Read the Docs build information
Build id: 1305527
Project: icb-scanpy
Version: latest
Commit: d64282a4c1b3de3e27fbcf904b16571887ac0865
Date: 2023-02-17T15:02:59.417625Z
State: finished
Success: True


[rtd-command-info] start-time: 2023-02-17T15:03:48.719517Z, end-time: 2023-02-17T15:03:51.365021Z, duration: 2, exit-code: 0
git clone --no-single-branch --depth 50 https://github.com/scverse/scanpy.git .
Cloning into '.'...

[rtd-command-info] start-time: 2023-02-17T15:03:51.656534Z, end-time: 2023-02-17T15:03:51.873604Z, duration: 0, exit-code: 0
git checkout --force origin/master
Note: switching to '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 switching back to a branch.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -c with the switch command. Example:

  git switch -c <new-branch-name>

Or undo this operation with:

  git switch -

Turn off this advice by setting config variable advice.detachedHead to false

HEAD is now at d64282a4 Revert "Stephen/spaceranger2.0 (#2296)" (#2422)

[rtd-command-info] start-time: 2023-02-17T15:03:52.189853Z, end-time: 2023-02-17T15:03:52.256285Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2023-02-17T15:03:52.549853Z, end-time: 2023-02-17T15:03:52.627924Z, duration: 0, exit-code: 0
git submodule sync


[rtd-command-info] start-time: 2023-02-17T15:03:52.978894Z, end-time: 2023-02-17T15:04:04.932432Z, duration: 11, exit-code: 0
git submodule update --init --force docs/tutorials
Submodule 'docs/tutorials' (https://github.com/scverse/scanpy-tutorials.git) registered for path 'docs/tutorials'
Cloning into '/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/tutorials'...
Submodule path 'docs/tutorials': checked out '75c5ebb5b63769aee65f38842a34b7f7e1bbd476'

[rtd-command-info] start-time: 2023-02-17T15:04:10.591726Z, end-time: 2023-02-17T15:04:10.704305Z, duration: 0, exit-code: 0
asdf global python 3.9.15


[rtd-command-info] start-time: 2023-02-17T15:04:11.206197Z, end-time: 2023-02-17T15:04:12.190552Z, duration: 0, exit-code: 0
python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH
created virtual environment CPython3.9.15.final.0-64 in 672ms
  creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest, clear=False, no_vcs_ignore=False, global=False)
  seeder FromAppData(download=False, pip=bundle, setuptools=bundle, wheel=bundle, via=copy, app_data_dir=/home/docs/.local/share/virtualenv)
    added seed packages: pip==21.2.3, setuptools==57.4.0, wheel==0.37.0
  activators BashActivator,CShellActivator,FishActivator,PowerShellActivator,PythonActivator

[rtd-command-info] start-time: 2023-02-17T15:04:12.370506Z, end-time: 2023-02-17T15:04:23.096774Z, duration: 10, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip setuptools<58.3.0
Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.9/site-packages (21.2.3)
Collecting pip
  Downloading pip-23.0-py3-none-any.whl (2.1 MB)
Requirement already satisfied: setuptools<58.3.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.9/site-packages (57.4.0)
Collecting setuptools<58.3.0
  Downloading setuptools-58.2.0-py3-none-any.whl (946 kB)
Installing collected packages: setuptools, pip
  Attempting uninstall: setuptools
    Found existing installation: setuptools 57.4.0
    Uninstalling setuptools-57.4.0:
      Successfully uninstalled setuptools-57.4.0
  Attempting uninstall: pip
    Found existing installation: pip 21.2.3
    Uninstalling pip-21.2.3:
      Successfully uninstalled pip-21.2.3
Successfully installed pip-23.0 setuptools-58.2.0

[rtd-command-info] start-time: 2023-02-17T15:04:23.329456Z, end-time: 2023-02-17T15:04:34.620837Z, duration: 11, exit-code: 0
python -m pip install --upgrade --no-cache-dir pillow mock==1.0.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.9.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<2.3 jinja2<3.1.0
Collecting pillow
  Downloading Pillow-9.4.0-cp39-cp39-manylinux_2_28_x86_64.whl (3.4 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.4/3.4 MB 62.3 MB/s eta 0:00:00
Collecting mock==1.0.1
  Downloading mock-1.0.1.zip (861 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 861.9/861.9 kB 156.2 MB/s eta 0:00:00
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting alabaster!=0.7.5,<0.8,>=0.7
  Downloading alabaster-0.7.13-py3-none-any.whl (13 kB)
Collecting commonmark==0.9.1
  Downloading commonmark-0.9.1-py2.py3-none-any.whl (51 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 51.1/51.1 kB 127.2 MB/s eta 0:00:00
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)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.1/3.1 MB 137.3 MB/s eta 0:00:00
Collecting sphinx-rtd-theme<0.5
  Downloading sphinx_rtd_theme-0.4.3-py2.py3-none-any.whl (6.4 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 6.4/6.4 MB 122.3 MB/s eta 0:00:00
Collecting readthedocs-sphinx-ext<2.3
  Downloading readthedocs_sphinx_ext-2.2.0-py2.py3-none-any.whl (11 kB)
Collecting jinja2<3.1.0
  Downloading Jinja2-3.0.3-py3-none-any.whl (133 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 133.6/133.6 kB 140.2 MB/s eta 0:00:00
Collecting docutils>=0.11
  Downloading docutils-0.19-py3-none-any.whl (570 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 570.5/570.5 kB 154.6 MB/s eta 0:00:00
  Downloading docutils-0.17.1-py2.py3-none-any.whl (575 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 575.5/575.5 kB 201.9 MB/s eta 0:00:00
Collecting imagesize
  Downloading imagesize-1.4.1-py2.py3-none-any.whl (8.8 kB)
Collecting babel!=2.0,>=1.3
  Downloading Babel-2.11.0-py3-none-any.whl (9.5 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 9.5/9.5 MB 135.1 MB/s eta 0:00:00
Collecting requests>=2.0.0
  Downloading requests-2.28.2-py3-none-any.whl (62 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.8/62.8 kB 122.3 MB/s eta 0:00:00
Collecting sphinxcontrib-websupport
  Downloading sphinxcontrib_websupport-1.2.4-py2.py3-none-any.whl (39 kB)
Collecting Pygments>=2.0
  Downloading Pygments-2.14.0-py3-none-any.whl (1.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 156.3 MB/s eta 0:00:00
Collecting packaging
  Downloading packaging-23.0-py3-none-any.whl (42 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 42.7/42.7 kB 114.6 MB/s eta 0:00:00
Collecting snowballstemmer>=1.1
  Downloading snowballstemmer-2.2.0-py2.py3-none-any.whl (93 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 93.0/93.0 kB 140.6 MB/s eta 0:00:00
Collecting six>=1.5
  Downloading six-1.16.0-py2.py3-none-any.whl (11 kB)
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.9/site-packages (from sphinx<2) (58.2.0)
Collecting MarkupSafe>=2.0
  Downloading MarkupSafe-2.1.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (25 kB)
Collecting pytz>=2015.7
  Downloading pytz-2022.7.1-py2.py3-none-any.whl (499 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 499.4/499.4 kB 170.0 MB/s eta 0:00:00
Collecting certifi>=2017.4.17
  Downloading certifi-2022.12.7-py3-none-any.whl (155 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 155.3/155.3 kB 156.3 MB/s eta 0:00:00
Collecting charset-normalizer<4,>=2
  Downloading charset_normalizer-3.0.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (198 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 198.8/198.8 kB 144.6 MB/s eta 0:00:00
Collecting urllib3<1.27,>=1.21.1
  Downloading urllib3-1.26.14-py2.py3-none-any.whl (140 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 140.6/140.6 kB 138.0 MB/s eta 0:00:00
Collecting idna<4,>=2.5
  Downloading idna-3.4-py3-none-any.whl (61 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 61.5/61.5 kB 107.2 MB/s eta 0:00:00
Collecting sphinxcontrib-serializinghtml
  Downloading sphinxcontrib_serializinghtml-1.1.5-py2.py3-none-any.whl (94 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 94.0/94.0 kB 138.5 MB/s eta 0:00:00
Building wheels for collected packages: mock
  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=b31de5b1de3f6d8c92aa8def31b55e85e4501848e7f4a5bfaf7a50b29285ddfd
  Stored in directory: /tmp/pip-ephem-wheel-cache-b6ne6r0k/wheels/44/dc/c7/e89296d3612588db0aa6545ee3305c23b7a48b3a9922916e1f
Successfully built mock
Installing collected packages: snowballstemmer, pytz, mock, commonmark, charset-normalizer, urllib3, sphinxcontrib-serializinghtml, six, Pygments, pillow, packaging, MarkupSafe, imagesize, idna, docutils, certifi, babel, alabaster, sphinxcontrib-websupport, requests, jinja2, sphinx, readthedocs-sphinx-ext, sphinx-rtd-theme, recommonmark
Successfully installed MarkupSafe-2.1.2 Pygments-2.14.0 alabaster-0.7.13 babel-2.11.0 certifi-2022.12.7 charset-normalizer-3.0.1 commonmark-0.9.1 docutils-0.17.1 idna-3.4 imagesize-1.4.1 jinja2-3.0.3 mock-1.0.1 packaging-23.0 pillow-9.4.0 pytz-2022.7.1 readthedocs-sphinx-ext-2.2.0 recommonmark-0.5.0 requests-2.28.2 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 urllib3-1.26.14

