Read the Docs build information
Build id: 2425100
Project: icb-anndata
Version: 1596
Commit: 0a5807c854a1e54c52f13ea4ba690f78a0f45e98
Date: 2024-08-19T15:39:40.725761Z
State: cancelled
Success: False


[rtd-command-info] start-time: 2024-08-19T15:39:41.944780Z, end-time: 2024-08-19T15:39:42.477253Z, duration: 0, exit-code: 0
git clone --depth 1 https://github.com/scverse/anndata.git .
Cloning into '.'...

[rtd-command-info] start-time: 2024-08-19T15:39:42.548439Z, end-time: 2024-08-19T15:39:43.029286Z, duration: 0, exit-code: 0
git fetch origin --force --prune --prune-tags --depth 50 pull/1596/head:external-1596
From https://github.com/scverse/anndata
 * [new ref]         refs/pull/1596/head -> external-1596

[rtd-command-info] start-time: 2024-08-19T15:39:43.165448Z, end-time: 2024-08-19T15:39:43.246435Z, duration: 0, exit-code: 0
git checkout --force 0a5807c854a1e54c52f13ea4ba690f78a0f45e98
Note: switching to '0a5807c854a1e54c52f13ea4ba690f78a0f45e98'.

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 0a5807c Update pyproject.toml

[rtd-command-info] start-time: 2024-08-19T15:39:43.337778Z, end-time: 2024-08-19T15:39:43.404870Z, 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: 2024-08-19T15:39:43.537342Z, end-time: 2024-08-19T15:39:43.617875Z, duration: 0, exit-code: 0
git submodule sync


[rtd-command-info] start-time: 2024-08-19T15:39:43.688298Z, end-time: 2024-08-19T15:39:44.340280Z, 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/1596/docs/tutorials/notebooks'...
Submodule path 'docs/tutorials/notebooks': checked out '9e186c5c694793bb04ea1397721d154d6e0b7069'

[rtd-command-info] start-time: 2024-08-19T15:39:50.990118Z, end-time: 2024-08-19T15:39:51.075889Z, duration: 0, exit-code: 0
asdf global python 3.12.3


[rtd-command-info] start-time: 2024-08-19T15:39:51.504671Z, end-time: 2024-08-19T15:39:52.733215Z, duration: 1, exit-code: 0
python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH
created virtual environment CPython3.12.3.final.0-64 in 841ms
  creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1596, 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: 2024-08-19T15:39:52.800792Z, end-time: 2024-08-19T15:40:10.122079Z, duration: 17, 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/1596/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 35.0 MB/s eta 0:00:00
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1596/lib/python3.12/site-packages (67.6.1)
Collecting setuptools
  Downloading setuptools-72.2.0-py3-none-any.whl (2.3 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.3/2.3 MB 99.8 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-72.2.0

