Read the Docs build information
Build id: 2442166
Project: icb-anndata
Version: 1558
Commit: b354e82b623b096fce6a06285a083e344f7a09f3
Date: 2024-08-27T09:34:17.137144Z
State: finished
Success: True


[rtd-command-info] start-time: 2024-08-27T09:34:19.219003Z, end-time: 2024-08-27T09:34:19.743873Z, duration: 0, exit-code: 0
git clone --depth 1 https://github.com/scverse/anndata.git .
Cloning into '.'...

[rtd-command-info] start-time: 2024-08-27T09:34:19.807489Z, end-time: 2024-08-27T09:34:20.323449Z, duration: 0, exit-code: 0
git fetch origin --force --prune --prune-tags --depth 50 pull/1558/head:external-1558
From https://github.com/scverse/anndata
 * [new ref]         refs/pull/1558/head -> external-1558

[rtd-command-info] start-time: 2024-08-27T09:34:20.452053Z, end-time: 2024-08-27T09:34:20.525003Z, duration: 0, exit-code: 0
git checkout --force b354e82b623b096fce6a06285a083e344f7a09f3
Note: switching to 'b354e82b623b096fce6a06285a083e344f7a09f3'.

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 b354e82 add numcodecs warning

[rtd-command-info] start-time: 2024-08-27T09:34:20.603126Z, end-time: 2024-08-27T09:34:20.670100Z, duration: 0, exit-code: 0
cat .readthedocs.yml
version: 2
build:
  os: ubuntu-20.04
  tools:
    python: "3.12"
sphinx:
  configuration: docs/conf.py
  fail_on_warning: true # do not change or you will be fired
python:
  install:
    - method: pip
      path: .
      extra_requirements:
        - doc
submodules:
  include:
    - "docs/tutorials/notebooks"
  recursive: true

[rtd-command-info] start-time: 2024-08-27T09:34:20.799602Z, end-time: 2024-08-27T09:34:20.891869Z, duration: 0, exit-code: 0
git submodule sync


[rtd-command-info] start-time: 2024-08-27T09:34:20.963912Z, end-time: 2024-08-27T09:34:21.560154Z, 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/1558/docs/tutorials/notebooks'...
Submodule path 'docs/tutorials/notebooks': checked out '9e186c5c694793bb04ea1397721d154d6e0b7069'

[rtd-command-info] start-time: 2024-08-27T09:34:28.097814Z, end-time: 2024-08-27T09:34:28.174532Z, duration: 0, exit-code: 0
asdf global python 3.12.3


[rtd-command-info] start-time: 2024-08-27T09:34:28.588055Z, end-time: 2024-08-27T09:34:29.697687Z, duration: 1, exit-code: 0
python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH
created virtual environment CPython3.12.3.final.0-64 in 761ms
  creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1558, 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: 2024-08-27T09:34:29.779091Z, end-time: 2024-08-27T09:34:44.188228Z, duration: 14, 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/1558/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 28.1 MB/s eta 0:00:00
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1558/lib/python3.12/site-packages (67.6.1)
Collecting setuptools
  Downloading setuptools-73.0.1-py3-none-any.whl (2.3 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.3/2.3 MB 107.4 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-73.0.1

[rtd-command-info] start-time: 2024-08-27T09:34:44.253816Z, end-time: 2024-08-27T09:34:53.534241Z, duration: 9, exit-code: 0
python -m pip install --upgrade --no-cache-dir sphinx readthedocs-sphinx-ext
Collecting sphinx
  Downloading sphinx-8.0.2-py3-none-any.whl.metadata (6.2 kB)
Collecting readthedocs-sphinx-ext
  Downloading readthedocs_sphinx_ext-2.2.5-py2.py3-none-any.whl.metadata (1.5 kB)
Collecting sphinxcontrib-applehelp (from sphinx)
  Downloading sphinxcontrib_applehelp-2.0.0-py3-none-any.whl.metadata (2.3 kB)
Collecting sphinxcontrib-devhelp (from sphinx)
  Downloading sphinxcontrib_devhelp-2.0.0-py3-none-any.whl.metadata (2.3 kB)
Collecting sphinxcontrib-jsmath (from sphinx)
  Downloading sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl.metadata (1.4 kB)
Collecting sphinxcontrib-htmlhelp>=2.0.0 (from sphinx)
  Downloading sphinxcontrib_htmlhelp-2.1.0-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 sphinxcontrib-qthelp (from sphinx)
  Downloading sphinxcontrib_qthelp-2.0.0-py3-none-any.whl.metadata (2.3 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-2.1.5-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.0 kB)
Collecting charset-normalizer<4,>=2 (from requests>=2.30.0->sphinx)
  Downloading charset_normalizer-3.3.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (33 kB)
Collecting idna<4,>=2.5 (from requests>=2.30.0->sphinx)
  Downloading idna-3.8-py3-none-any.whl.metadata (9.9 kB)
Collecting urllib3<3,>=1.21.1 (from requests>=2.30.0->sphinx)
  Downloading urllib3-2.2.2-py3-none-any.whl.metadata (6.4 kB)
Collecting certifi>=2017.4.17 (from requests>=2.30.0->sphinx)
  Downloading certifi-2024.7.4-py3-none-any.whl.metadata (2.2 kB)
Downloading sphinx-8.0.2-py3-none-any.whl (3.5 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.5/3.5 MB 91.6 MB/s eta 0:00:00
Downloading readthedocs_sphinx_ext-2.2.5-py2.py3-none-any.whl (11 kB)
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 158.0 MB/s eta 0:00:00
Downloading docutils-0.21.2-py3-none-any.whl (587 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 587.4/587.4 kB 332.2 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 338.1 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_htmlhelp-2.1.0-py3-none-any.whl (98 kB)
Downloading sphinxcontrib_serializinghtml-2.0.0-py3-none-any.whl (92 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_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 certifi-2024.7.4-py3-none-any.whl (162 kB)
Downloading charset_normalizer-3.3.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (141 kB)
Downloading idna-3.8-py3-none-any.whl (66 kB)
Downloading MarkupSafe-2.1.5-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (28 kB)
Downloading urllib3-2.2.2-py3-none-any.whl (121 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, readthedocs-sphinx-ext
Successfully installed Jinja2-3.1.4 MarkupSafe-2.1.5 Pygments-2.18.0 alabaster-1.0.0 babel-2.16.0 certifi-2024.7.4 charset-normalizer-3.3.2 docutils-0.21.2 idna-3.8 imagesize-1.4.1 packaging-24.1 readthedocs-sphinx-ext-2.2.5 requests-2.32.3 snowballstemmer-2.2.0 sphinx-8.0.2 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 urllib3-2.2.2

