Read the Docs build information Build id: 2074855 Project: icb-anndata Version: 1411 Commit: a3a042529d71e15bbae27df68073eaaa56d51216 Date: 2024-03-11T12:32:10.530391Z State: cancelled Success: False [rtd-command-info] start-time: 2024-03-11T12:36:04.446065Z, end-time: 2024-03-11T12:36:05.015561Z, duration: 0, exit-code: 0 git clone --depth 1 https://github.com/scverse/anndata.git . Cloning into '.'... [rtd-command-info] start-time: 2024-03-11T12:36:05.084292Z, end-time: 2024-03-11T12:36:05.657020Z, duration: 0, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 pull/1411/head:external-1411 From https://github.com/scverse/anndata * [new ref] refs/pull/1411/head -> external-1411 [rtd-command-info] start-time: 2024-03-11T12:36:05.775915Z, end-time: 2024-03-11T12:36:05.841106Z, duration: 0, exit-code: 0 git checkout --force a3a042529d71e15bbae27df68073eaaa56d51216 Note: switching to 'a3a042529d71e15bbae27df68073eaaa56d51216'. 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 Or undo this operation with: git switch - Turn off this advice by setting config variable advice.detachedHead to false HEAD is now at a3a0425 Release note [rtd-command-info] start-time: 2024-03-11T12:36:05.937513Z, end-time: 2024-03-11T12:36:05.995098Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2024-03-11T12:36:06.089372Z, end-time: 2024-03-11T12:36:06.145926Z, 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: 2024-03-11T12:36:06.287407Z, end-time: 2024-03-11T12:36:06.373427Z, duration: 0, exit-code: 0 git submodule sync [rtd-command-info] start-time: 2024-03-11T12:36:06.438655Z, end-time: 2024-03-11T12:36:07.068428Z, 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/1411/docs/tutorials/notebooks'... Submodule path 'docs/tutorials/notebooks': checked out '9e186c5c694793bb04ea1397721d154d6e0b7069' [rtd-command-info] start-time: 2024-03-11T12:36:13.192868Z, end-time: 2024-03-11T12:36:13.275935Z, duration: 0, exit-code: 0 asdf global python 3.12.0 [rtd-command-info] start-time: 2024-03-11T12:36:13.683000Z, end-time: 2024-03-11T12:36:14.856922Z, duration: 1, exit-code: 0 python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH created virtual environment CPython3.12.0.final.0-64 in 841ms creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1411, 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: 2024-03-11T12:36:14.918775Z, end-time: 2024-03-11T12:36:27.020203Z, duration: 12, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip setuptools Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1411/lib/python3.12/site-packages (23.1) Collecting pip Downloading pip-24.0-py3-none-any.whl (2.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.1/2.1 MB 44.4 MB/s eta 0:00:00 Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1411/lib/python3.12/site-packages (67.6.1) Collecting setuptools Downloading setuptools-69.1.1-py3-none-any.whl (819 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 819.3/819.3 kB 156.7 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-24.0 setuptools-69.1.1 [rtd-command-info] start-time: 2024-03-11T12:36:27.089727Z, end-time: 2024-03-11T12:36:34.972758Z, duration: 7, exit-code: 0 python -m pip install --upgrade --no-cache-dir sphinx readthedocs-sphinx-ext Collecting sphinx Downloading sphinx-7.2.6-py3-none-any.whl.metadata (5.9 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-1.0.8-py3-none-any.whl.metadata (2.3 kB) Collecting sphinxcontrib-devhelp (from sphinx) Downloading sphinxcontrib_devhelp-1.0.6-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-2.0.5-py3-none-any.whl.metadata (2.3 kB) Collecting sphinxcontrib-serializinghtml>=1.1.9 (from sphinx) Downloading sphinxcontrib_serializinghtml-1.1.10-py3-none-any.whl.metadata (2.4 kB) Collecting sphinxcontrib-qthelp (from sphinx) Downloading sphinxcontrib_qthelp-1.0.7-py3-none-any.whl.metadata (2.2 kB) Collecting