes/scanpy.pl.StackedViolin.add_dendrogram
writing output... [ 29%] generated/classes/scanpy.pl.StackedViolin.add_totals
writing output... [ 30%] generated/classes/scanpy.pl.StackedViolin.get_axes
writing output... [ 30%] generated/classes/scanpy.pl.StackedViolin.getdoc
writing output... [ 30%] generated/classes/scanpy.pl.StackedViolin.legend
writing output... [ 31%] generated/classes/scanpy.pl.StackedViolin.make_figure
writing output... [ 31%] generated/classes/scanpy.pl.StackedViolin.savefig
writing output... [ 31%] generated/classes/scanpy.pl.StackedViolin.show
writing output... [ 32%] generated/classes/scanpy.pl.StackedViolin.style
writing output... [ 32%] generated/classes/scanpy.pl.StackedViolin.swap_axes
writing output... [ 32%] generated/scanpy.Neighbors
writing output... [ 33%] generated/scanpy.Neighbors.compute_eigen
writing output... [ 33%] generated/scanpy.Neighbors.compute_neighbors
writing output... [ 33%] generated/scanpy.Neighbors.compute_transitions
writing output... [ 33%] generated/scanpy.Neighbors.connectivities
writing output... [ 34%] generated/scanpy.Neighbors.distances
writing output... [ 34%] generated/scanpy.Neighbors.distances_dpt
writing output... [ 34%] generated/scanpy.Neighbors.eigen_basis
writing output... [ 35%] generated/scanpy.Neighbors.eigen_values
writing output... [ 35%] generated/scanpy.Neighbors.getdoc
writing output... [ 35%] generated/scanpy.Neighbors.rp_forest
writing output... [ 36%] generated/scanpy.Neighbors.to_igraph
writing output... [ 36%] generated/scanpy.Neighbors.transitions
writing output... [ 36%] generated/scanpy.Neighbors.transitions_sym
writing output... [ 37%] generated/scanpy._settings.ScanpyConfig
writing output... [ 37%] generated/scanpy._settings.ScanpyConfig.autosave
writing output... [ 37%] generated/scanpy._settings.ScanpyConfig.autoshow
writing output... [ 38%] generated/scanpy._settings.ScanpyConfig.cache_compression
writing output... [ 38%] generated/scanpy._settings.ScanpyConfig.cachedir
writing output... [ 38%] generated/scanpy._settings.ScanpyConfig.categories_to_ignore
writing output... [ 39%] generated/scanpy._settings.ScanpyConfig.datasetdir
writing output... [ 39%] generated/scanpy._settings.ScanpyConfig.figdir
writing output... [ 39%] generated/scanpy._settings.ScanpyConfig.file_format_data
writing output... [ 40%] generated/scanpy._settings.ScanpyConfig.file_format_figs
writing output... [ 40%] generated/scanpy._settings.ScanpyConfig.logfile
writing output... [ 40%] generated/scanpy._settings.ScanpyConfig.logpath
writing output... [ 41%] generated/scanpy._settings.ScanpyConfig.max_memory
writing output... [ 41%] generated/scanpy._settings.ScanpyConfig.n_jobs
writing output... [ 41%] generated/scanpy._settings.ScanpyConfig.plot_suffix
writing output... [ 41%] generated/scanpy._settings.ScanpyConfig.set_figure_params
writing output... [ 42%] generated/scanpy._settings.ScanpyConfig.verbosity
writing output... [ 42%] generated/scanpy._settings.ScanpyConfig.writedir
writing output... [ 42%] generated/scanpy.datasets.blobs
writing output... [ 43%] generated/scanpy.datasets.ebi_expression_atlas
writing output... [ 43%] generated/scanpy.datasets.krumsiek11
writing output... [ 43%] generated/scanpy.datasets.moignard15
writing output... [ 44%] generated/scanpy.datasets.paul15
writing output... [ 44%] generated/scanpy.datasets.pbmc3k
writing output... [ 44%] generated/scanpy.datasets.pbmc3k_processed
writing output... [ 45%] generated/scanpy.datasets.pbmc68k_reduced
writing output... [ 45%] generated/scanpy.datasets.toggleswitch
writing output... [ 45%] generated/scanpy.datasets.visium_sge
writing output... [ 46%] generated/scanpy.external.exporting.cellbrowser
writing output... [ 46%] generated/scanpy.external.exporting.spring_project
writing output... [ 46%] generated/scanpy.external.pl.phate
writing output... [ 47%] generated/scanpy.external.pl.sam