[rtd-command-info] start-time: 2024-08-27T09:34:53.618159Z, end-time: 2024-08-27T09:35:29.919785Z, duration: 36, 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/1558
  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 array-api-compat!=1.5,>1.4 (from anndata==0.1.dev71+gb354e82)
  Downloading array_api_compat-1.8-py3-none-any.whl.metadata (1.5 kB)
Collecting h5py>=3.1 (from anndata==0.1.dev71+gb354e82)
  Downloading h5py-3.11.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.5 kB)
Collecting natsort (from anndata==0.1.dev71+gb354e82)
  Downloading natsort-8.4.0-py3-none-any.whl.metadata (21 kB)
Collecting numpy>=1.23 (from anndata==0.1.dev71+gb354e82)
  Downloading numpy-2.1.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB)
Requirement already satisfied: packaging>=20.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1558/lib/python3.12/site-packages (from anndata==0.1.dev71+gb354e82) (24.1)
Collecting pandas!=2.1.0rc0,!=2.1.2,>=1.4 (from anndata==0.1.dev71+gb354e82)
  Downloading pandas-2.2.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (19 kB)
Collecting scipy>1.8 (from anndata==0.1.dev71+gb354e82)
  Downloading scipy-1.14.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB)
Collecting awkward>=2.0.7 (from anndata==0.1.dev71+gb354e82)
  Downloading awkward-2.6.7-py3-none-any.whl.metadata (7.0 kB)
Collecting ipython (from anndata==0.1.dev71+gb354e82)
  Downloading ipython-8.26.0-py3-none-any.whl.metadata (5.0 kB)
Collecting myst-parser (from anndata==0.1.dev71+gb354e82)
  Downloading myst_parser-4.0.0-py3-none-any.whl.metadata (5.4 kB)
Collecting nbsphinx (from anndata==0.1.dev71+gb354e82)
  Downloading nbsphinx-0.9.5-py3-none-any.whl.metadata (2.1 kB)
Collecting readthedocs-sphinx-search (from anndata==0.1.dev71+gb354e82)
  Downloading readthedocs_sphinx_search-0.3.2-py3-none-any.whl.metadata (2.4 kB)
Collecting scanpydoc>=0.13.6 (from scanpydoc[theme,typehints]>=0.13.6; extra == "doc"->anndata==0.1.dev71+gb354e82)
  Downloading scanpydoc-0.13.6-py3-none-any.whl.metadata (2.7 kB)
Collecting sphinx-autodoc-typehints>=2.2.0 (from anndata==0.1.dev71+gb354e82)
  Downloading sphinx_autodoc_typehints-2.2.3-py3-none-any.whl.metadata (8.0 kB)
Collecting sphinx-book-theme>=1.1.0 (from anndata==0.1.dev71+gb354e82)
  Downloading sphinx_book_theme-1.1.3-py3-none-any.whl.metadata (5.7 kB)
Collecting sphinx-copybutton (from anndata==0.1.dev71+gb354e82)
  Downloading sphinx_copybutton-0.5.2-py3-none-any.whl.metadata (3.2 kB)
Collecting sphinx-design>=0.5.0 (from anndata==0.1.dev71+gb354e82)
  Downloading sphinx_design-0.6.1-py3-none-any.whl.metadata (5.5 kB)
Collecting sphinx-issues (from anndata==0.1.dev71+gb354e82)
  Downloading sphinx_issues-4.1.0-py3-none-any.whl.metadata (8.3 kB)
Collecting sphinx-toolbox (from anndata==0.1.dev71+gb354e82)
  Downloading sphinx_toolbox-3.8.0-py3-none-any.whl.metadata (8.1 kB)
Requirement already satisfied: sphinx>=7.4.6 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1558/lib/python3.12/site-packages (from anndata==0.1.dev71+gb354e82) (8.0.2)
Collecting sphinxext-opengraph (from anndata==0.1.dev71+gb354e82)
  Downloading sphinxext_opengraph-0.9.1-py3-none-any.whl.metadata (6.5 kB)
Collecting zarr (from anndata==0.1.dev71+gb354e82)
  Downloading zarr-2.18.2-py3-none-any.whl.metadata (5.7 kB)
Collecting awkward-cpp==37 (from awkward>=2.0.7->anndata==0.1.dev71+gb354e82)
  Downloading awkward_cpp-37-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.2 kB)
Collecting fsspec>=2022.11.0 (from awkward>=2.0.7->anndata==0.1.dev71+gb354e82)
  Downloading fsspec-2024.6.1-py3-none-any.whl.metadata (11 kB)
Collecting python-dateutil>=2.8.2 (from pandas!=2.1.0rc0,!=2.1.2,>=1.4->anndata==0.1.dev71+gb354e82)
  Downloading python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
Collecting pytz>=2020.1 (from pandas!=2.1.0rc0,!=2.1.2,>=1.4->anndata==0.1.dev71+gb354e82)
  Downloading pytz-2024.1-py2.py3-none-any.whl.metadata (22 kB)
Collecting tzdata>=2022.7 (from pandas!=2.1.0rc0,!=2.1.2,>=1.4->anndata==0.1.dev71+gb354e82)
  Downloading tzdata-2024.1-py2.py3-none-any.whl.metadata (1.4 kB)
Requirement already satisfied: sphinxcontrib-applehelp in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1558/lib/python3.12/site-packages (from sphinx>=7.4.6->anndata==0.1.dev71+gb354e82) (2.0.0)
Requirement already satisfied: sphinxcontrib-devhelp in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1558/lib/python3.12/site-packages (from sphinx>=7.4.6->anndata==0.1.dev71+gb354e82) (2.0.0)
Requirement already satisfied: sphinxcontrib-jsmath in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1558/lib/python3.12/site-packages (from sphinx>=7.4.6->anndata==0.1.dev71+gb354e82) (1.0.1)
Requirement already satisfied: sphinxcontrib-htmlhelp>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1558/lib/python3.12/site-packages (from sphinx>=7.4.6->anndata==0.1.dev71+gb354e82) (2.1.0)
Requirement already satisfied: sphinxcontrib-serializinghtml>=1.1.9 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1558/lib/python3.12/site-packages (from sphinx>=7.4.6->anndata==0.1.dev71+gb354e82) (2.0.0)
Requirement already satisfied: sphinxcontrib-qthelp in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1558/lib/python3.12/site-packages (from sphinx>=7.4.6->anndata==0.1.dev71+gb354e82) (2.0.0)
Requirement already satisfied: Jinja2>=3.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1558/lib/python3.12/site-packages (from sphinx>=7.4.6->anndata==0.1.dev71+gb354e82) (3.1.4)
Requirement already satisfied: Pygments>=2.17 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1558/lib/python3.12/site-packages (from sphinx>=7.4.6->anndata==0.1.dev71+gb354e82) (2.18.0)
Requirement already satisfied: docutils<0.22,>=0.20 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1558/lib/python3.12/site-packages (from sphinx>=7.4.6->anndata==0.1.dev71+gb354e82) (0.21.2)
Requirement already satisfied: snowballstemmer>=2.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1558/lib/python3.12/site-packages (from sphinx>=7.4.6->anndata==0.1.dev71+gb354e82) (2.2.0)
Requirement already satisfied: babel>=2.13 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1558/lib/python3.12/site-packages (from sphinx>=7.4.6->anndata==0.1.dev71+gb354e82) (2.16.0)
Requirement already satisfied: alabaster>=0.7.14 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1558/lib/python3.12/site-packages (from sphinx>=7.4.6->anndata==0.1.dev71+gb354e82) (1.0.0)
Requirement already satisfied: imagesize>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1558/lib/python3.12/site-packages (from sphinx>=7.4.6->anndata==0.1.dev71+gb354e82) (1.4.1)
Requirement already satisfied: requests>=2.30.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1558/lib/python3.12/site-packages (from sphinx>=7.4.6->anndata==0.1.dev71+gb354e82) (2.32.3)
Collecting pydata-sphinx-theme>=0.15.2 (from sphinx-book-theme>=1.1.0->anndata==0.1.dev71+gb354e82)
  Downloading pydata_sphinx_theme-0.15.4-py3-none-any.whl.metadata (7.5 kB)
Collecting decorator (from ipython->anndata==0.1.dev71+gb354e82)
  Downloading decorator-5.1.1-py3-none-any.whl.metadata (4.0 kB)
Collecting jedi>=0.16 (from ipython->anndata==0.1.dev71+gb354e82)
  Downloading jedi-0.19.1-py2.py3-none-any.whl.metadata (22 kB)
Collecting matplotlib-inline (from ipython->anndata==0.1.dev71+gb354e82)
  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->anndata==0.1.dev71+gb354e82)
  Downloading prompt_toolkit-3.0.47-py3-none-any.whl.metadata (6.4 kB)
Collecting stack-data (from ipython->anndata==0.1.dev71+gb354e82)
  Downloading stack_data-0.6.3-py3-none-any.whl.metadata (18 kB)
Collecting traitlets>=5.13.0 (from ipython->anndata==0.1.dev71+gb354e82)
  Downloading traitlets-5.14.3-py3-none-any.whl.metadata (10 kB)
Collecting pexpect>4.3 (from ipython->anndata==0.1.dev71+gb354e82)
  Downloading pexpect-4.9.0-py2.py3-none-any.whl.metadata (2.5 kB)
Collecting markdown-it-py~=3.0 (from myst-parser->anndata==0.1.dev71+gb354e82)
  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->anndata==0.1.dev71+gb354e82)
  Downloading mdit_py_plugins-0.4.1-py3-none-any.whl.metadata (2.8 kB)
Collecting pyyaml (from myst-parser->anndata==0.1.dev71+gb354e82)
  Downloading PyYAML-6.0.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB)
Collecting nbconvert!=5.4,>=5.3 (from nbsphinx->anndata==0.1.dev71+gb354e82)
  Downloading nbconvert-7.16.4-py3-none-any.whl.metadata (8.5 kB)
Collecting nbformat (from nbsphinx->anndata==0.1.dev71+gb354e82)
  Downloading nbformat-5.10.4-py3-none-any.whl.metadata (3.6 kB)
Collecting apeye>=0.4.0 (from sphinx-toolbox->anndata==0.1.dev71+gb354e82)
  Downloading apeye-1.4.1-py3-none-any.whl.metadata (7.3 kB)
Collecting autodocsumm>=0.2.0 (from sphinx-toolbox->anndata==0.1.dev71+gb354e82)
  Downloading autodocsumm-0.2.13-py3-none-any.whl.metadata (5.6 kB)
Collecting beautifulsoup4>=4.9.1 (from sphinx-toolbox->anndata==0.1.dev71+gb354e82)
  Downloading beautifulsoup4-4.12.3-py3-none-any.whl.metadata (3.8 kB)