Jinja2>=3.0 (from sphinx) Downloading Jinja2-3.1.3-py3-none-any.whl.metadata (3.3 kB) Collecting Pygments>=2.14 (from sphinx) Downloading pygments-2.17.2-py3-none-any.whl.metadata (2.6 kB) Collecting docutils<0.21,>=0.18.1 (from sphinx) Downloading docutils-0.20.1-py3-none-any.whl.metadata (2.8 kB) Collecting snowballstemmer>=2.0 (from sphinx) Downloading snowballstemmer-2.2.0-py2.py3-none-any.whl.metadata (6.5 kB) Collecting babel>=2.9 (from sphinx) Downloading Babel-2.14.0-py3-none-any.whl.metadata (1.6 kB) Collecting alabaster<0.8,>=0.7 (from sphinx) Downloading alabaster-0.7.16-py3-none-any.whl.metadata (2.9 kB) Collecting imagesize>=1.3 (from sphinx) Downloading imagesize-1.4.1-py2.py3-none-any.whl.metadata (1.5 kB) Collecting requests>=2.25.0 (from sphinx) Downloading requests-2.31.0-py3-none-any.whl.metadata (4.6 kB) Collecting packaging>=21.0 (from sphinx) Downloading packaging-24.0-py3-none-any.whl.metadata (3.2 kB) Collecting MarkupSafe>=2.0 (from Jinja2>=3.0->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>=2.25.0->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>=2.25.0->sphinx) Downloading idna-3.6-py3-none-any.whl.metadata (9.9 kB) Collecting urllib3<3,>=1.21.1 (from requests>=2.25.0->sphinx) Downloading urllib3-2.2.1-py3-none-any.whl.metadata (6.4 kB) Collecting certifi>=2017.4.17 (from requests>=2.25.0->sphinx) Downloading certifi-2024.2.2-py3-none-any.whl.metadata (2.2 kB) Downloading sphinx-7.2.6-py3-none-any.whl (3.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.2/3.2 MB 80.4 MB/s eta 0:00:00 Downloading readthedocs_sphinx_ext-2.2.5-py2.py3-none-any.whl (11 kB) Downloading alabaster-0.7.16-py3-none-any.whl (13 kB) Downloading Babel-2.14.0-py3-none-any.whl (11.0 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.0/11.0 MB 208.6 MB/s eta 0:00:00 Downloading docutils-0.20.1-py3-none-any.whl (572 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 572.7/572.7 kB 259.8 MB/s eta 0:00:00 Downloading imagesize-1.4.1-py2.py3-none-any.whl (8.8 kB) Downloading Jinja2-3.1.3-py3-none-any.whl (133 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 133.2/133.2 kB 247.0 MB/s eta 0:00:00 Downloading packaging-24.0-py3-none-any.whl (53 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 53.5/53.5 kB 209.9 MB/s eta 0:00:00 Downloading pygments-2.17.2-py3-none-any.whl (1.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 259.1 MB/s eta 0:00:00 Downloading requests-2.31.0-py3-none-any.whl (62 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.6/62.6 kB 225.0 MB/s eta 0:00:00 Downloading snowballstemmer-2.2.0-py2.py3-none-any.whl (93 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 93.0/93.0 kB 225.0 MB/s eta 0:00:00 Downloading sphinxcontrib_htmlhelp-2.0.5-py3-none-any.whl (99 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 99.2/99.2 kB 242.2 MB/s eta 0:00:00 Downloading sphinxcontrib_serializinghtml-1.1.10-py3-none-any.whl (92 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 92.7/92.7 kB 234.3 MB/s eta 0:00:00 Downloading sphinxcontrib_applehelp-1.0.8-py3-none-any.whl (120 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 120.0/120.0 kB 244.8 MB/s eta 0:00:00 Downloading sphinxcontrib_devhelp-1.0.6-py3-none-any.whl (83 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 83.5/83.5 kB 234.5 MB/s eta 0:00:00 Downloading sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB) Downloading sphinxcontrib_qthelp-1.0.7-py3-none-any.whl (89 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 89.4/89.4 kB 240.4 MB/s eta 0:00:00 Downloading certifi-2024.2.2-py3-none-any.whl (163 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 163.8/163.8 kB 261.3 MB/s eta 0:00:00 Downloading charset_normalizer-3.3.