[rtd-command-info] start-time: 2024-08-19T15:40:10.201148Z, end-time: 2024-08-19T15:40:18.139167Z, duration: 7, 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-3.7-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 118.1 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 201.3 MB/s eta 0:00:00
Downloading docutils-0.21.2-py3-none-any.whl (587 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 587.4/587.4 kB 323.2 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 338.8 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-3.7-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-3.7 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: 2024-08-19T15:40:18.227133Z, end-time: 2024-08-19T15:40:56.889978Z, duration: 38, 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/1596
  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.dev50+g0a5807c)
  Downloading array_api_compat-1.8-py3-none-any.whl.metadata (1.5 kB)
Collecting h5py>=3.1 (from anndata==0.1.dev50+g0a5807c)
  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.dev50+g0a5807c)
  Downloading natsort-8.4.0-py3-none-any.whl.metadata (21 kB)
Collecting numpy>=1.23 (from anndata==0.1.dev50+g0a5807c)
  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/1596/lib/python3.12/site-packages (from anndata==0.1.dev50+g0a5807c) (24.1)
Collecting pandas!=2.1.0rc0,!=2.1.2,>=1.4 (from anndata==0.1.dev50+g0a5807c)
  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.dev50+g0a5807c)
  Downloading scipy-1.14.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB)
Collecting awkward>=2.0.7 (from anndata==0.1.dev50+g0a5807c)
  Downloading awkward-2.6.7-py3-none-any.whl.metadata (7.0 kB)
Collecting ipython (from anndata==0.1.dev50+g0a5807c)
  Downloading ipython-8.26.0-py3-none-any.whl.metadata (5.0 kB)
Collecting myst-parser (from anndata==0.1.dev50+g0a5807c)
  Downloading myst_parser-4.0.0-py3-none-any.whl.metadata (5.4 kB)
Collecting nbsphinx (from anndata==0.1.dev50+g0a5807c)
  Downloading nbsphinx-0.9.5-py3-none-any.whl.metadata (2.1 kB)
Collecting readthedocs-sphinx-search (from anndata==0.1.dev50+g0a5807c)
  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.dev50+g0a5807c)
  Downloading scanpydoc-0.13.6-py3-none-any.whl.metadata (2.7 kB)
Collecting sphinx-autodoc-typehints>=2.2.0 (from anndata==0.1.dev50+g0a5807c)
  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.dev50+g0a5807c)
  Downloading sphinx_book_theme-1.1.3-py3-none-any.whl.metadata (5.7 kB)
Collecting sphinx-copybutton (from anndata==0.1.dev50+g0a5807c)
  Downloading sphinx_copybutton-0.5.2-py3-none-any.whl.metadata (3.2 kB)
Collecting sphinx-design>=0.5.0 (from anndata==0.1.dev50+g0a5807c)
  Downloading sphinx_design-0.6.1-py3-none-any.whl.metadata (5.5 kB)
Collecting sphinx-issues (from anndata==0.1.dev50+g0a5807c)
  Downloading sphinx_issues-4.1.0-py3-none-any.whl.metadata (8.3 kB)
Collecting sphinx-toolbox (from anndata==0.1.dev50+g0a5807c)
  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/1596/lib/python3.12/site-packages (from anndata==0.1.dev50+g0a5807c) (8.0.2)
Collecting sphinxext-opengraph (from anndata==0.1.dev50+g0a5807c)
  Downloading sphinxext_opengraph-0.9.1-py3-none-any.whl.metadata (6.5 kB)
Collecting zarr (from anndata==0.1.dev50+g0a5807c)
  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.dev50+g0a5807c)
  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.dev50+g0a5807c)
  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.dev50+g0a5807c)
  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.dev50+g0a5807c)
  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.dev50+g0a5807c)
  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/1596/lib/python3.12/site-packages (from sphinx>=7.4.6->anndata==0.1.dev50+g0a5807c) (2.0.0)
Requirement already satisfied: sphinxcontrib-devhelp in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1596/lib/python3.12/site-packages (from sphinx>=7.4.6->anndata==0.1.dev50+g0a5807c) (2.0.0)
Requirement already satisfied: sphinxcontrib-jsmath in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1596/lib/python3.12/site-packages (from sphinx>=7.4.6->anndata==0.1.dev50+g0a5807c) (1.0.1)
Requirement already satisfied: sphinxcontrib-htmlhelp>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1596/lib/python3.12/site-packages (from sphinx>=7.4.6->anndata==0.1.dev50+g0a5807c) (2.1.0)
Requirement already satisfied: sphinxcontrib-serializinghtml>=1.1.9 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1596/lib/python3.12/site-packages (from sphinx>=7.4.6->anndata==0.1.dev50+g0a5807c) (2.0.0)
Requirement already satisfied: sphinxcontrib-qthelp in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1596/lib/python3.12/site-packages (from sphinx>=7.4.6->anndata==0.1.dev50+g0a5807c) (2.0.0)
Requirement already satisfied: Jinja2>=3.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1596/lib/python3.12/site-packages (from sphinx>=7.4.6->anndata==0.1.dev50+g0a5807c) (3.1.4)
Requirement already satisfied: Pygments>=2.17 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1596/lib/python3.12/site-packages (from sphinx>=7.4.6->anndata==0.1.dev50+g0a5807c) (2.18.0)
Requirement already satisfied: docutils<0.22,>=0.20 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1596/lib/python3.12/site-packages (from sphinx>=7.4.6->anndata==0.1.dev50+g0a5807c) (0.21.2)
Requirement already satisfied: snowballstemmer>=2.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1596/lib/python3.12/site-packages (from sphinx>=7.4.6->anndata==0.1.dev50+g0a5807c) (2.2.0)
