Read the Docs build information
Build id: 1630280
Project: icb-anndata
Version: 949
Commit: e1452845832c71b1e8d1c61c20117143dbbf38ac
Date: 2023-07-30T20:06:15.936042Z
State: finished
Success: False


[rtd-command-info] start-time: 2023-07-30T20:06:19.532146Z, end-time: 2023-07-30T20:06:20.117938Z, duration: 0, exit-code: 0
git clone --depth 1 https://github.com/scverse/anndata.git .
Cloning into '.'...

[rtd-command-info] start-time: 2023-07-30T20:06:20.369624Z, end-time: 2023-07-30T20:06:21.662831Z, duration: 1, exit-code: 0
git fetch origin --force --prune --prune-tags --depth 50 pull/949/head:external-949
From https://github.com/scverse/anndata
 * [new ref]         refs/pull/949/head -> external-949
 * [new tag]         0.10.0.dev0        -> 0.10.0.dev0
 * [new tag]         0.9.0rc1           -> 0.9.0rc1

[rtd-command-info] start-time: 2023-07-30T20:06:22.152345Z, end-time: 2023-07-30T20:06:22.265448Z, duration: 0, exit-code: 0
git checkout --force e1452845832c71b1e8d1c61c20117143dbbf38ac
Note: switching to 'e1452845832c71b1e8d1c61c20117143dbbf38ac'.

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 e145284 (chore): bring in last changes from `read_backed` branch

[rtd-command-info] start-time: 2023-07-30T20:06:22.513654Z, end-time: 2023-07-30T20:06:22.575690Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2023-07-30T20:06:22.839140Z, end-time: 2023-07-30T20:06:22.948683Z, duration: 0, exit-code: 0
git submodule sync


[rtd-command-info] start-time: 2023-07-30T20:06:23.205257Z, end-time: 2023-07-30T20:06:23.856700Z, duration: 0, exit-code: 0
git submodule update --init --force --recursive docs/tutorials/notebooks
Submodule 'docs/tutorials/notebooks' (https://github.com/scverse/anndata-tutorials) registered for path 'docs/tutorials/notebooks'
Cloning into '/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/949/docs/tutorials/notebooks'...
Submodule path 'docs/tutorials/notebooks': checked out '9e186c5c694793bb04ea1397721d154d6e0b7069'

[rtd-command-info] start-time: 2023-07-30T20:06:24.096716Z, end-time: 2023-07-30T20:06:24.191921Z, duration: 0, exit-code: 0
cat .readthedocs.yml
version: 2
build:
  os: ubuntu-20.04
  tools:
    python: '3.10'
sphinx:
  configuration: docs/conf.py
python:
  install:
  - method: pip
    path: .
    extra_requirements:
    - doc
submodules:
    include:
        - "docs/tutorials/notebooks"
    recursive: true

[rtd-command-info] start-time: 2023-07-30T20:06:30.329438Z, end-time: 2023-07-30T20:06:30.478085Z, duration: 0, exit-code: 0
asdf global python 3.10.12


[rtd-command-info] start-time: 2023-07-30T20:06:31.011544Z, end-time: 2023-07-30T20:06:32.093419Z, duration: 1, exit-code: 0
python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH
created virtual environment CPython3.10.12.final.0-64 in 676ms
  creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/949, clear=False, no_vcs_ignore=False, global=False)
  seeder FromAppData(download=False, pip=bundle, setuptools=bundle, wheel=bundle, via=copy, app_data_dir=/home/docs/.local/share/virtualenv)
    added seed packages: pip==21.2.3, setuptools==57.4.0, wheel==0.37.0
  activators BashActivator,CShellActivator,FishActivator,PowerShellActivator,PythonActivator

[rtd-command-info] start-time: 2023-07-30T20:06:32.408759Z, end-time: 2023-07-30T20:06:44.445334Z, duration: 12, 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-anndata/envs/949/lib/python3.10/site-packages (21.2.3)
Collecting pip
  Downloading pip-23.2.1-py3-none-any.whl (2.1 MB)
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/949/lib/python3.10/site-packages (57.4.0)
Collecting setuptools
  Downloading setuptools-68.0.0-py3-none-any.whl (804 kB)
Installing collected packages: setuptools, pip
  Attempting uninstall: setuptools
    Found existing installation: setuptools 57.4.0
    Uninstalling setuptools-57.4.0:
      Successfully uninstalled setuptools-57.4.0
  Attempting uninstall: pip
    Found existing installation: pip 21.2.3
    Uninstalling pip-21.2.3:
      Successfully uninstalled pip-21.2.3
Successfully installed pip-23.2.1 setuptools-68.0.0