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (141 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 141.9/141.9 kB 251.8 MB/s eta 0:00:00 Downloading idna-3.6-py3-none-any.whl (61 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 61.6/61.6 kB 209.3 MB/s eta 0:00:00 Downloading MarkupSafe-2.1.5-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (28 kB) Downloading urllib3-2.2.1-py3-none-any.whl (121 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 121.1/121.1 kB 242.2 MB/s eta 0:00:00 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 Jinja2-3.1.3 MarkupSafe-2.1.5 Pygments-2.17.2 alabaster-0.7.16 babel-2.14.0 certifi-2024.2.2 charset-normalizer-3.3.2 docutils-0.20.1 idna-3.6 imagesize-1.4.1 packaging-24.0 readthedocs-sphinx-ext-2.2.5 requests-2.31.0 snowballstemmer-2.2.0 sphinx-7.2.6 sphinxcontrib-applehelp-1.0.8 sphinxcontrib-devhelp-1.0.6 sphinxcontrib-htmlhelp-2.0.5 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.7 sphinxcontrib-serializinghtml-1.1.10 urllib3-2.2.1 [rtd-command-info] start-time: 2024-03-11T12:36:35.046945Z, end-time: 2024-03-11T12:37:14.837599Z, duration: 39, 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/1411 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 (from anndata==0.1.dev50+ga3a0425) Downloading array_api_compat-1.4.1-py3-none-any.whl.metadata (13 kB) Collecting h5py>=3.1 (from anndata==0.1.dev50+ga3a0425) Downloading h5py-3.10.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.5 kB) Collecting natsort (from anndata==0.1.dev50+ga3a0425) Downloading natsort-8.4.0-py3-none-any.whl.metadata (21 kB) Collecting numpy>=1.23 (from anndata==0.1.dev50+ga3a0425) Downloading numpy-1.26.4-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (61 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 61.0/61.0 kB 7.7 MB/s eta 0:00:00 Requirement already satisfied: packaging>=20.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1411/lib/python3.12/site-packages (from anndata==0.1.dev50+ga3a0425) (24.0) Collecting pandas!=2.1.0rc0,!=2.1.2,>=1.4 (from anndata==0.1.dev50+ga3a0425) Downloading pandas-2.2.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (19 kB) Collecting scipy>1.8 (from anndata==0.1.dev50+ga3a0425) Downloading scipy-1.12.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 60.4/60.4 kB 174.1 MB/s eta 0:00:00 Collecting awkward>=2.0.7 (from anndata==0.1.dev50+ga3a0425) Downloading awkward-2.6.2-py3-none-any.whl.metadata (7.0 kB) Collecting ipython (from anndata==0.1.dev50+ga3a0425) Downloading ipython-8.22.2-py3-none-any.whl.metadata (4.8 kB) Collecting myst-parser (from anndata==0.1.dev50+ga3a0425) Downloading myst_parser-2.0.0-py3-none-any.whl.metadata (5.4 kB) Collecting nbsphinx (from anndata==0.1.dev50+ga3a0425) Downloading nbsphinx-0.9.3-py3-none-any.whl.metadata (2.1 kB) Collecting readthedocs-sphinx-search (from anndata==0.1.dev50+ga3a0425) Downloading readthedocs_sphinx_search-0.3.2-py3-none-any.whl.metadata (2.4 kB) Collecting scanpydoc>=0.13.4 (from scanpydoc[theme,typehints]>=0.13.4; extra == "doc"->anndata==0.1.dev50+ga3a0425) Downloading scanpydoc-0.13.4-py3-none-any.whl.metadata (2.6 kB) Collecting sphinx-autodoc-typehints>=1.11.0 (from anndata==0.1.dev50+ga3a0425) Downloading sphinx_autodoc_typehints-2.0.0-py3-none-any.whl.metadata (7.7 kB) Collecting sphinx-book-theme>=1.1.0 (from anndata==0.1.dev50+ga3a0425) Downloading sphinx_book_theme-1.1.2-py3-none-any.whl.metadata (5.7 kB) Collecting sphinx-copybutton (from anndata==0.1.dev50+ga3a0425) 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+ga3a0425) Downloading sphinx_design-0.5.0-py3-none-any.whl.metadata (5.1 kB) Collecting sphinx-issues (from anndata==0.1.dev50+ga3a0425) Downloading sphinx_issues-4.0.0-py3-none-any.whl.metadata (8.0 kB) Requirement already satisfied: sphinx>=4.4 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1411/lib/python3.12/site-packages (from anndata==0.1.dev50+ga3a0425) (7.2.6) Collecting sphinxext-opengraph (from anndata==0.1.dev50+ga3a0425) Downloading sphinxext_opengraph-0.9.1-py3-none-any.whl.metadata (6.5 kB) Collecting zarr (from anndata==0.1.dev50+ga3a0425) Downloading zarr-2.17.1-py3-none-any.whl.metadata (5.7 kB) Collecting awkward-cpp==30 (from awkward>=2.0.7->anndata==0.1.dev50+ga3a0425) Downloading awkward_cpp-30-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+ga3a0425) Downloading fsspec-2024.2.0-py3-none-any.whl.metadata (6.8 kB) Collecting python-dateutil>=2.8.2 (from pandas!