[rtd-command-info] start-time: 2023-02-17T15:04:34.823830Z, end-time: 2023-02-17T15:06:06.581429Z, duration: 91, exit-code: 0
python -m pip install --upgrade --upgrade-strategy eager --no-cache-dir .[doc,leiden]
Processing /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest
  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 numpy>=1.17.0
  Downloading numpy-1.24.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (17.3 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 17.3/17.3 MB 167.2 MB/s eta 0:00:00
Collecting seaborn
  Downloading seaborn-0.12.2-py3-none-any.whl (293 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 293.3/293.3 kB 202.7 MB/s eta 0:00:00
Collecting numba>=0.41.0
  Downloading numba-0.56.4-cp39-cp39-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (3.5 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.5/3.5 MB 187.8 MB/s eta 0:00:00
Collecting tqdm
  Downloading tqdm-4.64.1-py2.py3-none-any.whl (78 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 78.5/78.5 kB 198.9 MB/s eta 0:00:00
Collecting patsy
  Downloading patsy-0.5.3-py2.py3-none-any.whl (233 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 233.8/233.8 kB 241.2 MB/s eta 0:00:00
Collecting joblib
  Downloading joblib-1.2.0-py3-none-any.whl (297 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 298.0/298.0 kB 237.1 MB/s eta 0:00:00
Collecting statsmodels>=0.10.0rc2
  Downloading statsmodels-0.13.5-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (9.9 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 9.9/9.9 MB 105.4 MB/s eta 0:00:00
Collecting scipy>=1.4
  Downloading scipy-1.10.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (34.4 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 34.4/34.4 MB 177.3 MB/s eta 0:00:00
Collecting scikit-learn>=0.22
  Downloading scikit_learn-1.2.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (9.6 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 9.6/9.6 MB 179.2 MB/s eta 0:00:00
Collecting session-info
  Downloading session_info-1.0.0.tar.gz (24 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting umap-learn>=0.3.10
  Downloading umap-learn-0.5.3.tar.gz (88 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 88.2/88.2 kB 215.6 MB/s eta 0:00:00
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting natsort
  Downloading natsort-8.2.0-py3-none-any.whl (37 kB)
Collecting h5py>=3
  Downloading h5py-3.8.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.7 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.7/4.7 MB 202.7 MB/s eta 0:00:00
Collecting matplotlib>=3.4
  Downloading matplotlib-3.7.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.6 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.6/11.6 MB 173.5 MB/s eta 0:00:00
Collecting networkx>=2.3
  Downloading networkx-3.0-py3-none-any.whl (2.0 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.0/2.0 MB 237.9 MB/s eta 0:00:00
Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.9/site-packages (from scanpy==1.10.0.dev42+gd64282a4) (23.0)
Collecting pandas>=1.0
  Downloading pandas-1.5.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.2 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 12.2/12.2 MB 180.4 MB/s eta 0:00:00
Collecting anndata>=0.7.4
  Downloading anndata-0.8.0-py3-none-any.whl (96 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 96.1/96.1 kB 214.7 MB/s eta 0:00:00
Collecting ipython>=7.20
  Downloading ipython-8.10.0-py3-none-any.whl (784 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 784.3/784.3 kB 252.1 MB/s eta 0:00:00
Collecting sphinxext-opengraph
  Downloading sphinxext_opengraph-0.8.1-py3-none-any.whl (1.0 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.0/1.0 MB 251.9 MB/s eta 0:00:00
Collecting sphinx<5,>=4.4
  Downloading Sphinx-4.5.0-py3-none-any.whl (3.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.1/3.1 MB 174.0 MB/s eta 0:00:00
Collecting nbsphinx
  Downloading nbsphinx-0.8.12-py3-none-any.whl (26 kB)
Collecting scanpydoc[typehints]>=0.7.7
  Downloading scanpydoc-0.7.7-py3-none-any.whl (29 kB)
Collecting sphinx-design
  Downloading sphinx_design-0.3.0-py3-none-any.whl (2.2 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.2/2.2 MB 222.3 MB/s eta 0:00:00
Collecting sphinx-copybutton
  Downloading sphinx_copybutton-0.5.1-py3-none-any.whl (13 kB)
Collecting myst-parser
  Downloading myst_parser-0.18.1-py3-none-any.whl (58 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 58.2/58.2 kB 179.4 MB/s eta 0:00:00
Collecting sphinx-book-theme
  Downloading sphinx_book_theme-0.3.3-py3-none-any.whl (345 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 345.7/345.7 kB 248.3 MB/s eta 0:00:00
Collecting myst-nb
  Downloading myst_nb-0.17.1-py3-none-any.whl (78 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 78.6/78.6 kB 160.9 MB/s eta 0:00:00
Collecting python-igraph
  Downloading python-igraph-0.10.4.tar.gz (9.5 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting leidenalg
  Downloading leidenalg-0.9.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.3 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.3/1.3 MB 249.9 MB/s eta 0:00:00
Collecting backcall
  Downloading backcall-0.2.0-py2.py3-none-any.whl (11 kB)
Collecting decorator
  Downloading decorator-5.1.1-py3-none-any.whl (9.1 kB)
Collecting stack-data
  Downloading stack_data-0.6.2-py3-none-any.whl (24 kB)
Collecting prompt-toolkit<3.1.0,>=3.0.30
  Downloading prompt_toolkit-3.0.36-py3-none-any.whl (386 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 386.4/386.4 kB 245.3 MB/s eta 0:00:00
Requirement already satisfied: pygments>=2.4.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.9/site-packages (from ipython>=7.20->scanpy==1.10.0.dev42+gd64282a4) (2.14.0)
Collecting traitlets>=5
  Downloading traitlets-5.9.0-py3-none-any.whl (117 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 117.4/117.4 kB 227.8 MB/s eta 0:00:00
Collecting pexpect>4.3
  Downloading pexpect-4.8.0-py2.py3-none-any.whl (59 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 59.0/59.0 kB 208.0 MB/s eta 0:00:00
Collecting pickleshare
  Downloading pickleshare-0.7.5-py2.py3-none-any.whl (6.9 kB)
Collecting jedi>=0.16
  Downloading jedi-0.18.2-py2.py3-none-any.whl (1.6 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.6/1.6 MB 230.8 MB/s eta 0:00:00
Collecting matplotlib-inline
  Downloading matplotlib_inline-0.1.6-py3-none-any.whl (9.4 kB)
Collecting importlib-resources>=3.2.0
  Downloading importlib_resources-5.10.2-py3-none-any.whl (34 kB)
Collecting contourpy>=1.0.1
  Downloading contourpy-1.0.7-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (299 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 299.7/299.7 kB 235.4 MB/s eta 0:00:00
Requirement already satisfied: pillow>=6.2.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.9/site-packages (from matplotlib>=3.4->scanpy==1.10.0.dev42+gd64282a4) (9.4.0)
Collecting cycler>=0.10
  Downloading cycler-0.11.0-py3-none-any.whl (6.4 kB)
Collecting fonttools>=4.22.0
  Downloading fonttools-4.38.0-py3-none-any.whl (965 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 965.4/965.4 kB 253.3 MB/s eta 0:00:00
Collecting kiwisolver>=1.0.1
  Downloading kiwisolver-1.4.4-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (1.6 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.6/1.6 MB 238.9 MB/s eta 0:00:00
Collecting python-dateutil>=2.7
  Downloading python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 247.7/247.7 kB 243.5 MB/s eta 0:00:00
Collecting pyparsing>=2.3.1
  Downloading pyparsing-3.0.9-py3-none-any.whl (98 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 98.3/98.3 kB 199.1 MB/s eta 0:00:00
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.9/site-packages (from numba>=0.41.0->scanpy==1.10.0.dev42+gd64282a4) (58.2.0)
Collecting setuptools
  Downloading setuptools-67.3.2-py3-none-any.whl (1.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 254.3 MB/s eta 0:00:00
Collecting llvmlite<0.40,>=0.39.0dev0
  Downloading llvmlite-0.39.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (34.6 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 34.6/34.6 MB 178.5 MB/s eta 0:00:00
Collecting numpy>=1.17.0
  Downloading numpy-1.23.5-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (17.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 17.1/17.1 MB 188.9 MB/s eta 0:00:00
Requirement already satisfied: pytz>=2020.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.9/site-packages (from pandas>=1.0->scanpy==1.10.0.dev42+gd64282a4) (2022.7.1)
Collecting get_version
  Downloading get_version-3.5.4-py3-none-any.whl (18 kB)
Collecting sphinx-autodoc-typehints>=1.15.2
  Downloading sphinx_autodoc_typehints-1.22-py3-none-any.whl (17 kB)
Collecting threadpoolctl>=2.0.0
  Downloading threadpoolctl-3.1.0-py3-none-any.whl (14 kB)
Collecting sphinxcontrib-qthelp
  Downloading sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl (90 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 90.6/90.6 kB 214.9 MB/s eta 0:00:00
Collecting sphinxcontrib-jsmath
  Downloading sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB)
Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.9/site-packages (from sphinx<5,>=4.4->scanpy==1.10.0.dev42+gd64282a4) (2.2.0)
Collecting importlib-metadata>=4.4
  Downloading importlib_metadata-6.0.0-py3-none-any.whl (21 kB)
Requirement already satisfied: requests>=2.5.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.9/site-packages (from sphinx<5,>=4.4->scanpy==1.10.0.dev42+gd64282a4) (2.28.2)
Collecting sphinxcontrib-applehelp
  Downloading sphinxcontrib_applehelp-1.0.4-py3-none-any.whl (120 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 120.6/120.6 kB 208.6 MB/s eta 0:00:00
Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.9/site-packages (from sphinx<5,>=4.4->scanpy==1.10.0.dev42+gd64282a4) (3.0.3)
Collecting Jinja2>=2.3
  Downloading Jinja2-3.1.2-py3-none-any.whl (133 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 133.1/133.1 kB 217.9 MB/s eta 0:00:00
Collecting sphinxcontrib-htmlhelp>=2.0.0
  Downloading sphinxcontrib_htmlhelp-2.0.1-py3-none-any.whl (99 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 99.8/99.8 kB 202.4 MB/s eta 0:00:00
Requirement already satisfied: babel>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.9/site-packages (from sphinx<5,>=4.4->scanpy==1.10.0.dev42+gd64282a4) (2.11.0)
Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.9/site-packages (from sphinx<5,>=4.4->scanpy==1.10.0.dev42+gd64282a4) (0.7.13)
Requirement already satisfied: sphinxcontrib-serializinghtml>=1.1.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.9/site-packages (from sphinx<5,>=4.4->scanpy==1.10.0.dev42+gd64282a4) (1.1.5)
Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.9/site-packages (from sphinx<5,>=4.4->scanpy==1.10.0.dev42+gd64282a4) (1.4.1)
Collecting sphinxcontrib-devhelp
  Downloading sphinxcontrib_devhelp-1.0.2-py2.py3-none-any.whl (84 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 84.7/84.7 kB 213.5 MB/s eta 0:00:00
Requirement already satisfied: docutils<0.18,>=0.14 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.9/site-packages (from sphinx<5,>=4.4->scanpy==1.10.0.dev42+gd64282a4) (0.17.1)
Requirement already satisfied: six in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.9/site-packages (from patsy->scanpy==1.10.0.dev42+gd64282a4) (1.16.0)
Collecting pynndescent>=0.5
  Downloading pynndescent-0.5.8.tar.gz (1.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 253.6 MB/s eta 0:00:00
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting igraph<0.11,>=0.10.0
  Downloading igraph-0.10.4-cp39-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.3 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.3/3.3 MB 193.6 MB/s eta 0:00:00
Collecting pyyaml
  Downloading PyYAML-6.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (661 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 661.8/661.8 kB 255.2 MB/s eta 0:00:00
Collecting nbclient
  Downloading nbclient-0.7.2-py3-none-any.whl (71 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 72.0/72.0 kB 202.4 MB/s eta 0:00:00
Collecting nbformat~=5.0
  Downloading nbformat-5.7.3-py3-none-any.whl (78 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 78.1/78.1 kB 212.2 MB/s eta 0:00:00
Collecting jupyter-cache~=0.5.0
  Downloading jupyter_cache-0.5.0-py3-none-any.whl (34 kB)
Collecting ipykernel
  Downloading ipykernel-6.21.2-py3-none-any.whl (149 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 149.7/149.7 kB 235.9 MB/s eta 0:00:00
Collecting typing-extensions
  Downloading typing_extensions-4.5.0-py3-none-any.whl (27 kB)
Collecting mdit-py-plugins~=0.3.1
  Downloading mdit_py_plugins-0.3.3-py3-none-any.whl (50 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 50.5/50.5 kB 190.3 MB/s eta 0:00:00
Collecting markdown-it-py<3.0.0,>=1.0.0
  Downloading markdown_it_py-2.1.0-py3-none-any.whl (84 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 84.5/84.5 kB 212.5 MB/s eta 0:00:00
