Read the Docs build information
Build id: 2548202
Project: icb-scanpy
Version: 3289
Commit: 1a96f6e4c3a16ec643fa76c9d049e70d7b0bf5d8
Date: 2024-10-15T18:04:03.702331Z
State: finished
Success: True


[rtd-command-info] start-time: 2024-10-15T18:04:05.167743Z, end-time: 2024-10-15T18:04:06.262541Z, duration: 1, exit-code: 0
git clone --depth 1 https://github.com/scverse/scanpy.git .
Cloning into '.'...

[rtd-command-info] start-time: 2024-10-15T18:04:06.376819Z, end-time: 2024-10-15T18:04:06.997132Z, duration: 0, exit-code: 0
git fetch origin --force --prune --prune-tags --depth 50 pull/3289/head:external-3289
From https://github.com/scverse/scanpy
 * [new ref]         refs/pull/3289/head -> external-3289

[rtd-command-info] start-time: 2024-10-15T18:04:07.159716Z, end-time: 2024-10-15T18:04:07.367368Z, duration: 0, exit-code: 0
git checkout --force 1a96f6e4c3a16ec643fa76c9d049e70d7b0bf5d8
Note: switching to '1a96f6e4c3a16ec643fa76c9d049e70d7b0bf5d8'.

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 1a96f6e (fix): update fixture creation

[rtd-command-info] start-time: 2024-10-15T18:04:07.461511Z, end-time: 2024-10-15T18:04:07.525260Z, duration: 0, exit-code: 0
cat .readthedocs.yml
version: 2
submodules:
  include: all
build:
  os: ubuntu-24.04
  tools:
    python: '3.12'
  jobs:
    post_checkout:
      # unshallow so version can be derived from tag
      - git fetch --unshallow || true
    pre_build:
      # run towncrier to preview the next version’s release notes
      - ( find docs/release-notes -regex '[^.]+[.][^.]+.md' | grep -q . ) && towncrier build --keep || true
sphinx:
  fail_on_warning: true # do not change or you will be fired
  configuration: docs/conf.py
python:
  install:
  - method: pip
    path: .
    extra_requirements:
    - doc
    - dev  # for towncrier
    - leiden

[rtd-command-info] start-time: 2024-10-15T18:04:07.691534Z, end-time: 2024-10-15T18:04:08.098978Z, duration: 0, exit-code: 0
git submodule sync


[rtd-command-info] start-time: 2024-10-15T18:04:08.198001Z, end-time: 2024-10-15T18:04:23.867842Z, duration: 15, exit-code: 0
git submodule update --init --force --
Submodule 'notebooks' (https://github.com/scverse/scanpy-tutorials/) registered for path 'notebooks'
Cloning into '/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3289/notebooks'...
Submodule path 'notebooks': checked out '3385df77ce0f63987104bc644562a811c5d1b441'

[rtd-command-info] start-time: 2024-10-15T18:04:23.967379Z, end-time: 2024-10-15T18:04:26.694490Z, duration: 2, exit-code: 0
git fetch --unshallow || true
From https://github.com/scverse/scanpy
 * [new tag]           0.0         -> 0.0
 * [new tag]           0.1         -> 0.1
 * [new tag]           0.2         -> 0.2
 * [new tag]           0.2.1       -> 0.2.1
 * [new tag]           0.2.3       -> 0.2.3
 * [new tag]           0.2.3.5     -> 0.2.3.5
 * [new tag]           0.2.4       -> 0.2.4
 * [new tag]           0.2.5       -> 0.2.5
 * [new tag]           0.2.6       -> 0.2.6
 * [new tag]           0.2.7       -> 0.2.7
 * [new tag]           0.2.8       -> 0.2.8
 * [new tag]           0.2.9       -> 0.2.9
 * [new tag]           0.2.9.1     -> 0.2.9.1
 * [new tag]           0.3         -> 0.3
 * [new tag]           0.3.1       -> 0.3.1
 * [new tag]           0.3.2       -> 0.3.2
 * [new tag]           0.4         -> 0.4
 * [new tag]           0.4.1       -> 0.4.1
 * [new tag]           0.4.2       -> 0.4.2
 * [new tag]           0.4.2.post1 -> 0.4.2.post1
 * [new tag]           0.4.2.post2 -> 0.4.2.post2
 * [new tag]           0.4.3       -> 0.4.3
 * [new tag]           0.4.4       -> 0.4.4
 * [new tag]           1.0         -> 1.0
 * [new tag]           1.0.1       -> 1.0.1
 * [new tag]           1.0.2       -> 1.0.2
 * [new tag]           1.0.3       -> 1.0.3
 * [new tag]           1.0.4       -> 1.0.4
 * [new tag]           1.1         -> 1.1
 * [new tag]           1.10.0.dev0 -> 1.10.0.dev0
 * [new tag]           1.10.0rc1   -> 1.10.0rc1
 * [new tag]           1.1a1       -> 1.1a1
 * [new tag]           1.1a2       -> 1.1a2
 * [new tag]           1.2.0       -> 1.2.0
 * [new tag]           1.2.1       -> 1.2.1
 * [new tag]           1.2.2       -> 1.2.2
 * [new tag]           1.3         -> 1.3
 * [new tag]           1.3.1       -> 1.3.1
 * [new tag]           1.3.2       -> 1.3.2
 * [new tag]           1.3.3       -> 1.3.3
 * [new tag]           1.3.4       -> 1.3.4
 * [new tag]           1.3.5       -> 1.3.5
 * [new tag]           1.3.6       -> 1.3.6
 * [new tag]           1.3.7       -> 1.3.7
 * [new tag]           1.3.8       -> 1.3.8
 * [new tag]           1.4         -> 1.4
 * [new tag]           1.4.1       -> 1.4.1
 * [new tag]           1.4.2       -> 1.4.2
 * [new tag]           1.4.3       -> 1.4.3
 * [new tag]           1.4.4       -> 1.4.4
 * [new tag]           1.4.5       -> 1.4.5
 * [new tag]           1.4.5.1     -> 1.4.5.1
 * [new tag]           1.4.5.post1 -> 1.4.5.post1
 * [new tag]           1.4.5.post2 -> 1.4.5.post2
 * [new tag]           1.4.5.post3 -> 1.4.5.post3
 * [new tag]           1.4.6       -> 1.4.6
 * [new tag]           1.5.0       -> 1.5.0
 * [new tag]           1.5.0a1     -> 1.5.0a1
 * [new tag]           1.5.1       -> 1.5.1
 * [new tag]           1.6.0       -> 1.6.0
 * [new tag]           1.7.0rc1    -> 1.7.0rc1
 * [new tag]           1.8.0       -> 1.8.0
 * [new tag]           1.8.0.dev0  -> 1.8.0.dev0
 * [new tag]           1.9.0       -> 1.9.0
 * [new tag]           1.9.0.dev0  -> 1.9.0.dev0

[rtd-command-info] start-time: 2024-10-15T18:04:36.000810Z, end-time: 2024-10-15T18:04:38.299018Z, duration: 2, exit-code: 0
asdf global python 3.12.3


[rtd-command-info] start-time: 2024-10-15T18:04:40.869659Z, end-time: 2024-10-15T18:04:43.678424Z, duration: 2, exit-code: 0
python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH
created virtual environment CPython3.12.3.final.0-64 in 838ms
  creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3289, 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==23.1, setuptools==67.6.1, wheel==0.40.0
  activators BashActivator,CShellActivator,FishActivator,NushellActivator,PowerShellActivator,PythonActivator

[rtd-command-info] start-time: 2024-10-15T18:04:43.796497Z, end-time: 2024-10-15T18:04:54.949264Z, duration: 11, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip setuptools
Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3289/lib/python3.12/site-packages (23.1)
Collecting pip
  Downloading pip-24.2-py3-none-any.whl (1.8 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.8/1.8 MB 10.9 MB/s eta 0:00:00
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3289/lib/python3.12/site-packages (67.6.1)
Collecting setuptools
  Downloading setuptools-75.1.0-py3-none-any.whl (1.2 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 22.2 MB/s eta 0:00:00
Installing collected packages: setuptools, pip
  Attempting uninstall: setuptools
    Found existing installation: setuptools 67.6.1
    Uninstalling setuptools-67.6.1:
      Successfully uninstalled setuptools-67.6.1
  Attempting uninstall: pip
    Found existing installation: pip 23.1
    Uninstalling pip-23.1:
      Successfully uninstalled pip-23.1
Successfully installed pip-24.2 setuptools-75.1.0

[rtd-command-info] start-time: 2024-10-15T18:04:55.048684Z, end-time: 2024-10-15T18:05:01.514303Z, duration: 6, exit-code: 0
python -m pip install --upgrade --no-cache-dir sphinx
Collecting sphinx
  Downloading sphinx-8.1.3-py3-none-any.whl.metadata (6.4 kB)
Collecting sphinxcontrib-applehelp>=1.0.7 (from sphinx)
  Downloading sphinxcontrib_applehelp-2.0.0-py3-none-any.whl.metadata (2.3 kB)
Collecting sphinxcontrib-devhelp>=1.0.6 (from sphinx)
  Downloading sphinxcontrib_devhelp-2.0.0-py3-none-any.whl.metadata (2.3 kB)
Collecting sphinxcontrib-htmlhelp>=2.0.6 (from sphinx)
  Downloading sphinxcontrib_htmlhelp-2.1.0-py3-none-any.whl.metadata (2.3 kB)
Collecting sphinxcontrib-jsmath>=1.0.1 (from sphinx)
  Downloading sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl.metadata (1.4 kB)
Collecting sphinxcontrib-qthelp>=1.0.6 (from sphinx)
  Downloading sphinxcontrib_qthelp-2.0.0-py3-none-any.whl.metadata (2.3 kB)
Collecting sphinxcontrib-serializinghtml>=1.1.9 (from sphinx)
  Downloading sphinxcontrib_serializinghtml-2.0.0-py3-none-any.whl.metadata (2.4 kB)
Collecting Jinja2>=3.1 (from sphinx)
  Downloading jinja2-3.1.4-py3-none-any.whl.metadata (2.6 kB)
Collecting Pygments>=2.17 (from sphinx)
  Downloading pygments-2.18.0-py3-none-any.whl.metadata (2.5 kB)
Collecting docutils<0.22,>=0.20 (from sphinx)
  Downloading docutils-0.21.2-py3-none-any.whl.metadata (2.8 kB)
Collecting snowballstemmer>=2.2 (from sphinx)
  Downloading snowballstemmer-2.2.0-py2.py3-none-any.whl.metadata (6.5 kB)
Collecting babel>=2.13 (from sphinx)
  Downloading babel-2.16.0-py3-none-any.whl.metadata (1.5 kB)
Collecting alabaster>=0.7.14 (from sphinx)
  Downloading alabaster-1.0.0-py3-none-any.whl.metadata (2.8 kB)
Collecting imagesize>=1.3 (from sphinx)
  Downloading imagesize-1.4.1-py2.py3-none-any.whl.metadata (1.5 kB)
Collecting requests>=2.30.0 (from sphinx)
  Downloading requests-2.32.3-py3-none-any.whl.metadata (4.6 kB)
Collecting packaging>=23.0 (from sphinx)
  Downloading packaging-24.1-py3-none-any.whl.metadata (3.2 kB)
Collecting MarkupSafe>=2.0 (from Jinja2>=3.1->sphinx)
  Downloading MarkupSafe-3.0.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.0 kB)
Collecting charset-normalizer<4,>=2 (from requests>=2.30.0->sphinx)
  Downloading charset_normalizer-3.4.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (34 kB)
Collecting idna<4,>=2.5 (from requests>=2.30.0->sphinx)
  Downloading idna-3.10-py3-none-any.whl.metadata (10 kB)
Collecting urllib3<3,>=1.21.1 (from requests>=2.30.0->sphinx)
  Downloading urllib3-2.2.3-py3-none-any.whl.metadata (6.5 kB)
Collecting certifi>=2017.4.17 (from requests>=2.30.0->sphinx)
  Downloading certifi-2024.8.30-py3-none-any.whl.metadata (2.2 kB)
Downloading sphinx-8.1.3-py3-none-any.whl (3.5 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.5/3.5 MB 114.4 MB/s eta 0:00:00
Downloading alabaster-1.0.0-py3-none-any.whl (13 kB)
Downloading babel-2.16.0-py3-none-any.whl (9.6 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 9.6/9.6 MB 210.1 MB/s eta 0:00:00
Downloading docutils-0.21.2-py3-none-any.whl (587 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 587.4/587.4 kB 571.5 MB/s eta 0:00:00
Downloading imagesize-1.4.1-py2.py3-none-any.whl (8.8 kB)
Downloading jinja2-3.1.4-py3-none-any.whl (133 kB)
Downloading packaging-24.1-py3-none-any.whl (53 kB)
Downloading pygments-2.18.0-py3-none-any.whl (1.2 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 556.5 MB/s eta 0:00:00
Downloading requests-2.32.3-py3-none-any.whl (64 kB)
Downloading snowballstemmer-2.2.0-py2.py3-none-any.whl (93 kB)
Downloading sphinxcontrib_applehelp-2.0.0-py3-none-any.whl (119 kB)
Downloading sphinxcontrib_devhelp-2.0.0-py3-none-any.whl (82 kB)
Downloading sphinxcontrib_htmlhelp-2.1.0-py3-none-any.whl (98 kB)
Downloading sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB)
Downloading sphinxcontrib_qthelp-2.0.0-py3-none-any.whl (88 kB)
Downloading sphinxcontrib_serializinghtml-2.0.0-py3-none-any.whl (92 kB)
Downloading certifi-2024.8.30-py3-none-any.whl (167 kB)
Downloading charset_normalizer-3.4.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (143 kB)
Downloading idna-3.10-py3-none-any.whl (70 kB)
Downloading MarkupSafe-3.0.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (23 kB)
Downloading urllib3-2.2.3-py3-none-any.whl (126 kB)
Installing collected packages: snowballstemmer, urllib3, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, Pygments, packaging, MarkupSafe, imagesize, idna, docutils, charset-normalizer, certifi, babel, alabaster, requests, Jinja2, sphinx
Successfully installed Jinja2-3.1.4 MarkupSafe-3.0.1 Pygments-2.18.0 alabaster-1.0.0 babel-2.16.0 certifi-2024.8.30 charset-normalizer-3.4.0 docutils-0.21.2 idna-3.10 imagesize-1.4.1 packaging-24.1 requests-2.32.3 snowballstemmer-2.2.0 sphinx-8.1.3 sphinxcontrib-applehelp-2.0.0 sphinxcontrib-devhelp-2.0.0 sphinxcontrib-htmlhelp-2.1.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-2.0.0 sphinxcontrib-serializinghtml-2.0.0 urllib3-2.2.3