[rtd-command-info] start-time: 2023-07-30T20:06:44.706144Z, end-time: 2023-07-30T20:06:52.172899Z, duration: 7, exit-code: 0
python -m pip install --upgrade --no-cache-dir pillow mock==1.0.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.9.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<2.3 jinja2<3.1.0
Collecting pillow
  Obtaining dependency information for pillow from https://files.pythonhosted.org/packages/3d/36/e78f09d510354977e10102dd811e928666021d9c451e05df962d56477772/Pillow-10.0.0-cp310-cp310-manylinux_2_28_x86_64.whl.metadata
  Downloading Pillow-10.0.0-cp310-cp310-manylinux_2_28_x86_64.whl.metadata (9.5 kB)
Collecting mock==1.0.1
  Downloading mock-1.0.1.zip (861 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 861.9/861.9 kB 26.5 MB/s eta 0:00:00
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting alabaster!=0.7.5,<0.8,>=0.7
  Downloading alabaster-0.7.13-py3-none-any.whl (13 kB)
Collecting commonmark==0.9.1
  Downloading commonmark-0.9.1-py2.py3-none-any.whl (51 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 51.1/51.1 kB 216.3 MB/s eta 0:00:00
Collecting recommonmark==0.5.0
  Downloading recommonmark-0.5.0-py2.py3-none-any.whl (9.8 kB)
Collecting sphinx<2
  Downloading Sphinx-1.8.6-py2.py3-none-any.whl (3.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.1/3.1 MB 173.0 MB/s eta 0:00:00
Collecting sphinx-rtd-theme<0.5
  Downloading sphinx_rtd_theme-0.4.3-py2.py3-none-any.whl (6.4 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 6.4/6.4 MB 108.3 MB/s eta 0:00:00
Collecting readthedocs-sphinx-ext<2.3
  Obtaining dependency information for readthedocs-sphinx-ext<2.3 from https://files.pythonhosted.org/packages/8c/f1/3d783ebfc084a9d556123d54669116101760e5e0dbb894b006745bcb59ea/readthedocs_sphinx_ext-2.2.2-py2.py3-none-any.whl.metadata
  Downloading readthedocs_sphinx_ext-2.2.2-py2.py3-none-any.whl.metadata (1.5 kB)
Collecting jinja2<3.1.0
  Downloading Jinja2-3.0.3-py3-none-any.whl (133 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 133.6/133.6 kB 246.3 MB/s eta 0:00:00
Collecting docutils>=0.11 (from recommonmark==0.5.0)
  Obtaining dependency information for docutils>=0.11 from https://files.pythonhosted.org/packages/26/87/f238c0670b94533ac0353a4e2a1a771a0cc73277b88bff23d3ae35a256c1/docutils-0.20.1-py3-none-any.whl.metadata
  Downloading docutils-0.20.1-py3-none-any.whl.metadata (2.8 kB)
Collecting six>=1.5 (from sphinx<2)
  Downloading six-1.16.0-py2.py3-none-any.whl (11 kB)
Collecting Pygments>=2.0 (from sphinx<2)
  Downloading Pygments-2.15.1-py3-none-any.whl (1.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 284.3 MB/s eta 0:00:00
Collecting docutils>=0.11 (from recommonmark==0.5.0)
  Downloading docutils-0.17.1-py2.py3-none-any.whl (575 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 575.5/575.5 kB 290.2 MB/s eta 0:00:00
Collecting snowballstemmer>=1.1 (from sphinx<2)
  Downloading snowballstemmer-2.2.0-py2.py3-none-any.whl (93 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 93.0/93.0 kB 248.6 MB/s eta 0:00:00
Collecting babel!=2.0,>=1.3 (from sphinx<2)
  Downloading Babel-2.12.1-py3-none-any.whl (10.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 10.1/10.1 MB 120.6 MB/s eta 0:00:00
Collecting imagesize (from sphinx<2)
  Downloading imagesize-1.4.1-py2.py3-none-any.whl (8.8 kB)
Collecting requests>=2.0.0 (from sphinx<2)
  Obtaining dependency information for requests>=2.0.0 from https://files.pythonhosted.org/packages/70/8e/0e2d847013cb52cd35b38c009bb167a1a26b2ce6cd6965bf26b47bc0bf44/requests-2.31.0-py3-none-any.whl.metadata
  Downloading requests-2.31.0-py3-none-any.whl.metadata (4.6 kB)
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/949/lib/python3.10/site-packages (from sphinx<2) (68.0.0)
Collecting packaging (from sphinx<2)
  Downloading packaging-23.1-py3-none-any.whl (48 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 48.9/48.9 kB 210.3 MB/s eta 0:00:00
Collecting sphinxcontrib-websupport (from sphinx<2)
  Downloading sphinxcontrib_websupport-1.2.4-py2.py3-none-any.whl (39 kB)
Collecting MarkupSafe>=2.0 (from jinja2<3.1.0)
  Obtaining dependency information for MarkupSafe>=2.0 from https://files.pythonhosted.org/packages/12/b3/d9ed2c0971e1435b8a62354b18d3060b66c8cb1d368399ec0b9baa7c0ee5/MarkupSafe-2.1.3-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata
  Downloading MarkupSafe-2.1.3-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.0 kB)
Collecting charset-normalizer<4,>=2 (from requests>=2.0.0->sphinx<2)
  Obtaining dependency information for charset-normalizer<4,>=2 from https://files.pythonhosted.org/packages/a4/65/057bf29660aae6ade0816457f8db4e749e5c0bfa2366eb5f67db9912fa4c/charset_normalizer-3.2.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata
  Downloading charset_normalizer-3.2.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (31 kB)
Collecting idna<4,>=2.5 (from requests>=2.0.0->sphinx<2)
  Downloading idna-3.4-py3-none-any.whl (61 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 61.5/61.5 kB 225.4 MB/s eta 0:00:00
Collecting urllib3<3,>=1.21.1 (from requests>=2.0.0->sphinx<2)
  Obtaining dependency information for urllib3<3,>=1.21.1 from https://files.pythonhosted.org/packages/9b/81/62fd61001fa4b9d0df6e31d47ff49cfa9de4af03adecf339c7bc30656b37/urllib3-2.0.4-py3-none-any.whl.metadata
  Downloading urllib3-2.0.4-py3-none-any.whl.metadata (6.6 kB)
Collecting certifi>=2017.4.17 (from requests>=2.0.0->sphinx<2)
  Obtaining dependency information for certifi>=2017.4.17 from https://files.pythonhosted.org/packages/4c/dd/2234eab22353ffc7d94e8d13177aaa050113286e93e7b40eae01fbf7c3d9/certifi-2023.7.22-py3-none-any.whl.metadata
  Downloading certifi-2023.7.22-py3-none-any.whl.metadata (2.2 kB)
Collecting sphinxcontrib-serializinghtml (from sphinxcontrib-websupport->sphinx<2)
  Downloading sphinxcontrib_serializinghtml-1.1.5-py2.py3-none-any.whl (94 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 94.0/94.0 kB 250.4 MB/s eta 0:00:00
Downloading Pillow-10.0.0-cp310-cp310-manylinux_2_28_x86_64.whl (3.4 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.4/3.4 MB 203.3 MB/s eta 0:00:00
Downloading readthedocs_sphinx_ext-2.2.2-py2.py3-none-any.whl (11 kB)
Downloading MarkupSafe-2.1.3-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (25 kB)
Downloading requests-2.31.0-py3-none-any.whl (62 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.6/62.6 kB 226.3 MB/s eta 0:00:00
Downloading certifi-2023.7.22-py3-none-any.whl (158 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 158.3/158.3 kB 261.1 MB/s eta 0:00:00
Downloading charset_normalizer-3.2.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (201 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 201.8/201.8 kB 269.5 MB/s eta 0:00:00
Downloading urllib3-2.0.4-py3-none-any.whl (123 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 123.9/123.9 kB 249.9 MB/s eta 0:00:00
Building wheels for collected packages: mock
  Building wheel for mock (setup.py): started
  Building wheel for mock (setup.py): finished with status 'done'
  Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23753 sha256=d320a4ef452307de922d83120f09a6530abbd521208240344eeb535a1a16fd69
  Stored in directory: /tmp/pip-ephem-wheel-cache-zamg398g/wheels/df/9a/50/99d488b71fc0b027f0d316f4e447cdc9b973c67e1e7e4abc4b
Successfully built mock
Installing collected packages: snowballstemmer, mock, commonmark, urllib3, sphinxcontrib-serializinghtml, six, Pygments, pillow, packaging, MarkupSafe, imagesize, idna, docutils, charset-normalizer, certifi, babel, alabaster, sphinxcontrib-websupport, requests, jinja2, sphinx, readthedocs-sphinx-ext, sphinx-rtd-theme, recommonmark
Successfully installed MarkupSafe-2.1.3 Pygments-2.15.1 alabaster-0.7.13 babel-2.12.1 certifi-2023.7.22 charset-normalizer-3.2.0 commonmark-0.9.1 docutils-0.17.1 idna-3.4 imagesize-1.4.1 jinja2-3.0.3 mock-1.0.1 packaging-23.1 pillow-10.0.0 readthedocs-sphinx-ext-2.2.2 recommonmark-0.5.0 requests-2.31.0 six-1.16.0 snowballstemmer-2.2.0 sphinx-1.8.6 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.5 sphinxcontrib-websupport-1.2.4 urllib3-2.0.4