Collecting nbconvert!=5.4
  Downloading nbconvert-7.2.9-py3-none-any.whl (274 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 274.9/274.9 kB 246.6 MB/s eta 0:00:00
Collecting texttable>=1.6.2
  Downloading texttable-1.6.7-py2.py3-none-any.whl (10 kB)
Collecting stdlib_list
  Downloading stdlib_list-0.8.0-py3-none-any.whl (63 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 63.5/63.5 kB 199.7 MB/s eta 0:00:00
Collecting pydata-sphinx-theme~=0.8.0
  Downloading pydata_sphinx_theme-0.8.1-py3-none-any.whl (3.3 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.3/3.3 MB 192.5 MB/s eta 0:00:00
Collecting zipp>=0.5
  Downloading zipp-3.13.0-py3-none-any.whl (6.7 kB)
Collecting parso<0.9.0,>=0.8.0
  Downloading parso-0.8.3-py2.py3-none-any.whl (100 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100.8/100.8 kB 185.8 MB/s eta 0:00:00
Requirement already satisfied: MarkupSafe>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.9/site-packages (from Jinja2>=2.3->sphinx<5,>=4.4->scanpy==1.10.0.dev42+gd64282a4) (2.1.2)
Collecting tabulate
  Downloading tabulate-0.9.0-py3-none-any.whl (35 kB)
Collecting attrs
  Downloading attrs-22.2.0-py3-none-any.whl (60 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 60.0/60.0 kB 201.1 MB/s eta 0:00:00
Collecting nbclient
  Downloading nbclient-0.5.13-py3-none-any.whl (70 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 70.6/70.6 kB 214.5 MB/s eta 0:00:00
Collecting sqlalchemy<1.5,>=1.3.12
  Downloading SQLAlchemy-1.4.46-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.6 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.6/1.6 MB 253.4 MB/s eta 0:00:00
Collecting click
  Downloading click-8.1.3-py3-none-any.whl (96 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 96.6/96.6 kB 206.2 MB/s eta 0:00:00
Collecting mdurl~=0.1
  Downloading mdurl-0.1.2-py3-none-any.whl (10.0 kB)
Collecting nest-asyncio
  Downloading nest_asyncio-1.5.6-py3-none-any.whl (5.2 kB)
Collecting jupyter-client>=6.1.5
  Downloading jupyter_client-8.0.3-py3-none-any.whl (102 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 102.7/102.7 kB 221.4 MB/s eta 0:00:00
Collecting jupyterlab-pygments
  Downloading jupyterlab_pygments-0.2.2-py2.py3-none-any.whl (21 kB)
Collecting pandocfilters>=1.4.1
  Downloading pandocfilters-1.5.0-py2.py3-none-any.whl (8.7 kB)
Collecting jupyter-core>=4.7
  Downloading jupyter_core-5.2.0-py3-none-any.whl (94 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 94.3/94.3 kB 215.9 MB/s eta 0:00:00
Collecting mistune<3,>=2.0.3
  Downloading mistune-2.0.5-py2.py3-none-any.whl (24 kB)
Collecting bleach
  Downloading bleach-6.0.0-py3-none-any.whl (162 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 162.5/162.5 kB 242.8 MB/s eta 0:00:00
Collecting defusedxml
  Downloading defusedxml-0.7.1-py2.py3-none-any.whl (25 kB)
Collecting beautifulsoup4
  Downloading beautifulsoup4-4.11.2-py3-none-any.whl (129 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 129.4/129.4 kB 237.5 MB/s eta 0:00:00
Collecting tinycss2
  Downloading tinycss2-1.2.1-py3-none-any.whl (21 kB)
Collecting fastjsonschema
  Downloading fastjsonschema-2.16.2-py3-none-any.whl (22 kB)
Collecting jsonschema>=2.6
  Downloading jsonschema-4.17.3-py3-none-any.whl (90 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 90.4/90.4 kB 203.6 MB/s eta 0:00:00
Collecting ptyprocess>=0.5
  Downloading ptyprocess-0.7.0-py2.py3-none-any.whl (13 kB)
Collecting wcwidth
  Downloading wcwidth-0.2.6-py2.py3-none-any.whl (29 kB)
Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.9/site-packages (from requests>=2.5.0->sphinx<5,>=4.4->scanpy==1.10.0.dev42+gd64282a4) (2022.12.7)
Requirement already satisfied: idna<4,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.9/site-packages (from requests>=2.5.0->sphinx<5,>=4.4->scanpy==1.10.0.dev42+gd64282a4) (3.4)
Requirement already satisfied: charset-normalizer<4,>=2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.9/site-packages (from requests>=2.5.0->sphinx<5,>=4.4->scanpy==1.10.0.dev42+gd64282a4) (3.0.1)
Requirement already satisfied: urllib3<1.27,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.9/site-packages (from requests>=2.5.0->sphinx<5,>=4.4->scanpy==1.10.0.dev42+gd64282a4) (1.26.14)
Collecting sphinx-autodoc-typehints>=1.15.2
  Downloading sphinx_autodoc_typehints-1.21.8-py3-none-any.whl (17 kB)
  Downloading sphinx_autodoc_typehints-1.21.7-py3-none-any.whl (16 kB)
  Downloading sphinx_autodoc_typehints-1.21.6-py3-none-any.whl (16 kB)
  Downloading sphinx_autodoc_typehints-1.21.5-py3-none-any.whl (16 kB)
  Downloading sphinx_autodoc_typehints-1.21.4-py3-none-any.whl (16 kB)
  Downloading sphinx_autodoc_typehints-1.21.3-py3-none-any.whl (15 kB)
  Downloading sphinx_autodoc_typehints-1.21.2-py3-none-any.whl (13 kB)
  Downloading sphinx_autodoc_typehints-1.21.1-py3-none-any.whl (13 kB)
  Downloading sphinx_autodoc_typehints-1.21.0-py3-none-any.whl (13 kB)
  Downloading sphinx_autodoc_typehints-1.20.2-py3-none-any.whl (12 kB)
  Downloading sphinx_autodoc_typehints-1.20.1-py3-none-any.whl (12 kB)
  Downloading sphinx_autodoc_typehints-1.20.0-py3-none-any.whl (12 kB)
  Downloading sphinx_autodoc_typehints-1.19.5-py3-none-any.whl (12 kB)
  Downloading sphinx_autodoc_typehints-1.19.4-py3-none-any.whl (12 kB)
  Downloading sphinx_autodoc_typehints-1.19.3-py3-none-any.whl (12 kB)
  Downloading sphinx_autodoc_typehints-1.19.2-py3-none-any.whl (12 kB)
  Downloading sphinx_autodoc_typehints-1.19.1-py3-none-any.whl (12 kB)
Collecting dunamai
  Downloading dunamai-1.15.0-py3-none-any.whl (23 kB)
Collecting pyzmq>=20
  Downloading pyzmq-25.0.0-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (1.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 250.8 MB/s eta 0:00:00
Collecting debugpy>=1.6.5
  Downloading debugpy-1.6.6-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.1/3.1 MB 216.6 MB/s eta 0:00:00
Collecting comm>=0.1.1
  Downloading comm-0.1.2-py3-none-any.whl (6.5 kB)
Collecting psutil
  Downloading psutil-5.9.4-cp36-abi3-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (280 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 280.2/280.2 kB 227.3 MB/s eta 0:00:00
Collecting tornado>=6.1
  Downloading tornado-6.2-cp37-abi3-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (423 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 424.0/424.0 kB 248.9 MB/s eta 0:00:00
Collecting pure-eval
  Downloading pure_eval-0.2.2-py3-none-any.whl (11 kB)
Collecting asttokens>=2.1.0
  Downloading asttokens-2.2.1-py2.py3-none-any.whl (26 kB)
Collecting executing>=1.2.0
  Downloading executing-1.2.0-py2.py3-none-any.whl (24 kB)
Collecting pyrsistent!=0.17.0,!=0.17.1,!=0.17.2,>=0.14.0
  Downloading pyrsistent-0.19.3-py3-none-any.whl (57 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 57.5/57.5 kB 194.5 MB/s eta 0:00:00
Collecting platformdirs>=2.5
  Downloading platformdirs-3.0.0-py3-none-any.whl (14 kB)
Collecting greenlet!=0.4.17
  Downloading greenlet-2.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (610 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 610.9/610.9 kB 255.7 MB/s eta 0:00:00
Collecting soupsieve>1.2
  Downloading soupsieve-2.4-py3-none-any.whl (37 kB)
Collecting webencodings
  Downloading webencodings-0.5.1-py2.py3-none-any.whl (11 kB)
Building wheels for collected packages: umap-learn, python-igraph, scanpy, session-info, 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-0.5.3-py3-none-any.whl size=82830 sha256=a6c7472571fc83628c08ac81d08032d05c723d43fcb17624383e1ba135f4bd8d
  Stored in directory: /tmp/pip-ephem-wheel-cache-37vxhqmj/wheels/f4/3e/1c/596d0a463d17475af648688443fa4846fef624d1390339e7e9
  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-0.10.4-py3-none-any.whl size=9076 sha256=098b2c2a4c5aa5a5a187c230f5dd76b1f221456509d302c5fd60ab0dfa8fd16f
  Stored in directory: /tmp/pip-ephem-wheel-cache-37vxhqmj/wheels/dc/07/ac/bff79052fd6222d1239b228cd24a47222f227c2350f9c4df01
  Building wheel for scanpy (pyproject.toml): started
  Building wheel for scanpy (pyproject.toml): finished with status 'done'
  Created wheel for scanpy: filename=scanpy-1.10.0.dev42+gd64282a4-py3-none-any.whl size=11485454 sha256=55f2383e81ff862a790a96c68172629ca661df1491a121829aa5118d80ba394c
  Stored in directory: /tmp/pip-ephem-wheel-cache-37vxhqmj/wheels/2c/ca/a8/b038e303156487f1950e65fb14990e1642cd81a73929959d71
  Building wheel for session-info (setup.py): started
  Building wheel for session-info (setup.py): finished with status 'done'
  Created wheel for session-info: filename=session_info-1.0.0-py3-none-any.whl size=8045 sha256=af5e9496c94d0837f959f0a380e3cfc003ea705e7d154d12d3ecceca20873ee6
  Stored in directory: /tmp/pip-ephem-wheel-cache-37vxhqmj/wheels/d4/fc/2e/00ca60bac7954b84907efd41baa9b4853500eaeec4228410c6
  Building wheel for pynndescent (setup.py): started
  Building wheel for pynndescent (setup.py): finished with status 'done'
  Created wheel for pynndescent: filename=pynndescent-0.5.8-py3-none-any.whl size=55511 sha256=47f8a5c5d19466f9ad8c5ed7ea0591f41ce2b4ade3a64945df857b700f69a969
  Stored in directory: /tmp/pip-ephem-wheel-cache-37vxhqmj/wheels/b9/89/cc/59ab91ef5b21dc2ab3635528d7d227f49dfc9169905dcb959d
Successfully built umap-learn python-igraph scanpy session-info pynndescent
Installing collected packages: webencodings, wcwidth, texttable, stdlib_list, pure-eval, ptyprocess, pickleshare, mistune, fastjsonschema, executing, backcall, zipp, typing-extensions, traitlets, tqdm, tornado, tinycss2, threadpoolctl, tabulate, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, soupsieve, setuptools, session-info, pyzmq, pyyaml, python-dateutil, pyrsistent, pyparsing, psutil, prompt-toolkit, platformdirs, pexpect, parso, pandocfilters, numpy, networkx, nest-asyncio, natsort, mdurl, llvmlite, kiwisolver, jupyterlab-pygments, joblib, Jinja2, igraph, greenlet, fonttools, dunamai, defusedxml, decorator, debugpy, cycler, click, bleach, attrs, asttokens, stack-data, sqlalchemy, scipy, python-igraph, patsy, pandas, numba, matplotlib-inline, markdown-it-py, leidenalg, jupyter-core, jsonschema, jedi, importlib-resources, importlib-metadata, h5py, get_version, contourpy, comm, beautifulsoup4, statsmodels, sphinx, scikit-learn, nbformat, mdit-py-plugins, matplotlib, jupyter-client, ipython, anndata, sphinxext-opengraph, sphinx-design, sphinx-copybutton, sphinx-autodoc-typehints, seaborn, scanpydoc, pynndescent, pydata-sphinx-theme, nbclient, myst-parser, ipykernel, umap-learn, sphinx-book-theme, nbconvert, jupyter-cache, scanpy, nbsphinx, myst-nb
  Attempting uninstall: setuptools
    Found existing installation: setuptools 58.2.0
    Uninstalling setuptools-58.2.0:
      Successfully uninstalled setuptools-58.2.0
  Attempting uninstall: Jinja2
    Found existing installation: Jinja2 3.0.3
    Uninstalling Jinja2-3.0.3:
      Successfully uninstalled Jinja2-3.0.3
  Attempting uninstall: sphinx
    Found existing installation: Sphinx 1.8.6
    Uninstalling Sphinx-1.8.6:
      Successfully uninstalled Sphinx-1.8.6
Successfully installed Jinja2-3.1.2 anndata-0.8.0 asttokens-2.2.1 attrs-22.2.0 backcall-0.2.0 beautifulsoup4-4.11.2 bleach-6.0.0 click-8.1.3 comm-0.1.2 contourpy-1.0.7 cycler-0.11.0 debugpy-1.6.6 decorator-5.1.1 defusedxml-0.7.1 dunamai-1.15.0 executing-1.2.0 fastjsonschema-2.16.2 fonttools-4.38.0 get_version-3.5.4 greenlet-2.0.2 h5py-3.8.0 igraph-0.10.4 importlib-metadata-6.0.0 importlib-resources-5.10.2 ipykernel-6.21.2 ipython-8.10.0 jedi-0.18.2 joblib-1.2.0 jsonschema-4.17.3 jupyter-cache-0.5.0 jupyter-client-8.0.3 jupyter-core-5.2.0 jupyterlab-pygments-0.2.2 kiwisolver-1.4.4 leidenalg-0.9.1 llvmlite-0.39.1 markdown-it-py-2.1.0 matplotlib-3.7.0 matplotlib-inline-0.1.6 mdit-py-plugins-0.3.3 mdurl-0.1.2 mistune-2.0.5 myst-nb-0.17.1 myst-parser-0.18.1 natsort-8.2.0 nbclient-0.5.13 nbconvert-7.2.9 nbformat-5.7.3 nbsphinx-0.8.12 nest-asyncio-1.5.6 networkx-3.0 numba-0.56.4 numpy-1.23.5 pandas-1.5.3 pandocfilters-1.5.0 parso-0.8.3 patsy-0.5.3 pexpect-4.8.0 pickleshare-0.7.5 platformdirs-3.0.0 prompt-toolkit-3.0.36 psutil-5.9.4 ptyprocess-0.7.0 pure-eval-0.2.2 pydata-sphinx-theme-0.8.1 pynndescent-0.5.8 pyparsing-3.0.9 pyrsistent-0.19.3 python-dateutil-2.8.2 python-igraph-0.10.4 pyyaml-6.0 pyzmq-25.0.0 scanpy-1.10.0.dev42+gd64282a4 scanpydoc-0.7.7 scikit-learn-1.2.1 scipy-1.10.0 seaborn-0.12.2 session-info-1.0.0 setuptools-67.3.2 soupsieve-2.4 sphinx-4.5.0 sphinx-autodoc-typehints-1.19.1 sphinx-book-theme-0.3.3 sphinx-copybutton-0.5.1 sphinx-design-0.3.0 sphinxcontrib-applehelp-1.0.4 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.1 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 sphinxext-opengraph-0.8.1 sqlalchemy-1.4.46 stack-data-0.6.2 statsmodels-0.13.5 stdlib_list-0.8.0 tabulate-0.9.0 texttable-1.6.7 threadpoolctl-3.1.0 tinycss2-1.2.1 tornado-6.2 tqdm-4.64.1 traitlets-5.9.0 typing-extensions-4.5.0 umap-learn-0.5.3 wcwidth-0.2.6 webencodings-0.5.1 zipp-3.13.0