Collecting cachecontrol>=0.13.0 (from cachecontrol[filecache]>=0.13.0->sphinx-toolbox->anndata==0.1.dev71+gb354e82)
  Downloading cachecontrol-0.14.0-py3-none-any.whl.metadata (3.1 kB)
Collecting dict2css>=0.2.3 (from sphinx-toolbox->anndata==0.1.dev71+gb354e82)
  Downloading dict2css-0.3.0.post1-py3-none-any.whl.metadata (7.4 kB)
Collecting domdf-python-tools>=2.9.0 (from sphinx-toolbox->anndata==0.1.dev71+gb354e82)
  Downloading domdf_python_tools-3.9.0-py3-none-any.whl.metadata (8.9 kB)
Collecting filelock>=3.8.0 (from sphinx-toolbox->anndata==0.1.dev71+gb354e82)
  Downloading filelock-3.15.4-py3-none-any.whl.metadata (2.9 kB)
Collecting html5lib>=1.1 (from sphinx-toolbox->anndata==0.1.dev71+gb354e82)
  Downloading html5lib-1.1-py2.py3-none-any.whl.metadata (16 kB)
Collecting ruamel.yaml>=0.16.12 (from sphinx-toolbox->anndata==0.1.dev71+gb354e82)
  Downloading ruamel.yaml-0.18.6-py3-none-any.whl.metadata (23 kB)
Collecting sphinx-jinja2-compat>=0.1.0 (from sphinx-toolbox->anndata==0.1.dev71+gb354e82)
  Downloading sphinx_jinja2_compat-0.3.0-py3-none-any.whl.metadata (6.8 kB)
Collecting sphinx-prompt>=1.1.0 (from sphinx-toolbox->anndata==0.1.dev71+gb354e82)
  Downloading sphinx_prompt-1.9.0-py3-none-any.whl.metadata (3.2 kB)
Collecting sphinx-tabs<3.5.0,>=1.2.1 (from sphinx-toolbox->anndata==0.1.dev71+gb354e82)
  Downloading sphinx_tabs-3.4.5-py3-none-any.whl.metadata (6.3 kB)
Collecting tabulate>=0.8.7 (from sphinx-toolbox->anndata==0.1.dev71+gb354e82)
  Downloading tabulate-0.9.0-py3-none-any.whl.metadata (34 kB)
Collecting typing-extensions!=3.10.0.1,>=3.7.4.3 (from sphinx-toolbox->anndata==0.1.dev71+gb354e82)
  Downloading typing_extensions-4.12.2-py3-none-any.whl.metadata (3.0 kB)
Collecting asciitree (from zarr->anndata==0.1.dev71+gb354e82)
  Downloading asciitree-0.3.3.tar.gz (4.0 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting numcodecs>=0.10.0 (from zarr->anndata==0.1.dev71+gb354e82)
  Downloading numcodecs-0.13.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.9 kB)
Collecting fasteners (from zarr->anndata==0.1.dev71+gb354e82)
  Downloading fasteners-0.19-py3-none-any.whl.metadata (4.9 kB)
Collecting apeye-core>=1.0.0b2 (from apeye>=0.4.0->sphinx-toolbox->anndata==0.1.dev71+gb354e82)
  Downloading apeye_core-1.1.5-py3-none-any.whl.metadata (7.7 kB)
Collecting platformdirs>=2.3.0 (from apeye>=0.4.0->sphinx-toolbox->anndata==0.1.dev71+gb354e82)
  Downloading platformdirs-4.2.2-py3-none-any.whl.metadata (11 kB)
Collecting soupsieve>1.2 (from beautifulsoup4>=4.9.1->sphinx-toolbox->anndata==0.1.dev71+gb354e82)
  Downloading soupsieve-2.6-py3-none-any.whl.metadata (4.6 kB)
Collecting msgpack<2.0.0,>=0.5.2 (from cachecontrol>=0.13.0->cachecontrol[filecache]>=0.13.0->sphinx-toolbox->anndata==0.1.dev71+gb354e82)
  Downloading msgpack-1.0.8-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (9.1 kB)
Collecting cssutils>=2.2.0 (from dict2css>=0.2.3->sphinx-toolbox->anndata==0.1.dev71+gb354e82)
  Downloading cssutils-2.11.1-py3-none-any.whl.metadata (8.7 kB)
Collecting six>=1.9 (from html5lib>=1.1->sphinx-toolbox->anndata==0.1.dev71+gb354e82)
  Downloading six-1.16.0-py2.py3-none-any.whl.metadata (1.8 kB)
Collecting webencodings (from html5lib>=1.1->sphinx-toolbox->anndata==0.1.dev71+gb354e82)
  Downloading webencodings-0.5.1-py2.py3-none-any.whl.metadata (2.1 kB)
Collecting parso<0.9.0,>=0.8.3 (from jedi>=0.16->ipython->anndata==0.1.dev71+gb354e82)
  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-anndata/envs/1558/lib/python3.12/site-packages (from Jinja2>=3.1->sphinx>=7.4.6->anndata==0.1.dev71+gb354e82) (2.1.5)
Collecting mdurl~=0.1 (from markdown-it-py~=3.0->myst-parser->anndata==0.1.dev71+gb354e82)
  Downloading mdurl-0.1.2-py3-none-any.whl.metadata (1.6 kB)
Collecting bleach!=5.0.0 (from nbconvert!=5.4,>=5.3->nbsphinx->anndata==0.1.dev71+gb354e82)
  Downloading bleach-6.1.0-py3-none-any.whl.metadata (30 kB)
Collecting defusedxml (from nbconvert!=5.4,>=5.3->nbsphinx->anndata==0.1.dev71+gb354e82)
  Downloading defusedxml-0.7.1-py2.py3-none-any.whl.metadata (32 kB)
Collecting jupyter-core>=4.7 (from nbconvert!=5.4,>=5.3->nbsphinx->anndata==0.1.dev71+gb354e82)
  Downloading jupyter_core-5.7.2-py3-none-any.whl.metadata (3.4 kB)
Collecting jupyterlab-pygments (from nbconvert!=5.4,>=5.3->nbsphinx->anndata==0.1.dev71+gb354e82)
  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->anndata==0.1.dev71+gb354e82)
  Downloading mistune-3.0.2-py3-none-any.whl.metadata (1.7 kB)
Collecting nbclient>=0.5.0 (from nbconvert!=5.4,>=5.3->nbsphinx->anndata==0.1.dev71+gb354e82)
  Downloading nbclient-0.10.0-py3-none-any.whl.metadata (7.8 kB)
Collecting pandocfilters>=1.4.1 (from nbconvert!=5.4,>=5.3->nbsphinx->anndata==0.1.dev71+gb354e82)
  Downloading pandocfilters-1.5.1-py2.py3-none-any.whl.metadata (9.0 kB)
Collecting tinycss2 (from nbconvert!=5.4,>=5.3->nbsphinx->anndata==0.1.dev71+gb354e82)
  Downloading tinycss2-1.3.0-py3-none-any.whl.metadata (3.0 kB)
Collecting fastjsonschema>=2.15 (from nbformat->nbsphinx->anndata==0.1.dev71+gb354e82)
  Downloading fastjsonschema-2.20.0-py3-none-any.whl.metadata (2.1 kB)
Collecting jsonschema>=2.6 (from nbformat->nbsphinx->anndata==0.1.dev71+gb354e82)
  Downloading jsonschema-4.23.0-py3-none-any.whl.metadata (7.9 kB)
Collecting ptyprocess>=0.5 (from pexpect>4.3->ipython->anndata==0.1.dev71+gb354e82)
  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->anndata==0.1.dev71+gb354e82)
  Downloading wcwidth-0.2.13-py2.py3-none-any.whl.metadata (14 kB)
Collecting accessible-pygments (from pydata-sphinx-theme>=0.15.2->sphinx-book-theme>=1.1.0->anndata==0.1.dev71+gb354e82)
  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-anndata/envs/1558/lib/python3.12/site-packages (from requests>=2.30.0->sphinx>=7.4.6->anndata==0.1.dev71+gb354e82) (3.3.2)
Requirement already satisfied: idna<4,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1558/lib/python3.12/site-packages (from requests>=2.30.0->sphinx>=7.4.6->anndata==0.1.dev71+gb354e82) (3.8)
Requirement already satisfied: urllib3<3,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1558/lib/python3.12/site-packages (from requests>=2.30.0->sphinx>=7.4.6->anndata==0.1.dev71+gb354e82) (2.2.2)
Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1558/lib/python3.12/site-packages (from requests>=2.30.0->sphinx>=7.4.6->anndata==0.1.dev71+gb354e82) (2024.7.4)
Collecting ruamel.yaml.clib>=0.2.7 (from ruamel.yaml>=0.16.12->sphinx-toolbox->anndata==0.1.dev71+gb354e82)
  Downloading ruamel.yaml.clib-0.2.8-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_28_x86_64.whl.metadata (2.2 kB)
Collecting executing>=1.2.0 (from stack-data->ipython->anndata==0.1.dev71+gb354e82)
  Downloading executing-2.0.1-py2.py3-none-any.whl.metadata (9.0 kB)
Collecting asttokens>=2.1.0 (from stack-data->ipython->anndata==0.1.dev71+gb354e82)
  Downloading asttokens-2.4.1-py2.py3-none-any.whl.metadata (5.2 kB)
Collecting pure-eval (from stack-data->ipython->anndata==0.1.dev71+gb354e82)
  Downloading pure_eval-0.2.3-py3-none-any.whl.metadata (6.3 kB)
Collecting more-itertools (from cssutils>=2.2.0->dict2css>=0.2.3->sphinx-toolbox->anndata==0.1.dev71+gb354e82)
  Downloading more_itertools-10.4.0-py3-none-any.whl.metadata (36 kB)
Collecting attrs>=22.2.0 (from jsonschema>=2.6->nbformat->nbsphinx->anndata==0.1.dev71+gb354e82)
  Downloading attrs-24.2.0-py3-none-any.whl.metadata (11 kB)
Collecting jsonschema-specifications>=2023.03.6 (from jsonschema>=2.6->nbformat->nbsphinx->anndata==0.1.dev71+gb354e82)
  Downloading jsonschema_specifications-2023.12.1-py3-none-any.whl.metadata (3.0 kB)
Collecting referencing>=0.28.4 (from jsonschema>=2.6->nbformat->nbsphinx->anndata==0.1.dev71+gb354e82)
  Downloading referencing-0.35.1-py3-none-any.whl.metadata (2.8 kB)
Collecting rpds-py>=0.7.1 (from jsonschema>=2.6->nbformat->nbsphinx->anndata==0.1.dev71+gb354e82)
  Downloading rpds_py-0.20.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.2 kB)
Collecting jupyter-client>=6.1.12 (from nbclient>=0.5.0->nbconvert!=5.4,>=5.3->nbsphinx->anndata==0.1.dev71+gb354e82)
  Downloading jupyter_client-8.6.2-py3-none-any.whl.metadata (8.3 kB)
Collecting pyzmq>=23.0 (from jupyter-client>=6.1.12->nbclient>=0.5.0->nbconvert!=5.4,>=5.3->nbsphinx->anndata==0.1.dev71+gb354e82)
  Downloading pyzmq-26.2.0-cp312-cp312-manylinux_2_28_x86_64.whl.metadata (6.2 kB)
Collecting tornado>=6.2 (from jupyter-client>=6.1.12->nbclient>=0.5.0->nbconvert!=5.4,>=5.3->nbsphinx->anndata==0.1.dev71+gb354e82)
  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)
Downloading array_api_compat-1.8-py3-none-any.whl (38 kB)
Downloading awkward-2.6.7-py3-none-any.whl (827 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 827.4/827.4 kB 53.8 MB/s eta 0:00:00
Downloading awkward_cpp-37-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (636 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 636.7/636.7 kB 500.5 MB/s eta 0:00:00
Downloading h5py-3.11.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (5.4 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 5.4/5.4 MB 195.0 MB/s eta 0:00:00