[rtd-command-info] start-time: 2024-10-15T18:05:01.609899Z, end-time: 2024-10-15T18:06:54.190587Z, duration: 112, exit-code: 0
python -m pip install --upgrade --upgrade-strategy only-if-needed --no-cache-dir .[doc,dev,leiden]
Processing /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3289
  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'
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): finished with status 'done'
Collecting anndata>=0.8 (from scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading anndata-0.10.9-py3-none-any.whl.metadata (6.9 kB)
Collecting h5py>=3.6 (from scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading h5py-3.12.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.5 kB)
Collecting joblib (from scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading joblib-1.4.2-py3-none-any.whl.metadata (5.4 kB)
Collecting legacy-api-wrap>=1.4 (from scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading legacy_api_wrap-1.4-py3-none-any.whl.metadata (1.8 kB)
Collecting matplotlib>=3.6 (from scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading matplotlib-3.9.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (11 kB)
Collecting natsort (from scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading natsort-8.4.0-py3-none-any.whl.metadata (21 kB)
Collecting networkx>=2.7 (from scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading networkx-3.4.1-py3-none-any.whl.metadata (6.3 kB)
Collecting numba>=0.56 (from scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading numba-0.60.0-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (2.7 kB)
Collecting numpy>=1.23 (from scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading numpy-2.1.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB)
Requirement already satisfied: packaging>=21.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3289/lib/python3.12/site-packages (from scanpy==1.11.0.dev132+g1a96f6e4) (24.1)
Collecting pandas>=1.5 (from scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading pandas-2.2.3-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (89 kB)
Collecting patsy (from scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading patsy-0.5.6-py2.py3-none-any.whl.metadata (3.5 kB)
Collecting pynndescent>=0.5 (from scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading pynndescent-0.5.13-py3-none-any.whl.metadata (6.8 kB)
Collecting scikit-learn>=1.1 (from scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading scikit_learn-1.5.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (13 kB)
Collecting scipy>=1.8 (from scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading scipy-1.14.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB)
Collecting seaborn>=0.13 (from scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading seaborn-0.13.2-py3-none-any.whl.metadata (5.4 kB)
Collecting session-info (from scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading session_info-1.0.0.tar.gz (24 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting statsmodels>=0.13 (from scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading statsmodels-0.14.4-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (9.2 kB)
Collecting tqdm (from scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading tqdm-4.66.5-py3-none-any.whl.metadata (57 kB)
Collecting umap-learn!=0.5.0,>=0.5 (from scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading umap_learn-0.5.6-py3-none-any.whl.metadata (21 kB)
Collecting pre-commit (from scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading pre_commit-4.0.1-py2.py3-none-any.whl.metadata (1.3 kB)
Collecting setuptools-scm (from scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading setuptools_scm-8.1.0-py3-none-any.whl.metadata (6.6 kB)
Collecting towncrier (from scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading towncrier-24.8.0-py3-none-any.whl.metadata (4.2 kB)
Collecting dask (from scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading dask-2024.9.1-py3-none-any.whl.metadata (3.7 kB)
Collecting igraph (from scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading igraph-0.11.6-cp39-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.9 kB)
Collecting ipython>=7.20 (from scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading ipython-8.28.0-py3-none-any.whl.metadata (5.0 kB)
Collecting myst-nb>=1 (from scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading myst_nb-1.1.2-py3-none-any.whl.metadata (4.6 kB)
Collecting myst-parser>=2 (from scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading myst_parser-4.0.0-py3-none-any.whl.metadata (5.4 kB)
Collecting nbsphinx>=0.9 (from scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading nbsphinx-0.9.5-py3-none-any.whl.metadata (2.1 kB)
Collecting readthedocs-sphinx-search (from scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading readthedocs_sphinx_search-0.3.2-py3-none-any.whl.metadata (2.4 kB)
Collecting sam-algorithm (from scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading sam-algorithm-1.0.2.tar.gz (35 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting scanpydoc>=0.14.1 (from scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading scanpydoc-0.14.1-py3-none-any.whl.metadata (2.7 kB)
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3289/lib/python3.12/site-packages (from scanpy==1.11.0.dev132+g1a96f6e4) (75.1.0)
Collecting sphinx-autodoc-typehints>=1.25.2 (from scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading sphinx_autodoc_typehints-2.5.0-py3-none-any.whl.metadata (8.0 kB)
Collecting sphinx-book-theme>=1.1.0 (from scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading sphinx_book_theme-1.1.3-py3-none-any.whl.metadata (5.7 kB)
Collecting sphinx-copybutton (from scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading sphinx_copybutton-0.5.2-py3-none-any.whl.metadata (3.2 kB)
Collecting sphinx-design (from scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading sphinx_design-0.6.1-py3-none-any.whl.metadata (5.5 kB)
Collecting sphinx-tabs (from scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading sphinx_tabs-3.4.7-py3-none-any.whl.metadata (6.3 kB)
Requirement already satisfied: sphinx>=7 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3289/lib/python3.12/site-packages (from scanpy==1.11.0.dev132+g1a96f6e4) (8.1.3)
Collecting sphinxcontrib-bibtex (from scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading sphinxcontrib_bibtex-2.6.3-py3-none-any.whl.metadata (6.3 kB)
Collecting sphinxext-opengraph (from scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading sphinxext_opengraph-0.9.1-py3-none-any.whl.metadata (6.5 kB)
Collecting leidenalg>=0.9.0 (from scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading leidenalg-0.10.2-cp38-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (10 kB)
Collecting array-api-compat!=1.5,>1.4 (from anndata>=0.8->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading array_api_compat-1.9-py3-none-any.whl.metadata (1.5 kB)
Collecting texttable>=1.6.2 (from igraph->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading texttable-1.7.0-py2.py3-none-any.whl.metadata (9.8 kB)
Collecting decorator (from ipython>=7.20->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading decorator-5.1.1-py3-none-any.whl.metadata (4.0 kB)
Collecting jedi>=0.16 (from ipython>=7.20->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading jedi-0.19.1-py2.py3-none-any.whl.metadata (22 kB)
Collecting matplotlib-inline (from ipython>=7.20->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading matplotlib_inline-0.1.7-py3-none-any.whl.metadata (3.9 kB)
Collecting prompt-toolkit<3.1.0,>=3.0.41 (from ipython>=7.20->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading prompt_toolkit-3.0.48-py3-none-any.whl.metadata (6.4 kB)
Requirement already satisfied: pygments>=2.4.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3289/lib/python3.12/site-packages (from ipython>=7.20->scanpy==1.11.0.dev132+g1a96f6e4) (2.18.0)
Collecting stack-data (from ipython>=7.20->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading stack_data-0.6.3-py3-none-any.whl.metadata (18 kB)
Collecting traitlets>=5.13.0 (from ipython>=7.20->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading traitlets-5.14.3-py3-none-any.whl.metadata (10 kB)
Collecting pexpect>4.3 (from ipython>=7.20->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading pexpect-4.9.0-py2.py3-none-any.whl.metadata (2.5 kB)
Collecting contourpy>=1.0.1 (from matplotlib>=3.6->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading contourpy-1.3.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.4 kB)
Collecting cycler>=0.10 (from matplotlib>=3.6->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading cycler-0.12.1-py3-none-any.whl.metadata (3.8 kB)
Collecting fonttools>=4.22.0 (from matplotlib>=3.6->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading fonttools-4.54.1-cp312-cp312-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (163 kB)
Collecting kiwisolver>=1.3.1 (from matplotlib>=3.6->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading kiwisolver-1.4.7-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.3 kB)
Collecting pillow>=8 (from matplotlib>=3.6->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading pillow-11.0.0-cp312-cp312-manylinux_2_28_x86_64.whl.metadata (9.1 kB)
Collecting pyparsing>=2.3.1 (from matplotlib>=3.6->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading pyparsing-3.2.0-py3-none-any.whl.metadata (5.0 kB)
Collecting python-dateutil>=2.7 (from matplotlib>=3.6->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
Collecting importlib_metadata (from myst-nb>=1->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading importlib_metadata-8.5.0-py3-none-any.whl.metadata (4.8 kB)
Collecting jupyter-cache>=0.5 (from myst-nb>=1->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading jupyter_cache-1.0.0-py3-none-any.whl.metadata (5.8 kB)
Collecting nbclient (from myst-nb>=1->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading nbclient-0.10.0-py3-none-any.whl.metadata (7.8 kB)
Collecting nbformat>=5.0 (from myst-nb>=1->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading nbformat-5.10.4-py3-none-any.whl.metadata (3.6 kB)
Collecting pyyaml (from myst-nb>=1->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading PyYAML-6.0.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB)
Collecting typing-extensions (from myst-nb>=1->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading typing_extensions-4.12.2-py3-none-any.whl.metadata (3.0 kB)
Collecting ipykernel (from myst-nb>=1->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading ipykernel-6.29.5-py3-none-any.whl.metadata (6.3 kB)
Requirement already satisfied: docutils<0.22,>=0.19 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3289/lib/python3.12/site-packages (from myst-parser>=2->scanpy==1.11.0.dev132+g1a96f6e4) (0.21.2)
Requirement already satisfied: jinja2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3289/lib/python3.12/site-packages (from myst-parser>=2->scanpy==1.11.0.dev132+g1a96f6e4) (3.1.4)
Collecting markdown-it-py~=3.0 (from myst-parser>=2->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading markdown_it_py-3.0.0-py3-none-any.whl.metadata (6.9 kB)
Collecting mdit-py-plugins>=0.4.1,~=0.4 (from myst-parser>=2->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading mdit_py_plugins-0.4.2-py3-none-any.whl.metadata (2.8 kB)
Collecting nbconvert!=5.4,>=5.3 (from nbsphinx>=0.9->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading nbconvert-7.16.4-py3-none-any.whl.metadata (8.5 kB)
Collecting llvmlite<0.44,>=0.43.0dev0 (from numba>=0.56->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading llvmlite-0.43.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.8 kB)
Collecting numpy>=1.23 (from scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading numpy-2.0.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB)
Collecting pytz>=2020.1 (from pandas>=1.5->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading pytz-2024.2-py2.py3-none-any.whl.metadata (22 kB)
Collecting tzdata>=2022.7 (from pandas>=1.5->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading tzdata-2024.2-py2.py3-none-any.whl.metadata (1.4 kB)
Collecting threadpoolctl>=3.1.0 (from scikit-learn>=1.1->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading threadpoolctl-3.5.0-py3-none-any.whl.metadata (13 kB)
Requirement already satisfied: sphinxcontrib-applehelp>=1.0.7 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3289/lib/python3.12/site-packages (from sphinx>=7->scanpy==1.11.0.dev132+g1a96f6e4) (2.0.0)
Requirement already satisfied: sphinxcontrib-devhelp>=1.0.6 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3289/lib/python3.12/site-packages (from sphinx>=7->scanpy==1.11.0.dev132+g1a96f6e4) (2.0.0)
Requirement already satisfied: sphinxcontrib-htmlhelp>=2.0.6 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3289/lib/python3.12/site-packages (from sphinx>=7->scanpy==1.11.0.dev132+g1a96f6e4) (2.1.0)
Requirement already satisfied: sphinxcontrib-jsmath>=1.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3289/lib/python3.12/site-packages (from sphinx>=7->scanpy==1.11.0.dev132+g1a96f6e4) (1.0.1)
Requirement already satisfied: sphinxcontrib-qthelp>=1.0.6 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3289/lib/python3.12/site-packages (from sphinx>=7->scanpy==1.11.0.dev132+g1a96f6e4) (2.0.0)
Requirement already satisfied: sphinxcontrib-serializinghtml>=1.1.9 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3289/lib/python3.12/site-packages (from sphinx>=7->scanpy==1.11.0.dev132+g1a96f6e4) (2.0.0)
Requirement already satisfied: snowballstemmer>=2.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3289/lib/python3.12/site-packages (from sphinx>=7->scanpy==1.11.0.dev132+g1a96f6e4) (2.2.0)
Requirement already satisfied: babel>=2.13 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3289/lib/python3.12/site-packages (from sphinx>=7->scanpy==1.11.0.dev132+g1a96f6e4) (2.16.0)
Requirement already satisfied: alabaster>=0.7.14 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3289/lib/python3.12/site-packages (from sphinx>=7->scanpy==1.11.0.dev132+g1a96f6e4) (1.0.0)
Requirement already satisfied: imagesize>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3289/lib/python3.12/site-packages (from sphinx>=7->scanpy==1.11.0.dev132+g1a96f6e4) (1.4.1)
Requirement already satisfied: requests>=2.30.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3289/lib/python3.12/site-packages (from sphinx>=7->scanpy==1.11.0.dev132+g1a96f6e4) (2.32.3)
Collecting pydata-sphinx-theme>=0.15.2 (from sphinx-book-theme>=1.1.0->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading pydata_sphinx_theme-0.15.4-py3-none-any.whl.metadata (7.5 kB)
Collecting six (from patsy->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading six-1.16.0-py2.py3-none-any.whl.metadata (1.8 kB)
Collecting click>=8.1 (from dask->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading click-8.1.7-py3-none-any.whl.metadata (3.0 kB)
Collecting cloudpickle>=3.0.0 (from dask->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading cloudpickle-3.1.0-py3-none-any.whl.metadata (7.0 kB)
Collecting fsspec>=2021.09.0 (from dask->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading fsspec-2024.9.0-py3-none-any.whl.metadata (11 kB)
Collecting partd>=1.4.0 (from dask->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading partd-1.4.2-py3-none-any.whl.metadata (4.6 kB)
Collecting toolz>=0.10.0 (from dask->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading toolz-1.0.0-py3-none-any.whl.metadata (5.1 kB)
Collecting cfgv>=2.0.0 (from pre-commit->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading cfgv-3.4.0-py2.py3-none-any.whl.metadata (8.5 kB)
Collecting identify>=1.0.0 (from pre-commit->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading identify-2.6.1-py2.py3-none-any.whl.metadata (4.4 kB)
Collecting nodeenv>=0.11.1 (from pre-commit->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading nodeenv-1.9.1-py2.py3-none-any.whl.metadata (21 kB)
Collecting virtualenv>=20.10.0 (from pre-commit->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading virtualenv-20.26.6-py3-none-any.whl.metadata (4.5 kB)
Collecting dill (from sam-algorithm->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading dill-0.3.9-py3-none-any.whl.metadata (10 kB)
Collecting harmonypy (from sam-algorithm->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading harmonypy-0.0.10-py3-none-any.whl.metadata (3.9 kB)
Collecting hnswlib (from sam-algorithm->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading hnswlib-0.8.0.tar.gz (36 kB)
  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'
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): finished with status 'done'
Collecting stdlib_list (from session-info->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading stdlib_list-0.10.0-py3-none-any.whl.metadata (3.3 kB)
Collecting pybtex>=0.24 (from sphinxcontrib-bibtex->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading pybtex-0.24.0-py2.py3-none-any.whl.metadata (2.0 kB)
Collecting pybtex-docutils>=1.0.0 (from sphinxcontrib-bibtex->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading pybtex_docutils-1.0.3-py3-none-any.whl.metadata (4.3 kB)
Collecting parso<0.9.0,>=0.8.3 (from jedi>=0.16->ipython>=7.20->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading parso-0.8.4-py2.py3-none-any.whl.metadata (7.7 kB)
Requirement already satisfied: MarkupSafe>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3289/lib/python3.12/site-packages (from jinja2->myst-parser>=2->scanpy==1.11.0.dev132+g1a96f6e4) (3.0.1)
Collecting attrs (from jupyter-cache>=0.5->myst-nb>=1->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading attrs-24.2.0-py3-none-any.whl.metadata (11 kB)
Collecting sqlalchemy<3,>=1.3.12 (from jupyter-cache>=0.5->myst-nb>=1->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading SQLAlchemy-2.0.35-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (9.6 kB)
Collecting tabulate (from jupyter-cache>=0.5->myst-nb>=1->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading tabulate-0.9.0-py3-none-any.whl.metadata (34 kB)
Collecting mdurl~=0.1 (from markdown-it-py~=3.0->myst-parser>=2->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading mdurl-0.1.2-py3-none-any.whl.metadata (1.6 kB)
Collecting jupyter-client>=6.1.12 (from nbclient->myst-nb>=1->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading jupyter_client-8.6.3-py3-none-any.whl.metadata (8.3 kB)
Collecting jupyter-core!=5.0.*,>=4.12 (from nbclient->myst-nb>=1->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading jupyter_core-5.7.2-py3-none-any.whl.metadata (3.4 kB)
Collecting beautifulsoup4 (from nbconvert!=5.4,>=5.3->nbsphinx>=0.9->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading beautifulsoup4-4.12.3-py3-none-any.whl.metadata (3.8 kB)
Collecting bleach!=5.0.0 (from nbconvert!=5.4,>=5.3->nbsphinx>=0.9->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading bleach-6.1.0-py3-none-any.whl.metadata (30 kB)
Collecting defusedxml (from nbconvert!=5.4,>=5.3->nbsphinx>=0.9->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading defusedxml-0.7.1-py2.py3-none-any.whl.metadata (32 kB)
Collecting jupyterlab-pygments (from nbconvert!=5.4,>=5.3->nbsphinx>=0.9->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading jupyterlab_pygments-0.3.0-py3-none-any.whl.metadata (4.4 kB)
Collecting mistune<4,>=2.0.3 (from nbconvert!=5.4,>=5.3->nbsphinx>=0.9->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading mistune-3.0.2-py3-none-any.whl.metadata (1.7 kB)
Collecting pandocfilters>=1.4.1 (from nbconvert!=5.4,>=5.3->nbsphinx>=0.9->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading pandocfilters-1.5.1-py2.py3-none-any.whl.metadata (9.0 kB)
Collecting tinycss2 (from nbconvert!=5.4,>=5.3->nbsphinx>=0.9->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading tinycss2-1.3.0-py3-none-any.whl.metadata (3.0 kB)
Collecting fastjsonschema>=2.15 (from nbformat>=5.0->myst-nb>=1->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading fastjsonschema-2.20.0-py3-none-any.whl.metadata (2.1 kB)
Collecting jsonschema>=2.6 (from nbformat>=5.0->myst-nb>=1->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading jsonschema-4.23.0-py3-none-any.whl.metadata (7.9 kB)
Collecting locket (from partd>=1.4.0->dask->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading locket-1.0.0-py2.py3-none-any.whl.metadata (2.8 kB)