[rtd-command-info] start-time: 2023-07-30T20:06:52.402101Z, end-time: 2023-07-30T20:07:43.962139Z, duration: 51, exit-code: 0
python -m pip install --upgrade --upgrade-strategy only-if-needed --no-cache-dir .[doc]
Processing /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/949
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
  Installing backend dependencies: started
  Installing backend dependencies: finished with status 'done'
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): finished with status 'done'
Collecting pandas!=2.0.1,>=1.1.1 (from anndata==0.10.0.dev35+ge145284)
  Obtaining dependency information for pandas!=2.0.1,>=1.1.1 from https://files.pythonhosted.org/packages/e3/59/35a2892bf09ded9c1bf3804461efe772836a5261ef5dfb4e264ce813ff99/pandas-2.0.3-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata
  Downloading pandas-2.0.3-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (18 kB)
Collecting numpy>=1.16.5 (from anndata==0.10.0.dev35+ge145284)
  Obtaining dependency information for numpy>=1.16.5 from https://files.pythonhosted.org/packages/d0/55/559e6f455a066e12058330377259a106b7fefa41c15dbdb1b71070cec429/numpy-1.25.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata
  Downloading numpy-1.25.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.6 kB)
Collecting scipy>1.4 (from anndata==0.10.0.dev35+ge145284)
  Obtaining dependency information for scipy>1.4 from https://files.pythonhosted.org/packages/14/f2/10fa23f0a6b9b2439c01579ae4a9b1849d4822e972515c8f92584bfda5e9/scipy-1.11.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata
  Downloading scipy-1.11.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (59 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 59.1/59.1 kB 9.1 MB/s eta 0:00:00
Collecting h5py>=3 (from anndata==0.10.0.dev35+ge145284)
  Obtaining dependency information for h5py>=3 from https://files.pythonhosted.org/packages/0d/7a/e55589e4093cca1934db5e99644c1c2424a9b3aac104b7f6176605a5eeb7/h5py-3.9.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata
  Downloading h5py-3.9.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.5 kB)
Collecting natsort (from anndata==0.10.0.dev35+ge145284)
  Obtaining dependency information for natsort from https://files.pythonhosted.org/packages/ef/82/7a9d0550484a62c6da82858ee9419f3dd1ccc9aa1c26a1e43da3ecd20b0d/natsort-8.4.0-py3-none-any.whl.metadata
  Downloading natsort-8.4.0-py3-none-any.whl.metadata (21 kB)
Requirement already satisfied: packaging>=20 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/949/lib/python3.10/site-packages (from anndata==0.10.0.dev35+ge145284) (23.1)
Collecting sphinx>=4.4 (from anndata==0.10.0.dev35+ge145284)
  Obtaining dependency information for sphinx>=4.4 from https://files.pythonhosted.org/packages/c7/64/c3d5a265ebc2e96a6d1c1b3f5d23abdd3dde547d8638a4d06383aa8d2059/sphinx-7.1.1-py3-none-any.whl.metadata
  Downloading sphinx-7.1.1-py3-none-any.whl.metadata (5.8 kB)
Collecting sphinx-rtd-theme>=1.1.1 (from anndata==0.10.0.dev35+ge145284)
  Obtaining dependency information for sphinx-rtd-theme>=1.1.1 from https://files.pythonhosted.org/packages/85/32/9ccebf3a82c085e8fc12b67cc3dbf840789fb6c7835ed0d61686d6509aa9/sphinx_rtd_theme-1.2.2-py2.py3-none-any.whl.metadata
  Downloading sphinx_rtd_theme-1.2.2-py2.py3-none-any.whl.metadata (4.5 kB)
Collecting sphinx-autodoc-typehints>=1.11.0 (from anndata==0.10.0.dev35+ge145284)
  Obtaining dependency information for sphinx-autodoc-typehints>=1.11.0 from https://files.pythonhosted.org/packages/a4/a2/71ee28033c218b025348555747cb95993338179875bae75c197138be77ad/sphinx_autodoc_typehints-1.24.0-py3-none-any.whl.metadata
  Downloading sphinx_autodoc_typehints-1.24.0-py3-none-any.whl.metadata (7.8 kB)
Collecting sphinx_issues (from anndata==0.10.0.dev35+ge145284)
  Downloading sphinx_issues-3.0.1-py3-none-any.whl (8.2 kB)
Collecting sphinxext.opengraph (from anndata==0.10.0.dev35+ge145284)
  Downloading sphinxext_opengraph-0.8.2-py3-none-any.whl (1.0 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.0/1.0 MB 50.0 MB/s eta 0:00:00
Collecting nbsphinx (from anndata==0.10.0.dev35+ge145284)
  Obtaining dependency information for nbsphinx from https://files.pythonhosted.org/packages/9f/30/ee4dc91710a76c287128f205087544e8adb3a373959e70be6c555ddb40c2/nbsphinx-0.9.2-py3-none-any.whl.metadata
  Downloading nbsphinx-0.9.2-py3-none-any.whl.metadata (2.1 kB)
Collecting scanpydoc>=0.7.7 (from anndata==0.10.0.dev35+ge145284)
  Obtaining dependency information for scanpydoc>=0.7.7 from https://files.pythonhosted.org/packages/6e/04/d3668db9d9e6da91896c1bac0e25362cdcae582951f8b7bda14993174d26/scanpydoc-0.9.4-py3-none-any.whl.metadata
  Downloading scanpydoc-0.9.4-py3-none-any.whl.metadata (2.4 kB)
Collecting zarr (from anndata==0.10.0.dev35+ge145284)
  Obtaining dependency information for zarr from https://files.pythonhosted.org/packages/57/8e/b74c2a80c7df474c300bab3b761c35d6cfa6468d6d23f891d518ec7c828e/zarr-2.16.0-py3-none-any.whl.metadata
  Downloading zarr-2.16.0-py3-none-any.whl.metadata (5.4 kB)
Collecting awkward>=2.0.7 (from anndata==0.10.0.dev35+ge145284)
  Obtaining dependency information for awkward>=2.0.7 from https://files.pythonhosted.org/packages/00/41/80dec4455f993021f09943c1a954b32a76b7261065d62bd77de9012b6c70/awkward-2.3.1-py3-none-any.whl.metadata
  Downloading awkward-2.3.1-py3-none-any.whl.metadata (6.9 kB)
Collecting IPython (from anndata==0.10.0.dev35+ge145284)
  Obtaining dependency information for IPython from https://files.pythonhosted.org/packages/52/d1/f70cdafba20030cbc1412d7a7d6a89c5035071835cc50e47fc5ed8da553c/ipython-8.14.0-py3-none-any.whl.metadata
  Downloading ipython-8.14.0-py3-none-any.whl.metadata (5.8 kB)
Collecting myst_parser (from anndata==0.10.0.dev35+ge145284)
  Obtaining dependency information for myst_parser from https://files.pythonhosted.org/packages/1d/f6/6d61a023d758f488e36638076e8a4ec4447a2cdf86938cf6c60cf1c860e6/myst_parser-2.0.0-py3-none-any.whl.metadata
  Downloading myst_parser-2.0.0-py3-none-any.whl.metadata (5.4 kB)
Collecting awkward-cpp==21 (from awkward>=2.0.7->anndata==0.10.0.dev35+ge145284)
  Obtaining dependency information for awkward-cpp==21 from https://files.pythonhosted.org/packages/92/16/8d843e827bfda3790a9e5b19d78c9f4d21ce0e225b7f90f9de14521cfecd/awkward_cpp-21-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata
  Downloading awkward_cpp-21-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB)
Collecting typing-extensions>=4.1.0 (from awkward>=2.0.7->anndata==0.10.0.dev35+ge145284)
  Obtaining dependency information for typing-extensions>=4.1.0 from https://files.pythonhosted.org/packages/ec/6b/63cc3df74987c36fe26157ee12e09e8f9db4de771e0f3404263117e75b95/typing_extensions-4.7.1-py3-none-any.whl.metadata
  Downloading typing_extensions-4.7.1-py3-none-any.whl.metadata (3.1 kB)
Collecting python-dateutil>=2.8.2 (from pandas!=2.0.1,>=1.1.1->anndata==0.10.0.dev35+ge145284)
  Downloading python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 247.7/247.7 kB 260.4 MB/s eta 0:00:00
Collecting pytz>=2020.1 (from pandas!=2.0.1,>=1.1.1->anndata==0.10.0.dev35+ge145284)
  Downloading pytz-2023.3-py2.py3-none-any.whl (502 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 502.3/502.3 kB 272.4 MB/s eta 0:00:00
Collecting tzdata>=2022.1 (from pandas!=2.0.1,>=1.1.1->anndata==0.10.0.dev35+ge145284)
  Downloading tzdata-2023.3-py2.py3-none-any.whl (341 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 341.8/341.8 kB 275.5 MB/s eta 0:00:00
Collecting sphinxcontrib-applehelp (from sphinx>=4.4->anndata==0.10.0.dev35+ge145284)
  Downloading sphinxcontrib_applehelp-1.0.4-py3-none-any.whl (120 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 120.6/120.6 kB 253.2 MB/s eta 0:00:00
Collecting sphinxcontrib-devhelp (from sphinx>=4.4->anndata==0.10.0.dev35+ge145284)
  Downloading sphinxcontrib_devhelp-1.0.2-py2.py3-none-any.whl (84 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 84.7/84.7 kB 192.0 MB/s eta 0:00:00
Collecting sphinxcontrib-jsmath (from sphinx>=4.4->anndata==0.10.0.dev35+ge145284)
  Downloading sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB)
Collecting sphinxcontrib-htmlhelp>=2.0.0 (from sphinx>=4.4->anndata==0.10.0.dev35+ge145284)
  Downloading sphinxcontrib_htmlhelp-2.0.1-py3-none-any.whl (99 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 99.8/99.8 kB 247.2 MB/s eta 0:00:00
Requirement already satisfied: sphinxcontrib-serializinghtml>=1.1.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/949/lib/python3.10/site-packages (from sphinx>=4.4->anndata==0.10.0.dev35+ge145284) (1.1.5)
Collecting sphinxcontrib-qthelp (from sphinx>=4.4->anndata==0.10.0.dev35+ge145284)
  Downloading sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl (90 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 90.6/90.6 kB 247.9 MB/s eta 0:00:00
Requirement already satisfied: Jinja2>=3.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/949/lib/python3.10/site-packages (from sphinx>=4.4->anndata==0.10.0.dev35+ge145284) (3.0.3)
Requirement already satisfied: Pygments>=2.13 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/949/lib/python3.10/site-packages (from sphinx>=4.4->anndata==0.10.0.dev35+ge145284) (2.15.1)
Collecting docutils<0.21,>=0.18.1 (from sphinx>=4.4->anndata==0.10.0.dev35+ge145284)