[rtd-command-info] start-time: 2023-02-17T15:06:08.215297Z, end-time: 2023-02-17T15:06:08.284154Z, duration: 0, exit-code: 0
cat docs/conf.py
import os
import sys
import importlib.util
import inspect
import re
import subprocess
from pathlib import Path
from datetime import datetime
from typing import Any

import matplotlib  # noqa
from packaging.version import parse as parse_version

# 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 = '4.0'  # Nicer param docs
suppress_warnings = [
    'ref.citation',
    'myst.header',  # https://github.com/executablebooks/MyST-Parser/issues/262
]

# General information
project = 'Scanpy'
author = 'Scanpy development team'
repository_url = "https://github.com/scverse/scanpy"
copyright = f'{datetime.now():%Y}, the Scanpy development team.'
version = scanpy.__version__.replace('.dirty', '')

# Bumping the version updates all docs, so don't do that
if parse_version(version).is_devrelease:
    parsed = parse_version(version)
    version = f"{parsed.major}.{parsed.minor}.{parsed.micro}.dev"

release = version

# default settings
templates_path = ['_templates']
master_doc = 'index'
default_role = 'literal'
exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', '**.ipynb_checkpoints']

extensions = [
    'myst_nb',
    'sphinx_copybutton',
    'sphinx.ext.autodoc',
    'sphinx.ext.intersphinx',
    'sphinx.ext.doctest',
    'sphinx.ext.coverage',
    'sphinx.ext.mathjax',
    'sphinx.ext.napoleon',
    'sphinx.ext.autosummary',
    'sphinx.ext.linkcode',
    'sphinx.ext.extlinks',
    'matplotlib.sphinxext.plot_directive',
    'sphinx_autodoc_typehints',  # needs to be after napoleon
    'scanpydoc.autosummary_generate_imported',
    "sphinx_design",
    "sphinxext.opengraph",
    *[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
myst_enable_extensions = [
    "amsmath",
    "colon_fence",
    "deflist",
    "dollarmath",
    "html_image",
    "html_admonition",
]
myst_url_schemes = ("http", "https", "mailto")
nb_output_stderr = "remove"
nb_execution_mode = "off"
nb_merge_streams = True


ogp_site_url = "https://scanpy.readthedocs.io/en/stable/"
ogp_image = "https://scanpy.readthedocs.io/en/stable/_static/Scanpy_Logo_BrightFG.svg"

typehints_defaults = 'braces'

scanpy_tutorials_url = 'https://scanpy-tutorials.readthedocs.io/en/latest/'

pygments_style = "default"
pygments_dark_style = "native"

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=('https://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/stable/', None),
    networkx=('https://networkx.org/documentation/stable/', None),
    numpy=('https://numpy.org/doc/stable/', 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/', 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 = "sphinx_book_theme"
html_theme_options = {
    "repository_url": repository_url,
    "use_repository_button": True,
    "logo_only": True,
    "show_toc_level": 4,  # show all levels in the sidebar
}
html_static_path = ['_static']
html_css_files = ["css/override.css"]
html_show_sphinx = False
html_logo = '_static/img/Scanpy_Logo_BrightFG.svg'
html_title = "scanpy"


def setup(app):
    """App setup hook."""
    # TODO: fix all warnings in a future PR
    # Many come from the tutorials, like the workshop directory
    # which is not included in the docs
    #     app.warningiserror = on_rtd
    app.add_config_value(
        "recommonmark_config",
        {
            "auto_toc_tree_section": "Contents",
            "enable_auto_toc_tree": True,
            "enable_math": True,
            "enable_inline_math": False,
            "enable_eval_rst": True,
        },
        True,
    )


# -- 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

# Linkcode config


def git(*args):
    return subprocess.check_output(["git", *args]).strip().decode()


# https://github.com/DisnakeDev/disnake/blob/7853da70b13fcd2978c39c0b7efa59b34d298186/docs/conf.py#L192
# Current git reference. Uses branch/tag name if found, otherwise uses commit hash
git_ref = None
try:
    git_ref = git("name-rev", "--name-only", "--no-undefined", "HEAD")
    git_ref = re.sub(r"^(remotes/[^/]+|tags)/", "", git_ref)
except Exception:
    pass

# (if no name found or relative ref, use commit hash instead)
if not git_ref or re.search(r"[\^~]", git_ref):
    try:
        git_ref = git("rev-parse", "HEAD")
    except Exception:
        git_ref = "master"

# https://github.com/DisnakeDev/disnake/blob/7853da70b13fcd2978c39c0b7efa59b34d298186/docs/conf.py#L192
_module_path = os.path.dirname(importlib.util.find_spec("scanpy").origin)  # type: ignore


def linkcode_resolve(domain, info):
    if domain != "py":
        return None

    try:
        obj: Any = sys.modules[info["module"]]
        for part in info["fullname"].split("."):
            obj = getattr(obj, part)
        obj = inspect.unwrap(obj)

        if isinstance(obj, property):
            obj = inspect.unwrap(obj.fget)  # type: ignore

        path = os.path.relpath(inspect.getsourcefile(obj), start=_module_path)  # type: ignore
        src, lineno = inspect.getsourcelines(obj)
    except Exception:
        return None

    path = f"{path}#L{lineno}-L{lineno + len(src) - 1}"
    return f"{repository_url}/blob/{git_ref}/scanpy/{path}"


# extlinks config
extlinks = {
    "issue": ("https://github.com/scverse/scanpy/issues/%s", "issue%s"),
    "pr": ("https://github.com/scverse/scanpy/pull/%s", "pr%s"),
    "tutorial": (
        "https://github.com/scverse/scanpy-tutorials/%s.ipynb",
        "tutorial: %s",
    ),
}




###########################################################################
#          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/main/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:
    html_theme = 'sphinx_rtd_theme'
    html_style = None
    html_theme_options = {}


# This following legacy behavior will gradually be sliced out until its deprecated and removed.
# Skipped for Sphinx 6+
# Skipped by internal Feature flag SKIP_SPHINX_HTML_THEME_PATH
# Skipped by all new projects since SKIP_SPHINX_HTML_THEME_PATH's introduction (jan 2023)
if (
        using_rtd_theme
        and version_info < (6,0)
        and not False
    ):
    theme = importlib.import_module('sphinx_rtd_theme')
    if 'html_theme_path' in globals():
        html_theme_path.append(theme.get_html_theme_path())
    else:
        html_theme_path = [theme.get_html_theme_path()]

# Define websupport2_base_url and websupport2_static_url
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",
    'proxied_static_path': "/_/static/",
    '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': 'scverse',
    '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': 'd64282a4',
}

# 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/1305527/'

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: 2023-02-17T15:06:08.483404Z, end-time: 2023-02-17T15:10:03.794320Z, duration: 235, exit-code: 0
python -m sphinx -T -E -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html
Running Sphinx v4.5.0
Matplotlib is building the font cache; this may take a moment.
loading translations [en]... done
making output directory... done
myst v0.18.1: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions=['amsmath', 'colon_fence', 'deflist', 'dollarmath', 'html_image', 'html_admonition'], disable_syntax=[], all_links_external=False, url_schemes=('http', 'https', 'mailto'), ref_domains=None, highlight_code_blocks=True, number_code_blocks=[], title_to_header=False, heading_anchors=None, heading_slug_func=None, footnote_transition=True, words_per_minute=200, sub_delimiters=('{', '}'), linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area')
myst-nb v0.17.1: NbParserConfig(custom_formats={}, metadata_key='mystnb', cell_metadata_key='mystnb', kernel_rgx_aliases={}, execution_mode='off', execution_cache_path='', execution_excludepatterns=(), execution_timeout=30, execution_in_temp=False, execution_allow_errors=False, execution_raise_on_error=False, execution_show_tb=False, merge_streams=True, render_plugin='default', remove_code_source=False, remove_code_outputs=False, code_prompt_show='Show code cell {type}', code_prompt_hide='Hide code cell {type}', number_source_lines=False, output_stderr='remove', render_text_lexer='myst-ansi', render_error_lexer='ipythontb', render_image_options={}, render_figure_options={}, render_markdown_format='commonmark', output_folder='build', append_css=True, metadata_to_fm=False)
Using jupyter-cache at: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/_readthedocs/.jupyter_cache
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 https://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/stable/objects.inv...
loading intersphinx inventory from https://networkx.org/documentation/stable/objects.inv...
loading intersphinx inventory from https://numpy.org/doc/stable/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...
loading intersphinx inventory from https://docs.scipy.org/doc/scipy/objects.inv...
loading intersphinx inventory from https://seaborn.pydata.org/objects.inv...
loading intersphinx inventory from https://scikit-learn.org/stable/objects.inv...
loading intersphinx inventory from https://scanpy-tutorials.readthedocs.io/en/latest/objects.inv...
[autosummary] generating autosummary for: _tutorials.md, api/classes.md, api/datasets.md, api/deprecated.md, api/experimental.md, api/get.md, api/index.md, api/metrics.md, api/plotting.md, api/preprocessing.md, ..., tutorials/scanpy_workshop/day2_01_DE_Colabs.ipynb, tutorials/scanpy_workshop/day2_01_DifferentialExpression.ipynb, tutorials/scanpy_workshop/day2_02_GSEA_Colabs.ipynb, tutorials/scanpy_workshop/day2_02_GeneSetEnrichmentAnalysis.ipynb, tutorials/scanpy_workshop/day2_03_RNAvelocity.ipynb, tutorials/spatial/basic-analysis.ipynb, tutorials/spatial/integration-scanorama.ipynb, tutorials/tutorial_pearson_residuals.ipynb, tutorials/visualizing-marker-genes.rst, usage-principles.md
[autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.MatrixPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.StackedViolin.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.Neighbors.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy._settings.ScanpyConfig.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.datasets.blobs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.datasets.ebi_expression_atlas.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.datasets.krumsiek11.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.datasets.moignard15.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.datasets.paul15.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/external/generated/scanpy.external.tl.cyclone.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/external/generated/scanpy.external.tl.harmony_timeseries.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/external/generated/scanpy.external.tl.palantir.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/external/generated/scanpy.external.tl.palantir_results.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/external/generated/scanpy.external.tl.phate.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/external/generated/scanpy.external.tl.phenograph.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/external/generated/scanpy.external.tl.sam.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/external/generated/scanpy.external.tl.sandbag.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/external/generated/scanpy.external.tl.trimap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/external/generated/scanpy.external.tl.wishbone.rst
[autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_HEIGHT.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_WIDTH.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLORMAP.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_LEGEND_TITLE.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_ON.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGECOLOR.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGELW.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MAX.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MIN.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_LARGEST_DOT.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy._settings.ScanpyConfig.file_format_data.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy._settings.ScanpyConfig.file_format_figs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy._settings.ScanpyConfig.logfile.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy._settings.ScanpyConfig.logpath.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy._settings.ScanpyConfig.max_memory.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy._settings.ScanpyConfig.n_jobs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy._settings.ScanpyConfig.plot_suffix.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy._settings.ScanpyConfig.set_figure_params.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy._settings.ScanpyConfig.verbosity.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy._settings.ScanpyConfig.writedir.rst
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 96 source files that are out of date
updating environment: [new config] 351 added, 0 changed, 0 removed
reading sources... [  0%] _tutorials
reading sources... [  0%] api/classes
reading sources... [  0%] api/datasets
reading sources... [  1%] api/deprecated
reading sources... [  1%] api/experimental
reading sources... [  1%] api/generated/classes/scanpy.pl.DotPlot
reading sources... [  1%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_HEIGHT
reading sources... [  2%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_WIDTH
reading sources... [  2%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLORMAP
reading sources... [  2%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_LEGEND_TITLE
reading sources... [  3%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_ON
reading sources... [  3%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGECOLOR
reading sources... [  3%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGELW
reading sources... [  3%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MAX
reading sources... [  4%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MIN
reading sources... [  4%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_LARGEST_DOT
reading sources... [  4%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_LEGENDS_WIDTH
reading sources... [  5%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_PLOT_X_PADDING
reading sources... [  5%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_PLOT_Y_PADDING
reading sources... [  5%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_SAVE_PREFIX
reading sources... [  5%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_SIZE_EXPONENT
reading sources... [  6%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_SIZE_LEGEND_TITLE
reading sources... [  6%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_SMALLEST_DOT
reading sources... [  6%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_WSPACE
reading sources... [  7%] api/generated/classes/scanpy.pl.DotPlot.MAX_NUM_CATEGORIES
reading sources... [  7%] api/generated/classes/scanpy.pl.DotPlot.MIN_FIGURE_HEIGHT
reading sources... [  7%] api/generated/classes/scanpy.pl.DotPlot.add_dendrogram
reading sources... [  7%] api/generated/classes/scanpy.pl.DotPlot.add_totals
reading sources... [  8%] api/generated/classes/scanpy.pl.DotPlot.get_axes
reading sources... [  8%] api/generated/classes/scanpy.pl.DotPlot.getdoc
reading sources... [  8%] api/generated/classes/scanpy.pl.DotPlot.legend
reading sources... [  9%] api/generated/classes/scanpy.pl.DotPlot.make_figure
reading sources... [  9%] api/generated/classes/scanpy.pl.DotPlot.savefig
reading sources... [  9%] api/generated/classes/scanpy.pl.DotPlot.show
reading sources... [  9%] api/generated/classes/scanpy.pl.DotPlot.style
reading sources... [ 10%] api/generated/classes/scanpy.pl.DotPlot.swap_axes
reading sources... [ 10%] api/generated/classes/scanpy.pl.MatrixPlot
reading sources... [ 10%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_CATEGORY_HEIGHT
reading sources... [ 11%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_CATEGORY_WIDTH
reading sources... [ 11%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_COLORMAP
reading sources... [ 11%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_COLOR_LEGEND_TITLE
reading sources... [ 11%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_EDGE_COLOR
reading sources... [ 12%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_EDGE_LW
reading sources... [ 12%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_LEGENDS_WIDTH
reading sources... [ 12%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_SAVE_PREFIX
reading sources... [ 13%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_WSPACE
reading sources... [ 13%] api/generated/classes/scanpy.pl.MatrixPlot.MAX_NUM_CATEGORIES
reading sources... [ 13%] api/generated/classes/scanpy.pl.MatrixPlot.MIN_FIGURE_HEIGHT
reading sources... [ 13%] api/generated/classes/scanpy.pl.MatrixPlot.add_dendrogram
reading sources... [ 14%] api/generated/classes/scanpy.pl.MatrixPlot.add_totals
reading sources... [ 14%] api/generated/classes/scanpy.pl.MatrixPlot.get_axes
reading sources... [ 14%] api/generated/classes/scanpy.pl.MatrixPlot.getdoc
reading sources... [ 15%] api/generated/classes/scanpy.pl.MatrixPlot.legend
reading sources... [ 15%] api/generated/classes/scanpy.pl.MatrixPlot.make_figure
reading sources... [ 15%] api/generated/classes/scanpy.pl.MatrixPlot.savefig
reading sources... [ 15%] api/generated/classes/scanpy.pl.MatrixPlot.show
reading sources... [ 16%] api/generated/classes/scanpy.pl.MatrixPlot.style
reading sources... [ 16%] api/generated/classes/scanpy.pl.MatrixPlot.swap_axes
reading sources... [ 16%] api/generated/classes/scanpy.pl.StackedViolin
reading sources... [ 17%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_CATEGORY_HEIGHT
reading sources... [ 17%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_CATEGORY_WIDTH
reading sources... [ 17%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_COLORMAP
reading sources... [ 17%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_COLOR_LEGEND_TITLE
reading sources... [ 18%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_CUT
reading sources... [ 18%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_INNER
reading sources... [ 18%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_JITTER
reading sources... [ 19%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_JITTER_SIZE
reading sources... [ 19%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_LEGENDS_WIDTH
reading sources... [ 19%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_LINE_WIDTH
reading sources... [ 19%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_PLOT_X_PADDING
reading sources... [ 20%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_PLOT_YTICKLABELS
reading sources... [ 20%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_PLOT_Y_PADDING
reading sources... [ 20%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_ROW_PALETTE
reading sources... [ 21%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_SAVE_PREFIX
reading sources... [ 21%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_SCALE
reading sources... [ 21%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_STRIPPLOT
reading sources... [ 21%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_WSPACE
reading sources... [ 22%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_YLIM
reading sources... [ 22%] api/generated/classes/scanpy.pl.StackedViolin.MAX_NUM_CATEGORIES
reading sources... [ 22%] api/generated/classes/scanpy.pl.StackedViolin.MIN_FIGURE_HEIGHT
reading sources... [ 23%] api/generated/classes/scanpy.pl.StackedViolin.add_dendrogram
reading sources... [ 23%] api/generated/classes/scanpy.pl.StackedViolin.add_totals
reading sources... [ 23%] api/generated/classes/scanpy.pl.StackedViolin.get_axes
reading sources... [ 23%] api/generated/classes/scanpy.pl.StackedViolin.getdoc
reading sources... [ 24%] api/generated/classes/scanpy.pl.StackedViolin.legend
reading sources... [ 24%] api/generated/classes/scanpy.pl.StackedViolin.make_figure
reading sources... [ 24%] api/generated/classes/scanpy.pl.StackedViolin.savefig
reading sources... [ 25%] api/generated/classes/scanpy.pl.StackedViolin.show
reading sources... [ 25%] api/generated/classes/scanpy.pl.StackedViolin.style
reading sources... [ 25%] api/generated/classes/scanpy.pl.StackedViolin.swap_axes
reading sources... [ 25%] api/generated/scanpy.Neighbors
reading sources... [ 26%] api/generated/scanpy.Neighbors.compute_eigen
reading sources... [ 26%] api/generated/scanpy.Neighbors.compute_neighbors
reading sources... [ 26%] api/generated/scanpy.Neighbors.compute_transitions
reading sources... [ 27%] api/generated/scanpy.Neighbors.connectivities
reading sources... [ 27%] api/generated/scanpy.Neighbors.distances
reading sources... [ 27%] api/generated/scanpy.Neighbors.distances_dpt
reading sources... [ 27%] api/generated/scanpy.Neighbors.eigen_basis
reading sources... [ 28%] api/generated/scanpy.Neighbors.eigen_values
reading sources... [ 28%] api/generated/scanpy.Neighbors.getdoc
reading sources... [ 28%] api/generated/scanpy.Neighbors.rp_forest
reading sources... [ 29%] api/generated/scanpy.Neighbors.to_igraph
reading sources... [ 29%] api/generated/scanpy.Neighbors.transitions
reading sources... [ 29%] api/generated/scanpy.Neighbors.transitions_sym
reading sources... [ 29%] api/generated/scanpy._settings.ScanpyConfig
reading sources... [ 30%] api/generated/scanpy._settings.ScanpyConfig.autosave
reading sources... [ 30%] api/generated/scanpy._settings.ScanpyConfig.autoshow
reading sources... [ 30%] api/generated/scanpy._settings.ScanpyConfig.cache_compression
reading sources... [ 31%] api/generated/scanpy._settings.ScanpyConfig.cachedir
reading sources... [ 31%] api/generated/scanpy._settings.ScanpyConfig.categories_to_ignore
reading sources... [ 31%] api/generated/scanpy._settings.ScanpyConfig.datasetdir
reading sources... [ 31%] api/generated/scanpy._settings.ScanpyConfig.figdir
reading sources... [ 32%] api/generated/scanpy._settings.ScanpyConfig.file_format_data
reading sources... [ 32%] api/generated/scanpy._settings.ScanpyConfig.file_format_figs
reading sources... [ 32%] api/generated/scanpy._settings.ScanpyConfig.logfile
reading sources... [ 33%] api/generated/scanpy._settings.ScanpyConfig.logpath
reading sources... [ 33%] api/generated/scanpy._settings.ScanpyConfig.max_memory
reading sources... [ 33%] api/generated/scanpy._settings.ScanpyConfig.n_jobs
reading sources... [ 33%] api/generated/scanpy._settings.ScanpyConfig.plot_suffix
reading sources... [ 34%] api/generated/scanpy._settings.ScanpyConfig.set_figure_params
reading sources... [ 34%] api/generated/scanpy._settings.ScanpyConfig.verbosity
reading sources... [ 34%] api/generated/scanpy._settings.ScanpyConfig.writedir
reading sources... [ 35%] api/generated/scanpy.datasets.blobs
reading sources... [ 35%] api/generated/scanpy.datasets.ebi_expression_atlas
reading sources... [ 35%] api/generated/scanpy.datasets.krumsiek11
reading sources... [ 35%] api/generated/scanpy.datasets.moignard15
reading sources... [ 36%] api/generated/scanpy.datasets.paul15
reading sources... [ 36%] api/generated/scanpy.datasets.pbmc3k
reading sources... [ 36%] api/generated/scanpy.datasets.pbmc3k_processed
reading sources... [ 37%] api/generated/scanpy.datasets.pbmc68k_reduced
reading sources... [ 37%] api/generated/scanpy.datasets.toggleswitch
reading sources... [ 37%] api/generated/scanpy.datasets.visium_sge
reading sources... [ 37%] api/generated/scanpy.experimental.pp.highly_variable_genes
reading sources... [ 38%] api/generated/scanpy.experimental.pp.normalize_pearson_residuals
reading sources... [ 38%] api/generated/scanpy.experimental.pp.normalize_pearson_residuals_pca
reading sources... [ 38%] api/generated/scanpy.experimental.pp.recipe_pearson_residuals
reading sources... [ 39%] api/generated/scanpy.get.obs_df
reading sources... [ 39%] api/generated/scanpy.get.rank_genes_groups_df
reading sources... [ 39%] api/generated/scanpy.get.var_df
reading sources... [ 39%] api/generated/scanpy.logging.print_header
reading sources... [ 40%] api/generated/scanpy.logging.print_versions
reading sources... [ 40%] api/generated/scanpy.metrics.confusion_matrix
reading sources... [ 40%] api/generated/scanpy.metrics.gearys_c
reading sources... [ 41%] api/generated/scanpy.metrics.morans_i
reading sources... [ 41%] api/generated/scanpy.pl.clustermap
reading sources... [ 41%] api/generated/scanpy.pl.dendrogram
reading sources... [ 41%] api/generated/scanpy.pl.diffmap
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/scatterplots.py:392: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
reading sources... [ 42%] api/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.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_dotplot.py:748: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap', 'norm' will be ignored
  dot_ax.scatter(x, y, **kwds)
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/checkouts/latest/scanpy/plotting/_dotplot.py:748: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap', 'norm' will be ignored
  dot_ax.scatter(x, y, **kwds)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_dotplot.py:748: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap', 'norm' will be ignored
  dot_ax.scatter(x, y, **kwds)
reading sources... [ 42%] api/generated/scanpy.pl.dpt_groups_pseudotime
reading sources... [ 42%] api/generated/scanpy.pl.dpt_timeseries
reading sources... [ 43%] api/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`).
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/scatterplots.py:392: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/scatterplots.py:392: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
reading sources... [ 43%] api/generated/scanpy.pl.embedding
reading sources... [ 43%] api/generated/scanpy.pl.embedding_density
reading sources... [ 43%] api/generated/scanpy.pl.filter_genes_dispersion
reading sources... [ 44%] api/generated/scanpy.pl.heatmap
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_anndata.py:2414: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead.
  obs_tidy.index.value_counts(sort=False).iteritems()
reading sources... [ 44%] api/generated/scanpy.pl.highest_expr_genes
reading sources... [ 44%] api/generated/scanpy.pl.highly_variable_genes
reading sources... [ 45%] api/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... [ 45%] api/generated/scanpy.pl.paga