Downloading numpy-2.1.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (16.0 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 16.0/16.0 MB 198.7 MB/s eta 0:00:00
Downloading pandas-2.2.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.7 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 12.7/12.7 MB 199.4 MB/s eta 0:00:00
Downloading scanpydoc-0.13.6-py3-none-any.whl (32 kB)
Downloading scipy-1.14.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (40.8 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 40.8/40.8 MB 198.1 MB/s eta 0:00:00
Downloading sphinx_autodoc_typehints-2.2.3-py3-none-any.whl (19 kB)
Downloading sphinx_book_theme-1.1.3-py3-none-any.whl (430 kB)
Downloading sphinx_design-0.6.1-py3-none-any.whl (2.2 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.2/2.2 MB 284.7 MB/s eta 0:00:00
Downloading ipython-8.26.0-py3-none-any.whl (817 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 817.9/817.9 kB 505.8 MB/s eta 0:00:00
Downloading myst_parser-4.0.0-py3-none-any.whl (84 kB)
Downloading natsort-8.4.0-py3-none-any.whl (38 kB)
Downloading nbsphinx-0.9.5-py3-none-any.whl (31 kB)
Downloading readthedocs_sphinx_search-0.3.2-py3-none-any.whl (21 kB)
Downloading sphinx_copybutton-0.5.2-py3-none-any.whl (13 kB)
Downloading sphinx_issues-4.1.0-py3-none-any.whl (8.2 kB)
Downloading sphinx_toolbox-3.8.0-py3-none-any.whl (194 kB)
Downloading sphinxext_opengraph-0.9.1-py3-none-any.whl (1.0 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.0/1.0 MB 517.5 MB/s eta 0:00:00
Downloading zarr-2.18.2-py3-none-any.whl (210 kB)
Downloading apeye-1.4.1-py3-none-any.whl (107 kB)
Downloading autodocsumm-0.2.13-py3-none-any.whl (14 kB)
Downloading beautifulsoup4-4.12.3-py3-none-any.whl (147 kB)
Downloading cachecontrol-0.14.0-py3-none-any.whl (22 kB)
Downloading dict2css-0.3.0.post1-py3-none-any.whl (25 kB)
Downloading domdf_python_tools-3.9.0-py3-none-any.whl (127 kB)
Downloading filelock-3.15.4-py3-none-any.whl (16 kB)
Downloading fsspec-2024.6.1-py3-none-any.whl (177 kB)
Downloading html5lib-1.1-py2.py3-none-any.whl (112 kB)
Downloading jedi-0.19.1-py2.py3-none-any.whl (1.6 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.6/1.6 MB 539.3 MB/s eta 0:00:00
Downloading markdown_it_py-3.0.0-py3-none-any.whl (87 kB)
Downloading mdit_py_plugins-0.4.1-py3-none-any.whl (54 kB)
Downloading nbconvert-7.16.4-py3-none-any.whl (257 kB)
Downloading nbformat-5.10.4-py3-none-any.whl (78 kB)
Downloading numcodecs-0.13.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (8.8 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 8.8/8.8 MB 202.5 MB/s eta 0:00:00
Downloading pexpect-4.9.0-py2.py3-none-any.whl (63 kB)
Downloading prompt_toolkit-3.0.47-py3-none-any.whl (386 kB)
Downloading pydata_sphinx_theme-0.15.4-py3-none-any.whl (4.6 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.6/4.6 MB 249.0 MB/s eta 0:00:00
Downloading python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB)
Downloading pytz-2024.1-py2.py3-none-any.whl (505 kB)
Downloading ruamel.yaml-0.18.6-py3-none-any.whl (117 kB)
Downloading sphinx_jinja2_compat-0.3.0-py3-none-any.whl (7.9 kB)
Downloading sphinx_prompt-1.9.0-py3-none-any.whl (7.3 kB)
Downloading sphinx_tabs-3.4.5-py3-none-any.whl (9.9 kB)
Downloading tabulate-0.9.0-py3-none-any.whl (35 kB)
Downloading traitlets-5.14.3-py3-none-any.whl (85 kB)
Downloading typing_extensions-4.12.2-py3-none-any.whl (37 kB)
Downloading tzdata-2024.1-py2.py3-none-any.whl (345 kB)
Downloading decorator-5.1.1-py3-none-any.whl (9.1 kB)
Downloading fasteners-0.19-py3-none-any.whl (18 kB)
Downloading matplotlib_inline-0.1.7-py3-none-any.whl (9.9 kB)
Downloading PyYAML-6.0.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (767 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 767.5/767.5 kB 514.1 MB/s eta 0:00:00
Downloading stack_data-0.6.3-py3-none-any.whl (24 kB)
Downloading apeye_core-1.1.5-py3-none-any.whl (99 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 cssutils-2.11.1-py3-none-any.whl (385 kB)
Downloading executing-2.0.1-py2.py3-none-any.whl (24 kB)
Downloading fastjsonschema-2.20.0-py3-none-any.whl (23 kB)
Downloading jsonschema-4.23.0-py3-none-any.whl (88 kB)
Downloading jupyter_core-5.7.2-py3-none-any.whl (28 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 msgpack-1.0.8-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (408 kB)
Downloading nbclient-0.10.0-py3-none-any.whl (25 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-4.2.2-py3-none-any.whl (18 kB)
Downloading ptyprocess-0.7.0-py2.py3-none-any.whl (13 kB)
Downloading ruamel.yaml.clib-0.2.8-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_28_x86_64.whl (734 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 734.6/734.6 kB 494.5 MB/s eta 0:00:00
Downloading six-1.16.0-py2.py3-none-any.whl (11 kB)
Downloading soupsieve-2.6-py3-none-any.whl (36 kB)
Downloading accessible_pygments-0.0.5-py3-none-any.whl (1.4 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.4/1.4 MB 419.5 MB/s eta 0:00:00
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 pure_eval-0.2.3-py3-none-any.whl (11 kB)
Downloading tinycss2-1.3.0-py3-none-any.whl (22 kB)
Downloading webencodings-0.5.1-py2.py3-none-any.whl (11 kB)
Downloading wcwidth-0.2.13-py2.py3-none-any.whl (34 kB)
Downloading attrs-24.2.0-py3-none-any.whl (63 kB)
Downloading jsonschema_specifications-2023.12.1-py3-none-any.whl (18 kB)
Downloading jupyter_client-8.6.2-py3-none-any.whl (105 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 more_itertools-10.4.0-py3-none-any.whl (60 kB)
Downloading pyzmq-26.2.0-cp312-cp312-manylinux_2_28_x86_64.whl (860 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 860.6/860.6 kB 520.8 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)
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-0.1.dev71+gb354e82-py3-none-any.whl size=137387 sha256=304068be3e36dfe3ede6da66f6e095ee3943f2c664e12b942f40499a4e666bcd
  Stored in directory: /tmp/pip-ephem-wheel-cache-jio4_d8s/wheels/84/42/0c/6e2ced8c05dfb5eaca2e3f981a5fe9bb60ad4d5c6b1fac38e1
  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=4c4c5c8acd4602e7c301739ed0ea5bbc98b977b90d832aa2759d476b3d6b53a4
  Stored in directory: /tmp/pip-ephem-wheel-cache-jio4_d8s/wheels/a5/d7/98/f56ae733748cd0fa577172bda0e73e0b1f1793c98e09b9e458
Successfully built anndata asciitree
Installing collected packages: webencodings, wcwidth, pytz, pure-eval, ptyprocess, fastjsonschema, asciitree, array-api-compat, tzdata, typing-extensions, traitlets, tornado, tinycss2, tabulate, soupsieve, six, ruamel.yaml.clib, rpds-py, readthedocs-sphinx-search, pyzmq, pyyaml, prompt-toolkit, platformdirs, pexpect, parso, pandocfilters, numpy, natsort, msgpack, more-itertools, mistune, mdurl, jupyterlab-pygments, fsspec, filelock, fasteners, executing, defusedxml, decorator, attrs, accessible-pygments, sphinx-jinja2-compat, scipy, ruamel.yaml, referencing, python-dateutil, numcodecs, matplotlib-inline, markdown-it-py, jupyter-core, jedi, html5lib, h5py, domdf-python-tools, cssutils, cachecontrol, bleach, beautifulsoup4, awkward-cpp, asttokens, zarr, stack-data, sphinxext-opengraph, sphinx-tabs, sphinx-prompt, sphinx-issues, sphinx-design, sphinx-copybutton, sphinx-autodoc-typehints, scanpydoc, pydata-sphinx-theme, pandas, mdit-py-plugins, jupyter-client, jsonschema-specifications, dict2css, awkward, autodocsumm, apeye-core, sphinx-book-theme, myst-parser, jsonschema, ipython, apeye, anndata, sphinx-toolbox, nbformat, nbclient, nbconvert, nbsphinx
Successfully installed accessible-pygments-0.0.5 anndata-0.1.dev71+gb354e82 apeye-1.4.1 apeye-core-1.1.5 array-api-compat-1.8 asciitree-0.3.3 asttokens-2.4.1 attrs-24.2.0 autodocsumm-0.2.13 awkward-2.6.7 awkward-cpp-37 beautifulsoup4-4.12.3 bleach-6.1.0 cachecontrol-0.14.0 cssutils-2.11.1 decorator-5.1.1 defusedxml-0.7.1 dict2css-0.3.0.post1 domdf-python-tools-3.9.0 executing-2.0.1 fasteners-0.19 fastjsonschema-2.20.0 filelock-3.15.4 fsspec-2024.6.1 h5py-3.11.0 html5lib-1.1 ipython-8.26.0 jedi-0.19.1 jsonschema-4.23.0 jsonschema-specifications-2023.12.1 jupyter-client-8.6.2 jupyter-core-5.7.2 jupyterlab-pygments-0.3.0 markdown-it-py-3.0.0 matplotlib-inline-0.1.7 mdit-py-plugins-0.4.1 mdurl-0.1.2 mistune-3.0.2 more-itertools-10.4.0 msgpack-1.0.8 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 numcodecs-0.13.0 numpy-2.1.0 pandas-2.2.2 pandocfilters-1.5.1 parso-0.8.4 pexpect-4.9.0 platformdirs-4.2.2 prompt-toolkit-3.0.47 ptyprocess-0.7.0 pure-eval-0.2.3 pydata-sphinx-theme-0.15.4 python-dateutil-2.9.0.post0 pytz-2024.1 pyyaml-6.0.2 pyzmq-26.2.0 readthedocs-sphinx-search-0.3.2 referencing-0.35.1 rpds-py-0.20.0 ruamel.yaml-0.18.6 ruamel.yaml.clib-0.2.8 scanpydoc-0.13.6 scipy-1.14.1 six-1.16.0 soupsieve-2.6 sphinx-autodoc-typehints-2.2.3 sphinx-book-theme-1.1.3 sphinx-copybutton-0.5.2 sphinx-design-0.6.1 sphinx-issues-4.1.0 sphinx-jinja2-compat-0.3.0 sphinx-prompt-1.9.0 sphinx-tabs-3.4.5 sphinx-toolbox-3.8.0 sphinxext-opengraph-0.9.1 stack-data-0.6.3 tabulate-0.9.0 tinycss2-1.3.0 tornado-6.4.1 traitlets-5.14.3 typing-extensions-4.12.2 tzdata-2024.1 wcwidth-0.2.13 webencodings-0.5.1 zarr-2.18.2