  Obtaining dependency information for docutils<0.21,>=0.18.1 from https://files.pythonhosted.org/packages/26/87/f238c0670b94533ac0353a4e2a1a771a0cc73277b88bff23d3ae35a256c1/docutils-0.20.1-py3-none-any.whl.metadata
  Downloading docutils-0.20.1-py3-none-any.whl.metadata (2.8 kB)
Requirement already satisfied: snowballstemmer>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/949/lib/python3.10/site-packages (from sphinx>=4.4->anndata==0.10.0.dev35+ge145284) (2.2.0)
Requirement already satisfied: babel>=2.9 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/949/lib/python3.10/site-packages (from sphinx>=4.4->anndata==0.10.0.dev35+ge145284) (2.12.1)
Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/949/lib/python3.10/site-packages (from sphinx>=4.4->anndata==0.10.0.dev35+ge145284) (0.7.13)
Requirement already satisfied: imagesize>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/949/lib/python3.10/site-packages (from sphinx>=4.4->anndata==0.10.0.dev35+ge145284) (1.4.1)
Requirement already satisfied: requests>=2.25.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/949/lib/python3.10/site-packages (from sphinx>=4.4->anndata==0.10.0.dev35+ge145284) (2.31.0)
INFO: pip is looking at multiple versions of sphinx-rtd-theme to determine which version is compatible with other requirements. This could take a while.
Collecting sphinx-rtd-theme>=1.1.1 (from anndata==0.10.0.dev35+ge145284)
  Obtaining dependency information for sphinx-rtd-theme>=1.1.1 from https://files.pythonhosted.org/packages/c2/73/946cdd32f29c87843edaa059b9fc52ab9267d1137b3a76dee1d59d02a01a/sphinx_rtd_theme-1.2.1-py2.py3-none-any.whl.metadata
  Downloading sphinx_rtd_theme-1.2.1-py2.py3-none-any.whl.metadata (4.5 kB)
  Downloading sphinx_rtd_theme-1.2.0-py2.py3-none-any.whl (2.8 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.8/2.8 MB 222.4 MB/s eta 0:00:00
  Downloading sphinx_rtd_theme-1.1.1-py2.py3-none-any.whl (2.8 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.8/2.8 MB 249.7 MB/s eta 0:00:00
Collecting sphinx-autodoc-typehints>=1.11.0 (from anndata==0.10.0.dev35+ge145284)
  Obtaining dependency information for sphinx-autodoc-typehints>=1.11.0 from https://files.pythonhosted.org/packages/74/0b/da14533947c9d250917c3537a2ac4efd3d0f149c43ebfca63e718cfd5db8/sphinx_autodoc_typehints-1.23.3-py3-none-any.whl.metadata
  Downloading sphinx_autodoc_typehints-1.23.3-py3-none-any.whl.metadata (8.5 kB)
INFO: pip is still looking at multiple versions of sphinx-rtd-theme to determine which version is compatible with other requirements. This could take a while.
  Obtaining dependency information for sphinx-autodoc-typehints>=1.11.0 from https://files.pythonhosted.org/packages/81/81/fa50a8950f0028a1cc82f621e203db019322b3b0c82a72c92b31ff9df951/sphinx_autodoc_typehints-1.23.2-py3-none-any.whl.metadata
  Downloading sphinx_autodoc_typehints-1.23.2-py3-none-any.whl.metadata (8.5 kB)
  Obtaining dependency information for sphinx-autodoc-typehints>=1.11.0 from https://files.pythonhosted.org/packages/c2/21/c4e7ff41eea7c258bb63ffbe0907323908531d6f8f33c8f361dc95176d2a/sphinx_autodoc_typehints-1.23.1-py3-none-any.whl.metadata
  Downloading sphinx_autodoc_typehints-1.23.1-py3-none-any.whl.metadata (8.6 kB)
INFO: This is taking longer than usual. You might need to provide the dependency resolver with stricter constraints to reduce runtime. See https://pip.pypa.io/warnings/backtracking for guidance. If you want to abort this run, press Ctrl + C.
  Downloading sphinx_autodoc_typehints-1.23.0-py3-none-any.whl (17 kB)
Collecting sphinx>=4.4 (from anndata==0.10.0.dev35+ge145284)
  Downloading sphinx-6.2.1-py3-none-any.whl (3.0 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.0/3.0 MB 252.4 MB/s eta 0:00:00
Collecting docutils<0.21,>=0.18.1 (from sphinx>=4.4->anndata==0.10.0.dev35+ge145284)
  Downloading docutils-0.18.1-py2.py3-none-any.whl (570 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 570.0/570.0 kB 273.4 MB/s eta 0:00:00
Collecting sphinxcontrib-jquery<5,>=4 (from sphinx-rtd-theme>=1.1.1->anndata==0.10.0.dev35+ge145284)
  Downloading sphinxcontrib_jquery-4.1-py2.py3-none-any.whl (121 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 121.1/121.1 kB 249.7 MB/s eta 0:00:00
Collecting backcall (from IPython->anndata==0.10.0.dev35+ge145284)
  Downloading backcall-0.2.0-py2.py3-none-any.whl (11 kB)
Collecting decorator (from IPython->anndata==0.10.0.dev35+ge145284)
  Downloading decorator-5.1.1-py3-none-any.whl (9.1 kB)
Collecting jedi>=0.16 (from IPython->anndata==0.10.0.dev35+ge145284)
  Obtaining dependency information for jedi>=0.16 from https://files.pythonhosted.org/packages/8e/46/7e3ae3aa2dcfcffc5138c6cef5448523218658411c84a2000bf75c8d3ec1/jedi-0.19.0-py2.py3-none-any.whl.metadata
  Downloading jedi-0.19.0-py2.py3-none-any.whl.metadata (22 kB)
Collecting matplotlib-inline (from IPython->anndata==0.10.0.dev35+ge145284)
  Downloading matplotlib_inline-0.1.6-py3-none-any.whl (9.4 kB)
Collecting pickleshare (from IPython->anndata==0.10.0.dev35+ge145284)
  Downloading pickleshare-0.7.5-py2.py3-none-any.whl (6.9 kB)
Collecting prompt-toolkit!=3.0.37,<3.1.0,>=3.0.30 (from IPython->anndata==0.10.0.dev35+ge145284)
  Obtaining dependency information for prompt-toolkit!=3.0.37,<3.1.0,>=3.0.30 from https://files.pythonhosted.org/packages/a9/b4/ba77c84edf499877317225d7b7bc047a81f7c2eed9628eeb6bab0ac2e6c9/prompt_toolkit-3.0.39-py3-none-any.whl.metadata
  Downloading prompt_toolkit-3.0.39-py3-none-any.whl.metadata (6.4 kB)
Collecting stack-data (from IPython->anndata==0.10.0.dev35+ge145284)
  Downloading stack_data-0.6.2-py3-none-any.whl (24 kB)
Collecting traitlets>=5 (from IPython->anndata==0.10.0.dev35+ge145284)
  Downloading traitlets-5.9.0-py3-none-any.whl (117 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 117.4/117.4 kB 261.0 MB/s eta 0:00:00
Collecting pexpect>4.3 (from IPython->anndata==0.10.0.dev35+ge145284)
  Downloading pexpect-4.8.0-py2.py3-none-any.whl (59 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 59.0/59.0 kB 247.0 MB/s eta 0:00:00
Collecting markdown-it-py~=3.0 (from myst_parser->anndata==0.10.0.dev35+ge145284)
  Obtaining dependency information for markdown-it-py~=3.0 from https://files.pythonhosted.org/packages/42/d7/1ec15b46af6af88f19b8e5ffea08fa375d433c998b8a7639e76935c14f1f/markdown_it_py-3.0.0-py3-none-any.whl.metadata
  Downloading markdown_it_py-3.0.0-py3-none-any.whl.metadata (6.9 kB)
Collecting mdit-py-plugins~=0.4 (from myst_parser->anndata==0.10.0.dev35+ge145284)
  Obtaining dependency information for mdit-py-plugins~=0.4 from https://files.pythonhosted.org/packages/e5/3c/fe85f19699a7b40c8f9ce8ecee7e269b9b3c94099306df6f9891bdefeedd/mdit_py_plugins-0.4.0-py3-none-any.whl.metadata
  Downloading mdit_py_plugins-0.4.0-py3-none-any.whl.metadata (2.7 kB)
Collecting pyyaml (from myst_parser->anndata==0.10.0.dev35+ge145284)
  Obtaining dependency information for pyyaml from https://files.pythonhosted.org/packages/29/61/bf33c6c85c55bc45a29eee3195848ff2d518d84735eb0e2d8cb42e0d285e/PyYAML-6.0.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata
  Downloading PyYAML-6.0.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB)
Collecting nbconvert!=5.4 (from nbsphinx->anndata==0.10.0.dev35+ge145284)
  Obtaining dependency information for nbconvert!=5.4 from https://files.pythonhosted.org/packages/51/bd/ede955c9e981abf6d0e12a7583fd0f9256eedfb461073f25045770f3e717/nbconvert-7.7.3-py3-none-any.whl.metadata
  Downloading nbconvert-7.7.3-py3-none-any.whl.metadata (8.0 kB)
Collecting nbformat (from nbsphinx->anndata==0.10.0.dev35+ge145284)
  Obtaining dependency information for nbformat from https://files.pythonhosted.org/packages/01/e5/322b31448ba6b0ed6de740306367e85d8da2af0d91e67f7a2860bdf87f72/nbformat-5.9.1-py3-none-any.whl.metadata
  Downloading nbformat-5.9.1-py3-none-any.whl.metadata (3.3 kB)
Collecting matplotlib (from sphinxext.opengraph->anndata==0.10.0.dev35+ge145284)
  Obtaining dependency information for matplotlib from https://files.pythonhosted.org/packages/c2/da/a5622266952ab05dc3995d77689cba600e49ea9d6c51d469c077695cb719/matplotlib-3.7.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata
  Downloading matplotlib-3.7.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.6 kB)
Collecting asciitree (from zarr->anndata==0.10.0.dev35+ge145284)
  Downloading asciitree-0.3.3.tar.gz (4.0 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting fasteners (from zarr->anndata==0.10.0.dev35+ge145284)
  Downloading fasteners-0.18-py3-none-any.whl (18 kB)
Collecting numcodecs>=0.10.0 (from zarr->anndata==0.10.0.dev35+ge145284)
  Downloading numcodecs-0.11.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (6.7 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 6.7/6.7 MB 209.3 MB/s eta 0:00:00
Collecting parso<0.9.0,>=0.8.3 (from jedi>=0.16->IPython->anndata==0.10.0.dev35+ge145284)
  Downloading parso-0.8.3-py2.py3-none-any.whl (100 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100.8/100.8 kB 262.7 MB/s eta 0:00:00
Requirement already satisfied: MarkupSafe>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/949/lib/python3.10/site-packages (from Jinja2>=3.0->sphinx>=4.4->anndata==0.10.0.dev35+ge145284) (2.1.3)
Collecting mdurl~=0.1 (from markdown-it-py~=3.0->myst_parser->anndata==0.10.0.dev35+ge145284)
  Downloading mdurl-0.1.2-py3-none-any.whl (10.0 kB)
Collecting beautifulsoup4 (from nbconvert!=5.4->nbsphinx->anndata==0.10.0.dev35+ge145284)