writing output... [ 47%] generated/scanpy.external.pl.scrublet_score_distribution
writing output... [ 47%] generated/scanpy.external.pl.trimap
writing output... [ 48%] generated/scanpy.external.pl.wishbone_marker_trajectory
writing output... [ 48%] generated/scanpy.external.pp.bbknn
writing output... [ 48%] generated/scanpy.external.pp.dca
writing output... [ 49%] generated/scanpy.external.pp.harmony_integrate
writing output... [ 49%] generated/scanpy.external.pp.hashsolo
writing output... [ 49%] generated/scanpy.external.pp.magic
writing output... [ 50%] generated/scanpy.external.pp.mnn_correct
writing output... [ 50%] generated/scanpy.external.pp.scanorama_integrate
writing output... [ 50%] generated/scanpy.external.pp.scrublet
writing output... [ 50%] generated/scanpy.external.pp.scrublet_simulate_doublets
writing output... [ 51%] generated/scanpy.external.tl.cyclone
writing output... [ 51%] generated/scanpy.external.tl.harmony_timeseries
writing output... [ 51%] generated/scanpy.external.tl.palantir
writing output... [ 52%] generated/scanpy.external.tl.palantir_results
writing output... [ 52%] generated/scanpy.external.tl.phate
writing output... [ 52%] generated/scanpy.external.tl.phenograph
writing output... [ 53%] generated/scanpy.external.tl.sam
writing output... [ 53%] generated/scanpy.external.tl.sandbag
writing output... [ 53%] generated/scanpy.external.tl.trimap
writing output... [ 54%] generated/scanpy.external.tl.wishbone
writing output... [ 54%] generated/scanpy.get.obs_df
writing output... [ 54%] generated/scanpy.get.rank_genes_groups_df
writing output... [ 55%] generated/scanpy.get.var_df
writing output... [ 55%] generated/scanpy.logging.print_header
writing output... [ 55%] generated/scanpy.logging.print_versions
writing output... [ 56%] generated/scanpy.metrics.confusion_matrix
writing output... [ 56%] generated/scanpy.metrics.gearys_c
writing output... [ 56%] generated/scanpy.metrics.morans_i
writing output... [ 57%] generated/scanpy.pl.clustermap
writing output... [ 57%] generated/scanpy.pl.dendrogram
writing output... [ 57%] generated/scanpy.pl.diffmap
writing output... [ 58%] generated/scanpy.pl.dotplot
writing output... [ 58%] generated/scanpy.pl.dpt_groups_pseudotime
writing output... [ 58%] generated/scanpy.pl.dpt_timeseries
writing output... [ 58%] generated/scanpy.pl.draw_graph
writing output... [ 59%] generated/scanpy.pl.embedding
writing output... [ 59%] generated/scanpy.pl.embedding_density
writing output... [ 59%] generated/scanpy.pl.filter_genes_dispersion
writing output... [ 60%] generated/scanpy.pl.heatmap
writing output... [ 60%] generated/scanpy.pl.highest_expr_genes
writing output... [ 60%] generated/scanpy.pl.highly_variable_genes
writing output... [ 61%] generated/scanpy.pl.matrixplot
writing output... [ 61%] generated/scanpy.pl.paga
writing output... [ 61%] generated/scanpy.pl.paga_compare
writing output... [ 62%] generated/scanpy.pl.paga_path
writing output... [ 62%] generated/scanpy.pl.pca
writing output... [ 62%] generated/scanpy.pl.pca_loadings
writing output... [ 63%] generated/scanpy.pl.pca_overview
writing output... [ 63%] generated/scanpy.pl.pca_variance_ratio
writing output... [ 63%] generated/scanpy.pl.rank_genes_groups
writing output... [ 64%] generated/scanpy.pl.rank_genes_groups_dotplot
writing output... [ 64%] generated/scanpy.pl.rank_genes_groups_heatmap
writing output... [ 64%] generated/scanpy.pl.rank_genes_groups_matrixplot
writing output... [ 65%] generated/scanpy.pl.rank_genes_groups_stacked_violin
writing output... [ 65%] generated/scanpy.pl.rank_genes_groups_tracksplot
writing output... [ 65%] generated/scanpy.pl.rank_genes_groups_violin
writing output... [ 66%] generated/scanpy.pl.ranking
writing output... [ 66%] generated/scanpy.pl.scatter
writing output... [ 66%] generated/scanpy.pl.sim
writing output... [ 66%] generated/scanpy.pl.spatial
writing output... [ 67%] generated/scanpy.pl.stacked_violin