=2.1.0rc0,!=2.1.2,>=1.4->anndata==0.1.dev50+ga3a0425) 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+ga3a0425) 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+ga3a0425) 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/1411/lib/python3.12/site-packages (from sphinx>=4.4->anndata==0.1.dev50+ga3a0425) (1.0.8) Requirement already satisfied: sphinxcontrib-devhelp in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1411/lib/python3.12/site-packages (from sphinx>=4.4->anndata==0.1.dev50+ga3a0425) (1.0.6) Requirement already satisfied: sphinxcontrib-jsmath in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1411/lib/python3.12/site-packages (from sphinx>=4.4->anndata==0.1.dev50+ga3a0425) (1.0.1) Requirement already satisfied: sphinxcontrib-htmlhelp>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1411/lib/python3.12/site-packages (from sphinx>=4.4->anndata==0.1.dev50+ga3a0425) (2.0.5) Requirement already satisfied: sphinxcontrib-serializinghtml>=1.1.9 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1411/lib/python3.12/site-packages (from sphinx>=4.4->anndata==0.1.dev50+ga3a0425) (1.1.10) Requirement already satisfied: sphinxcontrib-qthelp in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1411/lib/python3.12/site-packages (from sphinx>=4.4->anndata==0.1.dev50+ga3a0425) (1.0.7) Requirement already satisfied: Jinja2>=3.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1411/lib/python3.12/site-packages (from sphinx>=4.4->anndata==0.1.dev50+ga3a0425) (3.1.3) Requirement already satisfied: Pygments>=2.14 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1411/lib/python3.12/site-packages (from sphinx>=4.4->anndata==0.1.dev50+ga3a0425) (2.17.2) Requirement already satisfied: docutils<0.21,>=0.18.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1411/lib/python3.12/site-packages (from sphinx>=4.4->anndata==0.1.dev50+ga3a0425) (0.20.1) Requirement already satisfied: snowballstemmer>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1411/lib/python3.12/site-packages (from sphinx>=4.4->anndata==0.1.dev50+ga3a0425) (2.2.0) Requirement already satisfied: babel>=2.9 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1411/lib/python3.12/site-packages (from sphinx>=4.4->anndata==0.1.dev50+ga3a0425) (2.14.0) Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1411/lib/python3.12/site-packages (from sphinx>=4.4->anndata==0.1.dev50+ga3a0425) (0.7.16) Requirement already satisfied: imagesize>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1411/lib/python3.12/site-packages (from sphinx>=4.4->anndata==0.1.dev50+ga3a0425) (1.4.1) Requirement already satisfied: requests>=2.25.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1411/lib/python3.12/site-packages (from sphinx>=4.4->anndata==0.1.dev50+ga3a0425) (2.31.0) Collecting pydata-sphinx-theme>=0.14 (from sphinx-book-theme>=1.1.0->anndata==0.1.dev50+ga3a0425) Downloading pydata_sphinx_theme-0.15.2-py3-none-any.whl.metadata (7.3 kB) Collecting decorator (from ipython->anndata==0.1.dev50+ga3a0425) Downloading decorator-5.1.1-py3-none-any.whl.metadata (4.0 kB) Collecting jedi>=0.16 (from ipython->anndata==0.1.dev50+ga3a0425) Downloading jedi-0.19.1-py2.py3-none-any.whl.metadata (22 kB) Collecting matplotlib-inline (from ipython->anndata==0.1.dev50+ga3a0425) Downloading matplotlib_inline-0.1.6-py3-none-any.whl.metadata (2.8 kB) Collecting prompt-toolkit<3.1.0,>=3.0.41 (from