Requirement already satisfied: babel>=2.13 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1596/lib/python3.12/site-packages (from sphinx>=7.4.6->anndata==0.1.dev50+g0a5807c) (2.16.0)
Requirement already satisfied: alabaster>=0.7.14 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1596/lib/python3.12/site-packages (from sphinx>=7.4.6->anndata==0.1.dev50+g0a5807c) (1.0.0)
Requirement already satisfied: imagesize>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1596/lib/python3.12/site-packages (from sphinx>=7.4.6->anndata==0.1.dev50+g0a5807c) (1.4.1)
Requirement already satisfied: requests>=2.30.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1596/lib/python3.12/site-packages (from sphinx>=7.4.6->anndata==0.1.dev50+g0a5807c) (2.32.3)
Collecting pydata-sphinx-theme>=0.15.2 (from sphinx-book-theme>=1.1.0->anndata==0.1.dev50+g0a5807c)
  Downloading pydata_sphinx_theme-0.15.4-py3-none-any.whl.metadata (7.5 kB)
Collecting decorator (from ipython->anndata==0.1.dev50+g0a5807c)
  Downloading decorator-5.1.1-py3-none-any.whl.metadata (4.0 kB)
Collecting jedi>=0.16 (from ipython->anndata==0.1.dev50+g0a5807c)
  Downloading jedi-0.19.1-py2.py3-none-any.whl.metadata (22 kB)
Collecting matplotlib-inline (from ipython->anndata==0.1.dev50+g0a5807c)
  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.dev50+g0a5807c)
  Downloading prompt_toolkit-3.0.47-py3-none-any.whl.metadata (6.4 kB)
Collecting stack-data (from ipython->anndata==0.1.dev50+g0a5807c)
  Downloading stack_data-0.6.3-py3-none-any.whl.metadata (18 kB)
Collecting traitlets>=5.13.0 (from ipython->anndata==0.1.dev50+g0a5807c)
  Downloading traitlets-5.14.3-py3-none-any.whl.metadata (10 kB)
Collecting pexpect>4.3 (from ipython->anndata==0.1.dev50+g0a5807c)
  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.dev50+g0a5807c)
  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.dev50+g0a5807c)
  Downloading mdit_py_plugins-0.4.1-py3-none-any.whl.metadata (2.8 kB)
Collecting pyyaml (from myst-parser->anndata==0.1.dev50+g0a5807c)
  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.dev50+g0a5807c)
  Downloading nbconvert-7.16.4-py3-none-any.whl.metadata (8.5 kB)
Collecting nbformat (from nbsphinx->anndata==0.1.dev50+g0a5807c)
  Downloading nbformat-5.10.4-py3-none-any.whl.metadata (3.6 kB)
Collecting apeye>=0.4.0 (from sphinx-toolbox->anndata==0.1.dev50+g0a5807c)
  Downloading apeye-1.4.1-py3-none-any.whl.metadata (7.3 kB)
Collecting autodocsumm>=0.2.0 (from sphinx-toolbox->anndata==0.1.dev50+g0a5807c)
  Downloading autodocsumm-0.2.13-py3-none-any.whl.metadata (5.6 kB)
Collecting beautifulsoup4>=4.9.1 (from sphinx-toolbox->anndata==0.1.dev50+g0a5807c)
  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.dev50+g0a5807c)
  Downloading cachecontrol-0.14.0-py3-none-any.whl.metadata (3.1 kB)
Collecting dict2css>=0.2.3 (from sphinx-toolbox->anndata==0.1.dev50+g0a5807c)
  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.dev50+g0a5807c)
  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.dev50+g0a5807c)
  Downloading filelock-3.15.4-py3-none-any.whl.metadata (2.9 kB)
Collecting html5lib>=1.1 (from sphinx-toolbox->anndata==0.1.dev50+g0a5807c)
  Downloading html5lib-1.1-py2.py3-none-any.whl.metadata (16 kB)
Collecting ruamel.yaml>=0.16.12 (from sphinx-toolbox->anndata==0.1.dev50+g0a5807c)
  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.dev50+g0a5807c)
  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.dev50+g0a5807c)
  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.dev50+g0a5807c)
  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.dev50+g0a5807c)
  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.dev50+g0a5807c)
  Downloading typing_extensions-4.12.2-py3-none-any.whl.metadata (3.0 kB)
Collecting asciitree (from zarr->anndata==0.1.dev50+g0a5807c)
  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.dev50+g0a5807c)
  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.dev50+g0a5807c)
  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.dev50+g0a5807c)
  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.dev50+g0a5807c)
  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.dev50+g0a5807c)
  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.dev50+g0a5807c)
  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.dev50+g0a5807c)
  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.dev50+g0a5807c)
  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.dev50+g0a5807c)
  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.dev50+g0a5807c)
  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/1596/lib/python3.12/site-packages (from Jinja2>=3.1->sphinx>=7.4.6->anndata==0.1.dev50+g0a5807c) (2.1.5)
Collecting mdurl~=0.1 (from markdown-it-py~=3.0->myst-parser->anndata==0.1.dev50+g0a5807c)
  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.dev50+g0a5807c)
  Downloading bleach-6.1.0-py3-none-any.whl.metadata (30 kB)
Collecting defusedxml (from nbconvert!=5.4,>=5.3->nbsphinx->anndata==0.1.dev50+g0a5807c)
  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.dev50+g0a5807c)
  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.dev50+g0a5807c)
  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.dev50+g0a5807c)
  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.dev50+g0a5807c)
  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.dev50+g0a5807c)