Collecting ptyprocess>=0.5 (from pexpect>4.3->ipython>=7.20->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading ptyprocess-0.7.0-py2.py3-none-any.whl.metadata (1.3 kB)
Collecting wcwidth (from prompt-toolkit<3.1.0,>=3.0.41->ipython>=7.20->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading wcwidth-0.2.13-py2.py3-none-any.whl.metadata (14 kB)
Collecting latexcodec>=1.0.4 (from pybtex>=0.24->sphinxcontrib-bibtex->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading latexcodec-3.0.0-py3-none-any.whl.metadata (4.9 kB)
Collecting accessible-pygments (from pydata-sphinx-theme>=0.15.2->sphinx-book-theme>=1.1.0->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading accessible_pygments-0.0.5-py3-none-any.whl.metadata (10 kB)
Requirement already satisfied: charset-normalizer<4,>=2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3289/lib/python3.12/site-packages (from requests>=2.30.0->sphinx>=7->scanpy==1.11.0.dev132+g1a96f6e4) (3.4.0)
Requirement already satisfied: idna<4,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3289/lib/python3.12/site-packages (from requests>=2.30.0->sphinx>=7->scanpy==1.11.0.dev132+g1a96f6e4) (3.10)
Requirement already satisfied: urllib3<3,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3289/lib/python3.12/site-packages (from requests>=2.30.0->sphinx>=7->scanpy==1.11.0.dev132+g1a96f6e4) (2.2.3)
Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3289/lib/python3.12/site-packages (from requests>=2.30.0->sphinx>=7->scanpy==1.11.0.dev132+g1a96f6e4) (2024.8.30)
Collecting distlib<1,>=0.3.7 (from virtualenv>=20.10.0->pre-commit->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading distlib-0.3.9-py2.py3-none-any.whl.metadata (5.2 kB)
Collecting filelock<4,>=3.12.2 (from virtualenv>=20.10.0->pre-commit->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading filelock-3.16.1-py3-none-any.whl.metadata (2.9 kB)
Collecting platformdirs<5,>=3.9.1 (from virtualenv>=20.10.0->pre-commit->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading platformdirs-4.3.6-py3-none-any.whl.metadata (11 kB)
Collecting zipp>=3.20 (from importlib_metadata->myst-nb>=1->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading zipp-3.20.2-py3-none-any.whl.metadata (3.7 kB)
Collecting comm>=0.1.1 (from ipykernel->myst-nb>=1->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading comm-0.2.2-py3-none-any.whl.metadata (3.7 kB)
Collecting debugpy>=1.6.5 (from ipykernel->myst-nb>=1->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading debugpy-1.8.7-cp312-cp312-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (1.1 kB)
Collecting nest-asyncio (from ipykernel->myst-nb>=1->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading nest_asyncio-1.6.0-py3-none-any.whl.metadata (2.8 kB)
Collecting psutil (from ipykernel->myst-nb>=1->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading psutil-6.0.0-cp36-abi3-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (21 kB)
Collecting pyzmq>=24 (from ipykernel->myst-nb>=1->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading pyzmq-26.2.0-cp312-cp312-manylinux_2_28_x86_64.whl.metadata (6.2 kB)
Collecting tornado>=6.1 (from ipykernel->myst-nb>=1->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading tornado-6.4.1-cp38-abi3-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.5 kB)
Collecting executing>=1.2.0 (from stack-data->ipython>=7.20->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading executing-2.1.0-py2.py3-none-any.whl.metadata (8.9 kB)
Collecting asttokens>=2.1.0 (from stack-data->ipython>=7.20->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading asttokens-2.4.1-py2.py3-none-any.whl.metadata (5.2 kB)
Collecting pure-eval (from stack-data->ipython>=7.20->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading pure_eval-0.2.3-py3-none-any.whl.metadata (6.3 kB)
Collecting webencodings (from bleach!=5.0.0->nbconvert!=5.4,>=5.3->nbsphinx>=0.9->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading webencodings-0.5.1-py2.py3-none-any.whl.metadata (2.1 kB)
Collecting jsonschema-specifications>=2023.03.6 (from jsonschema>=2.6->nbformat>=5.0->myst-nb>=1->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading jsonschema_specifications-2024.10.1-py3-none-any.whl.metadata (3.0 kB)
Collecting referencing>=0.28.4 (from jsonschema>=2.6->nbformat>=5.0->myst-nb>=1->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading referencing-0.35.1-py3-none-any.whl.metadata (2.8 kB)
Collecting rpds-py>=0.7.1 (from jsonschema>=2.6->nbformat>=5.0->myst-nb>=1->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading rpds_py-0.20.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.2 kB)
Collecting greenlet!=0.4.17 (from sqlalchemy<3,>=1.3.12->jupyter-cache>=0.5->myst-nb>=1->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading greenlet-3.1.1-cp312-cp312-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (3.8 kB)
Collecting soupsieve>1.2 (from beautifulsoup4->nbconvert!=5.4,>=5.3->nbsphinx>=0.9->scanpy==1.11.0.dev132+g1a96f6e4)
  Downloading soupsieve-2.6-py3-none-any.whl.metadata (4.6 kB)
Downloading anndata-0.10.9-py3-none-any.whl (128 kB)
Downloading h5py-3.12.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (5.4 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 5.4/5.4 MB 150.6 MB/s eta 0:00:00
Downloading igraph-0.11.6-cp39-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.1 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.1/3.1 MB 257.0 MB/s eta 0:00:00
Downloading ipython-8.28.0-py3-none-any.whl (819 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 819.5/819.5 kB 569.6 MB/s eta 0:00:00
Downloading legacy_api_wrap-1.4-py3-none-any.whl (15 kB)
Downloading leidenalg-0.10.2-cp38-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (2.0 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.0/2.0 MB 303.0 MB/s eta 0:00:00
Downloading matplotlib-3.9.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (8.3 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 8.3/8.3 MB 153.2 MB/s eta 0:00:00
Downloading myst_nb-1.1.2-py3-none-any.whl (80 kB)
Downloading myst_parser-4.0.0-py3-none-any.whl (84 kB)
Downloading nbsphinx-0.9.5-py3-none-any.whl (31 kB)
Downloading networkx-3.4.1-py3-none-any.whl (1.7 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.7/1.7 MB 331.1 MB/s eta 0:00:00
Downloading numba-0.60.0-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (3.8 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.8/3.8 MB 260.2 MB/s eta 0:00:00
Downloading numpy-2.0.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (19.2 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 19.2/19.2 MB 196.4 MB/s eta 0:00:00
Downloading pandas-2.2.3-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.7 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 12.7/12.7 MB 225.3 MB/s eta 0:00:00
Downloading pynndescent-0.5.13-py3-none-any.whl (56 kB)
Downloading joblib-1.4.2-py3-none-any.whl (301 kB)
Downloading scanpydoc-0.14.1-py3-none-any.whl (34 kB)
Downloading scikit_learn-1.5.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.9 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 12.9/12.9 MB 172.4 MB/s eta 0:00:00
Downloading scipy-1.14.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (40.8 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 40.8/40.8 MB 219.0 MB/s eta 0:00:00
Downloading seaborn-0.13.2-py3-none-any.whl (294 kB)
Downloading sphinx_autodoc_typehints-2.5.0-py3-none-any.whl (20 kB)
Downloading sphinx_book_theme-1.1.3-py3-none-any.whl (430 kB)
Downloading statsmodels-0.14.4-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (10.7 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 10.7/10.7 MB 234.4 MB/s eta 0:00:00
Downloading patsy-0.5.6-py2.py3-none-any.whl (233 kB)
Downloading umap_learn-0.5.6-py3-none-any.whl (85 kB)
Downloading dask-2024.9.1-py3-none-any.whl (1.3 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.3/1.3 MB 509.2 MB/s eta 0:00:00
Downloading natsort-8.4.0-py3-none-any.whl (38 kB)
Downloading pre_commit-4.0.1-py2.py3-none-any.whl (218 kB)
Downloading readthedocs_sphinx_search-0.3.2-py3-none-any.whl (21 kB)
Downloading setuptools_scm-8.1.0-py3-none-any.whl (43 kB)
Downloading sphinx_copybutton-0.5.2-py3-none-any.whl (13 kB)
Downloading sphinx_design-0.6.1-py3-none-any.whl (2.2 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.2/2.2 MB 178.5 MB/s eta 0:00:00
Downloading sphinx_tabs-3.4.7-py3-none-any.whl (9.7 kB)
Downloading sphinxcontrib_bibtex-2.6.3-py3-none-any.whl (40 kB)
Downloading sphinxext_opengraph-0.9.1-py3-none-any.whl (1.0 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.0/1.0 MB 563.5 MB/s eta 0:00:00
Downloading towncrier-24.8.0-py3-none-any.whl (56 kB)
Downloading tqdm-4.66.5-py3-none-any.whl (78 kB)
Downloading array_api_compat-1.9-py3-none-any.whl (49 kB)
Downloading cfgv-3.4.0-py2.py3-none-any.whl (7.2 kB)
Downloading click-8.1.7-py3-none-any.whl (97 kB)
Downloading cloudpickle-3.1.0-py3-none-any.whl (22 kB)
Downloading contourpy-1.3.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (320 kB)
Downloading cycler-0.12.1-py3-none-any.whl (8.3 kB)
Downloading fonttools-4.54.1-cp312-cp312-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.9 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.9/4.9 MB 215.9 MB/s eta 0:00:00
Downloading fsspec-2024.9.0-py3-none-any.whl (179 kB)
Downloading identify-2.6.1-py2.py3-none-any.whl (98 kB)
Downloading jedi-0.19.1-py2.py3-none-any.whl (1.6 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.6/1.6 MB 575.3 MB/s eta 0:00:00
Downloading jupyter_cache-1.0.0-py3-none-any.whl (33 kB)
Downloading kiwisolver-1.4.7-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.5 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.5/1.5 MB 493.0 MB/s eta 0:00:00
Downloading llvmlite-0.43.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (43.9 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 43.9/43.9 MB 224.1 MB/s eta 0:00:00
Downloading markdown_it_py-3.0.0-py3-none-any.whl (87 kB)
Downloading mdit_py_plugins-0.4.2-py3-none-any.whl (55 kB)
Downloading nbclient-0.10.0-py3-none-any.whl (25 kB)
Downloading nbconvert-7.16.4-py3-none-any.whl (257 kB)
Downloading nbformat-5.10.4-py3-none-any.whl (78 kB)
Downloading nodeenv-1.9.1-py2.py3-none-any.whl (22 kB)
Downloading partd-1.4.2-py3-none-any.whl (18 kB)
Downloading pexpect-4.9.0-py2.py3-none-any.whl (63 kB)
Downloading pillow-11.0.0-cp312-cp312-manylinux_2_28_x86_64.whl (4.4 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.4/4.4 MB 236.0 MB/s eta 0:00:00
Downloading prompt_toolkit-3.0.48-py3-none-any.whl (386 kB)
Downloading pybtex-0.24.0-py2.py3-none-any.whl (561 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 561.4/561.4 kB 552.4 MB/s eta 0:00:00
Downloading pybtex_docutils-1.0.3-py3-none-any.whl (6.4 kB)
Downloading pydata_sphinx_theme-0.15.4-py3-none-any.whl (4.6 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.6/4.6 MB 261.6 MB/s eta 0:00:00
Downloading pyparsing-3.2.0-py3-none-any.whl (106 kB)
Downloading python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB)
Downloading pytz-2024.2-py2.py3-none-any.whl (508 kB)
Downloading PyYAML-6.0.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (767 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 767.5/767.5 kB 559.1 MB/s eta 0:00:00
Downloading six-1.16.0-py2.py3-none-any.whl (11 kB)
Downloading texttable-1.7.0-py2.py3-none-any.whl (10 kB)
Downloading threadpoolctl-3.5.0-py3-none-any.whl (18 kB)
Downloading toolz-1.0.0-py3-none-any.whl (56 kB)
Downloading traitlets-5.14.3-py3-none-any.whl (85 kB)
Downloading tzdata-2024.2-py2.py3-none-any.whl (346 kB)
Downloading virtualenv-20.26.6-py3-none-any.whl (6.0 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 6.0/6.0 MB 248.9 MB/s eta 0:00:00
Downloading decorator-5.1.1-py3-none-any.whl (9.1 kB)
Downloading dill-0.3.9-py3-none-any.whl (119 kB)
Downloading harmonypy-0.0.10-py3-none-any.whl (20 kB)
Downloading importlib_metadata-8.5.0-py3-none-any.whl (26 kB)
Downloading ipykernel-6.29.5-py3-none-any.whl (117 kB)
Downloading matplotlib_inline-0.1.7-py3-none-any.whl (9.9 kB)
Downloading stack_data-0.6.3-py3-none-any.whl (24 kB)
Downloading stdlib_list-0.10.0-py3-none-any.whl (79 kB)
Downloading typing_extensions-4.12.2-py3-none-any.whl (37 kB)
Downloading asttokens-2.4.1-py2.py3-none-any.whl (27 kB)
Downloading bleach-6.1.0-py3-none-any.whl (162 kB)
Downloading comm-0.2.2-py3-none-any.whl (7.2 kB)
Downloading debugpy-1.8.7-cp312-cp312-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.2 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.2/4.2 MB 261.6 MB/s eta 0:00:00
Downloading distlib-0.3.9-py2.py3-none-any.whl (468 kB)
Downloading executing-2.1.0-py2.py3-none-any.whl (25 kB)
Downloading fastjsonschema-2.20.0-py3-none-any.whl (23 kB)
Downloading filelock-3.16.1-py3-none-any.whl (16 kB)
Downloading jsonschema-4.23.0-py3-none-any.whl (88 kB)
Downloading attrs-24.2.0-py3-none-any.whl (63 kB)
Downloading jupyter_client-8.6.3-py3-none-any.whl (106 kB)
Downloading jupyter_core-5.7.2-py3-none-any.whl (28 kB)
Downloading latexcodec-3.0.0-py3-none-any.whl (18 kB)
Downloading mdurl-0.1.2-py3-none-any.whl (10.0 kB)
Downloading mistune-3.0.2-py3-none-any.whl (47 kB)
Downloading pandocfilters-1.5.1-py2.py3-none-any.whl (8.7 kB)
Downloading parso-0.8.4-py2.py3-none-any.whl (103 kB)
Downloading platformdirs-4.3.6-py3-none-any.whl (18 kB)
Downloading ptyprocess-0.7.0-py2.py3-none-any.whl (13 kB)
Downloading pyzmq-26.2.0-cp312-cp312-manylinux_2_28_x86_64.whl (860 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 860.6/860.6 kB 516.9 MB/s eta 0:00:00
Downloading SQLAlchemy-2.0.35-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.2 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.2/3.2 MB 270.1 MB/s eta 0:00:00
Downloading tornado-6.4.1-cp38-abi3-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (436 kB)
Downloading zipp-3.20.2-py3-none-any.whl (9.2 kB)
Downloading accessible_pygments-0.0.5-py3-none-any.whl (1.4 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.4/1.4 MB 447.4 MB/s eta 0:00:00
Downloading beautifulsoup4-4.12.3-py3-none-any.whl (147 kB)
Downloading defusedxml-0.7.1-py2.py3-none-any.whl (25 kB)
Downloading jupyterlab_pygments-0.3.0-py3-none-any.whl (15 kB)
Downloading locket-1.0.0-py2.py3-none-any.whl (4.4 kB)
Downloading nest_asyncio-1.6.0-py3-none-any.whl (5.2 kB)
Downloading psutil-6.0.0-cp36-abi3-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (290 kB)
Downloading pure_eval-0.2.3-py3-none-any.whl (11 kB)
Downloading tabulate-0.9.0-py3-none-any.whl (35 kB)
Downloading tinycss2-1.3.0-py3-none-any.whl (22 kB)
Downloading wcwidth-0.2.13-py2.py3-none-any.whl (34 kB)
Downloading greenlet-3.1.1-cp312-cp312-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (613 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 613.1/613.1 kB 472.0 MB/s eta 0:00:00
Downloading jsonschema_specifications-2024.10.1-py3-none-any.whl (18 kB)
Downloading referencing-0.35.1-py3-none-any.whl (26 kB)
Downloading rpds_py-0.20.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (357 kB)
Downloading soupsieve-2.6-py3-none-any.whl (36 kB)
Downloading webencodings-0.5.1-py2.py3-none-any.whl (11 kB)
Building wheels for collected packages: scanpy, sam-algorithm, session-info, hnswlib
  Building wheel for scanpy (pyproject.toml): started
  Building wheel for scanpy (pyproject.toml): finished with status 'done'
  Created wheel for scanpy: filename=scanpy-1.11.0.dev132+g1a96f6e4-py3-none-any.whl size=2086102 sha256=73ebfd5ee84bad68147e8850a486a8248793d7750e8e4070307514a7d6d15307
  Stored in directory: /tmp/pip-ephem-wheel-cache-dig8pbh2/wheels/d2/b2/a3/d1b4e78e080f56810ec4926731515b6c904b40246b5fa8f06e
  Building wheel for sam-algorithm (setup.py): started
  Building wheel for sam-algorithm (setup.py): finished with status 'done'
  Created wheel for sam-algorithm: filename=sam_algorithm-1.0.2-py3-none-any.whl size=34579 sha256=ec672ae6e129504f639938cf172804646123201927365fb9af8828a8286ac50d
  Stored in directory: /tmp/pip-ephem-wheel-cache-dig8pbh2/wheels/57/54/be/ca87c5831826023e1d64b77d6680c582ff898a13844a7ed4ed
  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=8023 sha256=6d09cd6e38afbf3e01c5f44800da433f3cf7581d52562143bb91fa56e51fd17b
  Stored in directory: /tmp/pip-ephem-wheel-cache-dig8pbh2/wheels/23/da/7c/868424f4a5845ab58cd8686e0eb405e9e1e2d4152bf702c39d
  Building wheel for hnswlib (pyproject.toml): started
  Building wheel for hnswlib (pyproject.toml): finished with status 'done'
  Created wheel for hnswlib: filename=hnswlib-0.8.0-cp312-cp312-linux_x86_64.whl size=2288948 sha256=02714717f344981daeaee3a3c0c93fa6b9439f49d64118e6e82cde57f064c769
  Stored in directory: /tmp/pip-ephem-wheel-cache-dig8pbh2/wheels/ac/39/b3/cbd7f9cbb76501d2d5fbc84956e70d0b94e788aac87bda465e
Successfully built scanpy sam-algorithm session-info hnswlib
Installing collected packages: webencodings, wcwidth, texttable, pytz, pure-eval, ptyprocess, fastjsonschema, distlib, array-api-compat, zipp, tzdata, typing-extensions, traitlets, tqdm, tornado, toolz, tinycss2, threadpoolctl, tabulate, stdlib_list, soupsieve, six, setuptools-scm, rpds-py, readthedocs-sphinx-search, pyzmq, pyyaml, pyparsing, psutil, prompt-toolkit, platformdirs, pillow, pexpect, parso, pandocfilters, numpy, nodeenv, networkx, nest-asyncio, natsort, mistune, mdurl, locket, llvmlite, legacy-api-wrap, latexcodec, kiwisolver, jupyterlab-pygments, joblib, igraph, identify, greenlet, fsspec, fonttools, filelock, executing, dill, defusedxml, decorator, debugpy, cycler, cloudpickle, click, cfgv, attrs, accessible-pygments, virtualenv, towncrier, sqlalchemy, session-info, scipy, referencing, python-dateutil, pybtex, patsy, partd, numba, matplotlib-inline, markdown-it-py, leidenalg, jupyter-core, jedi, importlib_metadata, hnswlib, h5py, contourpy, comm, bleach, beautifulsoup4, asttokens, stack-data, sphinxext-opengraph, sphinx-tabs, sphinx-design, sphinx-copybutton, sphinx-autodoc-typehints, scikit-learn, scanpydoc, pydata-sphinx-theme, pybtex-docutils, pre-commit, pandas, mdit-py-plugins, matplotlib, jupyter-client, jsonschema-specifications, dask, statsmodels, sphinxcontrib-bibtex, sphinx-book-theme, seaborn, pynndescent, myst-parser, jsonschema, ipython, harmonypy, anndata, umap-learn, nbformat, ipykernel, scanpy, sam-algorithm, nbclient, nbconvert, jupyter-cache, nbsphinx, myst-nb
Successfully installed accessible-pygments-0.0.5 anndata-0.10.9 array-api-compat-1.9 asttokens-2.4.1 attrs-24.2.0 beautifulsoup4-4.12.3 bleach-6.1.0 cfgv-3.4.0 click-8.1.7 cloudpickle-3.1.0 comm-0.2.2 contourpy-1.3.0 cycler-0.12.1 dask-2024.9.1 debugpy-1.8.7 decorator-5.1.1 defusedxml-0.7.1 dill-0.3.9 distlib-0.3.9 executing-2.1.0 fastjsonschema-2.20.0 filelock-3.16.1 fonttools-4.54.1 fsspec-2024.9.0 greenlet-3.1.1 h5py-3.12.1 harmonypy-0.0.10 hnswlib-0.8.0 identify-2.6.1 igraph-0.11.6 importlib_metadata-8.5.0 ipykernel-6.29.5 ipython-8.28.0 jedi-0.19.1 joblib-1.4.2 jsonschema-4.23.0 jsonschema-specifications-2024.10.1 jupyter-cache-1.0.0 jupyter-client-8.6.3 jupyter-core-5.7.2 jupyterlab-pygments-0.3.0 kiwisolver-1.4.7 latexcodec-3.0.0 legacy-api-wrap-1.4 leidenalg-0.10.2 llvmlite-0.43.0 locket-1.0.0 markdown-it-py-3.0.0 matplotlib-3.9.2 matplotlib-inline-0.1.7 mdit-py-plugins-0.4.2 mdurl-0.1.2 mistune-3.0.2 myst-nb-1.1.2 myst-parser-4.0.0 natsort-8.4.0 nbclient-0.10.0 nbconvert-7.16.4 nbformat-5.10.4 nbsphinx-0.9.5 nest-asyncio-1.6.0 networkx-3.4.1 nodeenv-1.9.1 numba-0.60.0 numpy-2.0.2 pandas-2.2.3 pandocfilters-1.5.1 parso-0.8.4 partd-1.4.2 patsy-0.5.6 pexpect-4.9.0 pillow-11.0.0 platformdirs-4.3.6 pre-commit-4.0.1 prompt-toolkit-3.0.48 psutil-6.0.0 ptyprocess-0.7.0 pure-eval-0.2.3 pybtex-0.24.0 pybtex-docutils-1.0.3 pydata-sphinx-theme-0.15.4 pynndescent-0.5.13 pyparsing-3.2.0 python-dateutil-2.9.0.post0 pytz-2024.2 pyyaml-6.0.2 pyzmq-26.2.0 readthedocs-sphinx-search-0.3.2 referencing-0.35.1 rpds-py-0.20.0 sam-algorithm-1.0.2 scanpy-1.11.0.dev132+g1a96f6e4 scanpydoc-0.14.1 scikit-learn-1.5.2 scipy-1.14.1 seaborn-0.13.2 session-info-1.0.0 setuptools-scm-8.1.0 six-1.16.0 soupsieve-2.6 sphinx-autodoc-typehints-2.5.0 sphinx-book-theme-1.1.3 sphinx-copybutton-0.5.2 sphinx-design-0.6.1 sphinx-tabs-3.4.7 sphinxcontrib-bibtex-2.6.3 sphinxext-opengraph-0.9.1 sqlalchemy-2.0.35 stack-data-0.6.3 statsmodels-0.14.4 stdlib_list-0.10.0 tabulate-0.9.0 texttable-1.7.0 threadpoolctl-3.5.0 tinycss2-1.3.0 toolz-1.0.0 tornado-6.4.1 towncrier-24.8.0 tqdm-4.66.5 traitlets-5.14.3 typing-extensions-4.12.2 tzdata-2024.2 umap-learn-0.5.6 virtualenv-20.26.6 wcwidth-0.2.13 webencodings-0.5.1 zipp-3.20.2