ipython->anndata==0.1.dev50+ga3a0425) Downloading prompt_toolkit-3.0.43-py3-none-any.whl.metadata (6.5 kB) Collecting stack-data (from ipython->anndata==0.1.dev50+ga3a0425) Downloading stack_data-0.6.3-py3-none-any.whl.metadata (18 kB) Collecting traitlets>=5.13.0 (from ipython->anndata==0.1.dev50+ga3a0425) Downloading traitlets-5.14.1-py3-none-any.whl.metadata (10 kB) Collecting pexpect>4.3 (from ipython->anndata==0.1.dev50+ga3a0425) 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+ga3a0425) Downloading markdown_it_py-3.0.0-py3-none-any.whl.metadata (6.9 kB) Collecting mdit-py-plugins~=0.4 (from myst-parser->anndata==0.1.dev50+ga3a0425) Downloading mdit_py_plugins-0.4.0-py3-none-any.whl.metadata (2.7 kB) Collecting pyyaml (from myst-parser->anndata==0.1.dev50+ga3a0425) Downloading PyYAML-6.0.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB) Collecting nbconvert!=5.4 (from nbsphinx->anndata==0.1.dev50+ga3a0425) Downloading nbconvert-7.16.2-py3-none-any.whl.metadata (8.0 kB) Collecting nbformat (from nbsphinx->anndata==0.1.dev50+ga3a0425) Downloading nbformat-5.9.2-py3-none-any.whl.metadata (3.4 kB) Collecting asciitree (from zarr->anndata==0.1.dev50+ga3a0425) 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+ga3a0425) Downloading numcodecs-0.12.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.8 kB) Collecting fasteners (from zarr->anndata==0.1.dev50+ga3a0425) Downloading fasteners-0.19-py3-none-any.whl.metadata (4.9 kB) Collecting parso<0.9.0,>=0.8.3 (from jedi>=0.16->ipython->anndata==0.1.dev50+ga3a0425) Downloading parso-0.8.3-py2.py3-none-any.whl.metadata (7.5 kB) Requirement already satisfied: MarkupSafe>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1411/lib/python3.12/site-packages (from Jinja2>=3.0->sphinx>=4.4->anndata==0.1.dev50+ga3a0425) (2.1.5) Collecting mdurl~=0.1 (from markdown-it-py~=3.0->myst-parser->anndata==0.1.dev50+ga3a0425) Downloading mdurl-0.1.2-py3-none-any.whl.metadata (1.6 kB) Collecting beautifulsoup4 (from nbconvert!=5.4->nbsphinx->anndata==0.1.dev50+ga3a0425) Downloading beautifulsoup4-4.12.3-py3-none-any.whl.metadata (3.8 kB) Collecting bleach!=5.0.0 (from nbconvert!=5.4->nbsphinx->anndata==0.1.dev50+ga3a0425) Downloading bleach-6.1.0-py3-none-any.whl.metadata (30 kB) Collecting defusedxml (from nbconvert!=5.4->nbsphinx->anndata==0.1.dev50+ga3a0425) Downloading defusedxml-0.7.1-py2.py3-none-any.whl.metadata (32 kB) Collecting jupyter-core>=4.7 (from nbconvert!=5.4->nbsphinx->anndata==0.1.dev50+ga3a0425) Downloading jupyter_core-5.7.1-py3-none-any.whl.metadata (3.4 kB) Collecting jupyterlab-pygments (from nbconvert!=5.4->nbsphinx->anndata==0.1.dev50+ga3a0425) Downloading jupyterlab_pygments-0.3.0-py3-none-any.whl.metadata (4.4 kB) Collecting mistune<4,>=2.0.3 (from nbconvert!=5.4->nbsphinx->anndata==0.1.dev50+ga3a0425) Downloading mistune-3.0.2-py3-none-any.whl.metadata (1.7 kB) Collecting nbclient>=0.5.0 (from nbconvert!=5.4->nbsphinx->anndata==0.1.dev50+ga3a0425) Downloading nbclient-0.9.0-py3-none-any.whl.metadata (7.8 kB) Collecting pandocfilters>=1.4.1 (from nbconvert!=5.4->nbsphinx->anndata==0.1.dev50+ga3a0425) Downloading pandocfilters-1.5.1-py2.py3-none-any.whl.metadata (9.0 kB) Collecting tinycss2 (from nbconvert!=5.4->nbsphinx->anndata==0.1.dev50+ga3a0425) Downloading tinycss2-1.2.1-py3-none-any.whl.metadata (3.0 kB) Collecting fastjsonschema (from nbformat->nbsphinx->anndata==0.1.dev50+ga3a0425) Downloading fastjsonschema-2.19.1-py3-none-any.whl.metadata (2.1 kB) Collecting jsonschema>=2.6 (from nbformat->nbsphinx->anndata==0.1.dev50+ga3a0425) Downloading jsonschema-4.21.1-py3-none-any.whl.metadata (7.8 kB) Collecting ptyprocess>=0.5 (from pexpect>4.3->ipython->anndata==0.1.dev50+ga3a0425) 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+ga3a0425) Downloading wcwidth-0.2.13-py2.py3-none-any.whl.metadata (14 kB) Collecting accessible-pygments (from pydata-sphinx-theme>=0.14->sphinx-book-theme>=1.1.0->anndata==0.1.dev50+ga3a0425) Downloading accessible_pygments-0.0.4-py2.py3-none-any.whl.metadata (6.0 kB) Collecting typing-extensions (from pydata-sphinx-theme>=0.14->sphinx-book-theme>=1.1.0->anndata==0.1.dev50+ga3a0425) Downloading typing_extensions-4.10.0-py3-none-any.whl.metadata (3.0 kB) Collecting six>=1.5 (from python-dateutil>=2.8.2->pandas!