  0%|          | 0.00/23.5M [00:00<?, ?B/s]
 52%|█████▏    | 12.1M/23.5M [00:00<00:00, 127MB/s]
100%|██████████| 23.5M/23.5M [00:00<00:00, 158MB/s]
reading sources... [ 45%] api/generated/scanpy.pl.paga_compare
reading sources... [ 45%] api/generated/scanpy.pl.paga_path
reading sources... [ 46%] api/generated/scanpy.pl.pca
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/scatterplots.py:392: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap', 'norm' will be ignored
  cax = scatter(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/scatterplots.py:392: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
reading sources... [ 46%] api/generated/scanpy.pl.pca_loadings
reading sources... [ 46%] api/generated/scanpy.pl.pca_overview
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/scatterplots.py:392: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
reading sources... [ 47%] api/generated/scanpy.pl.pca_variance_ratio
reading sources... [ 47%] api/generated/scanpy.pl.rank_genes_groups
reading sources... [ 47%] api/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.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_dotplot.py:748: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap', 'norm' will be ignored
  dot_ax.scatter(x, y, **kwds)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_dotplot.py:748: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap', 'norm' will be ignored
  dot_ax.scatter(x, y, **kwds)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_dotplot.py:748: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap', 'norm' will be ignored
  dot_ax.scatter(x, y, **kwds)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_dotplot.py:748: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap', 'norm' will be ignored
  dot_ax.scatter(x, y, **kwds)
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/checkouts/latest/scanpy/plotting/_dotplot.py:748: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap', 'norm' will be ignored
  dot_ax.scatter(x, y, **kwds)
reading sources... [ 47%] api/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`
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_anndata.py:2414: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead.
  obs_tidy.index.value_counts(sort=False).iteritems()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_anndata.py:2414: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead.
  obs_tidy.index.value_counts(sort=False).iteritems()
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_anndata.py:2414: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead.
  obs_tidy.index.value_counts(sort=False).iteritems()
reading sources... [ 48%] api/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... [ 48%] api/generated/scanpy.pl.rank_genes_groups_stacked_violin
reading sources... [ 48%] api/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.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_anndata.py:2414: FutureWarning: iteritems is deprecated and will be removed in a future version. Use .items instead.
  obs_tidy.index.value_counts(sort=False).iteritems()
reading sources... [ 49%] api/generated/scanpy.pl.rank_genes_groups_violin
reading sources... [ 49%] api/generated/scanpy.pl.ranking
reading sources... [ 49%] api/generated/scanpy.pl.scatter
reading sources... [ 49%] api/generated/scanpy.pl.sim
reading sources... [ 50%] api/generated/scanpy.pl.spatial
reading sources... [ 50%] api/generated/scanpy.pl.stacked_violin
reading sources... [ 50%] api/generated/scanpy.pl.tracksplot
reading sources... [ 50%] api/generated/scanpy.pl.tsne
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/scatterplots.py:392: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
reading sources... [ 51%] api/generated/scanpy.pl.umap
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/scatterplots.py:392: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap', 'norm' will be ignored
  cax = scatter(
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/scatterplots.py:392: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored
  cax = scatter(
reading sources... [ 51%] api/generated/scanpy.pl.violin
reading sources... [ 51%] api/generated/scanpy.pp.calculate_qc_metrics

  0%|          | 0.00/5.58M [00:00<?, ?B/s]
  0%|          | 8.00k/5.58M [00:00<02:07, 46.0kB/s]
  1%|          | 32.0k/5.58M [00:00<00:58, 98.9kB/s]
  2%|▏         | 96.0k/5.58M [00:00<00:26, 219kB/s] 
  4%|▎         | 208k/5.58M [00:00<00:14, 382kB/s] 
  8%|▊         | 432k/5.58M [00:00<00:07, 699kB/s]
 16%|█▌        | 888k/5.58M [00:01<00:03, 1.33MB/s]
 31%|███       | 1.74M/5.58M [00:01<00:01, 2.55MB/s]
 54%|█████▍    | 3.02M/5.58M [00:01<00:00, 3.99MB/s]
 76%|███████▌  | 4.26M/5.58M [00:01<00:00, 4.85MB/s]
 99%|█████████▉| 5.53M/5.58M [00:01<00:00, 5.47MB/s]
100%|██████████| 5.58M/5.58M [00:01<00:00, 3.15MB/s]
reading sources... [ 52%] api/generated/scanpy.pp.combat
reading sources... [ 52%] api/generated/scanpy.pp.downsample_counts
reading sources... [ 52%] api/generated/scanpy.pp.filter_cells
reading sources... [ 52%] api/generated/scanpy.pp.filter_genes
reading sources... [ 53%] api/generated/scanpy.pp.filter_genes_dispersion
reading sources... [ 53%] api/generated/scanpy.pp.highly_variable_genes
reading sources... [ 53%] api/generated/scanpy.pp.log1p
reading sources... [ 54%] api/generated/scanpy.pp.neighbors
reading sources... [ 54%] api/generated/scanpy.pp.normalize_per_cell
reading sources... [ 54%] api/generated/scanpy.pp.normalize_total
reading sources... [ 54%] api/generated/scanpy.pp.pca
reading sources... [ 55%] api/generated/scanpy.pp.recipe_seurat
reading sources... [ 55%] api/generated/scanpy.pp.recipe_weinreb17
reading sources... [ 55%] api/generated/scanpy.pp.recipe_zheng17
reading sources... [ 56%] api/generated/scanpy.pp.regress_out
reading sources... [ 56%] api/generated/scanpy.pp.scale
reading sources... [ 56%] api/generated/scanpy.pp.subsample
reading sources... [ 56%] api/generated/scanpy.queries.biomart_annotations
reading sources... [ 57%] api/generated/scanpy.queries.enrich
reading sources... [ 57%] api/generated/scanpy.queries.gene_coordinates
reading sources... [ 57%] api/generated/scanpy.queries.mitochondrial_genes
reading sources... [ 58%] api/generated/scanpy.read
reading sources... [ 58%] api/generated/scanpy.read_10x_h5
reading sources... [ 58%] api/generated/scanpy.read_10x_mtx
reading sources... [ 58%] api/generated/scanpy.read_csv
reading sources... [ 59%] api/generated/scanpy.read_excel
reading sources... [ 59%] api/generated/scanpy.read_h5ad
reading sources... [ 59%] api/generated/scanpy.read_hdf
reading sources... [ 60%] api/generated/scanpy.read_loom
reading sources... [ 60%] api/generated/scanpy.read_mtx
reading sources... [ 60%] api/generated/scanpy.read_text
reading sources... [ 60%] api/generated/scanpy.read_umi_tools
reading sources... [ 61%] api/generated/scanpy.read_visium
reading sources... [ 61%] api/generated/scanpy.set_figure_params
reading sources... [ 61%] api/generated/scanpy.tl.dendrogram
reading sources... [ 62%] api/generated/scanpy.tl.diffmap
reading sources... [ 62%] api/generated/scanpy.tl.dpt
reading sources... [ 62%] api/generated/scanpy.tl.draw_graph
reading sources... [ 62%] api/generated/scanpy.tl.embedding_density
reading sources... [ 63%] api/generated/scanpy.tl.filter_rank_genes_groups
reading sources... [ 63%] api/generated/scanpy.tl.ingest
reading sources... [ 63%] api/generated/scanpy.tl.leiden
reading sources... [ 64%] api/generated/scanpy.tl.louvain
reading sources... [ 64%] api/generated/scanpy.tl.marker_gene_overlap
reading sources... [ 64%] api/generated/scanpy.tl.paga
reading sources... [ 64%] api/generated/scanpy.tl.pca
reading sources... [ 65%] api/generated/scanpy.tl.rank_genes_groups
reading sources... [ 65%] api/generated/scanpy.tl.score_genes
reading sources... [ 65%] api/generated/scanpy.tl.score_genes_cell_cycle
reading sources... [ 66%] api/generated/scanpy.tl.sim
reading sources... [ 66%] api/generated/scanpy.tl.tsne
reading sources... [ 66%] api/generated/scanpy.tl.umap
reading sources... [ 66%] api/get
reading sources... [ 67%] api/index
reading sources... [ 67%] api/metrics
reading sources... [ 67%] api/plotting
reading sources... [ 68%] api/preprocessing
reading sources... [ 68%] api/queries
reading sources... [ 68%] api/reading
reading sources... [ 68%] api/settings
reading sources... [ 69%] api/tools
reading sources... [ 69%] basic_usage
reading sources... [ 69%] community
reading sources... [ 70%] contributors
reading sources... [ 70%] dev/ci
reading sources... [ 70%] dev/code
reading sources... [ 70%] dev/documentation
reading sources... [ 71%] dev/getting-set-up
reading sources... [ 71%] dev/index
reading sources... [ 71%] dev/release
reading sources... [ 72%] dev/testing
reading sources... [ 72%] dev/versioning
reading sources... [ 72%] ecosystem
reading sources... [ 72%] external/exporting
reading sources... [ 73%] external/generated/scanpy.external.exporting.cellbrowser
reading sources... [ 73%] external/generated/scanpy.external.exporting.spring_project
reading sources... [ 73%] external/generated/scanpy.external.pl.phate
reading sources... [ 74%] external/generated/scanpy.external.pl.sam
reading sources... [ 74%] external/generated/scanpy.external.pl.scrublet_score_distribution
reading sources... [ 74%] external/generated/scanpy.external.pl.trimap
reading sources... [ 74%] external/generated/scanpy.external.pl.wishbone_marker_trajectory
reading sources... [ 75%] external/generated/scanpy.external.pp.bbknn
reading sources... [ 75%] external/generated/scanpy.external.pp.dca
reading sources... [ 75%] external/generated/scanpy.external.pp.harmony_integrate
reading sources... [ 76%] external/generated/scanpy.external.pp.hashsolo
reading sources... [ 76%] external/generated/scanpy.external.pp.magic
reading sources... [ 76%] external/generated/scanpy.external.pp.mnn_correct
reading sources... [ 76%] external/generated/scanpy.external.pp.scanorama_integrate
reading sources... [ 77%] external/generated/scanpy.external.pp.scrublet
reading sources... [ 77%] external/generated/scanpy.external.pp.scrublet_simulate_doublets
reading sources... [ 77%] external/generated/scanpy.external.tl.cyclone
reading sources... [ 78%] external/generated/scanpy.external.tl.harmony_timeseries
reading sources... [ 78%] external/generated/scanpy.external.tl.palantir
reading sources... [ 78%] external/generated/scanpy.external.tl.palantir_results
reading sources... [ 78%] external/generated/scanpy.external.tl.phate
reading sources... [ 79%] external/generated/scanpy.external.tl.phenograph
reading sources... [ 79%] external/generated/scanpy.external.tl.sam
reading sources... [ 79%] external/generated/scanpy.external.tl.sandbag
reading sources... [ 80%] external/generated/scanpy.external.tl.trimap
reading sources... [ 80%] external/generated/scanpy.external.tl.wishbone
reading sources... [ 80%] external/index
reading sources... [ 80%] external/plotting
reading sources... [ 81%] external/preprocessing
reading sources... [ 81%] external/tools
reading sources... [ 81%] index
reading sources... [ 82%] installation
reading sources... [ 82%] news
reading sources... [ 82%] references
reading sources... [ 82%] release-notes/0.1.0
reading sources... [ 83%] release-notes/0.2.1
reading sources... [ 83%] release-notes/0.2.9
reading sources... [ 83%] release-notes/0.3.0
reading sources... [ 84%] release-notes/0.3.2
reading sources... [ 84%] release-notes/0.4.0
reading sources... [ 84%] release-notes/0.4.2
reading sources... [ 84%] release-notes/0.4.3
reading sources... [ 85%] release-notes/0.4.4
reading sources... [ 85%] release-notes/1.0.0
reading sources... [ 85%] release-notes/1.1.0
reading sources... [ 86%] release-notes/1.10.0
reading sources... [ 86%] release-notes/1.2.0
reading sources... [ 86%] release-notes/1.2.1
reading sources... [ 86%] release-notes/1.3.1
reading sources... [ 87%] release-notes/1.3.3
reading sources... [ 87%] release-notes/1.3.4
reading sources... [ 87%] release-notes/1.3.5
reading sources... [ 88%] release-notes/1.3.6
reading sources... [ 88%] release-notes/1.3.7
reading sources... [ 88%] release-notes/1.3.8
reading sources... [ 88%] release-notes/1.4.1
reading sources... [ 89%] release-notes/1.4.2
reading sources... [ 89%] release-notes/1.4.3
reading sources... [ 89%] release-notes/1.4.4
reading sources... [ 90%] release-notes/1.4.5
reading sources... [ 90%] release-notes/1.4.6
reading sources... [ 90%] release-notes/1.5.0
reading sources... [ 90%] release-notes/1.5.1
reading sources... [ 91%] release-notes/1.6.0
reading sources... [ 91%] release-notes/1.7.0
reading sources... [ 91%] release-notes/1.7.1
reading sources... [ 92%] release-notes/1.7.2
reading sources... [ 92%] release-notes/1.8.0
reading sources... [ 92%] release-notes/1.8.1
reading sources... [ 92%] release-notes/1.8.2
reading sources... [ 93%] release-notes/1.9.0
reading sources... [ 93%] release-notes/1.9.1
reading sources... [ 93%] release-notes/1.9.2
reading sources... [ 94%] release-notes/index
reading sources... [ 94%] tutorials/README
reading sources... [ 94%] tutorials/index
reading sources... [ 94%] tutorials/integrating-data-using-ingest
reading sources... [ 95%] tutorials/paga-paul15
reading sources... [ 95%] tutorials/pbmc3k
reading sources... [ 95%] tutorials/plotting/core
reading sources... [ 96%] tutorials/scanpy_workshop/README
reading sources... [ 96%] tutorials/scanpy_workshop/day1_01
reading sources... [ 96%] tutorials/scanpy_workshop/day1_01_GColab
reading sources... [ 96%] tutorials/scanpy_workshop/day1_01_GColabs_solutions
reading sources... [ 97%] tutorials/scanpy_workshop/day1_01_solutions
reading sources... [ 97%] tutorials/scanpy_workshop/day2_01_DE_Colabs
reading sources... [ 97%] tutorials/scanpy_workshop/day2_01_DifferentialExpression
reading sources... [ 98%] tutorials/scanpy_workshop/day2_02_GSEA_Colabs
reading sources... [ 98%] tutorials/scanpy_workshop/day2_02_GeneSetEnrichmentAnalysis
reading sources... [ 98%] tutorials/scanpy_workshop/day2_03_RNAvelocity
reading sources... [ 98%] tutorials/spatial/basic-analysis
reading sources... [ 99%] tutorials/spatial/integration-scanorama
reading sources... [ 99%] tutorials/tutorial_pearson_residuals
reading sources... [ 99%] tutorials/visualizing-marker-genes
reading sources... [100%] usage-principles

looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/tutorials/index.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/tutorials/scanpy_workshop/README.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/tutorials/scanpy_workshop/day1_01.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/tutorials/scanpy_workshop/day1_01_GColab.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/tutorials/scanpy_workshop/day1_01_GColabs_solutions.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/tutorials/scanpy_workshop/day1_01_solutions.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/tutorials/scanpy_workshop/day2_01_DE_Colabs.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/tutorials/scanpy_workshop/day2_01_DifferentialExpression.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/tutorials/scanpy_workshop/day2_02_GSEA_Colabs.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/tutorials/scanpy_workshop/day2_02_GeneSetEnrichmentAnalysis.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/tutorials/scanpy_workshop/day2_03_RNAvelocity.ipynb: WARNING: document isn't included in any toctree
done
preparing documents... done
writing output... [  0%] _tutorials
writing output... [  0%] api/classes
writing output... [  0%] api/datasets
writing output... [  1%] api/deprecated
writing output... [  1%] api/experimental
writing output... [  1%] api/generated/classes/scanpy.pl.DotPlot
writing output... [  1%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_HEIGHT
writing output... [  2%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_WIDTH
writing output... [  2%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLORMAP
writing output... [  2%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_LEGEND_TITLE
writing output... [  3%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_ON
writing output... [  3%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGECOLOR
writing output... [  3%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGELW
writing output... [  3%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MAX
writing output... [  4%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MIN
writing output... [  4%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_LARGEST_DOT
writing output... [  4%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_LEGENDS_WIDTH
writing output... [  5%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_PLOT_X_PADDING
writing output... [  5%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_PLOT_Y_PADDING
writing output... [  5%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_SAVE_PREFIX
writing output... [  5%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_SIZE_EXPONENT
writing output... [  6%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_SIZE_LEGEND_TITLE
writing output... [  6%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_SMALLEST_DOT
writing output... [  6%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_WSPACE
writing output... [  7%] api/generated/classes/scanpy.pl.DotPlot.MAX_NUM_CATEGORIES
writing output... [  7%] api/generated/classes/scanpy.pl.DotPlot.MIN_FIGURE_HEIGHT
writing output... [  7%] api/generated/classes/scanpy.pl.DotPlot.add_dendrogram
writing output... [  7%] api/generated/classes/scanpy.pl.DotPlot.add_totals
writing output... [  8%] api/generated/classes/scanpy.pl.DotPlot.get_axes
writing output... [  8%] api/generated/classes/scanpy.pl.DotPlot.getdoc
writing output... [  8%] api/generated/classes/scanpy.pl.DotPlot.legend
writing output... [  9%] api/generated/classes/scanpy.pl.DotPlot.make_figure
writing output... [  9%] api/generated/classes/scanpy.pl.DotPlot.savefig
writing output... [  9%] api/generated/classes/scanpy.pl.DotPlot.show
writing output... [  9%] api/generated/classes/scanpy.pl.DotPlot.style
writing output... [ 10%] api/generated/classes/scanpy.pl.DotPlot.swap_axes
writing output... [ 10%] api/generated/classes/scanpy.pl.MatrixPlot
writing output... [ 10%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_CATEGORY_HEIGHT
writing output... [ 11%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_CATEGORY_WIDTH
writing output... [ 11%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_COLORMAP
writing output... [ 11%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_COLOR_LEGEND_TITLE
writing output... [ 11%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_EDGE_COLOR
writing output... [ 12%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_EDGE_LW
writing output... [ 12%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_LEGENDS_WIDTH
writing output... [ 12%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_SAVE_PREFIX
writing output... [ 13%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_WSPACE
writing output... [ 13%] api/generated/classes/scanpy.pl.MatrixPlot.MAX_NUM_CATEGORIES
writing output... [ 13%] api/generated/classes/scanpy.pl.MatrixPlot.MIN_FIGURE_HEIGHT
writing output... [ 13%] api/generated/classes/scanpy.pl.MatrixPlot.add_dendrogram
writing output... [ 14%] api/generated/classes/scanpy.pl.MatrixPlot.add_totals
writing output... [ 14%] api/generated/classes/scanpy.pl.MatrixPlot.get_axes
writing output... [ 14%] api/generated/classes/scanpy.pl.MatrixPlot.getdoc
writing output... [ 15%] api/generated/classes/scanpy.pl.MatrixPlot.legend
writing output... [ 15%] api/generated/classes/scanpy.pl.MatrixPlot.make_figure
writing output... [ 15%] api/generated/classes/scanpy.pl.MatrixPlot.savefig
writing output... [ 15%] api/generated/classes/scanpy.pl.MatrixPlot.show
writing output... [ 16%] api/generated/classes/scanpy.pl.MatrixPlot.style
writing output... [ 16%] api/generated/classes/scanpy.pl.MatrixPlot.swap_axes
writing output... [ 16%] api/generated/classes/scanpy.pl.StackedViolin
writing output... [ 17%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_CATEGORY_HEIGHT
writing output... [ 17%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_CATEGORY_WIDTH
writing output... [ 17%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_COLORMAP
writing output... [ 17%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_COLOR_LEGEND_TITLE
writing output... [ 18%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_CUT
writing output... [ 18%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_INNER
writing output... [ 18%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_JITTER
writing output... [ 19%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_JITTER_SIZE
writing output... [ 19%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_LEGENDS_WIDTH
writing output... [ 19%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_LINE_WIDTH
writing output... [ 19%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_PLOT_X_PADDING
writing output... [ 20%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_PLOT_YTICKLABELS
writing output... [ 20%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_PLOT_Y_PADDING
writing output... [ 20%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_ROW_PALETTE
writing output... [ 21%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_SAVE_PREFIX
writing output... [ 21%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_SCALE
writing output... [ 21%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_STRIPPLOT
writing output... [ 21%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_WSPACE
writing output... [ 22%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_YLIM
writing output... [ 22%] api/generated/classes/scanpy.pl.StackedViolin.MAX_NUM_CATEGORIES
writing output... [ 22%] api/generated/classes/scanpy.pl.StackedViolin.MIN_FIGURE_HEIGHT
writing output... [ 23%] api/generated/classes/scanpy.pl.StackedViolin.add_dendrogram
writing output... [ 23%] api/generated/classes/scanpy.pl.StackedViolin.add_totals
writing output... [ 23%] api/generated/classes/scanpy.pl.StackedViolin.get_axes
writing output... [ 23%] api/generated/classes/scanpy.pl.StackedViolin.getdoc
writing output... [ 24%] api/generated/classes/scanpy.pl.StackedViolin.legend
writing output... [ 24%] api/generated/classes/scanpy.pl.StackedViolin.make_figure
writing output... [ 24%] api/generated/classes/scanpy.pl.StackedViolin.savefig
writing output... [ 25%] api/generated/classes/scanpy.pl.StackedViolin.show
writing output... [ 25%] api/generated/classes/scanpy.pl.StackedViolin.style
writing output... [ 25%] api/generated/classes/scanpy.pl.StackedViolin.swap_axes
writing output... [ 25%] api/generated/scanpy.Neighbors
writing output... [ 26%] api/generated/scanpy.Neighbors.compute_eigen
writing output... [ 26%] api/generated/scanpy.Neighbors.compute_neighbors
writing output... [ 26%] api/generated/scanpy.Neighbors.compute_transitions
writing output... [ 27%] api/generated/scanpy.Neighbors.connectivities
writing output... [ 27%] api/generated/scanpy.Neighbors.distances
writing output... [ 27%] api/generated/scanpy.Neighbors.distances_dpt
writing output... [ 27%] api/generated/scanpy.Neighbors.eigen_basis
writing output... [ 28%] api/generated/scanpy.Neighbors.eigen_values
writing output... [ 28%] api/generated/scanpy.Neighbors.getdoc
writing output... [ 28%] api/generated/scanpy.Neighbors.rp_forest
writing output... [ 29%] api/generated/scanpy.Neighbors.to_igraph
writing output... [ 29%] api/generated/scanpy.Neighbors.transitions
writing output... [ 29%] api/generated/scanpy.Neighbors.transitions_sym
writing output... [ 29%] api/generated/scanpy._settings.ScanpyConfig
writing output... [ 30%] api/generated/scanpy._settings.ScanpyConfig.autosave
writing output... [ 30%] api/generated/scanpy._settings.ScanpyConfig.autoshow
writing output... [ 30%] api/generated/scanpy._settings.ScanpyConfig.cache_compression
writing output... [ 31%] api/generated/scanpy._settings.ScanpyConfig.cachedir
writing output... [ 31%] api/generated/scanpy._settings.ScanpyConfig.categories_to_ignore
writing output... [ 31%] api/generated/scanpy._settings.ScanpyConfig.datasetdir
writing output... [ 31%] api/generated/scanpy._settings.ScanpyConfig.figdir
writing output... [ 32%] api/generated/scanpy._settings.ScanpyConfig.file_format_data
writing output... [ 32%] api/generated/scanpy._settings.ScanpyConfig.file_format_figs
writing output... [ 32%] api/generated/scanpy._settings.ScanpyConfig.logfile
writing output... [ 33%] api/generated/scanpy._settings.ScanpyConfig.logpath
writing output... [ 33%] api/generated/scanpy._settings.ScanpyConfig.max_memory
writing output... [ 33%] api/generated/scanpy._settings.ScanpyConfig.n_jobs
writing output... [ 33%] api/generated/scanpy._settings.ScanpyConfig.plot_suffix
writing output... [ 34%] api/generated/scanpy._settings.ScanpyConfig.set_figure_params
writing output... [ 34%] api/generated/scanpy._settings.ScanpyConfig.verbosity
writing output... [ 34%] api/generated/scanpy._settings.ScanpyConfig.writedir
writing output... [ 35%] api/generated/scanpy.datasets.blobs
writing output... [ 35%] api/generated/scanpy.datasets.ebi_expression_atlas
writing output... [ 35%] api/generated/scanpy.datasets.krumsiek11
writing output... [ 35%] api/generated/scanpy.datasets.moignard15
writing output... [ 36%] api/generated/scanpy.datasets.paul15
writing output... [ 36%] api/generated/scanpy.datasets.pbmc3k
writing output... [ 36%] api/generated/scanpy.datasets.pbmc3k_processed
writing output... [ 37%] api/generated/scanpy.datasets.pbmc68k_reduced
writing output... [ 37%] api/generated/scanpy.datasets.toggleswitch
writing output... [ 37%] api/generated/scanpy.datasets.visium_sge
writing output... [ 37%] api/generated/scanpy.experimental.pp.highly_variable_genes
writing output... [ 38%] api/generated/scanpy.experimental.pp.normalize_pearson_residuals
writing output... [ 38%] api/generated/scanpy.experimental.pp.normalize_pearson_residuals_pca
writing output... [ 38%] api/generated/scanpy.experimental.pp.recipe_pearson_residuals
writing output... [ 39%] api/generated/scanpy.get.obs_df
writing output... [ 39%] api/generated/scanpy.get.rank_genes_groups_df
writing output... [ 39%] api/generated/scanpy.get.var_df
writing output... [ 39%] api/generated/scanpy.logging.print_header
writing output... [ 40%] api/generated/scanpy.logging.print_versions
writing output... [ 40%] api/generated/scanpy.metrics.confusion_matrix
writing output... [ 40%] api/generated/scanpy.metrics.gearys_c
writing output... [ 41%] api/generated/scanpy.metrics.morans_i
writing output... [ 41%] api/generated/scanpy.pl.clustermap
writing output... [ 41%] api/generated/scanpy.pl.dendrogram
writing output... [ 41%] api/generated/scanpy.pl.diffmap
writing output... [ 42%] api/generated/scanpy.pl.dotplot
writing output... [ 42%] api/generated/scanpy.pl.dpt_groups_pseudotime
writing output... [ 42%] api/generated/scanpy.pl.dpt_timeseries
writing output... [ 43%] api/generated/scanpy.pl.draw_graph
writing output... [ 43%] api/generated/scanpy.pl.embedding
writing output... [ 43%] api/generated/scanpy.pl.embedding_density
writing output... [ 43%] api/generated/scanpy.pl.filter_genes_dispersion
writing output... [ 44%] api/generated/scanpy.pl.heatmap
writing output... [ 44%] api/generated/scanpy.pl.highest_expr_genes
writing output... [ 44%] api/generated/scanpy.pl.highly_variable_genes
writing output... [ 45%] api/generated/scanpy.pl.matrixplot
writing output... [ 45%] api/generated/scanpy.pl.paga
writing output... [ 45%] api/generated/scanpy.pl.paga_compare
writing output... [ 45%] api/generated/scanpy.pl.paga_path
writing output... [ 46%] api/generated/scanpy.pl.pca
writing output... [ 46%] api/generated/scanpy.pl.pca_loadings
writing output... [ 46%] api/generated/scanpy.pl.pca_overview
writing output... [ 47%] api/generated/scanpy.pl.pca_variance_ratio
writing output... [ 47%] api/generated/scanpy.pl.rank_genes_groups
writing output... [ 47%] api/generated/scanpy.pl.rank_genes_groups_dotplot
writing output... [ 47%] api/generated/scanpy.pl.rank_genes_groups_heatmap
writing output... [ 48%] api/generated/scanpy.pl.rank_genes_groups_matrixplot
writing output... [ 48%] api/generated/scanpy.pl.rank_genes_groups_stacked_violin
writing output... [ 48%] api/generated/scanpy.pl.rank_genes_groups_tracksplot
writing output... [ 49%] api/generated/scanpy.pl.rank_genes_groups_violin
writing output... [ 49%] api/generated/scanpy.pl.ranking
writing output... [ 49%] api/generated/scanpy.pl.scatter
writing output... [ 49%] api/generated/scanpy.pl.sim
writing output... [ 50%] api/generated/scanpy.pl.spatial
writing output... [ 50%] api/generated/scanpy.pl.stacked_violin
writing output... [ 50%] api/generated/scanpy.pl.tracksplot
writing output... [ 50%] api/generated/scanpy.pl.tsne
writing output... [ 51%] api/generated/scanpy.pl.umap
writing output... [ 51%] api/generated/scanpy.pl.violin
writing output... [ 51%] api/generated/scanpy.pp.calculate_qc_metrics
writing output... [ 52%] api/generated/scanpy.pp.combat
writing output... [ 52%] api/generated/scanpy.pp.downsample_counts
writing output... [ 52%] api/generated/scanpy.pp.filter_cells
writing output... [ 52%] api/generated/scanpy.pp.filter_genes
writing output... [ 53%] api/generated/scanpy.pp.filter_genes_dispersion
writing output... [ 53%] api/generated/scanpy.pp.highly_variable_genes
writing output... [ 53%] api/generated/scanpy.pp.log1p
writing output... [ 54%] api/generated/scanpy.pp.neighbors
writing output... [ 54%] api/generated/scanpy.pp.normalize_per_cell
writing output... [ 54%] api/generated/scanpy.pp.normalize_total
writing output... [ 54%] api/generated/scanpy.pp.pca
writing output... [ 55%] api/generated/scanpy.pp.recipe_seurat
writing output... [ 55%] api/generated/scanpy.pp.recipe_weinreb17
writing output... [ 55%] api/generated/scanpy.pp.recipe_zheng17
writing output... [ 56%] api/generated/scanpy.pp.regress_out
writing output... [ 56%] api/generated/scanpy.pp.scale
writing output... [ 56%] api/generated/scanpy.pp.subsample
writing output... [ 56%] api/generated/scanpy.queries.biomart_annotations
writing output... [ 57%] api/generated/scanpy.queries.enrich
writing output... [ 57%] api/generated/scanpy.queries.gene_coordinates
writing output... [ 57%] api/generated/scanpy.queries.mitochondrial_genes
writing output... [ 58%] api/generated/scanpy.read
writing output... [ 58%] api/generated/scanpy.read_10x_h5
writing output... [ 58%] api/generated/scanpy.read_10x_mtx
writing output... [ 58%] api/generated/scanpy.read_csv
writing output... [ 59%] api/generated/scanpy.read_excel
writing output... [ 59%] api/generated/scanpy.read_h5ad
writing output... [ 59%] api/generated/scanpy.read_hdf
writing output... [ 60%] api/generated/scanpy.read_loom
writing output... [ 60%] api/generated/scanpy.read_mtx
writing output... [ 60%] api/generated/scanpy.read_text
writing output... [ 60%] api/generated/scanpy.read_umi_tools
writing output... [ 61%] api/generated/scanpy.read_visium
writing output... [ 61%] api/generated/scanpy.set_figure_params
writing output... [ 61%] api/generated/scanpy.tl.dendrogram
writing output... [ 62%] api/generated/scanpy.tl.diffmap
writing output... [ 62%] api/generated/scanpy.tl.dpt
writing output... [ 62%] api/generated/scanpy.tl.draw_graph
writing output... [ 62%] api/generated/scanpy.tl.embedding_density
writing output... [ 63%] api/generated/scanpy.tl.filter_rank_genes_groups
writing output... [ 63%] api/generated/scanpy.tl.ingest
writing output... [ 63%] api/generated/scanpy.tl.leiden
writing output... [ 64%] api/generated/scanpy.tl.louvain
writing output... [ 64%] api/generated/scanpy.tl.marker_gene_overlap
writing output... [ 64%] api/generated/scanpy.tl.paga
writing output... [ 64%] api/generated/scanpy.tl.pca
writing output... [ 65%] api/generated/scanpy.tl.rank_genes_groups
writing output... [ 65%] api/generated/scanpy.tl.score_genes
writing output... [ 65%] api/generated/scanpy.tl.score_genes_cell_cycle
writing output... [ 66%] api/generated/scanpy.tl.sim
writing output... [ 66%] api/generated/scanpy.tl.tsne
writing output... [ 66%] api/generated/scanpy.tl.umap
writing output... [ 66%] api/get
writing output... [ 67%] api/index
writing output... [ 67%] api/metrics
writing output... [ 67%] api/plotting
writing output... [ 68%] api/preprocessing
writing output... [ 68%] api/queries
writing output... [ 68%] api/reading
writing output... [ 68%] api/settings
writing output... [ 69%] api/tools
writing output... [ 69%] basic_usage
writing output... [ 69%] community
writing output... [ 70%] contributors
writing output... [ 70%] dev/ci
writing output... [ 70%] dev/code
writing output... [ 70%] dev/documentation
writing output... [ 71%] dev/getting-set-up
writing output... [ 71%] dev/index
writing output... [ 71%] dev/release
writing output... [ 72%] dev/testing
writing output... [ 72%] dev/versioning
writing output... [ 72%] ecosystem
writing output... [ 72%] external/exporting
writing output... [ 73%] external/generated/scanpy.external.exporting.cellbrowser
writing output... [ 73%] external/generated/scanpy.external.exporting.spring_project
writing output... [ 73%] external/generated/scanpy.external.pl.phate
writing output... [ 74%] external/generated/scanpy.external.pl.sam
writing output... [ 74%] external/generated/scanpy.external.pl.scrublet_score_distribution
writing output... [ 74%] external/generated/scanpy.external.pl.trimap
writing output... [ 74%] external/generated/scanpy.external.pl.wishbone_marker_trajectory
writing output... [ 75%] external/generated/scanpy.external.pp.bbknn
writing output... [ 75%] external/generated/scanpy.external.pp.dca
writing output... [ 75%] external/generated/scanpy.external.pp.harmony_integrate
writing output... [ 76%] external/generated/scanpy.external.pp.hashsolo
writing output... [ 76%] external/generated/scanpy.external.pp.magic
writing output... [ 76%] external/generated/scanpy.external.pp.mnn_correct
writing output... [ 76%] external/generated/scanpy.external.pp.scanorama_integrate
writing output... [ 77%] external/generated/scanpy.external.pp.scrublet
writing output... [ 77%] external/generated/scanpy.external.pp.scrublet_simulate_doublets
writing output... [ 77%] external/generated/scanpy.external.tl.cyclone
writing output... [ 78%] external/generated/scanpy.external.tl.harmony_timeseries
writing output... [ 78%] external/generated/scanpy.external.tl.palantir
writing output... [ 78%] external/generated/scanpy.external.tl.palantir_results
writing output... [ 78%] external/generated/scanpy.external.tl.phate
writing output... [ 79%] external/generated/scanpy.external.tl.phenograph
writing output... [ 79%] external/generated/scanpy.external.tl.sam
writing output... [ 79%] external/generated/scanpy.external.tl.sandbag
writing output... [ 80%] external/generated/scanpy.external.tl.trimap
writing output... [ 80%] external/generated/scanpy.external.tl.wishbone
writing output... [ 80%] external/index
writing output... [ 80%] external/plotting
writing output... [ 81%] external/preprocessing
writing output... [ 81%] external/tools
writing output... [ 81%] index
writing output... [ 82%] installation
writing output... [ 82%] news
writing output... [ 82%] references
writing output... [ 82%] release-notes/0.1.0
writing output... [ 83%] release-notes/0.2.1
writing output... [ 83%] release-notes/0.2.9
writing output... [ 83%] release-notes/0.3.0
writing output... [ 84%] release-notes/0.3.2
writing output... [ 84%] release-notes/0.4.0
writing output... [ 84%] release-notes/0.4.2
writing output... [ 84%] release-notes/0.4.3
writing output... [ 85%] release-notes/0.4.4
writing output... [ 85%] release-notes/1.0.0
writing output... [ 85%] release-notes/1.1.0
writing output... [ 86%] release-notes/1.10.0
writing output... [ 86%] release-notes/1.2.0
writing output... [ 86%] release-notes/1.2.1
writing output... [ 86%] release-notes/1.3.1
writing output... [ 87%] release-notes/1.3.3
writing output... [ 87%] release-notes/1.3.4
writing output... [ 87%] release-notes/1.3.5
writing output... [ 88%] release-notes/1.3.6
writing output... [ 88%] release-notes/1.3.7
writing output... [ 88%] release-notes/1.3.8
writing output... [ 88%] release-notes/1.4.1
writing output... [ 89%] release-notes/1.4.2
writing output... [ 89%] release-notes/1.4.3
writing output... [ 89%] release-notes/1.4.4
writing output... [ 90%] release-notes/1.4.5
writing output... [ 90%] release-notes/1.4.6
writing output... [ 90%] release-notes/1.5.0
writing output... [ 90%] release-notes/1.5.1
writing output... [ 91%] release-notes/1.6.0
writing output... [ 91%] release-notes/1.7.0
writing output... [ 91%] release-notes/1.7.1
writing output... [ 92%] release-notes/1.7.2
writing output... [ 92%] release-notes/1.8.0
writing output... [ 92%] release-notes/1.8.1
writing output... [ 92%] release-notes/1.8.2
writing output... [ 93%] release-notes/1.9.0
writing output... [ 93%] release-notes/1.9.1
writing output... [ 93%] release-notes/1.9.2
writing output... [ 94%] release-notes/index
writing output... [ 94%] tutorials/README
writing output... [ 94%] tutorials/index
writing output... [ 94%] tutorials/integrating-data-using-ingest
writing output... [ 95%] tutorials/paga-paul15
writing output... [ 95%] tutorials/pbmc3k
writing output... [ 95%] tutorials/plotting/core
writing output... [ 96%] tutorials/scanpy_workshop/README
writing output... [ 96%] tutorials/scanpy_workshop/day1_01
writing output... [ 96%] tutorials/scanpy_workshop/day1_01_GColab
writing output... [ 96%] tutorials/scanpy_workshop/day1_01_GColabs_solutions
writing output... [ 97%] tutorials/scanpy_workshop/day1_01_solutions
writing output... [ 97%] tutorials/scanpy_workshop/day2_01_DE_Colabs
writing output... [ 97%] tutorials/scanpy_workshop/day2_01_DifferentialExpression
writing output... [ 98%] tutorials/scanpy_workshop/day2_02_GSEA_Colabs
writing output... [ 98%] tutorials/scanpy_workshop/day2_02_GeneSetEnrichmentAnalysis
writing output... [ 98%] tutorials/scanpy_workshop/day2_03_RNAvelocity
writing output... [ 98%] tutorials/spatial/basic-analysis
writing output... [ 99%] tutorials/spatial/integration-scanorama
writing output... [ 99%] tutorials/tutorial_pearson_residuals
writing output... [ 99%] tutorials/visualizing-marker-genes
writing output... [100%] usage-principles