  Downloading beautifulsoup4-4.12.2-py3-none-any.whl (142 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 143.0/143.0 kB 266.1 MB/s eta 0:00:00
Collecting bleach!=5.0.0 (from nbconvert!=5.4->nbsphinx->anndata==0.10.0.dev35+ge145284)
  Downloading bleach-6.0.0-py3-none-any.whl (162 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 162.5/162.5 kB 271.2 MB/s eta 0:00:00
Collecting defusedxml (from nbconvert!=5.4->nbsphinx->anndata==0.10.0.dev35+ge145284)
  Downloading defusedxml-0.7.1-py2.py3-none-any.whl (25 kB)
Collecting jupyter-core>=4.7 (from nbconvert!=5.4->nbsphinx->anndata==0.10.0.dev35+ge145284)
  Obtaining dependency information for jupyter-core>=4.7 from https://files.pythonhosted.org/packages/8c/e0/3f9061c5e99a03612510f892647b15a91f910c5275b7b77c6c72edae1494/jupyter_core-5.3.1-py3-none-any.whl.metadata
  Downloading jupyter_core-5.3.1-py3-none-any.whl.metadata (3.4 kB)
Collecting jupyterlab-pygments (from nbconvert!=5.4->nbsphinx->anndata==0.10.0.dev35+ge145284)
  Downloading jupyterlab_pygments-0.2.2-py2.py3-none-any.whl (21 kB)
Collecting mistune<4,>=2.0.3 (from nbconvert!=5.4->nbsphinx->anndata==0.10.0.dev35+ge145284)
  Obtaining dependency information for mistune<4,>=2.0.3 from https://files.pythonhosted.org/packages/cc/c0/ac9587149e37cde62ae338e9db8241ae2fdc79a84bde8c8ba7caea2c22d8/mistune-3.0.1-py3-none-any.whl.metadata
  Downloading mistune-3.0.1-py3-none-any.whl.metadata (1.7 kB)
Collecting nbclient>=0.5.0 (from nbconvert!=5.4->nbsphinx->anndata==0.10.0.dev35+ge145284)
  Obtaining dependency information for nbclient>=0.5.0 from https://files.pythonhosted.org/packages/ac/5a/d670ca51e6c3d98574b9647599821590efcd811d71f58e9c89fc59a17685/nbclient-0.8.0-py3-none-any.whl.metadata
  Downloading nbclient-0.8.0-py3-none-any.whl.metadata (7.8 kB)
Collecting pandocfilters>=1.4.1 (from nbconvert!=5.4->nbsphinx->anndata==0.10.0.dev35+ge145284)
  Downloading pandocfilters-1.5.0-py2.py3-none-any.whl (8.7 kB)
Collecting tinycss2 (from nbconvert!=5.4->nbsphinx->anndata==0.10.0.dev35+ge145284)
  Downloading tinycss2-1.2.1-py3-none-any.whl (21 kB)
Collecting fastjsonschema (from nbformat->nbsphinx->anndata==0.10.0.dev35+ge145284)
  Obtaining dependency information for fastjsonschema from https://files.pythonhosted.org/packages/9d/93/a3ca3cdeb84065d7d8f8df4cb09ab44405f109183c1d2b915ec17574e6b1/fastjsonschema-2.18.0-py3-none-any.whl.metadata
  Downloading fastjsonschema-2.18.0-py3-none-any.whl.metadata (2.0 kB)
Collecting jsonschema>=2.6 (from nbformat->nbsphinx->anndata==0.10.0.dev35+ge145284)
  Obtaining dependency information for jsonschema>=2.6 from https://files.pythonhosted.org/packages/a1/ba/28ce987450c6afa8336373761193ddaadc1ba2004fbf23a6407db036f558/jsonschema-4.18.4-py3-none-any.whl.metadata
  Downloading jsonschema-4.18.4-py3-none-any.whl.metadata (7.8 kB)
Collecting entrypoints (from numcodecs>=0.10.0->zarr->anndata==0.10.0.dev35+ge145284)
  Downloading entrypoints-0.4-py3-none-any.whl (5.3 kB)
Collecting ptyprocess>=0.5 (from pexpect>4.3->IPython->anndata==0.10.0.dev35+ge145284)
  Downloading ptyprocess-0.7.0-py2.py3-none-any.whl (13 kB)
Collecting wcwidth (from prompt-toolkit!=3.0.37,<3.1.0,>=3.0.30->IPython->anndata==0.10.0.dev35+ge145284)
  Downloading wcwidth-0.2.6-py2.py3-none-any.whl (29 kB)
Requirement already satisfied: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/949/lib/python3.10/site-packages (from python-dateutil>=2.8.2->pandas!=2.0.1,>=1.1.1->anndata==0.10.0.dev35+ge145284) (1.16.0)
Requirement already satisfied: charset-normalizer<4,>=2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/949/lib/python3.10/site-packages (from requests>=2.25.0->sphinx>=4.4->anndata==0.10.0.dev35+ge145284) (3.2.0)
Requirement already satisfied: idna<4,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/949/lib/python3.10/site-packages (from requests>=2.25.0->sphinx>=4.4->anndata==0.10.0.dev35+ge145284) (3.4)
Requirement already satisfied: urllib3<3,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/949/lib/python3.10/site-packages (from requests>=2.25.0->sphinx>=4.4->anndata==0.10.0.dev35+ge145284) (2.0.4)
Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/949/lib/python3.10/site-packages (from requests>=2.25.0->sphinx>=4.4->anndata==0.10.0.dev35+ge145284) (2023.7.22)
Collecting contourpy>=1.0.1 (from matplotlib->sphinxext.opengraph->anndata==0.10.0.dev35+ge145284)
  Obtaining dependency information for contourpy>=1.0.1 from https://files.pythonhosted.org/packages/aa/55/02c6d24804592b862b38a85c9b3283edc245081390a520ccd11697b6b24f/contourpy-1.1.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata
  Downloading contourpy-1.1.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.7 kB)
Collecting cycler>=0.10 (from matplotlib->sphinxext.opengraph->anndata==0.10.0.dev35+ge145284)
  Downloading cycler-0.11.0-py3-none-any.whl (6.4 kB)
Collecting fonttools>=4.22.0 (from matplotlib->sphinxext.opengraph->anndata==0.10.0.dev35+ge145284)
  Obtaining dependency information for fonttools>=4.22.0 from https://files.pythonhosted.org/packages/4e/d8/53f22f89cf87fcb088293ac94888c1ecbbd5a1418379f2ad05114d924446/fonttools-4.41.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata
  Downloading fonttools-4.41.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (150 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 150.0/150.0 kB 267.8 MB/s eta 0:00:00
Collecting kiwisolver>=1.0.1 (from matplotlib->sphinxext.opengraph->anndata==0.10.0.dev35+ge145284)
  Downloading kiwisolver-1.4.4-cp310-cp310-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (1.6 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.6/1.6 MB 262.0 MB/s eta 0:00:00
Requirement already satisfied: pillow>=6.2.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/949/lib/python3.10/site-packages (from matplotlib->sphinxext.opengraph->anndata==0.10.0.dev35+ge145284) (10.0.0)
Collecting pyparsing<3.1,>=2.3.1 (from matplotlib->sphinxext.opengraph->anndata==0.10.0.dev35+ge145284)
  Downloading pyparsing-3.0.9-py3-none-any.whl (98 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 98.3/98.3 kB 255.5 MB/s eta 0:00:00
Collecting executing>=1.2.0 (from stack-data->IPython->anndata==0.10.0.dev35+ge145284)
  Downloading executing-1.2.0-py2.py3-none-any.whl (24 kB)
Collecting asttokens>=2.1.0 (from stack-data->IPython->anndata==0.10.0.dev35+ge145284)
  Downloading asttokens-2.2.1-py2.py3-none-any.whl (26 kB)
Collecting pure-eval (from stack-data->IPython->anndata==0.10.0.dev35+ge145284)
  Downloading pure_eval-0.2.2-py3-none-any.whl (11 kB)
Collecting webencodings (from bleach!=5.0.0->nbconvert!=5.4->nbsphinx->anndata==0.10.0.dev35+ge145284)
  Downloading webencodings-0.5.1-py2.py3-none-any.whl (11 kB)
Collecting attrs>=22.2.0 (from jsonschema>=2.6->nbformat->nbsphinx->anndata==0.10.0.dev35+ge145284)
  Downloading attrs-23.1.0-py3-none-any.whl (61 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 61.2/61.2 kB 241.6 MB/s eta 0:00:00
Collecting jsonschema-specifications>=2023.03.6 (from jsonschema>=2.6->nbformat->nbsphinx->anndata==0.10.0.dev35+ge145284)
  Obtaining dependency information for jsonschema-specifications>=2023.03.6 from https://files.pythonhosted.org/packages/1c/24/83349ac2189cc2435e84da3f69ba3c97314d3c0622628e55171c6798ed80/jsonschema_specifications-2023.7.1-py3-none-any.whl.metadata
  Downloading jsonschema_specifications-2023.7.1-py3-none-any.whl.metadata (2.8 kB)
Collecting referencing>=0.28.4 (from jsonschema>=2.6->nbformat->nbsphinx->anndata==0.10.0.dev35+ge145284)
  Obtaining dependency information for referencing>=0.28.4 from https://files.pythonhosted.org/packages/ea/c3/f75f0ce2cdacca3d68a70b1756635092a1add1002e34afb4895b9fb62598/referencing-0.30.0-py3-none-any.whl.metadata
  Downloading referencing-0.30.0-py3-none-any.whl.metadata (2.7 kB)
Collecting rpds-py>=0.7.1 (from jsonschema>=2.6->nbformat->nbsphinx->anndata==0.10.0.dev35+ge145284)
  Obtaining dependency information for rpds-py>=0.7.1 from https://files.pythonhosted.org/packages/e2/26/69fd9b7e0ec9c2d710eae3eac5db157f5384b7717f2342596948c14cb6a3/rpds_py-0.9.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata
  Downloading rpds_py-0.9.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.7 kB)
Collecting platformdirs>=2.5 (from jupyter-core>=4.7->nbconvert!=5.4->nbsphinx->anndata==0.10.0.dev35+ge145284)
  Obtaining dependency information for platformdirs>=2.5 from https://files.pythonhosted.org/packages/14/51/fe5a0d6ea589f0d4a1b97824fb518962ad48b27cd346dcdfa2405187997a/platformdirs-3.10.0-py3-none-any.whl.metadata
  Downloading platformdirs-3.10.0-py3-none-any.whl.metadata (11 kB)
Collecting jupyter-client>=6.1.12 (from nbclient>=0.5.0->nbconvert!=5.4->nbsphinx->anndata==0.10.0.dev35+ge145284)
  Obtaining dependency information for jupyter-client>=6.1.12 from https://files.pythonhosted.org/packages/29/24/0491f7837cedf39ae0f96d9b3e4db2fae31cc4dd5eac00a98ab0db996c9b/jupyter_client-8.3.0-py3-none-any.whl.metadata
  Downloading jupyter_client-8.3.0-py3-none-any.whl.metadata (8.5 kB)
Collecting soupsieve>1.2 (from beautifulsoup4->nbconvert!=5.4->nbsphinx->anndata==0.10.0.dev35+ge145284)
  Downloading soupsieve-2.4.1-py3-none-any.whl (36 kB)
Collecting pyzmq>=23.0 (from jupyter-client>=6.1.12->nbclient>=0.5.0->nbconvert!=5.4->nbsphinx->anndata==0.10.0.dev35+ge145284)