=2.1.0rc0,!=2.1.2,>=1.4->anndata==0.1.dev50+ga3a0425) Downloading six-1.16.0-py2.py3-none-any.whl.metadata (1.8 kB) Requirement already satisfied: charset-normalizer<4,>=2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1411/lib/python3.12/site-packages (from requests>=2.25.0->sphinx>=4.4->anndata==0.1.dev50+ga3a0425) (3.3.2) Requirement already satisfied: idna<4,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1411/lib/python3.12/site-packages (from requests>=2.25.0->sphinx>=4.4->anndata==0.1.dev50+ga3a0425) (3.6) Requirement already satisfied: urllib3<3,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1411/lib/python3.12/site-packages (from requests>=2.25.0->sphinx>=4.4->anndata==0.1.dev50+ga3a0425) (2.2.1) Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1411/lib/python3.12/site-packages (from requests>=2.25.0->sphinx>=4.4->anndata==0.1.dev50+ga3a0425) (2024.2.2) Collecting executing>=1.2.0 (from stack-data->ipython->anndata==0.1.dev50+ga3a0425) 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+ga3a0425) 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+ga3a0425) Downloading pure_eval-0.2.2-py3-none-any.whl.metadata (6.2 kB) Collecting webencodings (from bleach!=5.0.0->nbconvert!=5.4->nbsphinx->anndata==0.1.dev50+ga3a0425) Downloading webencodings-0.5.1-py2.py3-none-any.whl.metadata (2.1 kB) Collecting attrs>=22.2.0 (from jsonschema>=2.6->nbformat->nbsphinx->anndata==0.1.dev50+ga3a0425) Downloading attrs-23.2.0-py3-none-any.whl.metadata (9.5 kB) Collecting jsonschema-specifications>=2023.03.6 (from jsonschema>=2.6->nbformat->nbsphinx->anndata==0.1.dev50+ga3a0425) 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+ga3a0425) Downloading referencing-0.33.0-py3-none-any.whl.metadata (2.7 kB) Collecting rpds-py>=0.7.1 (from jsonschema>=2.6->nbformat->nbsphinx->anndata==0.1.dev50+ga3a0425) Downloading rpds_py-0.18.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.1 kB) Collecting platformdirs>=2.5 (from jupyter-core>=4.7->nbconvert!=5.4->nbsphinx->anndata==0.1.dev50+ga3a0425) Downloading platformdirs-4.2.0-py3-none-any.whl.metadata (11 kB) Collecting jupyter-client>=6.1.12 (from nbclient>=0.5.0->nbconvert!=5.4->nbsphinx->anndata==0.1.dev50+ga3a0425) Downloading jupyter_client-8.6.0-py3-none-any.whl.metadata (8.3 kB) Collecting soupsieve>1.2 (from beautifulsoup4->nbconvert!=5.4->nbsphinx->anndata==0.1.dev50+ga3a0425) Downloading soupsieve-2.5-py3-none-any.whl.metadata (4.7 kB) Collecting pyzmq>=23.0 (from jupyter-client>=6.1.12->nbclient>=0.5.0->nbconvert!=5.4->nbsphinx->anndata==0.1.dev50+ga3a0425) Downloading pyzmq-25.1.2-cp312-cp312-manylinux_2_28_x86_64.whl.metadata (4.9 kB) Collecting tornado>=6.2 (from jupyter-client>=6.1.12->nbclient>=0.5.0->nbconvert!=5.4->nbsphinx->anndata==0.1.dev50+ga3a0425) Downloading tornado-6.4-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-1.4.1-py3-none-any.whl (30 kB) Downloading awkward-2.6.2-py3-none-any.whl (774 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 774.7/774.7 kB 46.9 MB/s eta 0:00:00 Downloading awkward_cpp-30-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (707 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 707.7/707.7 kB 166.8 MB/s eta 0:00:00 Downloading h5py-3.10.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.7 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.7/4.7 MB 206.5 MB/s eta 0:00:00 Downloading numpy-1.26.4-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (18.0 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 18.0/18.0 MB 182.9 MB/s eta 0:00:00 Downloading pandas-2.2.