/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/index.md:10: WARNING: py:mod reference target not found: scanpy.external
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/preprocessing.md:: WARNING: py:mod reference target not found: scanpy.external
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/external/pp/_bbknn.py:docstring of scanpy.external.pp._bbknn.bbknn:28: WARNING: py:class reference target not found: sklearn.neighbors._distance_metric.DistanceMetric
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/index.md:44: WARNING: unknown document: external
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/release-notes/1.3.1.md:17: WARNING: unknown document: ../external
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/release-notes/1.3.1.md:18: WARNING: unknown document: ../external
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/tutorials/integrating-data-using-ingest.ipynb:310002: WARNING: 'myst' reference target not found: ftp://ngs.sanger.ac.uk/production/teichmann/BBKNN/objects-pancreas.zip
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/tutorials/spatial/basic-analysis.ipynb:20005: WARNING: 'myst' reference target not found: #MERFISH-example
generating indices... genindex py-modindex done
writing additional pages... search done
copying images... [  0%] _static/img/tutorials/170505_seurat/filter_genes_dispersion.png
copying images... [  0%] _static/img/tutorials/170505_seurat/louvain.png
copying images... [  1%] _static/img/tutorials/170505_seurat/NKG7.png
copying images... [  1%] _static/img/tutorials/170505_seurat/violin.png
copying images... [  1%] _static/img/tutorials/170505_seurat/cell_types.png
copying images... [  2%] _static/img/stacked_violin_dotplot_matrixplot.png
copying images... [  2%] _static/img/tutorials/paga_paul15.png
copying images... [  2%] _static/img/tutorials/paga_planaria.png
copying images... [  3%] _static/img/spatial-basic-analysis.png
copying images... [  3%] _static/img/tutorials/170522_visualizing_one_million_cells/tsne_1.3M.png
copying images... [  3%] _static/img/tutorials/170430_krumsiek11/timeseries.png
copying images... [  4%] _build/plot_directive/api/generated/classes/scanpy-pl-MatrixPlot-1.png
copying images... [  4%] _build/plot_directive/api/generated/classes/scanpy-pl-MatrixPlot-2.png
copying images... [  5%] _build/plot_directive/api/generated/classes/scanpy-pl-MatrixPlot-style-2.png
copying images... [  5%] _build/plot_directive/api/generated/scanpy-metrics-confusion_matrix-1.png
copying images... [  5%] _build/plot_directive/api/generated/scanpy-pl-dendrogram-1.png
copying images... [  6%] _build/plot_directive/api/generated/scanpy-pl-diffmap-1.png
copying images... [  6%] _build/plot_directive/api/generated/scanpy-pl-dotplot-1.png
copying images... [  6%] _build/plot_directive/api/generated/scanpy-pl-dotplot-2.png
copying images... [  7%] _build/plot_directive/api/generated/scanpy-pl-dotplot-3.png
copying images... [  7%] _build/plot_directive/api/generated/scanpy-pl-draw_graph-1.png
copying images... [  7%] _build/plot_directive/api/generated/scanpy-pl-embedding_density-2.png
copying images... [  8%] _build/plot_directive/api/generated/scanpy-pl-embedding_density-3.png
copying images... [  8%] _build/plot_directive/api/generated/scanpy-pl-heatmap-1.png
copying images... [  9%] _build/plot_directive/api/generated/scanpy-pl-matrixplot-1.png
copying images... [  9%] _build/plot_directive/api/generated/scanpy-pl-matrixplot-2.png
copying images... [  9%] _build/plot_directive/api/generated/scanpy-pl-matrixplot-3.png
copying images... [ 10%] _build/plot_directive/api/generated/scanpy-pl-paga-1.png
copying images... [ 10%] _build/plot_directive/api/generated/scanpy-pl-paga-2.png
copying images... [ 10%] _build/plot_directive/api/generated/scanpy-pl-pca-1.png
copying images... [ 11%] _build/plot_directive/api/generated/scanpy-pl-pca-2.png
copying images... [ 11%] _build/plot_directive/api/generated/scanpy-pl-pca-3.png
copying images... [ 11%] _build/plot_directive/api/generated/scanpy-pl-pca_loadings-2.png
copying images... [ 12%] _build/plot_directive/api/generated/scanpy-pl-pca_overview-1_00.png
copying images... [ 12%] _build/plot_directive/api/generated/scanpy-pl-pca_overview-1_01.png
copying images... [ 13%] _build/plot_directive/api/generated/scanpy-pl-pca_overview-1_02.png
copying images... [ 13%] _build/plot_directive/api/generated/scanpy-pl-rank_genes_groups-1.png
copying images... [ 13%] _build/plot_directive/api/generated/scanpy-pl-rank_genes_groups-2.png
copying images... [ 14%] _build/plot_directive/api/generated/scanpy-pl-rank_genes_groups_dotplot-2.png
copying images... [ 14%] _build/plot_directive/api/generated/scanpy-pl-rank_genes_groups_dotplot-3.png
copying images... [ 14%] _build/plot_directive/api/generated/scanpy-pl-rank_genes_groups_dotplot-4.png
copying images... [ 15%] _build/plot_directive/api/generated/scanpy-pl-rank_genes_groups_dotplot-5.png
copying images... [ 15%] _build/plot_directive/api/generated/scanpy-pl-rank_genes_groups_dotplot-6.png
copying images... [ 15%] _build/plot_directive/api/generated/scanpy-pl-rank_genes_groups_heatmap-1.png
copying images... [ 16%] _build/plot_directive/api/generated/scanpy-pl-rank_genes_groups_heatmap-2.png
copying images... [ 16%] _build/plot_directive/api/generated/scanpy-pl-rank_genes_groups_heatmap-3.png
copying images... [ 17%] _build/plot_directive/api/generated/scanpy-pl-rank_genes_groups_matrixplot-2.png
copying images... [ 17%] _build/plot_directive/api/generated/scanpy-pl-rank_genes_groups_matrixplot-3.png
copying images... [ 17%] _build/plot_directive/api/generated/scanpy-pl-rank_genes_groups_matrixplot-4.png
copying images... [ 18%] _build/plot_directive/api/generated/scanpy-pl-rank_genes_groups_tracksplot-1.png
copying images... [ 18%] _build/plot_directive/api/generated/scanpy-pl-tsne-1.png
copying images... [ 18%] _build/plot_directive/api/generated/scanpy-pl-umap-1.png
copying images... [ 19%] _build/plot_directive/api/generated/scanpy-pl-umap-2.png
copying images... [ 19%] _build/plot_directive/api/generated/scanpy-pl-umap-3.png
copying images... [ 19%] _build/plot_directive/api/generated/scanpy-pl-umap-4.png
copying images... [ 20%] _build/plot_directive/api/generated/scanpy-pl-violin-1.png
copying images... [ 20%] _build/plot_directive/api/generated/scanpy-pl-violin-2.png
copying images... [ 21%] _build/plot_directive/api/generated/scanpy-pl-violin-3.png
copying images... [ 21%] _build/plot_directive/api/generated/scanpy-pl-violin-4.png
copying images... [ 21%] _build/plot_directive/api/generated/scanpy-pl-violin-5.png
copying images... [ 22%] _build/plot_directive/api/generated/scanpy-pp-calculate_qc_metrics-1.png
copying images... [ 22%] _build/plot_directive/api/generated/scanpy-pp-calculate_qc_metrics-2.png
copying images... [ 22%] _build/plot_directive/api/generated/scanpy-tl-embedding_density-1.png
copying images... [ 23%] _build/plot_directive/api/generated/scanpy-tl-embedding_density-2.png
copying images... [ 23%] _static/img/ci_plot-view_tests-tab.png
copying images... [ 23%] _static/img/ci_plot-view_select-test.png
copying images... [ 24%] _static/img/ci_plot-view_attachment-tab.png
copying images... [ 24%] ../_readthedocs/jupyter_execute/542415f9bd02cc1108d982f182bea4116ed2a182764ad41d095c6a0a5d712cdc.png
copying images... [ 25%] ../_readthedocs/jupyter_execute/21423d090d5deec30ffffaf9fe999cabf3897e83fc08febea1ebcb0048b14b9e.png
copying images... [ 25%] ../_readthedocs/jupyter_execute/3fbf51d0bc0256b8b387de3510d6964aa24372f671d2085d798d1fc2bc1428c4.png
copying images... [ 25%] ../_readthedocs/jupyter_execute/fdbd63abd20448ff20607bdcd4da6f91db2db9c9c541e66f3520e04f1bedbadf.png
copying images... [ 26%] ../_readthedocs/jupyter_execute/1af1296c7ed0c06d2815caeb3a8c31b62d471620af488450173c8a05d54dad6d.png
copying images... [ 26%] ../_readthedocs/jupyter_execute/cc1dfa9ffb1eec5439a19e1ca9f612225a9597aa6a2a26b3e378009b972e942b.png
copying images... [ 26%] ../_readthedocs/jupyter_execute/c0104eda27200a144158abe264ff469d18727eb9bafbab10dba115548ca922af.png
copying images... [ 27%] ../_readthedocs/jupyter_execute/78103d8a616e5b464c6c563b549fc57bbadd4b155e2c0e305fcb9f28b4e1b40d.png
copying images... [ 27%] ../_readthedocs/jupyter_execute/cbdc500ce63e341c08c1ce211be52d703d16f4783b5666affe8f4f4a60e703b3.png
copying images... [ 27%] ../_readthedocs/jupyter_execute/409b2243634a8a3383d9f328335c9b5db8fc9315a4144d3a35b17edc6b9a4c0d.png
copying images... [ 28%] ../_readthedocs/jupyter_execute/ed18200ddf3d74f299e2d77ddb844cba0b52270d67c35b71be7a0d45b4b4b26e.png
copying images... [ 28%] ../_readthedocs/jupyter_execute/4492033e1eb9e476766c6942aabd46eaad2b3228f96b3e28cb643a2ad98fb4d1.png
copying images... [ 28%] ../_readthedocs/jupyter_execute/59119cceab24bf4920c184099992be16e9207c2857690ae3bb5455a637148f03.png
copying images... [ 29%] ../_readthedocs/jupyter_execute/a3a02c63f6cf5c59f8dd1f9cac14b4655adcff7c3fac1170691d96d654362e91.png
copying images... [ 29%] ../_readthedocs/jupyter_execute/7b578c69a2284b8fd485f3bd2dd0688e0c23240b49992062543b4fd78e1249d5.png
copying images... [ 30%] ../_readthedocs/jupyter_execute/8c6e16996372827af59a9307b99355e02a221d5dc9263dd06bf4b4c700e24a16.png
copying images... [ 30%] ../_readthedocs/jupyter_execute/f79e8a9231c64ac6ebd623f262089b4dd439d322200e42eb83bae3a4aff60025.png
copying images... [ 30%] ../_readthedocs/jupyter_execute/486b4fae6e599adc0c8bdce07b379475fc92dc6a22415e5b94705437c75588b3.png
copying images... [ 31%] ../_readthedocs/jupyter_execute/eeb0653d95013989aa1b7ee46828634e0c8b6b0986a0cc33b8d5dbe8d5996b30.png
copying images... [ 31%] ../_readthedocs/jupyter_execute/59d88b19dec14c20c6a54bbbdd29f6ed504dbd194b950c4a110d0c822137ade1.png
copying images... [ 31%] ../_readthedocs/jupyter_execute/0c6d4195d19a39ad2ac081136ad90cb848a6da29f81b06f72b7c82aa80ea9f2c.png
copying images... [ 32%] ../_readthedocs/jupyter_execute/651cfdb470bfbd2326d31865d359a62d8d959aa466ca2f63bb94fb6c321040c5.png
copying images... [ 32%] ../_readthedocs/jupyter_execute/7c168ae28a9840611590d3ad58b410b693b51e46f830cda886e2f99469ce8fd4.png
copying images... [ 32%] ../_readthedocs/jupyter_execute/081683db6a39c4abde3740c8cd84b316d79cad738ea30fe1ce3c0620f12f9637.png
copying images... [ 33%] ../_readthedocs/jupyter_execute/da0b4d5292de18d09c20ed43ef7633d9ba072045d3b2974b0ea8bbfb3cc5ffcc.png
copying images... [ 33%] ../_readthedocs/jupyter_execute/4416ae5fc46bbd5d02b02799ee3ddda64902b988d8d24a952d7698c7299277bd.png
copying images... [ 34%] ../_readthedocs/jupyter_execute/1d6e7e52ed4e9190b1a67aa5b3a65b3503013052f5ed5553403f98d1cb06cdba.png
copying images... [ 34%] ../_readthedocs/jupyter_execute/865e89925a12beab888d33e5716886fc688908b99fa93b35435c6ac102405c14.png
copying images... [ 34%] ../_readthedocs/jupyter_execute/2cf1ba79af276b658202deef3e4210c296d0e7fd6ad65f07dff40c48987ce5ef.png
copying images... [ 35%] ../_readthedocs/jupyter_execute/d199bf9408916eb70e6ddb841b7dc6f802334c8f93961cf5c2a99fd54cd24ef9.png
copying images... [ 35%] ../_readthedocs/jupyter_execute/efa37ab2f92d2b8b2f4dd1e25cd6ff9660087032f476c162c5c1e804e3198f3a.png
copying images... [ 35%] ../_readthedocs/jupyter_execute/e78d140b7896dda646c984f48653a5376417e4c28575aab9a0905d53dccbc9c1.png
copying images... [ 36%] ../_readthedocs/jupyter_execute/d1eebe95caa260c40f89bf9e8819c2dc48a3233329f819738277c8e0ef8c4ec6.png
copying images... [ 36%] ../_readthedocs/jupyter_execute/2b356b583aa88252c2fc18d54bfac7849e5cdbb99c8101df6e4f16dffaa12c80.png
copying images... [ 36%] ../_readthedocs/jupyter_execute/861b5ceaa4cdf231f6683610222a998453f994044750adc0a538dca4ae8ab775.png
copying images... [ 37%] ../_readthedocs/jupyter_execute/5137a445364556b183291a0069ff67b30eca0bc7ac814b4b91ce3ed59102e7a3.png
copying images... [ 37%] ../_readthedocs/jupyter_execute/6dd0ab29cd40f5bd5da9fbc62c5440295f55a740f5850b805841588f98938066.png
copying images... [ 38%] ../_readthedocs/jupyter_execute/2c5a4aab65279d1fbb6c7d7b8df200261693cbc5acb9d64c62acfb1f95b46837.png
copying images... [ 38%] ../_readthedocs/jupyter_execute/2fc1eedecb3bbedb7e197eed2cfb02a92080bb661a360241bb0d1a8bae9d46f6.png
copying images... [ 38%] ../_readthedocs/jupyter_execute/07f5dbbb7c79f153c7cd1d676e24c72b36e8347b369072f7d751fe8c5c7b434d.png
copying images... [ 39%] ../_readthedocs/jupyter_execute/f2d53d127b4bd5ed62ef629ecf4bb438fa264b5e142809f69d0f2458e151ee50.png
copying images... [ 39%] ../_readthedocs/jupyter_execute/adbdc0f2413270e8db74218ad4af9d73b872759dcf78a26d598922433343cde0.png
copying images... [ 39%] ../_readthedocs/jupyter_execute/740afa4ec3e68d88942e2de74ce868ca4306e09f97d9be023bb662769b6f0a31.png
copying images... [ 40%] ../_readthedocs/jupyter_execute/504e65d4d15aa127a9bb04c30daec818440418ee2c3345874dab91afd1d3f688.png
copying images... [ 40%] ../_readthedocs/jupyter_execute/38b04efe0ab3288cc5e15e030b63ba4c80ab0926ebcf1dc47435947510c0f0e2.png
copying images... [ 40%] ../_readthedocs/jupyter_execute/57c9d1c99a09f135f58f96f041a93271957ddeb1b610774a52c60e2969dd44e3.png
copying images... [ 41%] ../_readthedocs/jupyter_execute/a6826a9d47a447ccaadd639b3e6947880c921b863503752ded5ae98bd86f90ad.png
copying images... [ 41%] ../_readthedocs/jupyter_execute/e2937b6300af75a3a78bd50b97013f32898dffeb42b808138c2096b7a4be0fd3.png
copying images... [ 42%] ../_readthedocs/jupyter_execute/a71177da4a3b277b07b100e5afee095e83eb76164099780927efc749d03dd03b.png
copying images... [ 42%] ../_readthedocs/jupyter_execute/c02881da3f09ca9f25c58fffd95b27c0a7ce40a8948f33b9f19eea055accde29.png
copying images... [ 42%] ../_readthedocs/jupyter_execute/b169ad1f76731ee06bbd22d03d3e2c15b96e3b4722e13b307ea1984a1197f977.png
copying images... [ 43%] ../_readthedocs/jupyter_execute/b800985f889f1dafa10e4a258a4c69268ee7c37ac3a0bb03f165562a73e2e04f.png
copying images... [ 43%] ../_readthedocs/jupyter_execute/52ba7889fd560e19c87e3b2ef1bd3b0234de4cd9caa0d5faaa7fd3bd4b21d127.png
copying images... [ 43%] ../_readthedocs/jupyter_execute/92194f2b37e09a31b833fa795bf4e2ab0c191e2848e9e6d827b2703bb403b43d.png
copying images... [ 44%] ../_readthedocs/jupyter_execute/f387627c70c92b7ff2e6038c5072f648bdb9373bbdc385cb757d19ed643d5f7f.png
copying images... [ 44%] ../_readthedocs/jupyter_execute/a8968ca63b7862776270e23a5d986a56283ea6d70aa915c13130d0cf3c4e94ed.png
copying images... [ 44%] ../_readthedocs/jupyter_execute/ae3f2ea259fc5151ab429224e027e6eec5517a0f6b807297a8011cbd587d303a.png
copying images... [ 45%] ../_readthedocs/jupyter_execute/64a6d47221dc1db38ca03c235891d75c636e6c9d4b9ce391ab83be5384cf026a.png
copying images... [ 45%] ../_readthedocs/jupyter_execute/40f7d98f707439e8f9b35ff53e2794e460b0d3a1801c9a17d67483d7f13aba4d.png
copying images... [ 46%] ../_readthedocs/jupyter_execute/1e16af26eb54038d48e731cb94ee1ebc55d44f224ec8a22ff4c4effc3d91ba17.png
copying images... [ 46%] ../_readthedocs/jupyter_execute/67f8c032d4427ee38de513f59fb3752cea2a77a2e75071bf7d6acbaa383b63cb.png
copying images... [ 46%] ../_readthedocs/jupyter_execute/4ac99490c9b853f2d3352bff5b903bab9bd3408496f800c2f237eb9883b489a6.png
copying images... [ 47%] ../_readthedocs/jupyter_execute/62aed4305c66c941cc8065ed8e54d4684eb7cc948a124bb08531304a219cfd3f.png
copying images... [ 47%] ../_readthedocs/jupyter_execute/25b4dcf77d06fb425fad8a9424c7d361e30724ed395552d7318f31a577091295.png
copying images... [ 47%] ../_readthedocs/jupyter_execute/aa6d723e590c9d6149883b8906df0235564ce5951df38ae2a5ce14ffe3a52eaa.png
copying images... [ 48%] ../_readthedocs/jupyter_execute/572800a6e137744cdfeff49c7487d89d9bbf98ba527cd5693456370f6601e1a3.png
copying images... [ 48%] ../_readthedocs/jupyter_execute/2267781c7a5380f9b036365bc89e8d65610cc3a6ebc00e412bbf57949f2cbf84.png
copying images... [ 48%] ../_readthedocs/jupyter_execute/8ce22d00618f95f6fb7566ec8535864f591c14611b2f804e96758ce666796109.png
copying images... [ 49%] ../_readthedocs/jupyter_execute/011e78a639f1a241f375117fd321855f232688e9e9c91eb30a0acd8e6244bd4f.png
copying images... [ 49%] ../_readthedocs/jupyter_execute/f69e7b4a7d727d39254cecb5dbb0e94173e08e2c5fd84568acfc26e2dc0152ac.png
copying images... [ 50%] ../_readthedocs/jupyter_execute/2acc7599c8748508319cf48509ea4d9711d81246b6a9badf8a23ef7adcc05df0.png
copying images... [ 50%] ../_readthedocs/jupyter_execute/407eb0c191b94e49862f7eabd2ef032ed6e2d2e22b41294046dad1174ecb04a0.png
copying images... [ 50%] ../_readthedocs/jupyter_execute/52fefef374a98bfc46f34bed98f769d176d5c68924627b16763d25540e300e55.png
copying images... [ 51%] ../_readthedocs/jupyter_execute/c896044ab9112ea84486a06379fbd8fe520fc63b2da957fbc3e6f88d2e1dc1e0.png
copying images... [ 51%] ../_readthedocs/jupyter_execute/021d1003cbdbbad8a681835ca2d8750436dd6b8b1073d0d2209d5763d30530ea.png
copying images... [ 51%] ../_readthedocs/jupyter_execute/c19415bb12e67ca01b5de62f4f8d9806a7aced8662092a4df0ac75b04c2c4ef5.png
copying images... [ 52%] ../_readthedocs/jupyter_execute/f22e3f72784fd7bfac50b93602bccb6417a552eb4eaed14c3bbc966acd868fd7.png