[rtd-command-info] start-time: 2024-08-27T09:35:30.491453Z, end-time: 2024-08-27T09:35:30.545666Z, duration: 0, exit-code: 0
cat docs/conf.py
from __future__ import annotations

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

from docutils import nodes

if TYPE_CHECKING:
    from sphinx.application import Sphinx

HERE = Path(__file__).parent
sys.path[:0] = [str(HERE / "extensions")]


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

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

# default settings
templates_path = ["_templates"]
html_static_path = ["_static"]
source_suffix = {".rst": "restructuredtext", ".md": "markdown"}
master_doc = "index"
default_role = "literal"
exclude_patterns = [
    "_build",
    "Thumbs.db",
    ".DS_Store",
    "**.ipynb_checkpoints",
    "tutorials/notebooks/*.rst",
    # exclude all 0.x.y.md files, but not index.md
    "release-notes/[!i]*.md",
    "news.md",  # is `include`d into index.md
]
pygments_style = "sphinx"

extensions = [
    "myst_parser",
    "sphinx_copybutton",
    "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",
    "sphinx_design",
    "sphinx_search.extension",
    "sphinxext.opengraph",
    "scanpydoc",  # needs to be before linkcode
    "sphinx.ext.linkcode",
    "nbsphinx",
    "IPython.sphinxext.ipython_console_highlighting",
    "patch_sphinx_toolbox_autoprotocol",
    "sphinx_toolbox.more_autodoc.autoprotocol",
    "patch_myst_cite",
]
myst_enable_extensions = [
    "html_image",  # So README.md can be used on github and sphinx docs
]
myst_heading_anchors = 3

# Generate the API documentation when building
autosummary_generate = True
autodoc_member_order = "bysource"
issues_github_path = "scverse/anndata"
rtd_links_prefix = PurePosixPath("src")
# 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"]
    ],
    # TODO: sphinx’ builtin autodoc.typehints extension isn’t handled by `qualname_overrides` yet
    # https://github.com/theislab/scanpydoc/issues/140
    ("py:class", "h5py._hl.group.Group"),
    ("py:class", "h5py._hl.dataset.Dataset"),
    # for experimental callback exports
    ("py:class", "anndata.compat.ZappyArray"),
    ("py:class", "anndata.compat.DaskArray"),
    ("py:class", "anndata.compat.CupyArray"),
    ("py:class", "anndata.compat.CupySparseMatrix"),
    ("py:class", "numpy.ma.core.MaskedArray"),
    ("py:class", "dask.array.core.Array"),
    ("py:class", "awkward.highlevel.Array"),
    ("py:class", "anndata._core.sparse_dataset.BaseCompressedSparseDataset"),
    ("py:obj", "numpy._typing._array_like._ScalarType_co"),
]


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


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),
    dask=("https://docs.dask.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",
    "anndata._types.ReadCallback": "anndata.experimental.ReadCallback",
    "anndata._types.WriteCallback": "anndata.experimental.WriteCallback",
    "anndata._types.Read": "anndata.experimental.Read",
    "anndata._types.Write": "anndata.experimental.Write",
    "anndata._types.RWAble": "anndata.experimental.RWAble",
}
autodoc_type_aliases = dict(
    NDArray=":data:`~numpy.typing.NDArray`",
    RWAble=":data:`~anndata.experimental.RWAble`",
    **{
        f"{v}variantInMemoryType": ":data:`~anndata.experimental.InMemoryElem`"
        for v in ["In", "Co", "Contra"]
    },
)

# -- 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 ----------------------------------------------


# The theme is sphinx-book-theme, with patches for readthedocs-sphinx-search
html_theme = "scanpydoc"
html_theme_options = dict(
    use_repository_button=True,
    repository_url="https://github.com/scverse/anndata",
    repository_branch="main",
    navigation_with_keys=False,  # https://github.com/pydata/pydata-sphinx-theme/issues/1492
)
html_logo = "_static/img/anndata_schema.svg"
issues_github_path = "scverse/anndata"
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')

# Define this variable in case it's not defined by the user.
# It defaults to `alabaster` which is the default from Sphinx.
# https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_theme
html_theme = globals().get('html_theme', 'alabaster')

#Add project information to the template context.
context = {
    'html_theme': html_theme,
    'current_version': "1558",
    'version_slug': "1558",
    '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/"),
    ("0.10.x", "/en/0.10.x/"),
    ("0.9.x", "/en/0.9.x/"),
    ("0.8.x", "/en/0.8.x/"),
    ("0.7.x", "/en/0.7.x/"),
    ],
    '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': 'b354e82b623b096fce6a06285a083e344f7a09f3',
    'display_github': True,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': 'b354e82b623b096fce6a06285a083e344f7a09f3',
    'display_bitbucket': False,
    'gitlab_user': 'None',
    'gitlab_repo': 'None',
    'gitlab_version': 'b354e82b623b096fce6a06285a083e344f7a09f3',
    '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': 'b354e82b',
}

# 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/1558'
    readthedocs_build_url = 'https://readthedocs.com/projects/icb-anndata/builds/2442166/'