  Obtaining dependency information for pyzmq>=23.0 from https://files.pythonhosted.org/packages/ca/db/f9976803f1a660e753d0f2426065975bad5db8272fd5284efaf488dc0ce1/pyzmq-25.1.0-cp310-cp310-manylinux_2_28_x86_64.whl.metadata
  Downloading pyzmq-25.1.0-cp310-cp310-manylinux_2_28_x86_64.whl.metadata (4.8 kB)
Collecting tornado>=6.2 (from jupyter-client>=6.1.12->nbclient>=0.5.0->nbconvert!=5.4->nbsphinx->anndata==0.10.0.dev35+ge145284)
  Obtaining dependency information for tornado>=6.2 from https://files.pythonhosted.org/packages/31/51/894f260c1380853cc268f661fe599a4523a47d07e867386abb58f1f11278/tornado-6.3.2-cp38-abi3-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata
  Downloading tornado-6.3.2-cp38-abi3-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.5 kB)
Downloading awkward-2.3.1-py3-none-any.whl (631 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 631.2/631.2 kB 279.1 MB/s eta 0:00:00
Downloading awkward_cpp-21-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.0 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.0/1.0 MB 283.6 MB/s eta 0:00:00
Downloading h5py-3.9.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.8 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.8/4.8 MB 230.4 MB/s eta 0:00:00
Downloading numpy-1.25.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (17.6 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 17.6/17.6 MB 218.4 MB/s eta 0:00:00
Downloading pandas-2.0.3-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.3 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 12.3/12.3 MB 226.4 MB/s eta 0:00:00
Downloading scanpydoc-0.9.4-py3-none-any.whl (30 kB)
Downloading scipy-1.11.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (36.3 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 36.3/36.3 MB 228.7 MB/s eta 0:00:00
Downloading sphinx_rtd_theme-1.2.2-py2.py3-none-any.whl (2.8 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.8/2.8 MB 39.3 MB/s eta 0:00:00
Downloading ipython-8.14.0-py3-none-any.whl (798 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 798.7/798.7 kB 281.4 MB/s eta 0:00:00
Downloading myst_parser-2.0.0-py3-none-any.whl (77 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 77.2/77.2 kB 253.7 MB/s eta 0:00:00
Downloading natsort-8.4.0-py3-none-any.whl (38 kB)
Downloading nbsphinx-0.9.2-py3-none-any.whl (30 kB)
Downloading zarr-2.16.0-py3-none-any.whl (206 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 206.5/206.5 kB 279.5 MB/s eta 0:00:00
Downloading jedi-0.19.0-py2.py3-none-any.whl (1.6 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.6/1.6 MB 258.0 MB/s eta 0:00:00
Downloading markdown_it_py-3.0.0-py3-none-any.whl (87 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 87.5/87.5 kB 255.3 MB/s eta 0:00:00
Downloading mdit_py_plugins-0.4.0-py3-none-any.whl (54 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 54.1/54.1 kB 235.4 MB/s eta 0:00:00
Downloading nbconvert-7.7.3-py3-none-any.whl (254 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 254.7/254.7 kB 275.1 MB/s eta 0:00:00
Downloading nbformat-5.9.1-py3-none-any.whl (77 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 77.6/77.6 kB 251.8 MB/s eta 0:00:00
Downloading prompt_toolkit-3.0.39-py3-none-any.whl (385 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 385.2/385.2 kB 280.3 MB/s eta 0:00:00
Downloading typing_extensions-4.7.1-py3-none-any.whl (33 kB)
Downloading matplotlib-3.7.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.6 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.6/11.6 MB 213.1 MB/s eta 0:00:00
Downloading PyYAML-6.0.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (705 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 705.5/705.5 kB 284.7 MB/s eta 0:00:00
Downloading contourpy-1.1.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (300 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 300.7/300.7 kB 272.7 MB/s eta 0:00:00
Downloading fonttools-4.41.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.5 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.5/4.5 MB 244.6 MB/s eta 0:00:00
Downloading jsonschema-4.18.4-py3-none-any.whl (80 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 81.0/81.0 kB 231.0 MB/s eta 0:00:00
Downloading jupyter_core-5.3.1-py3-none-any.whl (93 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 93.7/93.7 kB 245.3 MB/s eta 0:00:00
Downloading mistune-3.0.1-py3-none-any.whl (47 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 48.0/48.0 kB 227.6 MB/s eta 0:00:00
Downloading nbclient-0.8.0-py3-none-any.whl (73 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 73.1/73.1 kB 232.1 MB/s eta 0:00:00
Downloading fastjsonschema-2.18.0-py3-none-any.whl (23 kB)
Downloading jsonschema_specifications-2023.7.1-py3-none-any.whl (17 kB)
Downloading jupyter_client-8.3.0-py3-none-any.whl (103 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 103.2/103.2 kB 251.4 MB/s eta 0:00:00
Downloading platformdirs-3.10.0-py3-none-any.whl (17 kB)
Downloading referencing-0.30.0-py3-none-any.whl (25 kB)
Downloading rpds_py-0.9.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.2 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 281.7 MB/s eta 0:00:00
Downloading pyzmq-25.1.0-cp310-cp310-manylinux_2_28_x86_64.whl (1.1 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 285.5 MB/s eta 0:00:00
Downloading tornado-6.3.2-cp38-abi3-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (426 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 426.9/426.9 kB 282.9 MB/s eta 0:00:00
Building wheels for collected packages: anndata, asciitree
  Building wheel for anndata (pyproject.toml): started
  Building wheel for anndata (pyproject.toml): finished with status 'done'
  Created wheel for anndata: filename=anndata-0.10.0.dev35+ge145284-py3-none-any.whl size=447736 sha256=70e14dd07cab22fda01c62fd143bbaf47622e317cdc38768f5c163ed9064b758
  Stored in directory: /tmp/pip-ephem-wheel-cache-tn335fbc/wheels/c5/16/50/20b0b1c30c0124f2fa780ee698faf4ec1a27a4d241d006c733
  Building wheel for asciitree (setup.py): started
  Building wheel for asciitree (setup.py): finished with status 'done'
  Created wheel for asciitree: filename=asciitree-0.3.3-py3-none-any.whl size=5033 sha256=4629d87b17d4662c32f4d194d31f0a009ffe47e8af4be00dea61c3be6f8f2972
  Stored in directory: /tmp/pip-ephem-wheel-cache-tn335fbc/wheels/7f/4e/be/1171b40f43b918087657ec57cf3b81fa1a2e027d8755baa184
Successfully built anndata asciitree
Installing collected packages: webencodings, wcwidth, pytz, pure-eval, ptyprocess, pickleshare, fastjsonschema, executing, backcall, asciitree, tzdata, typing-extensions, traitlets, tornado, tinycss2, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, soupsieve, rpds-py, pyzmq, pyyaml, python-dateutil, pyparsing, prompt-toolkit, platformdirs, pexpect, parso, pandocfilters, numpy, natsort, mistune, mdurl, kiwisolver, jupyterlab-pygments, fonttools, fasteners, entrypoints, docutils, defusedxml, decorator, cycler, bleach, attrs, asttokens, stack-data, sphinx, scipy, referencing, pandas, numcodecs, matplotlib-inline, markdown-it-py, jupyter-core, jedi, h5py, contourpy, beautifulsoup4, awkward-cpp, zarr, sphinxcontrib-jquery, sphinx_issues, sphinx-autodoc-typehints, scanpydoc, mdit-py-plugins, matplotlib, jupyter-client, jsonschema-specifications, IPython, awkward, anndata, sphinxext.opengraph, sphinx-rtd-theme, myst_parser, jsonschema, nbformat, nbclient, nbconvert, nbsphinx
  Attempting uninstall: docutils
    Found existing installation: docutils 0.17.1
    Uninstalling docutils-0.17.1:
      Successfully uninstalled docutils-0.17.1
  Attempting uninstall: sphinx
    Found existing installation: Sphinx 1.8.6
    Uninstalling Sphinx-1.8.6:
      Successfully uninstalled Sphinx-1.8.6
  Attempting uninstall: sphinx-rtd-theme
    Found existing installation: sphinx-rtd-theme 0.4.3
    Uninstalling sphinx-rtd-theme-0.4.3:
      Successfully uninstalled sphinx-rtd-theme-0.4.3
Successfully installed IPython-8.14.0 anndata-0.10.0.dev35+ge145284 asciitree-0.3.3 asttokens-2.2.1 attrs-23.1.0 awkward-2.3.1 awkward-cpp-21 backcall-0.2.0 beautifulsoup4-4.12.2 bleach-6.0.0 contourpy-1.1.0 cycler-0.11.0 decorator-5.1.1 defusedxml-0.7.1 docutils-0.18.1 entrypoints-0.4 executing-1.2.0 fasteners-0.18 fastjsonschema-2.18.0 fonttools-4.41.1 h5py-3.9.0 jedi-0.19.0 jsonschema-4.18.4 jsonschema-specifications-2023.7.1 jupyter-client-8.3.0 jupyter-core-5.3.1 jupyterlab-pygments-0.2.2 kiwisolver-1.4.4 markdown-it-py-3.0.0 matplotlib-3.7.2 matplotlib-inline-0.1.6 mdit-py-plugins-0.4.0 mdurl-0.1.2 mistune-3.0.1 myst_parser-2.0.0 natsort-8.4.0 nbclient-0.8.0 nbconvert-7.7.3 nbformat-5.9.1 nbsphinx-0.9.2 numcodecs-0.11.0 numpy-1.25.1 pandas-2.0.3 pandocfilters-1.5.0 parso-0.8.3 pexpect-4.8.0 pickleshare-0.7.5 platformdirs-3.10.0 prompt-toolkit-3.0.39 ptyprocess-0.7.0 pure-eval-0.2.2 pyparsing-3.0.9 python-dateutil-2.8.2 pytz-2023.3 pyyaml-6.0.1 pyzmq-25.1.0 referencing-0.30.0 rpds-py-0.9.2 scanpydoc-0.9.4 scipy-1.11.1 soupsieve-2.4.1 sphinx-6.2.1 sphinx-autodoc-typehints-1.23.0 sphinx-rtd-theme-1.2.2 sphinx_issues-3.0.1 sphinxcontrib-applehelp-1.0.4 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.1 sphinxcontrib-jquery-4.1 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 sphinxext.opengraph-0.8.2 stack-data-0.6.2 tinycss2-1.2.1 tornado-6.3.2 traitlets-5.9.0 typing-extensions-4.7.1 tzdata-2023.3 wcwidth-0.2.6 webencodings-0.5.1 zarr-2.16.0