copying images... [ 52%] ../_readthedocs/jupyter_execute/a4b9d8093019822c9418045cd0db3ebae0bef2399edd07c50bd0968b3638fb9a.png
copying images... [ 52%] ../_readthedocs/jupyter_execute/7789da93c99bce2b7e9af885a3191ae3926f2845efa3d5727b553c2ed812a60a.png
copying images... [ 53%] ../_readthedocs/jupyter_execute/655fa866fca72282db9a45e94957876f8b1414c82a637382f094bda928ffd141.png
copying images... [ 53%] ../_readthedocs/jupyter_execute/601657ef351c7e336e548bdbcae76880d7241197808cd887c55ccd2ee17e1ee6.png
copying images... [ 53%] ../_readthedocs/jupyter_execute/fa17550ad5d27d3eb2b5b797633a042cf6a9071b01cc2f8d22cccf0d4b12e69d.png
copying images... [ 54%] ../_readthedocs/jupyter_execute/d0b7857b6695d10c5d46792bfddbde92478c4a213f780f30331daf5a73511994.png
copying images... [ 54%] ../_readthedocs/jupyter_execute/afbb90bb5e072d2010a7e46e4b5cc33435d597ece4007c1bf69002ec56478889.png
copying images... [ 55%] ../_readthedocs/jupyter_execute/6343578116aa55bc8545845d7f8b9ba1ab567eeba70493d92c21d2490ae3e912.png
copying images... [ 55%] ../_readthedocs/jupyter_execute/1816927d44f18f95ca2c9fa15ffdc6f11f114045c581413a5d3ef3a987b8ce99.png
copying images... [ 55%] ../_readthedocs/jupyter_execute/8f2a8dbabb88e62f021c906fb7c3155991da1f0284c8be3b1cf978fe79e343a2.png
copying images... [ 56%] ../_readthedocs/jupyter_execute/5c9fc9efde217b5dbe37f2a152ec754f8826ed06e43bf617c7b395de0a158fef.png
copying images... [ 56%] ../_readthedocs/jupyter_execute/aa7927dc47e77e524448715687eaaa4391dcf0646088dfcefac13a54bce8df79.png
copying images... [ 56%] ../_readthedocs/jupyter_execute/17870f1708e80c042ffde63114d8c2e420d954fc1930f69d173da22a081717e3.png
copying images... [ 57%] ../_readthedocs/jupyter_execute/a67384043b1a315c6df9c8bf9ecc0d7cabf0a729398be8f70701166a19ba8d67.png
copying images... [ 57%] ../_readthedocs/jupyter_execute/6969ed239aba47e872a0947bc97407fce1b3e76aa2f2e6d101d26993ecfb7e32.png
copying images... [ 57%] ../_readthedocs/jupyter_execute/ec60708d94166fb9f35e8a74c4963ced76e7a59f74fff84562e8889137503b67.png
copying images... [ 58%] ../_readthedocs/jupyter_execute/3f664f9ca6fd8a53995bbca403748df003bba95dd5343f401d027589c8a58116.png
copying images... [ 58%] ../_readthedocs/jupyter_execute/88035d1592e6817b888d997ff02de62520c4496206968b8f93c7d373a30f5113.png
copying images... [ 59%] ../_readthedocs/jupyter_execute/73d5ac19ecf35199f9c4a2de1da58f4a640aba4c564c5935267654a0a287f5a9.png
copying images... [ 59%] ../_readthedocs/jupyter_execute/43ea4e9a1d33e1d4fa6bf854a7acd69673392d9d383f3edfcc2f522e763422cb.png
copying images... [ 59%] ../_readthedocs/jupyter_execute/de27a29bda7cd4ff5d997ad452eba37f697c39615cd39e272dd8691ed5d868bf.png
copying images... [ 60%] ../_readthedocs/jupyter_execute/781af9f8702018baa7e2d827037977e7b5b8468d26d5b09d59ccd8b59850f555.png
copying images... [ 60%] ../_readthedocs/jupyter_execute/4f60972e3185dc184d9533cd917873063a559cd0dfad26ad5597a959382a4fcb.png
copying images... [ 60%] ../_readthedocs/jupyter_execute/a600e85a4c337bf362817cabaa58da048ac6fdbe7c7265ab79cbf204cc7ed32d.png
copying images... [ 61%] ../_readthedocs/jupyter_execute/7719e9c4b0cd099ec336f131f729b6b5b87ea7e48389f91262a9a74574f303ff.png
copying images... [ 61%] ../_readthedocs/jupyter_execute/1281d7d24f0e6f26c4d6f9c72776fd28cadac7a7d33d6dc2ab9266e86e93ede7.png
copying images... [ 61%] ../_readthedocs/jupyter_execute/23eb91df75e5953fd0b15a7b5ab3ccb98a5b179a4fef599df59d940dbe0ac5a4.png
copying images... [ 62%] ../_readthedocs/jupyter_execute/2e91d68923cc357db8fccfcba3ca1bd95c3b6a2150c3ce6b35ba8bdcb140f765.png
copying images... [ 62%] ../_readthedocs/jupyter_execute/e6c73b711ff1ec19713a2327eb0f0e06ba8e081c2f840e1e28dd70d7cca08241.png
copying images... [ 63%] ../_readthedocs/jupyter_execute/13b52ba4d074507c2163c3ed7adb9c9ebe7e40c5faf9c2bcd1eaa85ebfb15eec.png
copying images... [ 63%] ../_readthedocs/jupyter_execute/97eccdbdbe8404656f87c28674694bc0a29a311821820a2cebb7d1eda7a3f8ff.png
copying images... [ 63%] ../_readthedocs/jupyter_execute/b26d08b6c1be29f6f4cb6276fbc1dcd9c066e744da32f03adf68b1a6105393db.png
copying images... [ 64%] ../_readthedocs/jupyter_execute/86aa83938fa64194d326c8a4ae08797378dc218267bd706c66c5a3e5c22dde78.png
copying images... [ 64%] ../_readthedocs/jupyter_execute/8b412280e1a080da76498f69949b04178ab6df4634365aa0fcb1712c92c03f08.png
copying images... [ 64%] ../_readthedocs/jupyter_execute/04f356e5e51e60cf8cca413d05f07fa14f282e0784f4f17541954b917dbb7ccc.png
copying images... [ 65%] ../_readthedocs/jupyter_execute/7c21a24633f9dbd1cb500d8e36288505d07acf93bf0579ab7a8b69ed17766feb.png
copying images... [ 65%] ../_readthedocs/jupyter_execute/4db77fe2b5b6c9b7eb989d4826f748236730537fd283e1eb4f1dfcf6cf248d37.png
copying images... [ 65%] ../_readthedocs/jupyter_execute/7985bedba6efb444956007a3e48dd032dab90f54048cab87444c14307aa7efd8.png
copying images... [ 66%] ../_readthedocs/jupyter_execute/0825f5ef74af6920e1f78086e86bc6fb67294bcf9ac735a6924ade9a83382d3b.png
copying images... [ 66%] ../_readthedocs/jupyter_execute/f092ddb9be38b04c110c8dcc12c13cdba89914b83ac172b4ac02d6da37ecc810.png
copying images... [ 67%] ../_readthedocs/jupyter_execute/0b9c4e9149097de19fa696abf3b20b7a8714e6488f408b04c21808fcc016939f.png
copying images... [ 67%] ../_readthedocs/jupyter_execute/4417033b5966dca87578910b7fc2334a00fb7f2d4350316ffe1bb938d957513e.png
copying images... [ 67%] ../_readthedocs/jupyter_execute/0bd7b21b63e4a88f40b5f940bf88605b463b76e214d9e71ea79ebab7d2beac3b.png
copying images... [ 68%] ../_readthedocs/jupyter_execute/f8253efe1869e2f75adfdf9ac64d6eaf0d8c37851e28c2454e372f0e85ff35b0.png
copying images... [ 68%] ../_readthedocs/jupyter_execute/397127b7f1241325f1d4b8af6accca9ab1678d36e8faf5689d0f1c63428409d6.png
copying images... [ 68%] ../_readthedocs/jupyter_execute/aaf990d76857ed90295cabb7979a0a6aa75d367976c5fefee745c031c04f42d8.png
copying images... [ 69%] ../_readthedocs/jupyter_execute/ecb8aa7cbb94fd7a0b07331b564e71b9373e0eb22002b4880e398784ab5803ce.png
copying images... [ 69%] ../_readthedocs/jupyter_execute/ff56caf2df62bc25222aac46522be28ae4dc2cce8da3df8605d9137622e3a1ea.png
copying images... [ 69%] ../_readthedocs/jupyter_execute/7618bdeee83d489da770b2705ce2c7a3f1464370c72da34b901e70635c47a48d.png
copying images... [ 70%] ../_readthedocs/jupyter_execute/bbe7fc09e16e1b4974bd2de1bcc6ca4568dfa8125d1214179d0ab0fb15e1db55.png
copying images... [ 70%] ../_readthedocs/jupyter_execute/be54264da202c6cf6857ff1310039c3381caf924b311ca0c6cc50365cb90aa78.png
copying images... [ 71%] ../_readthedocs/jupyter_execute/be51f0c4e33ee1db76c28a953f6f0fb417d7f51516f4f6a2118a5e78ab482f90.png
copying images... [ 71%] ../_readthedocs/jupyter_execute/6a52afb4202441fc68152e7b08d56cce3b4538806049309b9f177acd063fbca2.png
copying images... [ 71%] ../_readthedocs/jupyter_execute/839492908199287e24a29fade6b31a1fe95052f6d9fb6ca9b6b4cc7061bf547b.png
copying images... [ 72%] ../_readthedocs/jupyter_execute/53f0d6ca5e1e0988f7aedee5f29ed626dcc9023295d74811cdbb9212eee983e2.png
copying images... [ 72%] ../_readthedocs/jupyter_execute/dda832f87913e3db1cd4cd8e76c547b0cd5aa51de6de0fd5c40e04d77369e320.png
copying images... [ 72%] ../_readthedocs/jupyter_execute/5261e831ba693cd17cc14891cc2492b6659b34e0d67d177da606be08cafbdc76.png
copying images... [ 73%] ../_readthedocs/jupyter_execute/c29268d379a703bea33631b3c80c14123127bddc35d4ab4f7fe9a8e17c801787.png
copying images... [ 73%] ../_readthedocs/jupyter_execute/97bc3900a747c7199ee9ca388aff6bcae0e6065f5bd83d68856a343be28e83fa.png
copying images... [ 73%] ../_readthedocs/jupyter_execute/9603b7088fb2ddaac67db7f0c5808eb96daa6de1f1d8e0c6edb343e0647f9bcf.png
copying images... [ 74%] ../_readthedocs/jupyter_execute/4d04994ad30d036eb77b7a90f30d9b76587cd232cb08fcdab7c1e3b08a60db7f.png
copying images... [ 74%] ../_readthedocs/jupyter_execute/bf42b31ae17c7f42f5fbf83eb7bdb14b0302b682d1c732e790acab8e5fa04d64.png
copying images... [ 75%] ../_readthedocs/jupyter_execute/51c0c81b956d1bf5c1a52e5fc778279c5cc0e3ea918592b7b79afca3e9e7ef7e.png
copying images... [ 75%] ../_readthedocs/jupyter_execute/169adcd24ee47379e1ddac815791929e254b37506d50f6532614c3e45a9498f8.png
copying images... [ 75%] ../_readthedocs/jupyter_execute/6049597d2e5db7fade096c1df78349008d83450e9ac4b7200137a86e63c2f974.png
copying images... [ 76%] ../_readthedocs/jupyter_execute/4a931861464d8b9f9d72de734ffefb86e0d0353dfdaee51837df0ed839128317.png
copying images... [ 76%] ../_readthedocs/jupyter_execute/b5052bba1689bbf3564a4aaed52203967c803b492923ab6a0abf6c6015f5388f.png
copying images... [ 76%] ../_readthedocs/jupyter_execute/846016df9800a06e75d75b51e640fdaba1a61de8fbe6032d8baeabecfb2b9f8b.png
copying images... [ 77%] ../_readthedocs/jupyter_execute/cdbcbfdc10df1a55d4e6ed5befd7b1d35bc2cf4adef1efba1e94d800d2edd216.png
copying images... [ 77%] ../_readthedocs/jupyter_execute/7fbb52a51f56e7e3d97cda1051ab1112c816cbb45f2cafb185d5a878e86ce8ff.png
copying images... [ 77%] ../_readthedocs/jupyter_execute/f695dd1adcdc19f616d98f61f4d546941592d02fc07e5826629dbcb74f0977ac.png
copying images... [ 78%] ../_readthedocs/jupyter_execute/3961c14c60d52151b7b3af049fd2bb2d7de38fb06015dc14cd9753fff3fb18e7.png
copying images... [ 78%] ../_readthedocs/jupyter_execute/82522d015eb9c6a9d24cb3e3124cde4ad5b889d960fc4860dceea68293f85ca0.png
copying images... [ 78%] ../_readthedocs/jupyter_execute/73d29e69edf5338f74ae1268832b917a29ae5e8030d9de573a79569d2f0dce65.png
copying images... [ 79%] ../_readthedocs/jupyter_execute/7d7668bd238094eb7ef33514c35d265b0d494023bae6e27e48a45fc43c0d04cb.png
copying images... [ 79%] ../_readthedocs/jupyter_execute/ef7df478409d348d78082f7a48ac9666ca2500096f809664c27cc7ffb17c43e4.png
copying images... [ 80%] ../_readthedocs/jupyter_execute/f3a6ebca0709f866c4403bdaff46233abddf73ac5c717169ea2bffd3acf6e2a1.png
copying images... [ 80%] ../_readthedocs/jupyter_execute/7fc866dcb4bcc6f8c47570d8361201546a69e523bcb60aeaf40ae494c5c51db0.png
copying images... [ 80%] ../_readthedocs/jupyter_execute/8e1d7e535b6e41170e2e24bc828361bd9b4b4ca2ececb0577ed163188cf04c80.png
copying images... [ 81%] ../_readthedocs/jupyter_execute/2a08fca9f3852e53baacf72e8984e3a53e9565ab6df1173a1c97ca74dad64f1a.png
copying images... [ 81%] ../_readthedocs/jupyter_execute/bcd58ff2174798c3c40c6ed49c48b6d9ca3d5f479d57696475693e5d0800bce0.png
copying images... [ 81%] ../_readthedocs/jupyter_execute/628f6bb98a3f0351d445e545447637c2e6113b1a9be30fdb49fd8f0a1f4ef734.png
copying images... [ 82%] ../_readthedocs/jupyter_execute/92685adabb98c3db81ca567b860aeac8ee6dd7a695a9652f1335a2cc96bfae3c.png
copying images... [ 82%] ../_readthedocs/jupyter_execute/e2ce38c65be3d9c6b637e5a67942dce7bafb297f0f1b777617be590a055cfef8.png
copying images... [ 82%] ../_readthedocs/jupyter_execute/a5a8ba4ba2d14b2bc53ccaf21dfae211387244007cf158606fd3bf09d143df6e.png
copying images... [ 83%] ../_readthedocs/jupyter_execute/0f8a1d79fe2ddc7440f137a9e63e100627cde5690ea5b048eedd9020deb98120.png
copying images... [ 83%] ../_readthedocs/jupyter_execute/d35549b76805d3994432a0ad27387365c2476b374a20436237adda8b5498a536.png
copying images... [ 84%] ../_readthedocs/jupyter_execute/6aa0c661fde8522fa174abc83c63ba65dbeaaeaa954cde751ae38c3d1b910e22.png
copying images... [ 84%] ../_readthedocs/jupyter_execute/04a645201b72e801a3278ac9a4c381e35dc3754f89031c89a31ee48e09509af5.png
copying images... [ 84%] ../_readthedocs/jupyter_execute/e3f2ae5b1885d05a454605d2db9589547ef38fb5d29b0b0cd7cbbbedad8faacf.png
copying images... [ 85%] ../_readthedocs/jupyter_execute/7521a77aa731621602b80cfeb220a5190b53cad5980ae8f60b79c0b4f232c59c.png
copying images... [ 85%] ../_readthedocs/jupyter_execute/f931b64515e36f97e785c412ee7700d4c509f7d6355875ee081f4846119fa3df.png
copying images... [ 85%] ../_readthedocs/jupyter_execute/3736c0a4d08a5ee075a7ea70e259ed41e4d69d7ec255c10dd4199507a0a453d8.png
copying images... [ 86%] ../_readthedocs/jupyter_execute/e46c28102dbecf8be10b7084e46d8f0601ac7f08733ba7b78835d59728dfc5c4.png
copying images... [ 86%] ../_readthedocs/jupyter_execute/8af8c9cd8169df5f211f59c780163aff7d2ecace2bf7ab138238f9ebce90dbd8.png
copying images... [ 86%] ../_readthedocs/jupyter_execute/bf1e67ba2865d7e1473fa478ca0b9caab1d876096b39b49fad589a3986581326.png
copying images... [ 87%] ../_readthedocs/jupyter_execute/d5725796924b2b66e8c4ec9f5f51174f51bd42e56ee11d51d18b5d497d04da9b.png
copying images... [ 87%] ../_readthedocs/jupyter_execute/35cc5d9902f2b37b897765be7c9e364153151355dd8b679e892e4c5f846d1593.png
copying images... [ 88%] ../_readthedocs/jupyter_execute/53e5d91d91d28e94a586cdf15f364f81b5887c3a52f388eea135dfb1c005a4c4.png
copying images... [ 88%] ../_readthedocs/jupyter_execute/74c70fa041964807c51402dd1851ef58623a275027cc12dabbbfb6a77ec088e6.png
copying images... [ 88%] ../_readthedocs/jupyter_execute/68def390a95c772fff85be0b8592d40e69ed596c929ec89d8d0165b248dffb4a.png
copying images... [ 89%] ../_readthedocs/jupyter_execute/fd3d769b3c4d80143228147f8514ea3a90cb9815b32906ba0a6f5abc91a4e17e.png
copying images... [ 89%] ../_readthedocs/jupyter_execute/acee682c0d0cc21e182d5a0642cbed568938f659ebd6062f856f0ce5387dd331.png
copying images... [ 89%] ../_readthedocs/jupyter_execute/7f25c4204dbe12e4d961412943f62ef74723cda61a7d26372fb30c32b86e239b.png
copying images... [ 90%] ../_readthedocs/jupyter_execute/fcd4c779908b2b1a58297f2b306eced1e8fb377cad94acf6ef47c427fd3c2411.png
copying images... [ 90%] ../_readthedocs/jupyter_execute/c42802a1caae0d9ddcd1cf206384af44be8c3841ff03ded0c71fbdce60d2f1a5.png
copying images... [ 90%] ../_readthedocs/jupyter_execute/327c5e93600a7df085b78816a73e0aed8b42a0f7e06f9e380d97c4f1b3cdf212.png
copying images... [ 91%] ../_readthedocs/jupyter_execute/6f3a3370cd34b07dc6053d56879911358649be9ce01c90ea858f595879ab6a58.png
copying images... [ 91%] ../_readthedocs/jupyter_execute/88fde293a58133755a4c07b39d925fa21d625c9479792d070e4b8058f75b398c.png
copying images... [ 92%] ../_readthedocs/jupyter_execute/63cb311e3b6b322fd3ae318d37a968c371b6705e465787a11847d0b9ffcb262a.png
copying images... [ 92%] ../_readthedocs/jupyter_execute/8a2add2641febe81a4f51c4ec1a62b7bbbf5fe39585c824074d13aa40b6492f7.png
copying images... [ 92%] ../_readthedocs/jupyter_execute/77908aa8da20d7313c7086d7494e8b2405cafb83dcafbcb219ae50d70770dda0.png
copying images... [ 93%] ../_readthedocs/jupyter_execute/76a0cb815b7786864bf888d7b9ef971fffdcc14e8fe6128ce9a67a410bb6d823.png
copying images... [ 93%] ../_readthedocs/jupyter_execute/56b34842722fa1513975dcb37435bbb78a73e388dcf226524eb08266f589a6ce.png
copying images... [ 93%] ../_readthedocs/jupyter_execute/dd0f349c4576a687d647a389536353b4591dd91b68f6841f660852df76b833cf.png
copying images... [ 94%] ../_readthedocs/jupyter_execute/09e42930c1b3b87f5470762ac43418dc8258c0ee0e4754d55f567a8df3c2c686.png
copying images... [ 94%] ../_readthedocs/jupyter_execute/f3f2556462fa208576e4105c0990b01ed5f62ceb8cd0417983c8264ff497192b.png
copying images... [ 94%] ../_readthedocs/jupyter_execute/f5436d7982d4d648cd4d1e1e6f3283332833168cdb71c2787bb24e92c6aea47e.png
copying images... [ 95%] ../_readthedocs/jupyter_execute/d3568d4999db5293e3f8c01c409bdebfa426f2ebc02dbe87a2eacaabc43c6387.png
copying images... [ 95%] ../_readthedocs/jupyter_execute/d38084d6b8bfe2b740495e415be42b8ec92fadcac5e0f7623d93289fe54d59a4.png
copying images... [ 96%] ../_readthedocs/jupyter_execute/44b8fd2671e0858c778f5b3c83d34cf81e436f4b9d0791d51f539cfd870fe4b0.png
copying images... [ 96%] ../_readthedocs/jupyter_execute/bce9a915b8a1cd592dbc510f489b1266bfd8d6db507fbf7ddc0663522c839d68.png
copying images... [ 96%] ../_readthedocs/jupyter_execute/4ae8cd6b5ff5f117f98702df007b86761818ad6dc8fadbdc2c2038d696931b68.png
copying images... [ 97%] ../_readthedocs/jupyter_execute/9a0db0720b669e56949e1410761fa298e9dca65cd57a973f570e9b457feac727.png
copying images... [ 97%] ../_readthedocs/jupyter_execute/069ead95a68747bfd6dee6f8151bb0fc74bf4bfe2ab6db2632f86577ac44e7f5.png
copying images... [ 97%] ../_readthedocs/jupyter_execute/b9730f9381e8f22951364c5d95201054765d88ee51f89e8931757eb0a0fb3ae6.png
copying images... [ 98%] ../_readthedocs/jupyter_execute/780bc8f66e3c4c204005b30fc6b64a6f24101b14004cd04faa87f60e101408aa.png
copying images... [ 98%] ../_readthedocs/jupyter_execute/0b21a805ce850cf069ca37234d41b27f7ca1d9a4177403d6a2e431cfcefc6189.png
copying images... [ 98%] ../_readthedocs/jupyter_execute/4961dfebe54dbb86dfeddc974201c04fe644ca76cb707f14366eb25ba32558e1.png
copying images... [ 99%] ../_readthedocs/jupyter_execute/6c6b762975a6bee0b60ef0c4624f06a58cd738ec468ed3415c38efdd61b98972.png
copying images... [ 99%] ../_readthedocs/jupyter_execute/56c6302e6daa092f9f9ab1ce7e94582374b4c0b5f0abb278394cde4c296ebec1.png
copying images... [100%] ../_readthedocs/jupyter_execute/5119a748fccea79b64c2f078212604da9757595bc43551a0728f0f91e72aaf34.png

copying static files... done
copying extra files... done
dumping search index in English (code: en)... done
dumping object inventory... done
build succeeded, 19 warnings.

The HTML pages are in ../_readthedocs/html.
Updating searchtools for Read the Docs search...