writing output... [ 67%] generated/scanpy.pl.tracksplot
writing output... [ 67%] generated/scanpy.pl.tsne
writing output... [ 68%] generated/scanpy.pl.umap
writing output... [ 68%] generated/scanpy.pl.violin
writing output... [ 68%] generated/scanpy.pp.calculate_qc_metrics
writing output... [ 69%] generated/scanpy.pp.combat
writing output... [ 69%] generated/scanpy.pp.downsample_counts
writing output... [ 69%] generated/scanpy.pp.filter_cells
writing output... [ 70%] generated/scanpy.pp.filter_genes
writing output... [ 70%] generated/scanpy.pp.filter_genes_dispersion
writing output... [ 70%] generated/scanpy.pp.highly_variable_genes
writing output... [ 71%] generated/scanpy.pp.log1p
writing output... [ 71%] generated/scanpy.pp.neighbors
writing output... [ 71%] generated/scanpy.pp.normalize_per_cell
writing output... [ 72%] generated/scanpy.pp.normalize_total
writing output... [ 72%] generated/scanpy.pp.pca
writing output... [ 72%] generated/scanpy.pp.recipe_seurat
writing output... [ 73%] generated/scanpy.pp.recipe_weinreb17
writing output... [ 73%] generated/scanpy.pp.recipe_zheng17
writing output... [ 73%] generated/scanpy.pp.regress_out
writing output... [ 74%] generated/scanpy.pp.scale
writing output... [ 74%] generated/scanpy.pp.subsample
writing output... [ 74%] generated/scanpy.queries.biomart_annotations
writing output... [ 75%] generated/scanpy.queries.enrich
writing output... [ 75%] generated/scanpy.queries.gene_coordinates
writing output... [ 75%] generated/scanpy.queries.mitochondrial_genes
writing output... [ 75%] generated/scanpy.read
writing output... [ 76%] generated/scanpy.read_10x_h5
writing output... [ 76%] generated/scanpy.read_10x_mtx
writing output... [ 76%] generated/scanpy.read_csv
writing output... [ 77%] generated/scanpy.read_excel
writing output... [ 77%] generated/scanpy.read_h5ad
writing output... [ 77%] generated/scanpy.read_hdf
writing output... [ 78%] generated/scanpy.read_loom
writing output... [ 78%] generated/scanpy.read_mtx
writing output... [ 78%] generated/scanpy.read_text
writing output... [ 79%] generated/scanpy.read_umi_tools
writing output... [ 79%] generated/scanpy.read_visium
writing output... [ 79%] generated/scanpy.set_figure_params
writing output... [ 80%] generated/scanpy.tl.dendrogram
writing output... [ 80%] generated/scanpy.tl.diffmap
writing output... [ 80%] generated/scanpy.tl.dpt
writing output... [ 81%] generated/scanpy.tl.draw_graph
writing output... [ 81%] generated/scanpy.tl.embedding_density
writing output... [ 81%] generated/scanpy.tl.filter_rank_genes_groups
writing output... [ 82%] generated/scanpy.tl.ingest
writing output... [ 82%] generated/scanpy.tl.leiden
writing output... [ 82%] generated/scanpy.tl.louvain
writing output... [ 83%] generated/scanpy.tl.marker_gene_overlap
writing output... [ 83%] generated/scanpy.tl.paga
writing output... [ 83%] generated/scanpy.tl.pca
writing output... [ 83%] generated/scanpy.tl.rank_genes_groups
writing output... [ 84%] generated/scanpy.tl.score_genes
writing output... [ 84%] generated/scanpy.tl.score_genes_cell_cycle
writing output... [ 84%] generated/scanpy.tl.sim
writing output... [ 85%] generated/scanpy.tl.tsne
writing output... [ 85%] generated/scanpy.tl.umap
writing output... [ 85%] index
writing output... [ 86%] installation
writing output... [ 86%] news
writing output... [ 86%] references
writing output... [ 87%] release-notes/0.1.0
writing output... [ 87%] release-notes/0.2.1
writing output... [ 87%] release-notes/0.2.9
writing output... [ 88%] release-notes/0.3.0
writing output... [ 88%] release-notes/0.3.2
writing output... [ 88%] release-notes/0.4.0
writing output... [ 89%] release-notes/0.4.2
writing output... [ 89%] release-notes/0.4.3
writing output... [ 89%] release-notes/0.4.4
writing output... [ 90%] release-notes/1.0.0
writing output... [ 90%] release-notes/1.1.0
writing output... [ 90%] release-notes/1.2.0