[rtd-command-info] start-time: 2023-07-30T20:07:46.793253Z, end-time: 2023-07-30T20:07:46.884444Z, duration: 0, exit-code: 0
cat docs/conf.py
import sys
import logging
from pathlib import Path
from datetime import datetime

from sphinx.application import Sphinx

HERE = Path(__file__).parent
sys.path[:0] = [str(HERE.parent), str(HERE / "extensions")]
import anndata  # noqa


logger = logging.getLogger(__name__)

for generated in HERE.glob("anndata.*.rst"):
    generated.unlink()


# -- General configuration ------------------------------------------------


needs_sphinx = "1.7"  # autosummary bugfix

# General information
project = "anndata"
author = f"{project} developers"
copyright = f"{datetime.now():%Y}, {author}"
version = anndata.__version__.replace(".dirty", "")
release = version

# default settings
templates_path = ["_templates"]
html_static_path = ["_static"]
source_suffix = [".rst", ".md"]
master_doc = "index"
default_role = "literal"
exclude_patterns = [
    "_build",
    "Thumbs.db",
    ".DS_Store",
    "**.ipynb_checkpoints",
    "tutorials/notebooks/*.rst",
]
pygments_style = "sphinx"

extensions = [
    "myst_parser",
    "sphinx.ext.autodoc",
    "sphinx.ext.intersphinx",
    "sphinx.ext.doctest",
    "sphinx.ext.coverage",
    "sphinx.ext.mathjax",
    "sphinx.ext.napoleon",
    "sphinx.ext.autosummary",
    "sphinx_autodoc_typehints",  # needs to be after napoleon
    "sphinx_issues",
    "sphinxext.opengraph",
    "scanpydoc",
    "nbsphinx",
    "IPython.sphinxext.ipython_console_highlighting",
]
myst_enable_extensions = [
    "html_image",  # So README.md can be used on github and sphinx docs
]

# Generate the API documentation when building
autosummary_generate = True
autodoc_member_order = "bysource"
issues_github_path = "scverse/anndata"
# 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")]
typehints_defaults = "braces"
todo_include_todos = False
nitpicky = True  # Report broken links
nitpick_ignore = [
    ("py:class", "scipy.sparse.base.spmatrix"),
    ("py:meth", "pandas.DataFrame.iloc"),
    ("py:meth", "pandas.DataFrame.loc"),
    ("py:class", "anndata._core.views.ArrayView"),
    ("py:class", "anndata._core.raw.Raw"),
    *[
        ("py:class", f"anndata._core.aligned_mapping.{cls}{kind}")
        for cls in "Layers AxisArrays PairwiseArrays".split()
        for kind in ["", "View"]
    ],
]
suppress_warnings = [
    "ref.citation",
    "myst.header",  # https://github.com/executablebooks/MyST-Parser/issues/262
]


def setup(app: Sphinx):
    # Don’t allow broken links. DO NOT CHANGE THIS LINE, fix problems instead.
    app.warningiserror = False


intersphinx_mapping = dict(
    h5py=("https://docs.h5py.org/en/latest/", None),
    hdf5plugin=("https://hdf5plugin.readthedocs.io/en/latest/", None),
    loompy=("https://linnarssonlab.org/loompy/", None),
    numpy=("https://numpy.org/doc/stable/", None),
    pandas=("https://pandas.pydata.org/pandas-docs/stable/", None),
    python=("https://docs.python.org/3", None),
    scipy=("https://docs.scipy.org/doc/scipy/", None),
    sklearn=("https://scikit-learn.org/stable/", None),
    zarr=("https://zarr.readthedocs.io/en/stable/", None),
    xarray=("https://xarray.pydata.org/en/stable/", None),
)
qualname_overrides = {
    "h5py._hl.group.Group": "h5py.Group",
    "h5py._hl.files.File": "h5py.File",
    "h5py._hl.dataset.Dataset": "h5py.Dataset",
    "anndata._core.anndata.AnnData": "anndata.AnnData",
}