[rtd-command-info] start-time: 2024-10-15T18:06:54.614816Z, end-time: 2024-10-15T18:08:31.366404Z, duration: 96, exit-code: 0
( find docs/release-notes -regex '[^.]+[.][^.]+.md' | grep -q . ) && towncrier build --keep || true
Loading template...
Finding news fragments...
Rendering news fragments...
Matplotlib is building the font cache; this may take a moment.
Writing to newsfile...
Staging newsfile...
Keeping the following files:
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3289/docs/release-notes/3264.bugfix.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3289/docs/release-notes/3206.bugfix.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3289/docs/release-notes/3155.feature.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3289/docs/release-notes/3180.feature.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3289/docs/release-notes/2921.feature.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3289/docs/release-notes/3184.feature.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3289/docs/release-notes/3243.bugfix.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3289/docs/release-notes/3244.bugfix.md
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3289/docs/release-notes/3283.breaking.md
Done!

[rtd-command-info] start-time: 2024-10-15T18:08:31.528323Z, end-time: 2024-10-15T18:08:31.591194Z, duration: 0, exit-code: 0
cat docs/conf.py
from __future__ import annotations

import sys
from datetime import datetime
from functools import partial
from pathlib import Path, PurePosixPath
from typing import TYPE_CHECKING

import matplotlib  # noqa
from docutils import nodes
from packaging.version import 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

if TYPE_CHECKING:
    from sphinx.application import Sphinx


# -- 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 = [
    "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 Version(version).is_devrelease:
    parsed = Version(version)
    version = f"{parsed.major}.{parsed.minor}.{parsed.micro}.dev"

release = version

# Bibliography settings
bibtex_bibfiles = ["references.bib"]
bibtex_reference_style = "author_year"


# default settings
templates_path = ["_templates"]
master_doc = "index"
default_role = "literal"
exclude_patterns = [
    "_build",
    "Thumbs.db",
    ".DS_Store",
    "**.ipynb_checkpoints",
    # exclude all 0.x.y.md files, but not index.md
    "release-notes/[!i]*.md",
]

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.extlinks",
    "sphinxcontrib.bibtex",
    "matplotlib.sphinxext.plot_directive",
    "sphinx_autodoc_typehints",  # needs to be after napoleon
    "git_ref",  # needs to be before scanpydoc.rtd_github_links
    "scanpydoc",  # needs to be before sphinx.ext.linkcode
    "sphinx.ext.linkcode",
    "sphinx_design",
    "sphinx_tabs.tabs",
    "sphinx_search.extension",
    "sphinxext.opengraph",
    *[p.stem for p in (HERE / "extensions").glob("*.py") if p.stem not in {"git_ref"}],
]

# 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", "ftp")
myst_heading_anchors = 3
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"

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),
    cuml=("https://docs.rapids.ai/api/cuml/stable/", None),
    cycler=("https://matplotlib.org/cycler/", None),
    dask=("https://docs.dask.org/en/stable/", None),
    dask_ml=("https://ml.dask.org/", None),
    h5py=("https://docs.h5py.org/en/stable/", None),
    ipython=("https://ipython.readthedocs.io/en/stable/", None),
    igraph=("https://python.igraph.org/en/stable/api/", 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),
    pynndescent=("https://pynndescent.readthedocs.io/en/latest/", None),
    pytest=("https://docs.pytest.org/en/latest/", None),
    python=("https://docs.python.org/3", None),
    rapids_singlecell=("https://rapids-singlecell.readthedocs.io/en/latest/", None),
    scipy=("https://docs.scipy.org/doc/scipy/", None),
    seaborn=("https://seaborn.pydata.org/", None),
    sklearn=("https://scikit-learn.org/stable/", None),
)


# -- Options for HTML output ----------------------------------------------

# The theme is sphinx-book-theme, with patches for readthedocs-sphinx-search
html_theme = "scanpydoc"
html_theme_options = {
    "repository_url": repository_url,
    "use_repository_button": True,
}
html_static_path = ["_static"]
html_show_sphinx = False
html_logo = "_static/img/Scanpy_Logo_BrightFG.svg"
html_title = "scanpy"


def setup(app: Sphinx):
    """App setup hook."""
    app.add_generic_role("small", partial(nodes.inline, classes=["small"]))
    app.add_generic_role("smaller", partial(nodes.inline, classes=["smaller"]))
    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,  # noqa: FBT003
    )


# -- 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.metrics.DistanceMetric",
    "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",
    "numpy.bool_": "numpy.bool",  # Since numpy 2, numpy.bool is the canonical dtype
}

nitpick_ignore = [
    # Technical issues
    ("py:class", "numpy.int64"),  # documented as “attribute”
    ("py:class", "numpy._typing._dtype_like._SupportsDType"),
    ("py:class", "numpy._typing._dtype_like._DTypeDict"),
    # Will probably be documented
    ("py:class", "scanpy._settings.Verbosity"),
    ("py:class", "scanpy.neighbors.OnFlySymMatrix"),
    ("py:class", "scanpy.plotting._baseplot_class.BasePlot"),
    # Currently undocumented
    # https://github.com/mwaskom/seaborn/issues/1810
    ("py:class", "seaborn.matrix.ClusterGrid"),
    ("py:class", "samalg.SAM"),
    # Won’t be documented
    ("py:class", "scanpy.plotting._utils._AxesSubplot"),
    ("py:class", "scanpy._utils.Empty"),
    ("py:class", "numpy.random.mtrand.RandomState"),
    ("py:class", "scanpy.neighbors._types.KnnTransformerLike"),
    # 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

# link config
extlinks = {
    "issue": ("https://github.com/scverse/scanpy/issues/%s", "issue%s"),
    "pr": ("https://github.com/scverse/scanpy/pull/%s", "pr%s"),
}
rtd_links_prefix = PurePosixPath("src")

[rtd-command-info] start-time: 2024-10-15T18:08:31.700468Z, end-time: 2024-10-15T18:12:00.536903Z, duration: 208, exit-code: 0
python -m sphinx -T -W --keep-going -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html
Running Sphinx v8.1.3
loading translations [en]... done
making output directory... done
checking bibtex cache... out of date
parsing bibtex file /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3289/docs/references.bib... parsed 66 entries
myst v4.0.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions={'amsmath', 'html_image', 'dollarmath', 'colon_fence', 'deflist', 'html_admonition'}, disable_syntax=[], all_links_external=False, links_external_new_tab=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, fence_as_directive=set(), number_code_blocks=[], title_to_header=False, heading_anchors=3, heading_slug_func=None, html_meta={}, footnote_sort=True, footnote_transition=True, words_per_minute=200, substitutions={}, linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area', enable_checkboxes=False, suppress_warnings=[], highlight_code_blocks=True)
myst-nb v1.1.2: NbParserConfig(custom_formats={}, metadata_key='mystnb', cell_metadata_key='mystnb', kernel_rgx_aliases={}, eval_name_regex='^[a-zA-Z_][a-zA-Z0-9_]*$', 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/3289/_readthedocs/.jupyter_cache
loading intersphinx inventory 'anndata' from https://anndata.readthedocs.io/en/stable/objects.inv ...
loading intersphinx inventory 'bbknn' from https://bbknn.readthedocs.io/en/latest/objects.inv ...
loading intersphinx inventory 'cuml' from https://docs.rapids.ai/api/cuml/stable/objects.inv ...
loading intersphinx inventory 'cycler' from https://matplotlib.org/cycler/objects.inv ...
loading intersphinx inventory 'dask' from https://docs.dask.org/en/stable/objects.inv ...
loading intersphinx inventory 'dask_ml' from https://ml.dask.org/objects.inv ...
loading intersphinx inventory 'h5py' from https://docs.h5py.org/en/stable/objects.inv ...
loading intersphinx inventory 'ipython' from https://ipython.readthedocs.io/en/stable/objects.inv ...
loading intersphinx inventory 'igraph' from https://python.igraph.org/en/stable/api/objects.inv ...
loading intersphinx inventory 'leidenalg' from https://leidenalg.readthedocs.io/en/latest/objects.inv ...
loading intersphinx inventory 'louvain' from https://louvain-igraph.readthedocs.io/en/latest/objects.inv ...
loading intersphinx inventory 'matplotlib' from https://matplotlib.org/stable/objects.inv ...
loading intersphinx inventory 'networkx' from https://networkx.org/documentation/stable/objects.inv ...
loading intersphinx inventory 'numpy' from https://numpy.org/doc/stable/objects.inv ...
loading intersphinx inventory 'pandas' from https://pandas.pydata.org/pandas-docs/stable/objects.inv ...
loading intersphinx inventory 'pynndescent' from https://pynndescent.readthedocs.io/en/latest/objects.inv ...
loading intersphinx inventory 'pytest' from https://docs.pytest.org/en/latest/objects.inv ...
loading intersphinx inventory 'python' from https://docs.python.org/3/objects.inv ...
loading intersphinx inventory 'rapids_singlecell' from https://rapids-singlecell.readthedocs.io/en/latest/objects.inv ...
loading intersphinx inventory 'scipy' from https://docs.scipy.org/doc/scipy/objects.inv ...
loading intersphinx inventory 'seaborn' from https://seaborn.pydata.org/objects.inv ...
loading intersphinx inventory 'sklearn' from https://scikit-learn.org/stable/objects.inv ...
[autosummary] generating autosummary for: 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, api/queries.md, ..., tutorials/index.md, tutorials/plotting/advanced.ipynb, tutorials/plotting/core.ipynb, tutorials/plotting/index.md, tutorials/spatial/basic-analysis.ipynb, tutorials/spatial/index.md, tutorials/spatial/integration-scanorama.ipynb, tutorials/trajectories/index.md, tutorials/trajectories/paga-paul15.ipynb, usage-principles.md
[autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3289/docs/api/generated/classes/scanpy.pl.DotPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3289/docs/api/generated/classes/scanpy.pl.MatrixPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3289/docs/api/generated/classes/scanpy.pl.StackedViolin.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3289/docs/api/generated/scanpy.pl.diffmap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3289/docs/api/generated/scanpy.pl.dpt_groups_pseudotime.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3289/docs/api/generated/scanpy.pl.dpt_timeseries.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3289/docs/api/generated/scanpy.pl.draw_graph.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3289/docs/api/generated/scanpy.pl.embedding.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3289/docs/api/generated/scanpy.pl.embedding_density.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3289/docs/api/generated/scanpy.pl.filter_genes_dispersion.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3289/docs/generated/scanpy.tl.leiden.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3289/docs/generated/scanpy.tl.louvain.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3289/docs/generated/scanpy.tl.marker_gene_overlap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3289/docs/generated/scanpy.tl.paga.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3289/docs/generated/scanpy.tl.rank_genes_groups.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3289/docs/generated/scanpy.tl.score_genes.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3289/docs/generated/scanpy.tl.score_genes_cell_cycle.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3289/docs/generated/scanpy.tl.sim.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3289/docs/generated/scanpy.tl.tsne.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3289/docs/generated/scanpy.tl.umap.rst
[autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3289/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_HEIGHT.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3289/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_WIDTH.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3289/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLORMAP.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3289/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_LEGEND_TITLE.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3289/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_ON.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3289/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGECOLOR.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3289/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGELW.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3289/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MAX.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3289/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MIN.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3289/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_LARGEST_DOT.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3289/docs/generated/scanpy._settings.ScanpyConfig.file_format_data.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3289/docs/generated/scanpy._settings.ScanpyConfig.file_format_figs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3289/docs/generated/scanpy._settings.ScanpyConfig.logfile.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3289/docs/generated/scanpy._settings.ScanpyConfig.logpath.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3289/docs/generated/scanpy._settings.ScanpyConfig.max_memory.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3289/docs/generated/scanpy._settings.ScanpyConfig.n_jobs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3289/docs/generated/scanpy._settings.ScanpyConfig.plot_suffix.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3289/docs/generated/scanpy._settings.ScanpyConfig.set_figure_params.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3289/docs/generated/scanpy._settings.ScanpyConfig.verbosity.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3289/docs/generated/scanpy._settings.ScanpyConfig.writedir.rst
building [mo]: targets for 0 po files that are out of date
writing output... 
building [html]: targets for 55 source files that are out of date
updating environment: [new config] 311 added, 0 changed, 0 removed
reading sources... [  0%] api/classes
reading sources... [  1%] api/datasets
reading sources... [  1%] api/deprecated
reading sources... [  1%] api/experimental
reading sources... [  2%] api/generated/classes/scanpy.pl.DotPlot
reading sources... [  2%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_HEIGHT
reading sources... [  2%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_WIDTH
reading sources... [  3%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLORMAP
reading sources... [  3%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_LEGEND_TITLE
reading sources... [  3%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_ON
reading sources... [  4%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGECOLOR
reading sources... [  4%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGELW
reading sources... [  4%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MAX
reading sources... [  5%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MIN
reading sources... [  5%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_LARGEST_DOT
reading sources... [  5%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_LEGENDS_WIDTH
reading sources... [  5%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_PLOT_X_PADDING
reading sources... [  6%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_PLOT_Y_PADDING
reading sources... [  6%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_SAVE_PREFIX
reading sources... [  6%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_SIZE_EXPONENT
reading sources... [  7%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_SIZE_LEGEND_TITLE
reading sources... [  7%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_SMALLEST_DOT
reading sources... [  7%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_WSPACE
reading sources... [  8%] api/generated/classes/scanpy.pl.DotPlot.MAX_NUM_CATEGORIES
reading sources... [  8%] api/generated/classes/scanpy.pl.DotPlot.MIN_FIGURE_HEIGHT
reading sources... [  8%] api/generated/classes/scanpy.pl.DotPlot.add_dendrogram
reading sources... [  9%] api/generated/classes/scanpy.pl.DotPlot.add_totals
reading sources... [  9%] api/generated/classes/scanpy.pl.DotPlot.get_axes
reading sources... [  9%] api/generated/classes/scanpy.pl.DotPlot.getdoc
reading sources... [ 10%] api/generated/classes/scanpy.pl.DotPlot.legend
reading sources... [ 10%] api/generated/classes/scanpy.pl.DotPlot.make_figure
reading sources... [ 10%] api/generated/classes/scanpy.pl.DotPlot.savefig
reading sources... [ 11%] api/generated/classes/scanpy.pl.DotPlot.show
reading sources... [ 11%] api/generated/classes/scanpy.pl.DotPlot.style
reading sources... [ 11%] api/generated/classes/scanpy.pl.DotPlot.swap_axes
reading sources... [ 12%] api/generated/classes/scanpy.pl.MatrixPlot
reading sources... [ 12%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_CATEGORY_HEIGHT
reading sources... [ 12%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_CATEGORY_WIDTH
reading sources... [ 13%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_COLORMAP
reading sources... [ 13%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_COLOR_LEGEND_TITLE
reading sources... [ 13%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_EDGE_COLOR
reading sources... [ 14%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_EDGE_LW
reading sources... [ 14%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_LEGENDS_WIDTH
reading sources... [ 14%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_SAVE_PREFIX
reading sources... [ 14%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_WSPACE
reading sources... [ 15%] api/generated/classes/scanpy.pl.MatrixPlot.MAX_NUM_CATEGORIES
reading sources... [ 15%] api/generated/classes/scanpy.pl.MatrixPlot.MIN_FIGURE_HEIGHT
reading sources... [ 15%] api/generated/classes/scanpy.pl.MatrixPlot.add_dendrogram
reading sources... [ 16%] api/generated/classes/scanpy.pl.MatrixPlot.add_totals
reading sources... [ 16%] api/generated/classes/scanpy.pl.MatrixPlot.get_axes
reading sources... [ 16%] api/generated/classes/scanpy.pl.MatrixPlot.getdoc
reading sources... [ 17%] api/generated/classes/scanpy.pl.MatrixPlot.legend
reading sources... [ 17%] api/generated/classes/scanpy.pl.MatrixPlot.make_figure
reading sources... [ 17%] api/generated/classes/scanpy.pl.MatrixPlot.savefig
reading sources... [ 18%] api/generated/classes/scanpy.pl.MatrixPlot.show
reading sources... [ 18%] api/generated/classes/scanpy.pl.MatrixPlot.style
reading sources... [ 18%] api/generated/classes/scanpy.pl.MatrixPlot.swap_axes
reading sources... [ 19%] api/generated/classes/scanpy.pl.StackedViolin
reading sources... [ 19%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_CATEGORY_HEIGHT
reading sources... [ 19%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_CATEGORY_WIDTH
reading sources... [ 20%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_COLORMAP
reading sources... [ 20%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_COLOR_LEGEND_TITLE
reading sources... [ 20%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_CUT
reading sources... [ 21%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_DENSITY_NORM
reading sources... [ 21%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_INNER
reading sources... [ 21%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_JITTER
reading sources... [ 22%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_JITTER_SIZE
reading sources... [ 22%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_LEGENDS_WIDTH
reading sources... [ 22%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_LINE_WIDTH
reading sources... [ 23%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_PLOT_X_PADDING
reading sources... [ 23%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_PLOT_YTICKLABELS
reading sources... [ 23%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_PLOT_Y_PADDING
reading sources... [ 23%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_ROW_PALETTE
reading sources... [ 24%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_SAVE_PREFIX
reading sources... [ 24%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_STRIPPLOT
reading sources... [ 24%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_WSPACE
reading sources... [ 25%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_YLIM
reading sources... [ 25%] api/generated/classes/scanpy.pl.StackedViolin.MAX_NUM_CATEGORIES
reading sources... [ 25%] api/generated/classes/scanpy.pl.StackedViolin.MIN_FIGURE_HEIGHT
reading sources... [ 26%] api/generated/classes/scanpy.pl.StackedViolin.add_dendrogram
reading sources... [ 26%] api/generated/classes/scanpy.pl.StackedViolin.add_totals
reading sources... [ 26%] api/generated/classes/scanpy.pl.StackedViolin.get_axes
reading sources... [ 27%] api/generated/classes/scanpy.pl.StackedViolin.getdoc
reading sources... [ 27%] api/generated/classes/scanpy.pl.StackedViolin.legend
reading sources... [ 27%] api/generated/classes/scanpy.pl.StackedViolin.make_figure
reading sources... [ 28%] api/generated/classes/scanpy.pl.StackedViolin.savefig
reading sources... [ 28%] api/generated/classes/scanpy.pl.StackedViolin.show
reading sources... [ 28%] api/generated/classes/scanpy.pl.StackedViolin.style
reading sources... [ 29%] api/generated/classes/scanpy.pl.StackedViolin.swap_axes
reading sources... [ 29%] api/generated/scanpy.pl.diffmap
reading sources... [ 29%] api/generated/scanpy.pl.dpt_groups_pseudotime
reading sources... [ 30%] api/generated/scanpy.pl.dpt_timeseries
reading sources... [ 30%] api/generated/scanpy.pl.draw_graph
WARNING: Package 'fa2-modified' is not installed, falling back to layout 'fr'.To use the faster and better ForceAtlas2 layout, install package 'fa2-modified' (`pip install fa2-modified`).
reading sources... [ 30%] api/generated/scanpy.pl.embedding
reading sources... [ 31%] api/generated/scanpy.pl.embedding_density
:65: (ERROR/3) no path specified
:75: (ERROR/3) no path specified
:82: (ERROR/3) no path specified
reading sources... [ 31%] api/generated/scanpy.pl.filter_genes_dispersion
reading sources... [ 31%] api/generated/scanpy.pl.highest_expr_genes
reading sources... [ 32%] api/generated/scanpy.pl.highly_variable_genes
reading sources... [ 32%] api/generated/scanpy.pl.paga