writing output... [ 91%] release-notes/1.2.1
writing output... [ 91%] release-notes/1.3.1
writing output... [ 91%] release-notes/1.3.3
writing output... [ 91%] release-notes/1.3.4
writing output... [ 92%] release-notes/1.3.5
writing output... [ 92%] release-notes/1.3.6
writing output... [ 92%] release-notes/1.3.7
writing output... [ 93%] release-notes/1.3.8
writing output... [ 93%] release-notes/1.4.1
writing output... [ 93%] release-notes/1.4.2
writing output... [ 94%] release-notes/1.4.3
writing output... [ 94%] release-notes/1.4.4
writing output... [ 94%] release-notes/1.4.5
writing output... [ 95%] release-notes/1.4.6
writing output... [ 95%] release-notes/1.5.0
writing output... [ 95%] release-notes/1.5.1
writing output... [ 96%] release-notes/1.6.0
writing output... [ 96%] release-notes/1.7.0
writing output... [ 96%] release-notes/1.7.1
writing output... [ 97%] release-notes/1.7.2
writing output... [ 97%] release-notes/1.8.0
writing output... [ 97%] release-notes/1.8.1
writing output... [ 98%] release-notes/1.8.2
writing output... [ 98%] release-notes/1.8.3
writing output... [ 98%] release-notes/1.9.0
writing output... [ 99%] release-notes/index
writing output... [ 99%] release-notes/release-latest
writing output... [ 99%] tutorials
writing output... [100%] usage-principles



Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2055/lib/python3.8/site-packages/sphinx/cmd/build.py", line 280, in build_main
    app.build(args.force_all, filenames)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2055/lib/python3.8/site-packages/sphinx/application.py", line 343, in build
    self.builder.build_update()
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2055/lib/python3.8/site-packages/sphinx/builders/__init__.py", line 293, in build_update
    self.build(to_build,
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2055/lib/python3.8/site-packages/sphinx/builders/__init__.py", line 357, in build
    self.write(docnames, list(updated_docnames), method)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2055/lib/python3.8/site-packages/sphinx/builders/__init__.py", line 531, in write
    self._write_serial(sorted(docnames))
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2055/lib/python3.8/site-packages/sphinx/builders/__init__.py", line 541, in _write_serial
    self.write_doc(docname, doctree)
  File "/home/docs/.pyenv/versions/3.8.6/lib/python3.8/contextlib.py", line 120, in __exit__
    next(self.gen)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2055/lib/python3.8/site-packages/sphinx/util/logging.py", line 213, in pending_warnings
    memhandler.flushTo(logger)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2055/lib/python3.8/site-packages/sphinx/util/logging.py", line 178, in flushTo
    logger.handle(record)
  File "/home/docs/.pyenv/versions/3.8.6/lib/python3.8/logging/__init__.py", line 1587, in handle
    self.callHandlers(record)
  File "/home/docs/.pyenv/versions/3.8.6/lib/python3.8/logging/__init__.py", line 1649, in callHandlers
    hdlr.handle(record)
  File "/home/docs/.pyenv/versions/3.8.6/lib/python3.8/logging/__init__.py", line 946, in handle
    rv = self.filter(record)
  File "/home/docs/.pyenv/versions/3.8.6/lib/python3.8/logging/__init__.py", line 807, in filter
    result = f.filter(record)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2055/lib/python3.8/site-packages/sphinx/util/logging.py", line 423, in filter
    raise exc
sphinx.errors.SphinxWarning: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2055/scanpy/plotting/_tools/paga.py:docstring of scanpy.plotting._tools.paga.paga:97:py:class reference target not found: matplotlib.colorbar.ColorbarBase

Warning, treated as error:
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2055/scanpy/plotting/_tools/paga.py:docstring of scanpy.plotting._tools.paga.paga:97:py:class reference target not found: matplotlib.colorbar.ColorbarBase