  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.dev50+g0a5807c)
  Downloading tinycss2-1.3.0-py3-none-any.whl.metadata (3.0 kB)
Collecting fastjsonschema>=2.15 (from nbformat->nbsphinx->anndata==0.1.dev50+g0a5807c)
  Downloading fastjsonschema-2.20.0-py3-none-any.whl.metadata (2.1 kB)
Collecting jsonschema>=2.6 (from nbformat->nbsphinx->anndata==0.1.dev50+g0a5807c)
  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.dev50+g0a5807c)
  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.dev50+g0a5807c)
  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.dev50+g0a5807c)
  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/1596/lib/python3.12/site-packages (from requests>=2.30.0->sphinx>=7.4.6->anndata==0.1.dev50+g0a5807c) (3.3.2)
Requirement already satisfied: idna<4,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1596/lib/python3.12/site-packages (from requests>=2.30.0->sphinx>=7.4.6->anndata==0.1.dev50+g0a5807c) (3.7)
Requirement already satisfied: urllib3<3,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1596/lib/python3.12/site-packages (from requests>=2.30.0->sphinx>=7.4.6->anndata==0.1.dev50+g0a5807c) (2.2.2)
Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1596/lib/python3.12/site-packages (from requests>=2.30.0->sphinx>=7.4.6->anndata==0.1.dev50+g0a5807c) (2024.7.4)
Collecting ruamel.yaml.clib>=0.2.7 (from ruamel.yaml>=0.16.12->sphinx-toolbox->anndata==0.1.dev50+g0a5807c)
  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.dev50+g0a5807c)
  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.dev50+g0a5807c)
  Downloading asttokens-2.4.1-py2.py3-none-any.whl.metadata (5.2 kB)
Collecting pure-eval (from stack-data->ipython->anndata==0.1.dev50+g0a5807c)
  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.dev50+g0a5807c)
  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.dev50+g0a5807c)
  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.dev50+g0a5807c)
  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.dev50+g0a5807c)
  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.dev50+g0a5807c)
  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.dev50+g0a5807c)
  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.dev50+g0a5807c)
  Downloading pyzmq-26.1.1-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.dev50+g0a5807c)
  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 54.2 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 438.2 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 227.7 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 202.9 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 205.8 MB/s eta 0:00:00
Downloading scanpydoc-0.13.6-py3-none-any.whl (32 kB)
Downloading scipy-1.14.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (40.8 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 40.8/40.8 MB 202.0 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 294.2 MB/s eta 0:00:00
Downloading ipython-8.26.0-py3-none-any.whl (817 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 817.9/817.9 kB 473.9 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 508.3 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 537.8 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 229.2 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 238.3 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 496.9 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 510.6 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 508.8 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-26.1.1-cp312-cp312-manylinux_2_28_x86_64.whl (860 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 860.6/860.6 kB 493.8 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.dev50+g0a5807c-py3-none-any.whl size=136664 sha256=ad5508ef773eaa4003ee9375b0e2a5ae60e1cb84cfd644d6e6b1f6e7d7f7d3f7
  Stored in directory: /tmp/pip-ephem-wheel-cache-7uz2r4dz/wheels/b0/17/5b/073369c6ac602fef1dc9b56a544b559677e13c44eaac1e2605
  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=a2ae9802c7b4136eddcf2d7388aca1a775c77fb5509c9a972ca63d657fa70890
  Stored in directory: /tmp/pip-ephem-wheel-cache-7uz2r4dz/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.dev50+g0a5807c 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-26.1.1 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-1.14.0 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: 2024-08-19T15:40:57.522403Z, end-time: 2024-08-19T15:40:57.585145Z, 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",
]
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",
]
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"),
]
suppress_warnings = [
    "ref.citation",
    "myst.header",  # https://github.com/executablebooks/MyST-Parser/issues/262
]


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': "1596",
    'version_slug': "1596",
    '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': '0a5807c854a1e54c52f13ea4ba690f78a0f45e98',
    'display_github': True,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': '0a5807c854a1e54c52f13ea4ba690f78a0f45e98',
    'display_bitbucket': False,
    'gitlab_user': 'None',
    'gitlab_repo': 'None',
    'gitlab_version': '0a5807c854a1e54c52f13ea4ba690f78a0f45e98',
    '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': '0a5807c8',
}

# 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/1596'
    readthedocs_build_url = 'https://readthedocs.com/projects/icb-anndata/builds/2425100/'

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'])