  0%|          | 0.00/23.5M [00:00<?, ?B/s]
 35%|███▍      | 8.22M/23.5M [00:00<00:00, 86.0MB/s]
 98%|█████████▊| 23.1M/23.5M [00:00<00:00, 127MB/s] 
100%|██████████| 23.5M/23.5M [00:00<00:00, 121MB/s]
reading sources... [ 32%] api/generated/scanpy.pl.paga_compare
reading sources... [ 32%] api/generated/scanpy.pl.paga_path
reading sources... [ 33%] api/generated/scanpy.pl.pca
reading sources... [ 33%] api/generated/scanpy.pl.pca_loadings
reading sources... [ 33%] api/generated/scanpy.pl.pca_overview
reading sources... [ 34%] api/generated/scanpy.pl.pca_variance_ratio
reading sources... [ 34%] api/generated/scanpy.pl.rank_genes_groups
reading sources... [ 34%] api/generated/scanpy.pl.rank_genes_groups_dotplot
WARNING: dendrogram data not found (using key=dendrogram_bulk_labels). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.
WARNING: Groups are not reordered because the `groupby` categories and the `var_group_labels` are different.
categories: CD4+/CD25 T Reg, CD4+/CD45RA+/CD25- Naive T, CD4+/CD45RO+ Memory, etc.
var_group_labels: T-cell, B-cell, myeloid
reading sources... [ 35%] api/generated/scanpy.pl.rank_genes_groups_heatmap
WARNING: dendrogram data not found (using key=dendrogram_bulk_labels). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.
WARNING: Gene labels are not shown when more than 50 genes are visualized. To show gene labels set `show_gene_labels=True`
reading sources... [ 35%] api/generated/scanpy.pl.rank_genes_groups_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... [ 35%] api/generated/scanpy.pl.rank_genes_groups_stacked_violin
reading sources... [ 36%] api/generated/scanpy.pl.rank_genes_groups_tracksplot
WARNING: dendrogram data not found (using key=dendrogram_bulk_labels). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.
reading sources... [ 36%] api/generated/scanpy.pl.rank_genes_groups_violin
reading sources... [ 36%] api/generated/scanpy.pl.scrublet_score_distribution
reading sources... [ 37%] api/generated/scanpy.pl.sim
reading sources... [ 37%] api/generated/scanpy.pl.spatial
reading sources... [ 37%] api/generated/scanpy.pl.tsne
reading sources... [ 38%] api/generated/scanpy.pl.umap
reading sources... [ 38%] api/generated/scanpy.pp.combat
reading sources... [ 38%] api/generated/scanpy.pp.neighbors
reading sources... [ 39%] api/generated/scanpy.pp.recipe_seurat
reading sources... [ 39%] api/generated/scanpy.pp.recipe_weinreb17
reading sources... [ 39%] api/generated/scanpy.pp.recipe_zheng17
reading sources... [ 40%] api/generated/scanpy.pp.scrublet
reading sources... [ 40%] api/generated/scanpy.pp.scrublet_simulate_doublets
reading sources... [ 40%] api/get
reading sources... [ 41%] api/index
reading sources... [ 41%] api/metrics
:17: (ERROR/3) no path specified
reading sources... [ 41%] api/plotting
:65: (ERROR/3) no path specified
:75: (ERROR/3) no path specified
:82: (ERROR/3) no path specified
reading sources... [ 41%] api/preprocessing
reading sources... [ 42%] api/queries
reading sources... [ 42%] api/reading
reading sources... [ 42%] api/settings
reading sources... [ 43%] api/tools
reading sources... [ 43%] basic_usage
reading sources... [ 43%] community
reading sources... [ 44%] contributors
reading sources... [ 44%] dev/ci
reading sources... [ 44%] dev/code
reading sources... [ 45%] dev/documentation
reading sources... [ 45%] dev/getting-set-up
reading sources... [ 45%] dev/index
reading sources... [ 46%] dev/release
reading sources... [ 46%] dev/testing
reading sources... [ 46%] dev/versioning
reading sources... [ 47%] ecosystem
reading sources... [ 47%] external/exporting
reading sources... [ 47%] external/generated/scanpy.external.tl.cyclone
reading sources... [ 48%] external/generated/scanpy.external.tl.harmony_timeseries
reading sources... [ 48%] external/generated/scanpy.external.tl.palantir
reading sources... [ 48%] external/generated/scanpy.external.tl.palantir_results
reading sources... [ 49%] external/generated/scanpy.external.tl.phate
reading sources... [ 49%] external/generated/scanpy.external.tl.phenograph
reading sources... [ 49%] external/generated/scanpy.external.tl.sam
reading sources... [ 50%] external/generated/scanpy.external.tl.sandbag
reading sources... [ 50%] external/generated/scanpy.external.tl.trimap
reading sources... [ 50%] external/generated/scanpy.external.tl.wishbone
reading sources... [ 50%] external/index
reading sources... [ 51%] external/plotting
reading sources... [ 51%] external/preprocessing
reading sources... [ 51%] external/tools
reading sources... [ 52%] generated/scanpy.Neighbors
reading sources... [ 52%] generated/scanpy.Neighbors.compute_eigen
reading sources... [ 52%] generated/scanpy.Neighbors.compute_neighbors
reading sources... [ 53%] generated/scanpy.Neighbors.compute_transitions
reading sources... [ 53%] generated/scanpy.Neighbors.connectivities
reading sources... [ 53%] generated/scanpy.Neighbors.distances
reading sources... [ 54%] generated/scanpy.Neighbors.distances_dpt
reading sources... [ 54%] generated/scanpy.Neighbors.eigen_basis
reading sources... [ 54%] generated/scanpy.Neighbors.eigen_values
reading sources... [ 55%] generated/scanpy.Neighbors.getdoc
reading sources... [ 55%] generated/scanpy.Neighbors.rp_forest
reading sources... [ 55%] generated/scanpy.Neighbors.to_igraph
reading sources... [ 56%] generated/scanpy.Neighbors.transitions
reading sources... [ 56%] generated/scanpy.Neighbors.transitions_sym
reading sources... [ 56%] generated/scanpy._settings.ScanpyConfig
reading sources... [ 57%] generated/scanpy._settings.ScanpyConfig.N_PCS
reading sources... [ 57%] generated/scanpy._settings.ScanpyConfig.autosave
reading sources... [ 57%] generated/scanpy._settings.ScanpyConfig.autoshow
reading sources... [ 58%] generated/scanpy._settings.ScanpyConfig.cache_compression
reading sources... [ 58%] generated/scanpy._settings.ScanpyConfig.cachedir
reading sources... [ 58%] generated/scanpy._settings.ScanpyConfig.categories_to_ignore
reading sources... [ 59%] generated/scanpy._settings.ScanpyConfig.datasetdir
reading sources... [ 59%] generated/scanpy._settings.ScanpyConfig.figdir
reading sources... [ 59%] generated/scanpy._settings.ScanpyConfig.file_format_data
reading sources... [ 59%] generated/scanpy._settings.ScanpyConfig.file_format_figs
reading sources... [ 60%] generated/scanpy._settings.ScanpyConfig.logfile
reading sources... [ 60%] generated/scanpy._settings.ScanpyConfig.logpath
reading sources... [ 60%] generated/scanpy._settings.ScanpyConfig.max_memory
reading sources... [ 61%] generated/scanpy._settings.ScanpyConfig.n_jobs
reading sources... [ 61%] generated/scanpy._settings.ScanpyConfig.plot_suffix
reading sources... [ 61%] generated/scanpy._settings.ScanpyConfig.set_figure_params
reading sources... [ 62%] generated/scanpy._settings.ScanpyConfig.verbosity
reading sources... [ 62%] generated/scanpy._settings.ScanpyConfig.writedir
reading sources... [ 62%] generated/scanpy.datasets.blobs
reading sources... [ 63%] generated/scanpy.datasets.ebi_expression_atlas
reading sources... [ 63%] generated/scanpy.datasets.krumsiek11
reading sources... [ 63%] generated/scanpy.datasets.moignard15
reading sources... [ 64%] generated/scanpy.datasets.paul15
reading sources... [ 64%] generated/scanpy.datasets.pbmc3k
reading sources... [ 64%] generated/scanpy.datasets.pbmc3k_processed
reading sources... [ 65%] generated/scanpy.datasets.pbmc68k_reduced
reading sources... [ 65%] generated/scanpy.datasets.toggleswitch
reading sources... [ 65%] generated/scanpy.datasets.visium_sge
reading sources... [ 66%] generated/scanpy.experimental.pp.highly_variable_genes
reading sources... [ 66%] generated/scanpy.experimental.pp.normalize_pearson_residuals
reading sources... [ 66%] generated/scanpy.experimental.pp.normalize_pearson_residuals_pca
reading sources... [ 67%] generated/scanpy.experimental.pp.recipe_pearson_residuals
reading sources... [ 67%] generated/scanpy.external.exporting.cellbrowser
reading sources... [ 67%] generated/scanpy.external.exporting.spring_project
reading sources... [ 68%] generated/scanpy.external.pl.phate
reading sources... [ 68%] generated/scanpy.external.pl.sam
reading sources... [ 68%] generated/scanpy.external.pl.trimap
reading sources... [ 68%] generated/scanpy.external.pl.wishbone_marker_trajectory
reading sources... [ 69%] generated/scanpy.external.pp.bbknn
reading sources... [ 69%] generated/scanpy.external.pp.dca
reading sources... [ 69%] generated/scanpy.external.pp.harmony_integrate
reading sources... [ 70%] generated/scanpy.external.pp.hashsolo
reading sources... [ 70%] generated/scanpy.external.pp.magic
reading sources... [ 70%] generated/scanpy.external.pp.mnn_correct
reading sources... [ 71%] generated/scanpy.external.pp.scanorama_integrate
reading sources... [ 71%] generated/scanpy.get.aggregate
reading sources... [ 71%] generated/scanpy.get.obs_df
reading sources... [ 72%] generated/scanpy.get.rank_genes_groups_df
reading sources... [ 72%] generated/scanpy.get.var_df
reading sources... [ 72%] generated/scanpy.logging.print_header
reading sources... [ 73%] generated/scanpy.logging.print_versions
reading sources... [ 73%] generated/scanpy.metrics.confusion_matrix
:17: (ERROR/3) no path specified
reading sources... [ 73%] generated/scanpy.metrics.gearys_c
reading sources... [ 74%] generated/scanpy.metrics.morans_i
reading sources... [ 74%] generated/scanpy.pl.clustermap
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3289/lib/python3.12/site-packages/anndata/_core/anndata.py:1754: UserWarning: Observation names are not unique. To make them unique, call `.obs_names_make_unique`.
  utils.warn_names_duplicates("obs")
reading sources... [ 74%] generated/scanpy.pl.dendrogram
reading sources... [ 75%] generated/scanpy.pl.dotplot
WARNING: dendrogram data not found (using key=dendrogram_bulk_labels). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.
WARNING: Groups are not reordered because the `groupby` categories and the `var_group_labels` are different.
categories: CD4+/CD25 T Reg, CD4+/CD45RA+/CD25- Naive T, CD4+/CD45RO+ Memory, etc.
var_group_labels: T-cell, B-cell, myeloid
reading sources... [ 75%] generated/scanpy.pl.heatmap
reading sources... [ 75%] 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... [ 76%] generated/scanpy.pl.ranking
reading sources... [ 76%] generated/scanpy.pl.scatter
reading sources... [ 76%] generated/scanpy.pl.stacked_violin
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... [ 77%] generated/scanpy.pl.tracksplot
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... [ 77%] generated/scanpy.pl.violin
reading sources... [ 77%] generated/scanpy.pp.calculate_qc_metrics