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: 2024-08-27T09:35:30.624309Z, end-time: 2024-08-27T09:36:18.334553Z, duration: 47, exit-code: 0
python -m sphinx -T -W --keep-going -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html
Running Sphinx v8.0.2
loading translations [en]... done
matplotlib is not installed, social cards will not be generated
making output directory... done
myst v4.0.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions={'html_image'}, 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)
loading intersphinx inventory 'h5py' from https://docs.h5py.org/en/latest//objects.inv ...
loading intersphinx inventory 'hdf5plugin' from https://hdf5plugin.readthedocs.io/en/latest//objects.inv ...
loading intersphinx inventory 'loompy' from https://linnarssonlab.org/loompy//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 'python' from https://docs.python.org/3/objects.inv ...
intersphinx inventory has moved: https://hdf5plugin.readthedocs.io/en/latest//objects.inv -> https://hdf5plugin.readthedocs.io/en/latest/objects.inv
loading intersphinx inventory 'scipy' from https://docs.scipy.org/doc/scipy//objects.inv ...
loading intersphinx inventory 'sklearn' from https://scikit-learn.org/stable//objects.inv ...
loading intersphinx inventory 'zarr' from https://zarr.readthedocs.io/en/stable//objects.inv ...
intersphinx inventory has moved: https://docs.h5py.org/en/latest//objects.inv -> https://docs.h5py.org/en/latest/objects.inv
loading intersphinx inventory 'xarray' from https://xarray.pydata.org/en/stable//objects.inv ...
loading intersphinx inventory 'dask' from https://docs.dask.org/en/stable//objects.inv ...
intersphinx inventory has moved: https://zarr.readthedocs.io/en/stable//objects.inv -> https://zarr.readthedocs.io/en/stable/objects.inv
intersphinx inventory has moved: https://docs.dask.org/en/stable//objects.inv -> https://docs.dask.org/en/stable/objects.inv
intersphinx inventory has moved: https://xarray.pydata.org/en/stable//objects.inv -> https://docs.xarray.dev/en/stable/objects.inv
[autosummary] generating autosummary for: _key_contributors.rst, api.md, benchmark-read-write.ipynb, benchmarks.md, concatenation.rst, contributing.md, fileformat-prose.md, index.md, interoperability.md, references.rst, release-notes/index.md, tutorials/index.md, tutorials/notebooks/anncollection-annloader.ipynb, tutorials/notebooks/anncollection.ipynb, tutorials/notebooks/anndata_dask_array.ipynb, tutorials/notebooks/annloader.ipynb, tutorials/notebooks/awkward-arrays.ipynb, tutorials/notebooks/getting-started.ipynb, tutorials/notebooks/{read,write}_dispatched.ipynb
[autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/1558/docs/generated/anndata.AnnData.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/1558/docs/generated/anndata.AnnData.write.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/1558/docs/generated/anndata.AnnData.write_csvs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/1558/docs/generated/anndata.AnnData.write_loom.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/1558/docs/generated/anndata.AnnData.write_zarr.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/1558/docs/generated/anndata.ImplicitModificationWarning.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/1558/docs/generated/anndata.concat.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/1558/docs/generated/anndata.experimental.AnnCollection.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/1558/docs/generated/anndata.experimental.AnnLoader.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/1558/docs/generated/anndata.experimental.CSCDataset.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/1558/docs/generated/anndata.read_excel.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/1558/docs/generated/anndata.read_h5ad.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/1558/docs/generated/anndata.read_hdf.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/1558/docs/generated/anndata.read_loom.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/1558/docs/generated/anndata.read_mtx.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/1558/docs/generated/anndata.read_text.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/1558/docs/generated/anndata.read_umi_tools.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/1558/docs/generated/anndata.read_zarr.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/1558/docs/generated/anndata.settings.override.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/1558/docs/generated/anndata.settings.rst
[autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/1558/docs/generated/anndata.AnnData.T.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/1558/docs/generated/anndata.AnnData.X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/1558/docs/generated/anndata.AnnData.chunk_X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/1558/docs/generated/anndata.AnnData.chunked_X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/1558/docs/generated/anndata.AnnData.concatenate.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/1558/docs/generated/anndata.AnnData.copy.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/1558/docs/generated/anndata.AnnData.filename.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/1558/docs/generated/anndata.AnnData.is_view.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/1558/docs/generated/anndata.AnnData.isbacked.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/1558/docs/generated/anndata.AnnData.layers.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/1558/docs/generated/anndata.experimental.StorageType.HDF5Dataset.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/1558/docs/generated/anndata.experimental.StorageType.Masked.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/1558/docs/generated/anndata.experimental.StorageType.Sparse.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/1558/docs/generated/anndata.experimental.StorageType.SparseArray.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/1558/docs/generated/anndata.experimental.StorageType.ZappyArray.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/1558/docs/generated/anndata.experimental.StorageType.ZarrArray.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/1558/docs/generated/anndata.experimental.StorageType.classes.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/1558/docs/generated/anndata.experimental.StorageType.cls.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/1558/docs/generated/anndata.experimental.StorageType.qualname.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/1558/docs/generated/anndata.experimental.StorageType.qualnames.rst
building [mo]: targets for 0 po files that are out of date
writing output... 
building [html]: targets for 19 source files that are out of date
updating environment: [new config] 145 added, 0 changed, 0 removed
reading sources... [  1%] _key_contributors
reading sources... [  1%] api
reading sources... [  2%] benchmark-read-write
/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1558/lib/python3.12/site-packages/nbsphinx/__init__.py:1074: RuntimeWarning: You are using an unsupported version of pandoc (2.5).
Your version must be at least (2.9.2) but less than (4.0.0).
Refer to https://pandoc.org/installing.html.
Continuing with doubts...
  nbconvert.utils.pandoc.check_pandoc_version()
reading sources... [  3%] benchmarks
reading sources... [  3%] concatenation
reading sources... [  4%] contributing
reading sources... [  5%] fileformat-prose
reading sources... [  6%] generated/anndata.AnnData
reading sources... [  6%] generated/anndata.AnnData.T
reading sources... [  7%] generated/anndata.AnnData.X
reading sources... [  8%] generated/anndata.AnnData.chunk_X
reading sources... [  8%] generated/anndata.AnnData.chunked_X
reading sources... [  9%] generated/anndata.AnnData.concatenate
reading sources... [ 10%] generated/anndata.AnnData.copy
reading sources... [ 10%] generated/anndata.AnnData.filename
reading sources... [ 11%] generated/anndata.AnnData.is_view
reading sources... [ 12%] generated/anndata.AnnData.isbacked
reading sources... [ 12%] generated/anndata.AnnData.layers
reading sources... [ 13%] generated/anndata.AnnData.n_obs
reading sources... [ 14%] generated/anndata.AnnData.n_vars
reading sources... [ 14%] generated/anndata.AnnData.obs
reading sources... [ 15%] generated/anndata.AnnData.obs_keys
reading sources... [ 16%] generated/anndata.AnnData.obs_names
reading sources... [ 17%] generated/anndata.AnnData.obs_names_make_unique
reading sources... [ 17%] generated/anndata.AnnData.obs_vector
reading sources... [ 18%] generated/anndata.AnnData.obsm
reading sources... [ 19%] generated/anndata.AnnData.obsm_keys
reading sources... [ 19%] generated/anndata.AnnData.obsp
reading sources... [ 20%] generated/anndata.AnnData.raw
reading sources... [ 21%] generated/anndata.AnnData.rename_categories
reading sources... [ 21%] generated/anndata.AnnData.shape
reading sources... [ 22%] generated/anndata.AnnData.strings_to_categoricals
reading sources... [ 23%] generated/anndata.AnnData.to_df
reading sources... [ 23%] generated/anndata.AnnData.to_memory
reading sources... [ 24%] generated/anndata.AnnData.transpose
reading sources... [ 25%] generated/anndata.AnnData.uns
reading sources... [ 26%] generated/anndata.AnnData.uns_keys
reading sources... [ 26%] generated/anndata.AnnData.var
reading sources... [ 27%] generated/anndata.AnnData.var_keys
reading sources... [ 28%] generated/anndata.AnnData.var_names
reading sources... [ 28%] generated/anndata.AnnData.var_names_make_unique
reading sources... [ 29%] generated/anndata.AnnData.var_vector
reading sources... [ 30%] generated/anndata.AnnData.varm
reading sources... [ 30%] generated/anndata.AnnData.varm_keys
reading sources... [ 31%] generated/anndata.AnnData.varp
reading sources... [ 32%] generated/anndata.AnnData.write
reading sources... [ 32%] generated/anndata.AnnData.write_csvs
reading sources... [ 33%] generated/anndata.AnnData.write_h5ad
reading sources... [ 34%] generated/anndata.AnnData.write_loom
reading sources... [ 34%] generated/anndata.AnnData.write_zarr
reading sources... [ 35%] generated/anndata.ImplicitModificationWarning
reading sources... [ 36%] generated/anndata.concat
reading sources... [ 37%] generated/anndata.experimental.AnnCollection
reading sources... [ 37%] generated/anndata.experimental.AnnCollection.attrs_keys
reading sources... [ 38%] generated/anndata.experimental.AnnCollection.convert
reading sources... [ 39%] generated/anndata.experimental.AnnCollection.has_backed
reading sources... [ 39%] generated/anndata.experimental.AnnCollection.iterate_axis
reading sources... [ 40%] generated/anndata.experimental.AnnCollection.lazy_attr
reading sources... [ 41%] generated/anndata.experimental.AnnCollection.n_obs
reading sources... [ 41%] generated/anndata.experimental.AnnCollection.n_vars
reading sources... [ 42%] generated/anndata.experimental.AnnCollection.obs
reading sources... [ 43%] generated/anndata.experimental.AnnCollection.obsm
reading sources... [ 43%] generated/anndata.experimental.AnnCollection.shape
reading sources... [ 44%] generated/anndata.experimental.AnnCollection.to_adata
reading sources... [ 45%] generated/anndata.experimental.AnnLoader
reading sources... [ 46%] generated/anndata.experimental.CSCDataset
reading sources... [ 46%] generated/anndata.experimental.CSCDataset.append
reading sources... [ 47%] generated/anndata.experimental.CSCDataset.backend
reading sources... [ 48%] generated/anndata.experimental.CSCDataset.dtype
reading sources... [ 48%] generated/anndata.experimental.CSCDataset.format
reading sources... [ 49%] generated/anndata.experimental.CSCDataset.format_str
reading sources... [ 50%] generated/anndata.experimental.CSCDataset.group
reading sources... [ 50%] generated/anndata.experimental.CSCDataset.indptr
reading sources... [ 51%] generated/anndata.experimental.CSCDataset.name
reading sources... [ 52%] generated/anndata.experimental.CSCDataset.shape
reading sources... [ 52%] generated/anndata.experimental.CSCDataset.to_memory
reading sources... [ 53%] generated/anndata.experimental.CSCDataset.value
reading sources... [ 54%] generated/anndata.experimental.CSRDataset
reading sources... [ 54%] generated/anndata.experimental.CSRDataset.append
reading sources... [ 55%] generated/anndata.experimental.CSRDataset.backend
reading sources... [ 56%] generated/anndata.experimental.CSRDataset.dtype
reading sources... [ 57%] generated/anndata.experimental.CSRDataset.format
reading sources... [ 57%] generated/anndata.experimental.CSRDataset.format_str
reading sources... [ 58%] generated/anndata.experimental.CSRDataset.group
reading sources... [ 59%] generated/anndata.experimental.CSRDataset.indptr
reading sources... [ 59%] generated/anndata.experimental.CSRDataset.name
reading sources... [ 60%] generated/anndata.experimental.CSRDataset.shape
reading sources... [ 61%] generated/anndata.experimental.CSRDataset.to_memory
reading sources... [ 61%] generated/anndata.experimental.CSRDataset.value
reading sources... [ 62%] generated/anndata.experimental.IOSpec
reading sources... [ 63%] generated/anndata.experimental.IOSpec.encoding_type
reading sources... [ 63%] generated/anndata.experimental.IOSpec.encoding_version
reading sources... [ 64%] generated/anndata.experimental.InMemoryElem
reading sources... [ 65%] generated/anndata.experimental.RWAble
reading sources... [ 66%] generated/anndata.experimental.Read
reading sources... [ 66%] generated/anndata.experimental.ReadCallback
reading sources... [ 67%] generated/anndata.experimental.StorageType
reading sources... [ 68%] generated/anndata.experimental.StorageType.Array
reading sources... [ 68%] generated/anndata.experimental.StorageType.AwkArray
reading sources... [ 69%] generated/anndata.experimental.StorageType.BackedSparseMatrix
reading sources... [ 70%] generated/anndata.experimental.StorageType.CupyArray
reading sources... [ 70%] generated/anndata.experimental.StorageType.CupySparseMatrix
reading sources... [ 71%] generated/anndata.experimental.StorageType.DaskArray
reading sources... [ 72%] generated/anndata.experimental.StorageType.HDF5Dataset
reading sources... [ 72%] generated/anndata.experimental.StorageType.Masked
reading sources... [ 73%] generated/anndata.experimental.StorageType.Sparse
reading sources... [ 74%] generated/anndata.experimental.StorageType.SparseArray
reading sources... [ 74%] generated/anndata.experimental.StorageType.ZappyArray
reading sources... [ 75%] generated/anndata.experimental.StorageType.ZarrArray
reading sources... [ 76%] generated/anndata.experimental.StorageType.classes
reading sources... [ 77%] generated/anndata.experimental.StorageType.cls
reading sources... [ 77%] generated/anndata.experimental.StorageType.qualname
reading sources... [ 78%] generated/anndata.experimental.StorageType.qualnames
reading sources... [ 79%] generated/anndata.experimental.Write
reading sources... [ 79%] generated/anndata.experimental.WriteCallback
reading sources... [ 80%] generated/anndata.experimental.concat_on_disk
reading sources... [ 81%] generated/anndata.experimental.read_dispatched
reading sources... [ 81%] generated/anndata.experimental.read_elem
reading sources... [ 82%] generated/anndata.experimental.read_elem_as_dask
reading sources... [ 83%] generated/anndata.experimental.sparse_dataset
reading sources... [ 83%] generated/anndata.experimental.write_dispatched
reading sources... [ 84%] generated/anndata.experimental.write_elem
reading sources... [ 85%] generated/anndata.read_csv
reading sources... [ 86%] generated/anndata.read_excel
reading sources... [ 86%] generated/anndata.read_h5ad
reading sources... [ 87%] generated/anndata.read_hdf
reading sources... [ 88%] generated/anndata.read_loom
reading sources... [ 88%] generated/anndata.read_mtx
reading sources... [ 89%] generated/anndata.read_text
reading sources... [ 90%] generated/anndata.read_umi_tools
reading sources... [ 90%] generated/anndata.read_zarr
reading sources... [ 91%] generated/anndata.settings
reading sources... [ 92%] generated/anndata.settings.override
reading sources... [ 92%] index
reading sources... [ 93%] interoperability
reading sources... [ 94%] references
reading sources... [ 94%] release-notes/index
reading sources... [ 95%] tutorials/index
reading sources... [ 96%] tutorials/notebooks/anncollection
reading sources... [ 97%] tutorials/notebooks/anncollection-annloader
reading sources... [ 97%] tutorials/notebooks/anndata_dask_array
reading sources... [ 98%] tutorials/notebooks/annloader
reading sources... [ 99%] tutorials/notebooks/awkward-arrays
reading sources... [ 99%] tutorials/notebooks/getting-started
reading sources... [100%] tutorials/notebooks/{read,write}_dispatched

looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
copying assets... 
copying static files... done
copying extra files... done
copying assets: done
writing output... [  1%] _key_contributors
/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1558/lib/python3.12/site-packages/readthedocs_ext/readthedocs.py:106: RemovedInSphinx90Warning: 'sphinx.builders.html.StandaloneHTMLBuilder.css_files' is deprecated. Check CHANGES for Sphinx API modifications.
  if inject_css and theme_css not in app.builder.css_files:
/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1558/lib/python3.12/site-packages/readthedocs_ext/readthedocs.py:106: RemovedInSphinx90Warning: The str interface for _CascadingStyleSheet objects is deprecated. Use css.filename instead.
  if inject_css and theme_css not in app.builder.css_files:
/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1558/lib/python3.12/site-packages/readthedocs_ext/readthedocs.py:120: RemovedInSphinx90Warning: 'sphinx.builders.html.StandaloneHTMLBuilder.script_files' is deprecated. Check CHANGES for Sphinx API modifications.
  hasattr(app.builder, 'script_files'),
/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1558/lib/python3.12/site-packages/readthedocs_ext/readthedocs.py:121: RemovedInSphinx90Warning: 'sphinx.builders.html.StandaloneHTMLBuilder.script_files' is deprecated. Check CHANGES for Sphinx API modifications.
  js_file not in app.builder.script_files,
/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1558/lib/python3.12/site-packages/readthedocs_ext/readthedocs.py:121: RemovedInSphinx90Warning: The str interface for _JavaScript objects is deprecated. Use js.filename instead.
  js_file not in app.builder.script_files,
writing output... [  1%] api
writing output... [  2%] benchmark-read-write
writing output... [  3%] benchmarks
writing output... [  3%] concatenation
writing output... [  4%] contributing
writing output... [  5%] fileformat-prose
writing output... [  6%] generated/anndata.AnnData
writing output... [  6%] generated/anndata.AnnData.T
writing output... [  7%] generated/anndata.AnnData.X
writing output... [  8%] generated/anndata.AnnData.chunk_X
writing output... [  8%] generated/anndata.AnnData.chunked_X
writing output... [  9%] generated/anndata.AnnData.concatenate
writing output... [ 10%] generated/anndata.AnnData.copy
writing output... [ 10%] generated/anndata.AnnData.filename
writing output... [ 11%] generated/anndata.AnnData.is_view
writing output... [ 12%] generated/anndata.AnnData.isbacked
writing output... [ 12%] generated/anndata.AnnData.layers
writing output... [ 13%] generated/anndata.AnnData.n_obs
writing output... [ 14%] generated/anndata.AnnData.n_vars
writing output... [ 14%] generated/anndata.AnnData.obs
writing output... [ 15%] generated/anndata.AnnData.obs_keys
writing output... [ 16%] generated/anndata.AnnData.obs_names
writing output... [ 17%] generated/anndata.AnnData.obs_names_make_unique
writing output... [ 17%] generated/anndata.AnnData.obs_vector
writing output... [ 18%] generated/anndata.AnnData.obsm
writing output... [ 19%] generated/anndata.AnnData.obsm_keys
writing output... [ 19%] generated/anndata.AnnData.obsp
writing output... [ 20%] generated/anndata.AnnData.raw
writing output... [ 21%] generated/anndata.AnnData.rename_categories
writing output... [ 21%] generated/anndata.AnnData.shape
writing output... [ 22%] generated/anndata.AnnData.strings_to_categoricals
writing output... [ 23%] generated/anndata.AnnData.to_df
writing output... [ 23%] generated/anndata.AnnData.to_memory
writing output... [ 24%] generated/anndata.AnnData.transpose
writing output... [ 25%] generated/anndata.AnnData.uns
writing output... [ 26%] generated/anndata.AnnData.uns_keys
writing output... [ 26%] generated/anndata.AnnData.var
writing output... [ 27%] generated/anndata.AnnData.var_keys
writing output... [ 28%] generated/anndata.AnnData.var_names
writing output... [ 28%] generated/anndata.AnnData.var_names_make_unique
writing output... [ 29%] generated/anndata.AnnData.var_vector
writing output... [ 30%] generated/anndata.AnnData.varm
writing output... [ 30%] generated/anndata.AnnData.varm_keys
writing output... [ 31%] generated/anndata.AnnData.varp
writing output... [ 32%] generated/anndata.AnnData.write
writing output... [ 32%] generated/anndata.AnnData.write_csvs
writing output... [ 33%] generated/anndata.AnnData.write_h5ad
writing output... [ 34%] generated/anndata.AnnData.write_loom
writing output... [ 34%] generated/anndata.AnnData.write_zarr
writing output... [ 35%] generated/anndata.ImplicitModificationWarning
writing output... [ 36%] generated/anndata.concat
writing output... [ 37%] generated/anndata.experimental.AnnCollection
writing output... [ 37%] generated/anndata.experimental.AnnCollection.attrs_keys
writing output... [ 38%] generated/anndata.experimental.AnnCollection.convert
writing output... [ 39%] generated/anndata.experimental.AnnCollection.has_backed
writing output... [ 39%] generated/anndata.experimental.AnnCollection.iterate_axis
writing output... [ 40%] generated/anndata.experimental.AnnCollection.lazy_attr
writing output... [ 41%] generated/anndata.experimental.AnnCollection.n_obs
writing output... [ 41%] generated/anndata.experimental.AnnCollection.n_vars
writing output... [ 42%] generated/anndata.experimental.AnnCollection.obs
writing output... [ 43%] generated/anndata.experimental.AnnCollection.obsm
writing output... [ 43%] generated/anndata.experimental.AnnCollection.shape
writing output... [ 44%] generated/anndata.experimental.AnnCollection.to_adata
writing output... [ 45%] generated/anndata.experimental.AnnLoader
writing output... [ 46%] generated/anndata.experimental.CSCDataset
writing output... [ 46%] generated/anndata.experimental.CSCDataset.append
writing output... [ 47%] generated/anndata.experimental.CSCDataset.backend
writing output... [ 48%] generated/anndata.experimental.CSCDataset.dtype
writing output... [ 48%] generated/anndata.experimental.CSCDataset.format
writing output... [ 49%] generated/anndata.experimental.CSCDataset.format_str
writing output... [ 50%] generated/anndata.experimental.CSCDataset.group
writing output... [ 50%] generated/anndata.experimental.CSCDataset.indptr
writing output... [ 51%] generated/anndata.experimental.CSCDataset.name
writing output... [ 52%] generated/anndata.experimental.CSCDataset.shape
writing output... [ 52%] generated/anndata.experimental.CSCDataset.to_memory
writing output... [ 53%] generated/anndata.experimental.CSCDataset.value
writing output... [ 54%] generated/anndata.experimental.CSRDataset
writing output... [ 54%] generated/anndata.experimental.CSRDataset.append
writing output... [ 55%] generated/anndata.experimental.CSRDataset.backend
writing output... [ 56%] generated/anndata.experimental.CSRDataset.dtype
writing output... [ 57%] generated/anndata.experimental.CSRDataset.format
writing output... [ 57%] generated/anndata.experimental.CSRDataset.format_str
writing output... [ 58%] generated/anndata.experimental.CSRDataset.group
writing output... [ 59%] generated/anndata.experimental.CSRDataset.indptr
writing output... [ 59%] generated/anndata.experimental.CSRDataset.name
writing output... [ 60%] generated/anndata.experimental.CSRDataset.shape
writing output... [ 61%] generated/anndata.experimental.CSRDataset.to_memory
writing output... [ 61%] generated/anndata.experimental.CSRDataset.value
writing output... [ 62%] generated/anndata.experimental.IOSpec
writing output... [ 63%] generated/anndata.experimental.IOSpec.encoding_type
writing output... [ 63%] generated/anndata.experimental.IOSpec.encoding_version
writing output... [ 64%] generated/anndata.experimental.InMemoryElem
writing output... [ 65%] generated/anndata.experimental.RWAble
writing output... [ 66%] generated/anndata.experimental.Read
writing output... [ 66%] generated/anndata.experimental.ReadCallback
writing output... [ 67%] generated/anndata.experimental.StorageType
writing output... [ 68%] generated/anndata.experimental.StorageType.Array
writing output... [ 68%] generated/anndata.experimental.StorageType.AwkArray
writing output... [ 69%] generated/anndata.experimental.StorageType.BackedSparseMatrix
writing output... [ 70%] generated/anndata.experimental.StorageType.CupyArray
writing output... [ 70%] generated/anndata.experimental.StorageType.CupySparseMatrix
writing output... [ 71%] generated/anndata.experimental.StorageType.DaskArray
writing output... [ 72%] generated/anndata.experimental.StorageType.HDF5Dataset
writing output... [ 72%] generated/anndata.experimental.StorageType.Masked
writing output... [ 73%] generated/anndata.experimental.StorageType.Sparse
writing output... [ 74%] generated/anndata.experimental.StorageType.SparseArray
writing output... [ 74%] generated/anndata.experimental.StorageType.ZappyArray
writing output... [ 75%] generated/anndata.experimental.StorageType.ZarrArray
writing output... [ 76%] generated/anndata.experimental.StorageType.classes
writing output... [ 77%] generated/anndata.experimental.StorageType.cls
writing output... [ 77%] generated/anndata.experimental.StorageType.qualname
writing output... [ 78%] generated/anndata.experimental.StorageType.qualnames
writing output... [ 79%] generated/anndata.experimental.Write
writing output... [ 79%] generated/anndata.experimental.WriteCallback
writing output... [ 80%] generated/anndata.experimental.concat_on_disk
writing output... [ 81%] generated/anndata.experimental.read_dispatched
writing output... [ 81%] generated/anndata.experimental.read_elem
writing output... [ 82%] generated/anndata.experimental.read_elem_as_dask
writing output... [ 83%] generated/anndata.experimental.sparse_dataset
writing output... [ 83%] generated/anndata.experimental.write_dispatched
writing output... [ 84%] generated/anndata.experimental.write_elem
writing output... [ 85%] generated/anndata.read_csv
writing output... [ 86%] generated/anndata.read_excel
writing output... [ 86%] generated/anndata.read_h5ad
writing output... [ 87%] generated/anndata.read_hdf
writing output... [ 88%] generated/anndata.read_loom
writing output... [ 88%] generated/anndata.read_mtx
writing output... [ 89%] generated/anndata.read_text
writing output... [ 90%] generated/anndata.read_umi_tools
writing output... [ 90%] generated/anndata.read_zarr
writing output... [ 91%] generated/anndata.settings
writing output... [ 92%] generated/anndata.settings.override
writing output... [ 92%] index
writing output... [ 93%] interoperability
writing output... [ 94%] references
writing output... [ 94%] release-notes/index
writing output... [ 95%] tutorials/index
writing output... [ 96%] tutorials/notebooks/anncollection
writing output... [ 97%] tutorials/notebooks/anncollection-annloader
writing output... [ 97%] tutorials/notebooks/anndata_dask_array
writing output... [ 98%] tutorials/notebooks/annloader
writing output... [ 99%] tutorials/notebooks/awkward-arrays
writing output... [ 99%] tutorials/notebooks/getting-started
writing output... [100%] tutorials/notebooks/{read,write}_dispatched