# -- Social cards ---------------------------------------------------------

ogp_site_url = "https://anndata.readthedocs.io/"
ogp_image = "https://anndata.readthedocs.io/en/latest/_static/img/anndata_schema.svg"

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


html_theme = "scanpydoc"
html_theme_options = dict(navigation_depth=4)
html_context = dict(
    display_github=True,  # Integrate GitHub
    github_user="scverse",  # Username
    github_repo="anndata",  # Repo name
    github_version="main",  # Version
    conf_py_path="/docs/",  # Path in the checkout to the docs root
)
issues_github_path = "{github_user}/{github_repo}".format_map(html_context)
html_show_sphinx = False


# -- 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",
    )
]




###########################################################################
#          auto-created readthedocs.org specific configuration            #
###########################################################################


#
# The following code was added during an automated build on readthedocs.org
# It is auto created and injected for every build. The result is based on the
# conf.py.tmpl file found in the readthedocs.org codebase:
# https://github.com/rtfd/readthedocs.org/blob/main/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl
#
# Note: this file shouldn't rely on extra dependencies.

import importlib
import sys
import os.path

# Borrowed from six.
PY3 = sys.version_info[0] == 3
string_types = str if PY3 else basestring

from sphinx import version_info

# Get suffix for proper linking to GitHub
# This is deprecated in Sphinx 1.3+,
# as each page can have its own suffix
if globals().get('source_suffix', False):
    if isinstance(source_suffix, string_types):
        SUFFIX = source_suffix
    elif isinstance(source_suffix, (list, tuple)):
        # Sphinx >= 1.3 supports list/tuple to define multiple suffixes
        SUFFIX = source_suffix[0]
    elif isinstance(source_suffix, dict):
        # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes
        SUFFIX = list(source_suffix.keys())[0]  # make a ``list()`` for py2/py3 compatibility
    else:
        # default to .rst
        SUFFIX = '.rst'
else:
    SUFFIX = '.rst'

# Add RTD Static Path. Add to the end because it overwrites previous files.
if not 'html_static_path' in globals():
    html_static_path = []
if os.path.exists('_static'):
    html_static_path.append('_static')

# Add RTD Theme only if they aren't overriding it already
using_rtd_theme = (
    (
        'html_theme' in globals() and
        html_theme in ['default'] and
        # Allow people to bail with a hack of having an html_style
        'html_style' not in globals()
    ) or 'html_theme' not in globals()
)
if using_rtd_theme:
    html_theme = 'sphinx_rtd_theme'
    html_style = None
    html_theme_options = {}


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

# Define websupport2_base_url and websupport2_static_url
if globals().get('websupport2_base_url', False):
    websupport2_base_url = 'https://readthedocs.com/websupport'
    websupport2_static_url = 'https://assets.readthedocs.com/'


#Add project information to the template context.
context = {
    'using_theme': using_rtd_theme,
    'html_theme': html_theme,
    'current_version': "949",
    'version_slug': "949",
    'MEDIA_URL': "https://media.readthedocs.com/media/",
    'STATIC_URL': "https://assets.readthedocs.com/",
    'PRODUCTION_DOMAIN': "readthedocs.com",
    'proxied_static_path': "/_/static/",
    'versions': [
    ("latest", "/en/latest/"),
    ("stable", "/en/stable/"),
    ("0.7.8", "/en/0.7.8/"),
    ("0.4.1", "/en/0.4.1/"),
    ("0.3", "/en/0.3/"),
    ],
    'downloads': [ 
    ],
    'subprojects': [ 
    ],
    'slug': 'icb-anndata',
    'name': u'anndata',
    'rtd_language': u'en',
    'programming_language': u'py',
    'canonical_url': '',
    'analytics_code': 'None',
    'single_version': False,
    'conf_py_path': '/docs/',
    'api_host': 'https://readthedocs.com',
    'github_user': 'scverse',
    'proxied_api_host': '/_',
    'github_repo': 'anndata',
    'github_version': 'e1452845832c71b1e8d1c61c20117143dbbf38ac',
    'display_github': True,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': 'e1452845832c71b1e8d1c61c20117143dbbf38ac',
    'display_bitbucket': False,
    'gitlab_user': 'None',
    'gitlab_repo': 'None',
    'gitlab_version': 'e1452845832c71b1e8d1c61c20117143dbbf38ac',
    'display_gitlab': False,
    'READTHEDOCS': True,
    'using_theme': (html_theme == "default"),
    'new_theme': (html_theme == "sphinx_rtd_theme"),
    'source_suffix': SUFFIX,
    'ad_free': False,
    'docsearch_disabled': False,
    'user_analytics_code': '',
    'global_analytics_code': 'UA-17997319-2',
    'commit': 'e1452845',
}

# For sphinx >=1.8 we can use html_baseurl to set the canonical URL.
# https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_baseurl
if version_info >= (1, 8):
    if not globals().get('html_baseurl'):
        html_baseurl = context['canonical_url']
    context['canonical_url'] = None





if 'html_context' in globals():
    for key in context:
        if key not in html_context:
            html_context[key] = context[key]
else:
    html_context = context

# Add custom RTD extension
if 'extensions' in globals():
    # Insert at the beginning because it can interfere
    # with other extensions.
    # See https://github.com/rtfd/readthedocs.org/pull/4054
    extensions.insert(0, "readthedocs_ext.readthedocs")
else:
    extensions = ["readthedocs_ext.readthedocs"]

# Add External version warning banner to the external version documentation
if 'external' == 'external':
    extensions.insert(1, "readthedocs_ext.external_version_warning")
    readthedocs_vcs_url = 'https://github.com/scverse/anndata/pull/949'
    readthedocs_build_url = 'https://readthedocs.com/projects/icb-anndata/builds/1630280/'

project_language = 'en'

# User's Sphinx configurations
language_user = globals().get('language', None)
latex_engine_user = globals().get('latex_engine', None)
latex_elements_user = globals().get('latex_elements', None)

# Remove this once xindy gets installed in Docker image and XINDYOPS
# env variable is supported
# https://github.com/rtfd/readthedocs-docker-images/pull/98
latex_use_xindy = False

chinese = any([
    language_user in ('zh_CN', 'zh_TW'),
    project_language in ('zh_CN', 'zh_TW'),
])

japanese = any([
    language_user == 'ja',
    project_language == 'ja',
])

if chinese:
    latex_engine = latex_engine_user or 'xelatex'

    latex_elements_rtd = {
        'preamble': '\\usepackage[UTF8]{ctex}\n',
    }
    latex_elements = latex_elements_user or latex_elements_rtd
elif japanese:
    latex_engine = latex_engine_user or 'platex'

# Make sure our build directory is always excluded
exclude_patterns = globals().get('exclude_patterns', [])
exclude_patterns.extend(['_build'])

[rtd-command-info] start-time: 2023-07-30T20:07:47.274888Z, end-time: 2023-07-30T20:08:15.203700Z, duration: 27, exit-code: 2
python -m sphinx -T -E -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html
Running Sphinx v6.2.1
Matplotlib is building the font cache; this may take a moment.
making output directory... done

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/949/lib/python3.10/site-packages/sphinx/theming.py", line 81, in __init__
    self.base = factory.create(inherit)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/949/lib/python3.10/site-packages/sphinx/theming.py", line 228, in create
    raise ThemeError(__('no theme named %r found (missing theme.conf?)') % name)
sphinx.errors.ThemeError: no theme named 'sphinx_book_theme' found (missing theme.conf?)

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/949/lib/python3.10/site-packages/sphinx/cmd/build.py", line 280, in build_main
    app = Sphinx(args.sourcedir, args.confdir, args.outputdir,
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/949/lib/python3.10/site-packages/sphinx/application.py", line 268, in __init__
    self._init_builder()
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/949/lib/python3.10/site-packages/sphinx/application.py", line 340, in _init_builder
    self.builder.init()
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/949/lib/python3.10/site-packages/sphinx/builders/html/__init__.py", line 253, in init
    self.init_templates()
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/949/lib/python3.10/site-packages/sphinx/builders/html/__init__.py", line 304, in init_templates
    self.theme = theme_factory.create(themename)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/949/lib/python3.10/site-packages/sphinx/theming.py", line 230, in create
    return Theme(name, self.themes[name], factory=self)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/949/lib/python3.10/site-packages/sphinx/theming.py", line 83, in __init__
    raise ThemeError(__('no theme named %r found, inherited by %r') %
sphinx.errors.ThemeError: no theme named 'sphinx_book_theme' found, inherited by 'scanpydoc'

Theme error:
no theme named 'sphinx_book_theme' found, inherited by 'scanpydoc'