  0%|          | 0.00/5.58M [00:00<?, ?B/s]
  0%|          | 8.00k/5.58M [00:00<02:03, 47.4kB/s]
  1%|          | 32.0k/5.58M [00:00<00:57, 102kB/s] 
  2%|▏         | 96.0k/5.58M [00:00<00:25, 225kB/s]
  3%|▎         | 200k/5.58M [00:00<00:15, 375kB/s] 
  7%|▋         | 416k/5.58M [00:00<00:07, 692kB/s]
 15%|█▍        | 856k/5.58M [00:01<00:03, 1.32MB/s]
 30%|███       | 1.69M/5.58M [00:01<00:01, 2.54MB/s]
 57%|█████▋    | 3.20M/5.58M [00:01<00:00, 4.60MB/s]
 85%|████████▍ | 4.74M/5.58M [00:01<00:00, 6.02MB/s]
100%|██████████| 5.58M/5.58M [00:01<00:00, 3.60MB/s]
reading sources... [ 77%] generated/scanpy.pp.downsample_counts
reading sources... [ 78%] generated/scanpy.pp.filter_cells
reading sources... [ 78%] generated/scanpy.pp.filter_genes
reading sources... [ 78%] generated/scanpy.pp.filter_genes_dispersion
reading sources... [ 79%] generated/scanpy.pp.highly_variable_genes
reading sources... [ 79%] generated/scanpy.pp.log1p
reading sources... [ 79%] generated/scanpy.pp.normalize_per_cell
reading sources... [ 80%] generated/scanpy.pp.normalize_total
reading sources... [ 80%] generated/scanpy.pp.pca
reading sources... [ 80%] generated/scanpy.pp.regress_out
reading sources... [ 81%] generated/scanpy.pp.scale
reading sources... [ 81%] generated/scanpy.pp.subsample
reading sources... [ 81%] generated/scanpy.queries.biomart_annotations
reading sources... [ 82%] generated/scanpy.queries.enrich
reading sources... [ 82%] generated/scanpy.queries.gene_coordinates
reading sources... [ 82%] generated/scanpy.queries.mitochondrial_genes
reading sources... [ 83%] generated/scanpy.read
reading sources... [ 83%] generated/scanpy.read_10x_h5
reading sources... [ 83%] generated/scanpy.read_10x_mtx
reading sources... [ 84%] generated/scanpy.read_csv
reading sources... [ 84%] generated/scanpy.read_excel
reading sources... [ 84%] generated/scanpy.read_h5ad
reading sources... [ 85%] generated/scanpy.read_hdf
reading sources... [ 85%] generated/scanpy.read_loom
reading sources... [ 85%] generated/scanpy.read_mtx
reading sources... [ 86%] generated/scanpy.read_text
reading sources... [ 86%] generated/scanpy.read_umi_tools
reading sources... [ 86%] generated/scanpy.read_visium
reading sources... [ 86%] generated/scanpy.set_figure_params
reading sources... [ 87%] generated/scanpy.tl.dendrogram
reading sources... [ 87%] generated/scanpy.tl.diffmap
reading sources... [ 87%] generated/scanpy.tl.dpt
reading sources... [ 88%] generated/scanpy.tl.draw_graph
reading sources... [ 88%] generated/scanpy.tl.embedding_density
reading sources... [ 88%] generated/scanpy.tl.filter_rank_genes_groups
reading sources... [ 89%] generated/scanpy.tl.ingest
reading sources... [ 89%] generated/scanpy.tl.leiden
reading sources... [ 89%] generated/scanpy.tl.louvain
reading sources... [ 90%] generated/scanpy.tl.marker_gene_overlap
reading sources... [ 90%] generated/scanpy.tl.paga
reading sources... [ 90%] generated/scanpy.tl.rank_genes_groups
reading sources... [ 91%] generated/scanpy.tl.score_genes
reading sources... [ 91%] generated/scanpy.tl.score_genes_cell_cycle
reading sources... [ 91%] generated/scanpy.tl.sim
reading sources... [ 92%] generated/scanpy.tl.tsne
reading sources... [ 92%] generated/scanpy.tl.umap
reading sources... [ 92%] how-to/index
reading sources... [ 93%] how-to/knn-transformers
reading sources... [ 93%] how-to/plotting-with-marsilea
reading sources... [ 93%] index
reading sources... [ 94%] installation
reading sources... [ 94%] news
reading sources... [ 94%] references
reading sources... [ 95%] release-notes/index
reading sources... [ 95%] tutorials/basics/clustering
reading sources... [ 95%] tutorials/basics/clustering-2017
reading sources... [ 95%] tutorials/basics/index
reading sources... [ 96%] tutorials/basics/integrating-data-using-ingest
reading sources... [ 96%] tutorials/experimental/dask
reading sources... [ 96%] tutorials/experimental/index
reading sources... [ 97%] tutorials/experimental/pearson_residuals
reading sources... [ 97%] tutorials/index
reading sources... [ 97%] tutorials/plotting/advanced
reading sources... [ 98%] tutorials/plotting/core
reading sources... [ 98%] tutorials/plotting/index
reading sources... [ 98%] tutorials/spatial/basic-analysis
reading sources... [ 99%] tutorials/spatial/index
reading sources... [ 99%] tutorials/spatial/integration-scanorama
reading sources... [ 99%] tutorials/trajectories/index
reading sources... [100%] tutorials/trajectories/paga-paul15
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/3289/docs/external/generated/scanpy.external.tl.palantir.rst: document is referenced in multiple toctrees: ['external/tools', 'external/tools'], selecting: external/tools <- external/generated/scanpy.external.tl.palantir
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3289/docs/generated/scanpy.pp.pca.rst: document is referenced in multiple toctrees: ['api/preprocessing', 'api/tools'], selecting: api/tools <- generated/scanpy.pp.pca
done
preparing documents... done
copying assets... 
copying static files... 
Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3289/_readthedocs/html/_static/basic.css
Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3289/_readthedocs/html/_static/language_data.js
Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3289/_readthedocs/html/_static/documentation_options.js
Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3289/_readthedocs/html/_static/copybutton.js
copying static files: done
copying extra files... 
copying extra files: done
copying assets: done
writing output... [  0%] api/classes
writing output... [  1%] api/datasets
writing output... [  1%] api/deprecated
writing output... [  1%] api/experimental
writing output... [  2%] api/generated/classes/scanpy.pl.DotPlot
writing output... [  2%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_HEIGHT
writing output... [  2%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_WIDTH
writing output... [  3%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLORMAP
writing output... [  3%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_LEGEND_TITLE
writing output... [  3%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_ON
writing output... [  4%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGECOLOR
writing output... [  4%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGELW
writing output... [  4%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MAX
writing output... [  5%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MIN
writing output... [  5%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_LARGEST_DOT
writing output... [  5%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_LEGENDS_WIDTH
writing output... [  5%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_PLOT_X_PADDING
writing output... [  6%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_PLOT_Y_PADDING
writing output... [  6%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_SAVE_PREFIX
writing output... [  6%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_SIZE_EXPONENT
writing output... [  7%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_SIZE_LEGEND_TITLE
writing output... [  7%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_SMALLEST_DOT
writing output... [  7%] api/generated/classes/scanpy.pl.DotPlot.DEFAULT_WSPACE
writing output... [  8%] api/generated/classes/scanpy.pl.DotPlot.MAX_NUM_CATEGORIES
writing output... [  8%] api/generated/classes/scanpy.pl.DotPlot.MIN_FIGURE_HEIGHT
writing output... [  8%] api/generated/classes/scanpy.pl.DotPlot.add_dendrogram
writing output... [  9%] api/generated/classes/scanpy.pl.DotPlot.add_totals
writing output... [  9%] api/generated/classes/scanpy.pl.DotPlot.get_axes
writing output... [  9%] api/generated/classes/scanpy.pl.DotPlot.getdoc
writing output... [ 10%] api/generated/classes/scanpy.pl.DotPlot.legend
writing output... [ 10%] api/generated/classes/scanpy.pl.DotPlot.make_figure
writing output... [ 10%] api/generated/classes/scanpy.pl.DotPlot.savefig
writing output... [ 11%] api/generated/classes/scanpy.pl.DotPlot.show
writing output... [ 11%] api/generated/classes/scanpy.pl.DotPlot.style
writing output... [ 11%] api/generated/classes/scanpy.pl.DotPlot.swap_axes
writing output... [ 12%] api/generated/classes/scanpy.pl.MatrixPlot
writing output... [ 12%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_CATEGORY_HEIGHT
writing output... [ 12%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_CATEGORY_WIDTH
writing output... [ 13%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_COLORMAP
writing output... [ 13%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_COLOR_LEGEND_TITLE
writing output... [ 13%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_EDGE_COLOR
writing output... [ 14%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_EDGE_LW
writing output... [ 14%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_LEGENDS_WIDTH
writing output... [ 14%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_SAVE_PREFIX
writing output... [ 14%] api/generated/classes/scanpy.pl.MatrixPlot.DEFAULT_WSPACE
writing output... [ 15%] api/generated/classes/scanpy.pl.MatrixPlot.MAX_NUM_CATEGORIES
writing output... [ 15%] api/generated/classes/scanpy.pl.MatrixPlot.MIN_FIGURE_HEIGHT
writing output... [ 15%] api/generated/classes/scanpy.pl.MatrixPlot.add_dendrogram
writing output... [ 16%] api/generated/classes/scanpy.pl.MatrixPlot.add_totals
writing output... [ 16%] api/generated/classes/scanpy.pl.MatrixPlot.get_axes
writing output... [ 16%] api/generated/classes/scanpy.pl.MatrixPlot.getdoc
writing output... [ 17%] api/generated/classes/scanpy.pl.MatrixPlot.legend
writing output... [ 17%] api/generated/classes/scanpy.pl.MatrixPlot.make_figure
writing output... [ 17%] api/generated/classes/scanpy.pl.MatrixPlot.savefig
writing output... [ 18%] api/generated/classes/scanpy.pl.MatrixPlot.show
writing output... [ 18%] api/generated/classes/scanpy.pl.MatrixPlot.style
writing output... [ 18%] api/generated/classes/scanpy.pl.MatrixPlot.swap_axes
writing output... [ 19%] api/generated/classes/scanpy.pl.StackedViolin
writing output... [ 19%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_CATEGORY_HEIGHT
writing output... [ 19%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_CATEGORY_WIDTH
writing output... [ 20%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_COLORMAP
writing output... [ 20%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_COLOR_LEGEND_TITLE
writing output... [ 20%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_CUT
writing output... [ 21%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_DENSITY_NORM
writing output... [ 21%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_INNER
writing output... [ 21%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_JITTER
writing output... [ 22%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_JITTER_SIZE
writing output... [ 22%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_LEGENDS_WIDTH
writing output... [ 22%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_LINE_WIDTH
writing output... [ 23%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_PLOT_X_PADDING
writing output... [ 23%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_PLOT_YTICKLABELS
writing output... [ 23%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_PLOT_Y_PADDING
writing output... [ 23%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_ROW_PALETTE
writing output... [ 24%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_SAVE_PREFIX
writing output... [ 24%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_STRIPPLOT
writing output... [ 24%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_WSPACE
writing output... [ 25%] api/generated/classes/scanpy.pl.StackedViolin.DEFAULT_YLIM
writing output... [ 25%] api/generated/classes/scanpy.pl.StackedViolin.MAX_NUM_CATEGORIES
writing output... [ 25%] api/generated/classes/scanpy.pl.StackedViolin.MIN_FIGURE_HEIGHT
writing output... [ 26%] api/generated/classes/scanpy.pl.StackedViolin.add_dendrogram
writing output... [ 26%] api/generated/classes/scanpy.pl.StackedViolin.add_totals
writing output... [ 26%] api/generated/classes/scanpy.pl.StackedViolin.get_axes
writing output... [ 27%] api/generated/classes/scanpy.pl.StackedViolin.getdoc
writing output... [ 27%] api/generated/classes/scanpy.pl.StackedViolin.legend
writing output... [ 27%] api/generated/classes/scanpy.pl.StackedViolin.make_figure
writing output... [ 28%] api/generated/classes/scanpy.pl.StackedViolin.savefig
writing output... [ 28%] api/generated/classes/scanpy.pl.StackedViolin.show
writing output... [ 28%] api/generated/classes/scanpy.pl.StackedViolin.style
writing output... [ 29%] api/generated/classes/scanpy.pl.StackedViolin.swap_axes
writing output... [ 29%] api/generated/scanpy.pl.diffmap
writing output... [ 29%] api/generated/scanpy.pl.dpt_groups_pseudotime
writing output... [ 30%] api/generated/scanpy.pl.dpt_timeseries
writing output... [ 30%] api/generated/scanpy.pl.draw_graph
writing output... [ 30%] api/generated/scanpy.pl.embedding
writing output... [ 31%] api/generated/scanpy.pl.embedding_density
writing output... [ 31%] api/generated/scanpy.pl.filter_genes_dispersion
writing output... [ 31%] api/generated/scanpy.pl.highest_expr_genes
writing output... [ 32%] api/generated/scanpy.pl.highly_variable_genes
writing output... [ 32%] api/generated/scanpy.pl.paga
writing output... [ 32%] api/generated/scanpy.pl.paga_compare
writing output... [ 32%] api/generated/scanpy.pl.paga_path
writing output... [ 33%] api/generated/scanpy.pl.pca
writing output... [ 33%] api/generated/scanpy.pl.pca_loadings
writing output... [ 33%] api/generated/scanpy.pl.pca_overview
writing output... [ 34%] api/generated/scanpy.pl.pca_variance_ratio
writing output... [ 34%] api/generated/scanpy.pl.rank_genes_groups
writing output... [ 34%] api/generated/scanpy.pl.rank_genes_groups_dotplot
writing output... [ 35%] api/generated/scanpy.pl.rank_genes_groups_heatmap
writing output... [ 35%] api/generated/scanpy.pl.rank_genes_groups_matrixplot
writing output... [ 35%] api/generated/scanpy.pl.rank_genes_groups_stacked_violin
writing output... [ 36%] api/generated/scanpy.pl.rank_genes_groups_tracksplot
writing output... [ 36%] api/generated/scanpy.pl.rank_genes_groups_violin
writing output... [ 36%] api/generated/scanpy.pl.scrublet_score_distribution
writing output... [ 37%] api/generated/scanpy.pl.sim
writing output... [ 37%] api/generated/scanpy.pl.spatial
writing output... [ 37%] api/generated/scanpy.pl.tsne
writing output... [ 38%] api/generated/scanpy.pl.umap
writing output... [ 38%] api/generated/scanpy.pp.combat
writing output... [ 38%] api/generated/scanpy.pp.neighbors
writing output... [ 39%] api/generated/scanpy.pp.recipe_seurat
writing output... [ 39%] api/generated/scanpy.pp.recipe_weinreb17
writing output... [ 39%] api/generated/scanpy.pp.recipe_zheng17
writing output... [ 40%] api/generated/scanpy.pp.scrublet
writing output... [ 40%] api/generated/scanpy.pp.scrublet_simulate_doublets
writing output... [ 40%] api/get
writing output... [ 41%] api/index
writing output... [ 41%] api/metrics
writing output... [ 41%] api/plotting
writing output... [ 41%] api/preprocessing
writing output... [ 42%] api/queries
writing output... [ 42%] api/reading
writing output... [ 42%] api/settings
writing output... [ 43%] api/tools
writing output... [ 43%] basic_usage
writing output... [ 43%] community
writing output... [ 44%] contributors
writing output... [ 44%] dev/ci
writing output... [ 44%] dev/code
writing output... [ 45%] dev/documentation
writing output... [ 45%] dev/getting-set-up
writing output... [ 45%] dev/index
writing output... [ 46%] dev/release
writing output... [ 46%] dev/testing
writing output... [ 46%] dev/versioning
writing output... [ 47%] ecosystem
writing output... [ 47%] external/exporting
writing output... [ 47%] external/generated/scanpy.external.tl.cyclone
writing output... [ 48%] external/generated/scanpy.external.tl.harmony_timeseries
writing output... [ 48%] external/generated/scanpy.external.tl.palantir
writing output... [ 48%] external/generated/scanpy.external.tl.palantir_results
writing output... [ 49%] external/generated/scanpy.external.tl.phate
writing output... [ 49%] external/generated/scanpy.external.tl.phenograph
writing output... [ 49%] external/generated/scanpy.external.tl.sam
writing output... [ 50%] external/generated/scanpy.external.tl.sandbag
writing output... [ 50%] external/generated/scanpy.external.tl.trimap
writing output... [ 50%] external/generated/scanpy.external.tl.wishbone
writing output... [ 50%] external/index
writing output... [ 51%] external/plotting
writing output... [ 51%] external/preprocessing
writing output... [ 51%] external/tools
writing output... [ 52%] generated/scanpy.Neighbors
writing output... [ 52%] generated/scanpy.Neighbors.compute_eigen
writing output... [ 52%] generated/scanpy.Neighbors.compute_neighbors
writing output... [ 53%] generated/scanpy.Neighbors.compute_transitions
writing output... [ 53%] generated/scanpy.Neighbors.connectivities
writing output... [ 53%] generated/scanpy.Neighbors.distances
writing output... [ 54%] generated/scanpy.Neighbors.distances_dpt
writing output... [ 54%] generated/scanpy.Neighbors.eigen_basis
writing output... [ 54%] generated/scanpy.Neighbors.eigen_values
writing output... [ 55%] generated/scanpy.Neighbors.getdoc
writing output... [ 55%] generated/scanpy.Neighbors.rp_forest
writing output... [ 55%] generated/scanpy.Neighbors.to_igraph
writing output... [ 56%] generated/scanpy.Neighbors.transitions
writing output... [ 56%] generated/scanpy.Neighbors.transitions_sym
writing output... [ 56%] generated/scanpy._settings.ScanpyConfig
writing output... [ 57%] generated/scanpy._settings.ScanpyConfig.N_PCS
writing output... [ 57%] generated/scanpy._settings.ScanpyConfig.autosave
writing output... [ 57%] generated/scanpy._settings.ScanpyConfig.autoshow
writing output... [ 58%] generated/scanpy._settings.ScanpyConfig.cache_compression
writing output... [ 58%] generated/scanpy._settings.ScanpyConfig.cachedir
writing output... [ 58%] generated/scanpy._settings.ScanpyConfig.categories_to_ignore
writing output... [ 59%] generated/scanpy._settings.ScanpyConfig.datasetdir
writing output... [ 59%] generated/scanpy._settings.ScanpyConfig.figdir
writing output... [ 59%] generated/scanpy._settings.ScanpyConfig.file_format_data
writing output... [ 59%] generated/scanpy._settings.ScanpyConfig.file_format_figs
writing output... [ 60%] generated/scanpy._settings.ScanpyConfig.logfile
writing output... [ 60%] generated/scanpy._settings.ScanpyConfig.logpath
writing output... [ 60%] generated/scanpy._settings.ScanpyConfig.max_memory
writing output... [ 61%] generated/scanpy._settings.ScanpyConfig.n_jobs
writing output... [ 61%] generated/scanpy._settings.ScanpyConfig.plot_suffix
writing output... [ 61%] generated/scanpy._settings.ScanpyConfig.set_figure_params
writing output... [ 62%] generated/scanpy._settings.ScanpyConfig.verbosity
writing output... [ 62%] generated/scanpy._settings.ScanpyConfig.writedir
writing output... [ 62%] generated/scanpy.datasets.blobs
writing output... [ 63%] generated/scanpy.datasets.ebi_expression_atlas
writing output... [ 63%] generated/scanpy.datasets.krumsiek11
writing output... [ 63%] generated/scanpy.datasets.moignard15
writing output... [ 64%] generated/scanpy.datasets.paul15
writing output... [ 64%] generated/scanpy.datasets.pbmc3k
writing output... [ 64%] generated/scanpy.datasets.pbmc3k_processed
writing output... [ 65%] generated/scanpy.datasets.pbmc68k_reduced
writing output... [ 65%] generated/scanpy.datasets.toggleswitch
writing output... [ 65%] generated/scanpy.datasets.visium_sge
writing output... [ 66%] generated/scanpy.experimental.pp.highly_variable_genes
writing output... [ 66%] generated/scanpy.experimental.pp.normalize_pearson_residuals
writing output... [ 66%] generated/scanpy.experimental.pp.normalize_pearson_residuals_pca
writing output... [ 67%] generated/scanpy.experimental.pp.recipe_pearson_residuals
writing output... [ 67%] generated/scanpy.external.exporting.cellbrowser
writing output... [ 67%] generated/scanpy.external.exporting.spring_project
writing output... [ 68%] generated/scanpy.external.pl.phate
writing output... [ 68%] generated/scanpy.external.pl.sam
writing output... [ 68%] generated/scanpy.external.pl.trimap
writing output... [ 68%] generated/scanpy.external.pl.wishbone_marker_trajectory
writing output... [ 69%] generated/scanpy.external.pp.bbknn
writing output... [ 69%] generated/scanpy.external.pp.dca
writing output... [ 69%] generated/scanpy.external.pp.harmony_integrate
writing output... [ 70%] generated/scanpy.external.pp.hashsolo
writing output... [ 70%] generated/scanpy.external.pp.magic
writing output... [ 70%] generated/scanpy.external.pp.mnn_correct
writing output... [ 71%] generated/scanpy.external.pp.scanorama_integrate
writing output... [ 71%] generated/scanpy.get.aggregate
writing output... [ 71%] generated/scanpy.get.obs_df
writing output... [ 72%] generated/scanpy.get.rank_genes_groups_df
writing output... [ 72%] generated/scanpy.get.var_df
writing output... [ 72%] generated/scanpy.logging.print_header
writing output... [ 73%] generated/scanpy.logging.print_versions
writing output... [ 73%] generated/scanpy.metrics.confusion_matrix
writing output... [ 73%] generated/scanpy.metrics.gearys_c
writing output... [ 74%] generated/scanpy.metrics.morans_i
writing output... [ 74%] generated/scanpy.pl.clustermap
writing output... [ 74%] generated/scanpy.pl.dendrogram
writing output... [ 75%] generated/scanpy.pl.dotplot
writing output... [ 75%] generated/scanpy.pl.heatmap
writing output... [ 75%] generated/scanpy.pl.matrixplot
writing output... [ 76%] generated/scanpy.pl.ranking
writing output... [ 76%] generated/scanpy.pl.scatter
writing output... [ 76%] generated/scanpy.pl.stacked_violin
writing output... [ 77%] generated/scanpy.pl.tracksplot
writing output... [ 77%] generated/scanpy.pl.violin
writing output... [ 77%] generated/scanpy.pp.calculate_qc_metrics
writing output... [ 77%] generated/scanpy.pp.downsample_counts
writing output... [ 78%] generated/scanpy.pp.filter_cells
writing output... [ 78%] generated/scanpy.pp.filter_genes
writing output... [ 78%] generated/scanpy.pp.filter_genes_dispersion
writing output... [ 79%] generated/scanpy.pp.highly_variable_genes
writing output... [ 79%] generated/scanpy.pp.log1p
writing output... [ 79%] generated/scanpy.pp.normalize_per_cell
writing output... [ 80%] generated/scanpy.pp.normalize_total
writing output... [ 80%] generated/scanpy.pp.pca
writing output... [ 80%] generated/scanpy.pp.regress_out
writing output... [ 81%] generated/scanpy.pp.scale
writing output... [ 81%] generated/scanpy.pp.subsample
writing output... [ 81%] generated/scanpy.queries.biomart_annotations
writing output... [ 82%] generated/scanpy.queries.enrich
writing output... [ 82%] generated/scanpy.queries.gene_coordinates
writing output... [ 82%] generated/scanpy.queries.mitochondrial_genes
writing output... [ 83%] generated/scanpy.read
writing output... [ 83%] generated/scanpy.read_10x_h5
writing output... [ 83%] generated/scanpy.read_10x_mtx
writing output... [ 84%] generated/scanpy.read_csv
writing output... [ 84%] generated/scanpy.read_excel
writing output... [ 84%] generated/scanpy.read_h5ad
writing output... [ 85%] generated/scanpy.read_hdf
writing output... [ 85%] generated/scanpy.read_loom
writing output... [ 85%] generated/scanpy.read_mtx
writing output... [ 86%] generated/scanpy.read_text
writing output... [ 86%] generated/scanpy.read_umi_tools
writing output... [ 86%] generated/scanpy.read_visium
writing output... [ 86%] generated/scanpy.set_figure_params
writing output... [ 87%] generated/scanpy.tl.dendrogram
writing output... [ 87%] generated/scanpy.tl.diffmap
writing output... [ 87%] generated/scanpy.tl.dpt
writing output... [ 88%] generated/scanpy.tl.draw_graph
writing output... [ 88%] generated/scanpy.tl.embedding_density
writing output... [ 88%] generated/scanpy.tl.filter_rank_genes_groups
writing output... [ 89%] generated/scanpy.tl.ingest
writing output... [ 89%] generated/scanpy.tl.leiden
writing output... [ 89%] generated/scanpy.tl.louvain
writing output... [ 90%] generated/scanpy.tl.marker_gene_overlap
writing output... [ 90%] generated/scanpy.tl.paga
writing output... [ 90%] generated/scanpy.tl.rank_genes_groups
writing output... [ 91%] generated/scanpy.tl.score_genes
writing output... [ 91%] generated/scanpy.tl.score_genes_cell_cycle
writing output... [ 91%] generated/scanpy.tl.sim
writing output... [ 92%] generated/scanpy.tl.tsne
writing output... [ 92%] generated/scanpy.tl.umap
writing output... [ 92%] how-to/index
writing output... [ 93%] how-to/knn-transformers
writing output... [ 93%] how-to/plotting-with-marsilea
writing output... [ 93%] index
writing output... [ 94%] installation
writing output... [ 94%] news
writing output... [ 94%] references
writing output... [ 95%] release-notes/index
writing output... [ 95%] tutorials/basics/clustering
writing output... [ 95%] tutorials/basics/clustering-2017
writing output... [ 95%] tutorials/basics/index
writing output... [ 96%] tutorials/basics/integrating-data-using-ingest
writing output... [ 96%] tutorials/experimental/dask
writing output... [ 96%] tutorials/experimental/index
writing output... [ 97%] tutorials/experimental/pearson_residuals
writing output... [ 97%] tutorials/index
writing output... [ 97%] tutorials/plotting/advanced
writing output... [ 98%] tutorials/plotting/core
writing output... [ 98%] tutorials/plotting/index
writing output... [ 98%] tutorials/spatial/basic-analysis
writing output... [ 99%] tutorials/spatial/index
writing output... [ 99%] tutorials/spatial/integration-scanorama
writing output... [ 99%] tutorials/trajectories/index
writing output... [100%] tutorials/trajectories/paga-paul15
writing output... [100%] usage-principles