generating indices... genindex py-modindex done
copying linked files... 
copying notebooks ... [ 12%] benchmark-read-write.ipynb
copying notebooks ... [ 25%] tutorials/notebooks/anncollection.ipynb
copying notebooks ... [ 38%] tutorials/notebooks/anncollection-annloader.ipynb
copying notebooks ... [ 50%] tutorials/notebooks/anndata_dask_array.ipynb
copying notebooks ... [ 62%] tutorials/notebooks/annloader.ipynb
copying notebooks ... [ 75%] tutorials/notebooks/awkward-arrays.ipynb
copying notebooks ... [ 88%] tutorials/notebooks/getting-started.ipynb
copying notebooks ... [100%] tutorials/notebooks/{read,write}_dispatched.ipynb

writing additional pages... search done
copying images... [  7%] _static/img/anndata_schema.svg
copying images... [ 14%] _build/doctrees/nbsphinx/tutorials_notebooks_anncollection_86_1.png
copying images... [ 21%] _build/doctrees/nbsphinx/tutorials_notebooks_anncollection_87_0.png
copying images... [ 29%] tutorials/notebooks/_static/semisup_cvae.jpg
copying images... [ 36%] _build/doctrees/nbsphinx/tutorials_notebooks_anncollection-annloader_38_1.png
copying images... [ 43%] _build/doctrees/nbsphinx/tutorials_notebooks_anncollection-annloader_42_0.png
copying images... [ 50%] _build/doctrees/nbsphinx/tutorials_notebooks_anndata_dask_array_11_0.png
copying images... [ 57%] _build/doctrees/nbsphinx/tutorials_notebooks_anndata_dask_array_15_0.png
copying images... [ 64%] _build/doctrees/nbsphinx/tutorials_notebooks_anndata_dask_array_17_0.png
copying images... [ 71%] _build/doctrees/nbsphinx/tutorials_notebooks_anndata_dask_array_26_0.png
copying images... [ 79%] _build/doctrees/nbsphinx/tutorials_notebooks_anndata_dask_array_29_0.png
copying images... [ 86%] tutorials/notebooks/_static/sup_cvae.jpg
copying images... [ 93%] _build/doctrees/nbsphinx/tutorials_notebooks_annloader_18_0.png
copying images... [100%] _build/doctrees/nbsphinx/tutorials_notebooks_annloader_58_0.png

dumping search index in English (code: en)... done
dumping object inventory... done
Updating searchtools for Read the Docs search... build succeeded.

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