generating indices... genindex py-modindex done
writing additional pages... search done
copying images... [  0%] _build/plot_directive/api/generated/classes/scanpy-pl-MatrixPlot-1.png
copying images... [  1%] _build/plot_directive/api/generated/classes/scanpy-pl-MatrixPlot-2.png
copying images... [  1%] _build/plot_directive/api/generated/classes/scanpy-pl-MatrixPlot-style-2.png
copying images... [  2%] _build/plot_directive/api/generated/scanpy-pl-diffmap-1.png
copying images... [  2%] _build/plot_directive/api/generated/scanpy-pl-draw_graph-1.png
copying images... [  3%] _build/plot_directive/api/generated/scanpy-pl-embedding_density-2.png
copying images... [  3%] _build/plot_directive/api/generated/scanpy-pl-embedding_density-3.png
copying images... [  4%] _build/plot_directive/api/generated/scanpy-pl-paga-1.png
copying images... [  4%] _build/plot_directive/api/generated/scanpy-pl-paga-2.png
copying images... [  4%] _build/plot_directive/api/generated/scanpy-pl-pca-1.png
copying images... [  5%] _build/plot_directive/api/generated/scanpy-pl-pca-2.png
copying images... [  5%] _build/plot_directive/api/generated/scanpy-pl-pca-3.png
copying images... [  6%] _build/plot_directive/api/generated/scanpy-pl-pca_loadings-2.png
copying images... [  6%] _build/plot_directive/api/generated/scanpy-pl-pca_overview-1_00.png
copying images... [  7%] _build/plot_directive/api/generated/scanpy-pl-pca_overview-1_01.png
copying images... [  7%] _build/plot_directive/api/generated/scanpy-pl-pca_overview-1_02.png
copying images... [  8%] _build/plot_directive/api/generated/scanpy-pl-rank_genes_groups-1.png
copying images... [  8%] _build/plot_directive/api/generated/scanpy-pl-rank_genes_groups-2.png
copying images... [  9%] _build/plot_directive/api/generated/scanpy-pl-rank_genes_groups_dotplot-2.png
copying images... [  9%] _build/plot_directive/api/generated/scanpy-pl-rank_genes_groups_dotplot-3.png
copying images... [  9%] _build/plot_directive/api/generated/scanpy-pl-rank_genes_groups_dotplot-4.png
copying images... [ 10%] _build/plot_directive/api/generated/scanpy-pl-rank_genes_groups_dotplot-5.png
copying images... [ 10%] _build/plot_directive/api/generated/scanpy-pl-rank_genes_groups_dotplot-6.png
copying images... [ 11%] _build/plot_directive/api/generated/scanpy-pl-rank_genes_groups_heatmap-1.png
copying images... [ 11%] _build/plot_directive/api/generated/scanpy-pl-rank_genes_groups_heatmap-2.png
copying images... [ 12%] _build/plot_directive/api/generated/scanpy-pl-rank_genes_groups_heatmap-3.png
copying images... [ 12%] _build/plot_directive/api/generated/scanpy-pl-rank_genes_groups_matrixplot-2.png
copying images... [ 13%] _build/plot_directive/api/generated/scanpy-pl-rank_genes_groups_matrixplot-3.png
copying images... [ 13%] _build/plot_directive/api/generated/scanpy-pl-rank_genes_groups_matrixplot-4.png
copying images... [ 13%] _build/plot_directive/api/generated/scanpy-pl-rank_genes_groups_tracksplot-1.png
copying images... [ 14%] _build/plot_directive/api/generated/scanpy-pl-tsne-1.png
copying images... [ 14%] _build/plot_directive/api/generated/scanpy-pl-umap-1.png
copying images... [ 15%] _build/plot_directive/api/generated/scanpy-pl-umap-2.png
copying images... [ 15%] _build/plot_directive/api/generated/scanpy-pl-umap-3.png
copying images... [ 16%] _build/plot_directive/api/generated/scanpy-pl-umap-4.png
copying images... [ 16%] _static/img/ci_plot-view_tests-tab.png
copying images... [ 17%] _static/img/ci_plot-view_select-test.png
copying images... [ 17%] _static/img/ci_plot-view_attachment-tab.png
copying images... [ 17%] _build/plot_directive/generated/scanpy-metrics-confusion_matrix-1.png
copying images... [ 18%] _build/plot_directive/generated/scanpy-pl-clustermap-1.png
copying images... [ 18%] _build/plot_directive/generated/scanpy-pl-clustermap-2.png
copying images... [ 19%] _build/plot_directive/generated/scanpy-pl-dendrogram-1.png
copying images... [ 19%] _build/plot_directive/generated/scanpy-pl-dotplot-1.png
copying images... [ 20%] _build/plot_directive/generated/scanpy-pl-dotplot-2.png
copying images... [ 20%] _build/plot_directive/generated/scanpy-pl-dotplot-3.png
copying images... [ 21%] _build/plot_directive/generated/scanpy-pl-heatmap-1.png
copying images... [ 21%] _build/plot_directive/generated/scanpy-pl-matrixplot-1.png
copying images... [ 22%] _build/plot_directive/generated/scanpy-pl-matrixplot-2.png
copying images... [ 22%] _build/plot_directive/generated/scanpy-pl-matrixplot-3.png
copying images... [ 22%] _build/plot_directive/generated/scanpy-pl-stacked_violin-1.png
copying images... [ 23%] _build/plot_directive/generated/scanpy-pl-stacked_violin-2.png
copying images... [ 23%] _build/plot_directive/generated/scanpy-pl-stacked_violin-3.png
copying images... [ 24%] _build/plot_directive/generated/scanpy-pl-tracksplot-1.png
copying images... [ 24%] _build/plot_directive/generated/scanpy-pl-tracksplot-2.png
copying images... [ 25%] _build/plot_directive/generated/scanpy-pl-violin-1.png
copying images... [ 25%] _build/plot_directive/generated/scanpy-pl-violin-2.png
copying images... [ 26%] _build/plot_directive/generated/scanpy-pl-violin-3.png
copying images... [ 26%] _build/plot_directive/generated/scanpy-pl-violin-4.png
copying images... [ 26%] _build/plot_directive/generated/scanpy-pl-violin-5.png
copying images... [ 27%] _build/plot_directive/generated/scanpy-pp-calculate_qc_metrics-1.png
copying images... [ 27%] _build/plot_directive/generated/scanpy-pp-calculate_qc_metrics-2.png
copying images... [ 28%] _build/plot_directive/generated/scanpy-tl-embedding_density-1.png
copying images... [ 28%] _build/plot_directive/generated/scanpy-tl-embedding_density-2.png
copying images... [ 29%] ../_readthedocs/jupyter_execute/ad8d8a4b869e02ab2b2ca1c0cddab9f8150214bfc27e6036a49ab5d854f5983c.png
copying images... [ 29%] ../_readthedocs/jupyter_execute/ba1422e2b60f77f4c59fc07a3c5ba6e7f359b149f5b44d7efe832e736794d28e.png
copying images... [ 30%] ../_readthedocs/jupyter_execute/2ad8c5624f6b1b9c504a9523579d15ea2f93a9fd5b609091b38786f953fe046b.png
copying images... [ 30%] ../_readthedocs/jupyter_execute/da883131a1fe9eb22a8c860e07c36a34e00e64e4442b006d9dde552fc2a40ead.png
copying images... [ 30%] ../_readthedocs/jupyter_execute/d81354fd0bdf8a72378abcefbc182d8285486fa17d8bd53f0c1f47b6cd1d28c4.png
copying images... [ 31%] ../_readthedocs/jupyter_execute/2d213968ea3f453f2cae74ae49e17f1fec45a53a476ae046b14010f283eda1a7.png
copying images... [ 31%] ../_readthedocs/jupyter_execute/4d8511ed85ad86dbf378823408503c528a42a79cd98b0e04f7be0f949decd72d.png
copying images... [ 32%] ../_readthedocs/jupyter_execute/4391834d507f58697345693f7e02b03afbb9057c3fe0d8386df4a8596d54803d.png
copying images... [ 32%] ../_readthedocs/jupyter_execute/e1ed4633b95cd6bec57e431a9b5349d46a96ac78dd24940d173cd3fca0428694.png
copying images... [ 33%] ../_readthedocs/jupyter_execute/a8fd5ce09328052fe68df76c87130f355b9a63a46d81cbfd679a2c87cb6ab4e7.png
copying images... [ 33%] ../_readthedocs/jupyter_execute/28915039aa4b875685c8d73a7139b94924f2a96e9041916eaeb5d593c3bace11.png
copying images... [ 34%] ../_readthedocs/jupyter_execute/2369cb7f97a8853b39251e0ca2ccae217e8613cbea0bf8c599d13adfed54622b.png
copying images... [ 34%] ../_readthedocs/jupyter_execute/3385e74bc3cd67483b2cc40687bbe1089c590fd399799f887c24323ea25ea637.png
copying images... [ 35%] ../_readthedocs/jupyter_execute/83a982f840b154da4420735c806689e16b150ad10ab64372e4ad9c0404390dd3.png
copying images... [ 35%] ../_readthedocs/jupyter_execute/9a168f2d7a68905521ea3fb1ef5a0ac2a22d65e6a5e7c3796a55da1c24c28cb1.png
copying images... [ 35%] ../_readthedocs/jupyter_execute/bd436a0a79afac682ff8132b32d4c90d3f74738d57e07f5743a03a55d9f82f68.png
copying images... [ 36%] ../_readthedocs/jupyter_execute/12e4e27cf02e408effd640d9a5846b20c0b4ea4856511e9af58f5743897aaf38.png
copying images... [ 36%] ../_readthedocs/jupyter_execute/e77d6bf9cd6e938808b2d57ffd8840f0d1aa27233c819a4f8f7b9fdd1d6a44cb.png
copying images... [ 37%] ../_readthedocs/jupyter_execute/610d17bf258b0cc0d840713ebac7867cf292c626df2e807ebd78b459a03ebd28.png
copying images... [ 37%] ../_readthedocs/jupyter_execute/08cb70daba840353bbf8529bf9f27d6121451a8200114c5b77f581df4bbf1a7b.png
copying images... [ 38%] ../_readthedocs/jupyter_execute/2b92963adeb5c28502e023b24967f509deb537d668944e8bec22585c1e66e341.png
copying images... [ 38%] ../_readthedocs/jupyter_execute/7c615842aa3a955f46581c1333bbb91b74a2fb9d38b7f18966a67a39cb1ce0f2.png
copying images... [ 39%] ../_readthedocs/jupyter_execute/17e024239d09ec7c14e90bdb43ea70d7959aab70f7e5d3d2f1620a8f96b77809.png
copying images... [ 39%] ../_readthedocs/jupyter_execute/e103233bd60eaaf71b1bee1293d49a4732a3e96a1e206df311d8166de065a188.png
copying images... [ 39%] ../_readthedocs/jupyter_execute/d016caf498b3b59f81afddca30abfa1354fc0d904eaa8c69776bf7c4e305996e.png
copying images... [ 40%] ../_readthedocs/jupyter_execute/ed9881bebcd5953137fcf30e4944fcbce5e7c4c12ab667db72f7d3f36f30058c.png
copying images... [ 40%] ../_readthedocs/jupyter_execute/4e88edca93fd310f0fe7af62ca93ebfc2a687d57d4b7e1a304672ab51a7c334c.png
copying images... [ 41%] ../_readthedocs/jupyter_execute/78c4088c92321073845e76b14c463511cf819c903177837bab5830af28206b6d.png
copying images... [ 41%] ../_readthedocs/jupyter_execute/4b7f38e2f2ae84492a518033c5ea9acdf496e9d985c703a948461b7224ab7c7e.png
copying images... [ 42%] ../_readthedocs/jupyter_execute/b11c7408eca682f8840ad5974baf5b67ddf7f8dcd9cdc8fec16a159855c0f9df.png
copying images... [ 42%] ../_readthedocs/jupyter_execute/d6b0abc906341f62df41f52067ab313e90d255581ce270e098053d39cae128ca.png
copying images... [ 43%] ../_readthedocs/jupyter_execute/e1560db6d51bccaee68e079db3ad3949f757e8912b9f99e206553e29a0915a22.png
copying images... [ 43%] ../_readthedocs/jupyter_execute/27d036a5d6d7facd8c3477df4c73077f64a6e637dc2e9373ab748835bc0c164b.png
copying images... [ 43%] ../_readthedocs/jupyter_execute/1924a655d8cbd9eb7a2434785ace6d9aacb7671af2c4035e48f24c59b88c548b.png
copying images... [ 44%] ../_readthedocs/jupyter_execute/63c86bf6eddeeee0e414bda8b8a6fb8f5b5fff1ed3e150d9a7fc31e7bade41a2.png
copying images... [ 44%] ../_readthedocs/jupyter_execute/a62ffd0e54feefbc602c045f8a44b87eb8c34389dfcc494602106f48897f1c30.png
copying images... [ 45%] ../_readthedocs/jupyter_execute/b7b449588533a3dbf01ca62c09659bf7e37fc69e7752917ed5db79f675cdb568.png
copying images... [ 45%] ../_readthedocs/jupyter_execute/fe768d7ddf7cad3bd2ecb53b2fd22e523e633ea9b3eac51aa68263e887dde546.png
copying images... [ 46%] ../_readthedocs/jupyter_execute/ef86c97c8ed4bb775254b9ca517c73b155da3fe8a0ebafc5362d55cfe0bb712b.png
copying images... [ 46%] ../_readthedocs/jupyter_execute/fb6b92c2fa4efe78b509bf4ad1bf17229de0a8a52f82b3c916ad107243b3e292.png
copying images... [ 47%] ../_readthedocs/jupyter_execute/48194bcf5b08aeaa814cd6e68a786a20c47d7bd3da16610cfa322d2e5d7f8a44.png
copying images... [ 47%] ../_readthedocs/jupyter_execute/0297752065ba2b790aec52ff2e6d24fdd469b5050fd81c8e19f31499648d8bad.png
copying images... [ 48%] ../_readthedocs/jupyter_execute/66235fc964a35fcf52eb3497082c6feb3d49f0259d6371adb9c4ff0bf06bbb1a.png
copying images... [ 48%] ../_readthedocs/jupyter_execute/3110dba6d70db7bd0b80ed087dd44f51240ba3687de97ed076f4e169e921a37f.png
copying images... [ 48%] ../_readthedocs/jupyter_execute/8243aacd081a724d22b1322a34b4ef92378fbb60712907853dbebc8a8f5de106.png
copying images... [ 49%] ../_readthedocs/jupyter_execute/542415f9bd02cc1108d982f182bea4116ed2a182764ad41d095c6a0a5d712cdc.png
copying images... [ 49%] ../_readthedocs/jupyter_execute/21423d090d5deec30ffffaf9fe999cabf3897e83fc08febea1ebcb0048b14b9e.png
copying images... [ 50%] ../_readthedocs/jupyter_execute/3fbf51d0bc0256b8b387de3510d6964aa24372f671d2085d798d1fc2bc1428c4.png
copying images... [ 50%] ../_readthedocs/jupyter_execute/fdbd63abd20448ff20607bdcd4da6f91db2db9c9c541e66f3520e04f1bedbadf.png
copying images... [ 51%] ../_readthedocs/jupyter_execute/1af1296c7ed0c06d2815caeb3a8c31b62d471620af488450173c8a05d54dad6d.png
copying images... [ 51%] ../_readthedocs/jupyter_execute/cc1dfa9ffb1eec5439a19e1ca9f612225a9597aa6a2a26b3e378009b972e942b.png
copying images... [ 52%] ../_readthedocs/jupyter_execute/c0104eda27200a144158abe264ff469d18727eb9bafbab10dba115548ca922af.png
copying images... [ 52%] ../_readthedocs/jupyter_execute/78103d8a616e5b464c6c563b549fc57bbadd4b155e2c0e305fcb9f28b4e1b40d.png
copying images... [ 52%] ../_readthedocs/jupyter_execute/cbdc500ce63e341c08c1ce211be52d703d16f4783b5666affe8f4f4a60e703b3.png
copying images... [ 53%] ../_readthedocs/jupyter_execute/409b2243634a8a3383d9f328335c9b5db8fc9315a4144d3a35b17edc6b9a4c0d.png
copying images... [ 53%] ../_readthedocs/jupyter_execute/ed18200ddf3d74f299e2d77ddb844cba0b52270d67c35b71be7a0d45b4b4b26e.png
copying images... [ 54%] ../_readthedocs/jupyter_execute/4492033e1eb9e476766c6942aabd46eaad2b3228f96b3e28cb643a2ad98fb4d1.png
copying images... [ 54%] ../_readthedocs/jupyter_execute/59119cceab24bf4920c184099992be16e9207c2857690ae3bb5455a637148f03.png
copying images... [ 55%] ../_readthedocs/jupyter_execute/f1c33f7271e9dd8c8f62f05945b8ceb1aed19e37619e234afc2be95ecc9ba5a6.png
copying images... [ 55%] ../_readthedocs/jupyter_execute/18f10d98f7b0d26476b4fd0d77cf726419d9db9db0ac6c051c7fccd57ebddc83.png
copying images... [ 56%] ../_readthedocs/jupyter_execute/13cc6c1d53e9a3aba72799cd93759ce396bc0cf762f3b46d5a762e2e276cd168.png
copying images... [ 56%] ../_readthedocs/jupyter_execute/5f159fa54af4fc9b8f206c572e1b24b1f1eb24f3711032a9892df784cc5bdd7c.png
copying images... [ 57%] ../_readthedocs/jupyter_execute/2eba1ec7ea236ae4f0ec8644785ccb3e4c08e44a3615eb1f0fcecbf277c408ae.png
copying images... [ 57%] ../_readthedocs/jupyter_execute/67a8f588f5e935db5d190240996d7ef24c757b99131454c54c9a4463823244a5.png
copying images... [ 57%] ../_readthedocs/jupyter_execute/915d74a745633da1ae5a4b91ea8bde5ace438f0cb3c103f3908c86e8166b46b1.png
copying images... [ 58%] ../_readthedocs/jupyter_execute/2e949f6382ce68273faebe569154569a3ee12f69ebcd948c449e0354db3c3858.png
copying images... [ 58%] ../_readthedocs/jupyter_execute/c4c7363df186dd1e25bb52b3ab60a88f27e65c5fd273d15d0e8e90d084b61a10.png
copying images... [ 59%] ../_readthedocs/jupyter_execute/58a1e8c7549f5784c7d394c45d782825e39f1bdf074e3fdded8f85138303dbb8.png
copying images... [ 59%] ../_readthedocs/jupyter_execute/f70cfa87abeee08705f1c0f68850c7f473f43cd828bd61d505236881b3929ea3.png
copying images... [ 60%] ../_readthedocs/jupyter_execute/18bc84a5f8b79b26336676391d299a04a557a748cf1d07ed08e6e8cac7da4c96.png
copying images... [ 60%] ../_readthedocs/jupyter_execute/db7abd6c2ccafd0838aad46c2bc2b048630dbb12171d5517102e5c05ff61195e.png
copying images... [ 61%] ../_readthedocs/jupyter_execute/dfecea44c594db8a640293ba3b83b768f0f8fffb11feb06bb02a9db87ac88f07.png
copying images... [ 61%] ../_readthedocs/jupyter_execute/dd9bd20407057e3f381a408e020551eab4a8158f49ffb9a4a5df3182d2245762.png
copying images... [ 61%] ../_readthedocs/jupyter_execute/5894ed27c5482d0a22c852ad7ec122674a5403866dfc7b981dc53aaa358cd43c.png
copying images... [ 62%] ../_readthedocs/jupyter_execute/9dde4846823e894d0bd646d737d64babb11955d44121dd294a676ecda2030ff7.png
copying images... [ 62%] ../_readthedocs/jupyter_execute/56b1242b1fc93eb876458f16b792cfc8f378a7ecc1fd970d8a885833f3d7a134.png
copying images... [ 63%] ../_readthedocs/jupyter_execute/75e95ac30061d0a6c4b5bbf3d3e5a9680b19ff08269fe2d8ea59ab10a023914e.png
copying images... [ 63%] ../_readthedocs/jupyter_execute/71c776827198f5562510afe4c17873f7d10a2a35357ffe4aeaa128a78e788e1b.png
copying images... [ 64%] ../_readthedocs/jupyter_execute/2d65107bba327ff05ed6987cc4c2777b641bed01c1ba09b6cc252a8e67c11998.png
copying images... [ 64%] ../_readthedocs/jupyter_execute/656a59ad999749dafe447f6f02f9dc776d629197c94870a322466e09d20cb963.png
copying images... [ 65%] ../_readthedocs/jupyter_execute/1e16be2728eeb5c9ab9542cc63fb3644e3b7c76f944de373115f046e2bddaa41.png
copying images... [ 65%] ../_readthedocs/jupyter_execute/00e09d35a6edfcfa22e4469241715ce73a888cecd411514d94cd40d382f41e22.png
copying images... [ 65%] ../_readthedocs/jupyter_execute/fec4e153d5cfd92a83fcba1cc62c2cdec87e8e91e1cb6f6b083ba8bf0f20f406.png
copying images... [ 66%] ../_readthedocs/jupyter_execute/5a26fa44dcc471d706f3f7ecf801d3cf31743edbb836a393073e937ab85c7237.png
copying images... [ 66%] ../_readthedocs/jupyter_execute/a7ed97e5192d909da6c3aef055bd93d31530c357a5110bf8219524f59aea1f47.png
copying images... [ 67%] ../_readthedocs/jupyter_execute/114213c032705aeaf87f170cedba7f54024e21f20b59eff12c40067b3eff9d64.png
copying images... [ 67%] ../_readthedocs/jupyter_execute/4b80a8ebb2fe694a361810d5829ad423339dec1272a186549a7f918f37259dd9.png
copying images... [ 68%] ../_readthedocs/jupyter_execute/0f9a0935c010d0ca3f3e91c8fa02275b0be7c9ee8e544f273cbb72a6a0ce3350.png
copying images... [ 68%] ../_readthedocs/jupyter_execute/03cce8ccfd5513f7ddc46190831f275b68395b19629c77570c13b7bb2ef5c0fd.png
copying images... [ 69%] ../_readthedocs/jupyter_execute/95d4d301cb8d8f1010e6cd414b366f4226bcaa19ee061e88e0366e862ceca920.png
copying images... [ 69%] ../_readthedocs/jupyter_execute/d5a3a68c99b881daa67c137c3d7bc76e191396f0a10909e3c86a00a4a5c3075c.png
copying images... [ 70%] ../_readthedocs/jupyter_execute/fc25f73c02ceb1211cb72c585ad3dc7b21852f9c79f8a4477e41a704f851dbaf.png
copying images... [ 70%] ../_readthedocs/jupyter_execute/f8a3a5f206cfdbc8fb57787377fb9f7ed9aee4755e69529878a36325eb9d9d3e.png
copying images... [ 70%] ../_readthedocs/jupyter_execute/014721e47639c9d7f9c1d1a707959e3c7d87bee55dab814b24034ef26bee0cd8.png
copying images... [ 71%] ../_readthedocs/jupyter_execute/82bf8185351514bbacde2d71cdbed19bd39ad9914092251bd40b07b1cc9ec0dc.png
copying images... [ 71%] ../_readthedocs/jupyter_execute/47e219415022be69ebab4ddc0dc565d07df0d0e7ec71e622d328381286b0cdb3.png
copying images... [ 72%] ../_readthedocs/jupyter_execute/bc2843555a0c778a2bc285fea5f772e8357d4f62eff7531e77a08e1c58094456.png
copying images... [ 72%] ../_readthedocs/jupyter_execute/57be388755512bf1c4bece588c87eeb6fc5c9961ca87791671a11abb9472dcf6.png
copying images... [ 73%] ../_readthedocs/jupyter_execute/f5fb8a678ef83c003c35c7b020573f9e2aab56cddf2a5a701e28f2735f83422b.png
copying images... [ 73%] ../_readthedocs/jupyter_execute/d21985bcdf27832fccc189399bdaef7bee22ef093bdd40da4061dc10b9b1baed.png
copying images... [ 74%] ../_readthedocs/jupyter_execute/2aa081589d93ba1ae17c10722df228186adf87c3c43905fc2b887185d1dde828.png
copying images... [ 74%] ../_readthedocs/jupyter_execute/95d9bc0fcfc65573d6ce802c62532cbda2ce8ecbc4ad06e1f1a731afa50527b3.png
copying images... [ 74%] ../_readthedocs/jupyter_execute/02d019ffed26debe94c69e5adbb17bb52797c8b6b9a7a18512cbf8c7d7fb59ac.png
copying images... [ 75%] ../_readthedocs/jupyter_execute/4d533bc71a9c43e23187261bcaf2bf4886d883f16a387ccd810c160d2568eeb4.png
copying images... [ 75%] ../_readthedocs/jupyter_execute/cbc036ce11fe42ce6583bcbd1e43942af679d7892b61bca04050a791bacbf83b.png
copying images... [ 76%] ../_readthedocs/jupyter_execute/477a99eb112ecbc4b0e1c526f14ec5a27a1fb25bb6eae3c49e5ec57142142d0d.png
copying images... [ 76%] ../_readthedocs/jupyter_execute/8bde7de95a2351bd40bce07c97f561d37524ee1a236956626ee6b2b73d5637bd.png
copying images... [ 77%] ../_readthedocs/jupyter_execute/6b10b32141a9383cc2d3ec112957ac1cfbee8154c449683ff9be2f612420b6f0.png
copying images... [ 77%] ../_readthedocs/jupyter_execute/de3758d79d14fbdb767d6a7bd7e4168274b76a9681e24a4e9fd8ecbb3a422b66.png
copying images... [ 78%] ../_readthedocs/jupyter_execute/b092a195a2e9e7d9ca1d9584a76b5b83ff3ad24c61bf77ffc0b61536bb8a4265.png
copying images... [ 78%] ../_readthedocs/jupyter_execute/72018721bf8762bbb23bdd5d118ce8c53e823e86f38104920ff825660e8251a2.png
copying images... [ 78%] ../_readthedocs/jupyter_execute/94d6e876d08841a146bf45d65240823eb8a13b2445b54ed983aea66c19f19d74.png
copying images... [ 79%] ../_readthedocs/jupyter_execute/eca426ba0c175565e5e34a5fb0e16eb75ea1933a4008b87634d6251931bab373.png
copying images... [ 79%] ../_readthedocs/jupyter_execute/8a5b9a3a844761620a81333f1f9aa834f42f58dbe1c07556eede789fa73d3821.png
copying images... [ 80%] ../_readthedocs/jupyter_execute/5cba17b1487a5b9f8e4f82747a7b5402b238afd0f8b9771329cc2cafe762323f.png
copying images... [ 80%] ../_readthedocs/jupyter_execute/d92ac8cff005d3d675db226476fcf16ce95c0103d3028eb2770e7aa8c5ae5f78.png
copying images... [ 81%] ../_readthedocs/jupyter_execute/33587a56c76354a9006e5432138fc644f0098910297dce64d387667ac6ad53f6.png
copying images... [ 81%] ../_readthedocs/jupyter_execute/a8f32a9fad1c3bca6c889411fa6340403d93cff435aa8365331db6d409594068.png
copying images... [ 82%] ../_readthedocs/jupyter_execute/26e16bbaa5daced14abe7dc8619f966a7bc30f364dba20e461e1a8b3f272ba98.png
copying images... [ 82%] ../_readthedocs/jupyter_execute/e1d9a1ff1adb3487a37c60f6580f69b4d4c0da2a2d01025db06e83cca852729b.png
copying images... [ 83%] ../_readthedocs/jupyter_execute/100284609ffeda2f93a6b1a417142135c4b7efe38bdf3c2883769701a7b4299d.png
copying images... [ 83%] ../_readthedocs/jupyter_execute/9e13c66be5f38fec2706fb5171b52fed4f99fce233114d52b1dec726fbb68961.png
copying images... [ 83%] ../_readthedocs/jupyter_execute/4d34fb0bcd64d9de622e9376144625d1cee775569df40d6c2953ef9c5c7eb989.png
copying images... [ 84%] ../_readthedocs/jupyter_execute/23de59d1185f3141aad01dd923dd8751ace35d6223b6dd3283d195b4b5a35bda.png
copying images... [ 84%] ../_readthedocs/jupyter_execute/d392ef9bf7bccb0cfa92bd7cfd20f15708623f461850d487d268ace8881bacbe.png
copying images... [ 85%] ../_readthedocs/jupyter_execute/9be6cbb75c066ca431aa1697c02b3bbc6387d91d32376e5cb2fff533a28d0dcf.png
copying images... [ 85%] ../_readthedocs/jupyter_execute/0f430485100fa1e738391c6c573147391e3b05235873271ca76308ff27873f8b.png
copying images... [ 86%] ../_readthedocs/jupyter_execute/07218b82400958fd118f851eba7a1c593d3d083f790cbb9b46c10ea4dffa173c.png
copying images... [ 86%] ../_readthedocs/jupyter_execute/3d1d0aaab00e772893316173eaca085db98615b901a1ac7ade4d25dff68a672e.png
copying images... [ 87%] ../_readthedocs/jupyter_execute/d468b69af1c7f0af35798c70c6312a99e836c25fd2134bb9edbdbbe4b7e9cded.png
copying images... [ 87%] ../_readthedocs/jupyter_execute/b12877b4e058b5310108e83e7b492a837cf49fb4203e4b68e48c678b612e34d8.png
copying images... [ 87%] ../_readthedocs/jupyter_execute/82fb18ee734c4f9cf6e5db6d5dae523a02126bdf21455165648b95d5e1ea9fb9.png
copying images... [ 88%] ../_readthedocs/jupyter_execute/1b81b6f79760bb6741c2b9380ca11b84580ab2d627bb5951de0c2fa33b0ca737.png
copying images... [ 88%] ../_readthedocs/jupyter_execute/2f5a89c96ba3e65e79d6df85263d5a0c8d329a9fbbf73368d313d9bd3376ddf7.png
copying images... [ 89%] ../_readthedocs/jupyter_execute/1a2073e231dc9f8a81d50a9246c9580eac9fe004d3120bc381bbdad20609aa17.png
copying images... [ 89%] ../_readthedocs/jupyter_execute/6a45269efcf7bf7309f92cdf684948b9e91beb3f8a4c89840b3c60f86714ef5c.png
copying images... [ 90%] ../_readthedocs/jupyter_execute/8bb74c11eb99e1b14e0880107a9753a8e071e0ec20559b95b1f62d62c305f727.png
copying images... [ 90%] ../_readthedocs/jupyter_execute/4e2619b85a5be447dac180b3c70c37c168b0c7b0ecd8f69f1be50d7affe1f3cf.png
copying images... [ 91%] ../_readthedocs/jupyter_execute/f9cb1d875449d2a6faf59b88ce54262f14da3235d5f3e2cfe981905019f54ac6.png
copying images... [ 91%] ../_readthedocs/jupyter_execute/c338f76d64435e9b5406ec7868ce4ce5ec689c79d85e81a3899b4b1c4e516596.png
copying images... [ 91%] ../_readthedocs/jupyter_execute/bc93727098434daa1d8fa343ed071898822b86804a4b6b5bde64fcf79cce718d.png
copying images... [ 92%] ../_readthedocs/jupyter_execute/0aa302a1f4bf30aa75db66d47f0fc3987e884c42844f031120f7dc7031474ab8.png
copying images... [ 92%] ../_readthedocs/jupyter_execute/bfe25bb9302cd7a75ccbf42ab54fc7f6959353702280cbca997127ffc101a624.png
copying images... [ 93%] ../_readthedocs/jupyter_execute/30c1584beee6097cbafde187fdf0ba2353becd3323c4576d4f1058810a225ad1.png
copying images... [ 93%] ../_readthedocs/jupyter_execute/2e1a1edf647822811b189ca73ec66e34a33709aa8699370b77bc0aca99020345.png
copying images... [ 94%] ../_readthedocs/jupyter_execute/7058d282c4bf34508fb7060e8002a81692aebe757bed798259814c4ba05aad98.png
copying images... [ 94%] ../_readthedocs/jupyter_execute/c201abda2ed90687a4dfe6dda241b5cfc7a3a42c22b761cb195227a4e228a3f1.png
copying images... [ 95%] ../_readthedocs/jupyter_execute/523261eadb2e967d20b517a2c1f5ef653e65e8f02a58da98cd5d4bcf08a6e398.png
copying images... [ 95%] ../_readthedocs/jupyter_execute/72825cab1ce202e45f5ed8347ed1c2be71e66760b993d8f5b0df3021da541f25.png
copying images... [ 96%] _static/img/tutorials/paga_planaria.png
copying images... [ 96%] ../_readthedocs/jupyter_execute/a3a02c63f6cf5c59f8dd1f9cac14b4655adcff7c3fac1170691d96d654362e91.png
copying images... [ 96%] ../_readthedocs/jupyter_execute/7b578c69a2284b8fd485f3bd2dd0688e0c23240b49992062543b4fd78e1249d5.png
copying images... [ 97%] ../_readthedocs/jupyter_execute/8c6e16996372827af59a9307b99355e02a221d5dc9263dd06bf4b4c700e24a16.png
copying images... [ 97%] ../_readthedocs/jupyter_execute/f79e8a9231c64ac6ebd623f262089b4dd439d322200e42eb83bae3a4aff60025.png
copying images... [ 98%] ../_readthedocs/jupyter_execute/486b4fae6e599adc0c8bdce07b379475fc92dc6a22415e5b94705437c75588b3.png
copying images... [ 98%] ../_readthedocs/jupyter_execute/eeb0653d95013989aa1b7ee46828634e0c8b6b0986a0cc33b8d5dbe8d5996b30.png
copying images... [ 99%] ../_readthedocs/jupyter_execute/59d88b19dec14c20c6a54bbbdd29f6ed504dbd194b950c4a110d0c822137ade1.png
copying images... [ 99%] ../_readthedocs/jupyter_execute/0c6d4195d19a39ad2ac081136ad90cb848a6da29f81b06f72b7c82aa80ea9f2c.png
copying images... [100%] ../_readthedocs/jupyter_execute/651cfdb470bfbd2326d31865d359a62d8d959aa466ca2f63bb94fb6c321040c5.png
copying images... [100%] ../_readthedocs/jupyter_execute/7c168ae28a9840611590d3ad58b410b693b51e46f830cda886e2f99469ce8fd4.png

dumping search index in English (code: en)... done
dumping object inventory... done
Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3289/_readthedocs/html/_static/js/rtd_search_config.js
build succeeded.

The HTML pages are in ../_readthedocs/html.