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.7 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 12.7/12.7 MB 198.4 MB/s eta 0:00:00 Downloading scanpydoc-0.13.4-py3-none-any.whl (32 kB) Downloading scipy-1.12.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (37.8 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 37.8/37.8 MB 202.1 MB/s eta 0:00:00 Downloading sphinx_autodoc_typehints-2.0.0-py3-none-any.whl (19 kB) Downloading sphinx_book_theme-1.1.2-py3-none-any.whl (400 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 400.8/400.8 kB 268.5 MB/s eta 0:00:00 Downloading sphinx_design-0.5.0-py3-none-any.whl (2.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.2/2.2 MB 227.2 MB/s eta 0:00:00 Downloading ipython-8.22.2-py3-none-any.whl (811 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 812.0/812.0 kB 266.2 MB/s eta 0:00:00 Downloading myst_parser-2.0.0-py3-none-any.whl (77 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 77.2/77.2 kB 241.5 MB/s eta 0:00:00 Downloading natsort-8.4.0-py3-none-any.whl (38 kB) Downloading nbsphinx-0.9.3-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-4.0.0-py3-none-any.whl (8.1 kB) Downloading sphinxext_opengraph-0.9.1-py3-none-any.whl (1.0 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.0/1.0 MB 269.6 MB/s eta 0:00:00 Downloading zarr-2.17.1-py3-none-any.whl (207 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 207.5/207.5 kB 247.3 MB/s eta 0:00:00 Downloading fsspec-2024.2.0-py3-none-any.whl (170 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 170.9/170.9 kB 260.1 MB/s eta 0:00:00 Downloading jedi-0.19.1-py2.py3-none-any.whl (1.6 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.6/1.6 MB 271.6 MB/s eta 0:00:00 Downloading markdown_it_py-3.0.0-py3-none-any.whl (87 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 87.5/87.5 kB 210.5 MB/s eta 0:00:00 Downloading mdit_py_plugins-0.4.0-py3-none-any.whl (54 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 54.1/54.1 kB 190.0 MB/s eta 0:00:00 Downloading nbconvert-7.16.2-py3-none-any.whl (257 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 257.3/257.3 kB 260.8 MB/s eta 0:00:00 Downloading nbformat-5.9.2-py3-none-any.whl (77 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 77.6/77.6 kB 237.0 MB/s eta 0:00:00 Downloading numcodecs-0.12.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (7.9 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 7.9/7.9 MB 186.4 MB/s eta 0:00:00 Downloading pexpect-4.9.0-py2.py3-none-any.whl (63 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 63.8/63.8 kB 231.7 MB/s eta 0:00:00 Downloading prompt_toolkit-3.0.43-py3-none-any.whl (386 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 386.1/386.1 kB 263.3 MB/s eta 0:00:00 Downloading pydata_sphinx_theme-0.15.2-py3-none-any.whl (4.5 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.5/4.5 MB 240.7 MB/s eta 0:00:00 Downloading python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 229.9/229.9 kB 246.0 MB/s eta 0:00:00 Downloading pytz-2024.1-py2.py3-none-any.whl (505 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 505.5/505.5 kB 270.5 MB/s eta 0:00:00 Downloading traitlets-5.14.1-py3-none-any.whl (85 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 85.4/85.4 kB 237.4 MB/s eta 0:00:00 Downloading tzdata-2024.1-py2.py3-none-any.whl (345 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 345.4/345.4 kB 266.9 MB/s eta 0:00:00 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-0.1.6-py3-none-any.whl (9.4 kB) Downloading PyYAML-6.0.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (724 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 725.0/725.0 kB 271.7 MB/s eta 0:00:00 Downloading stack_data-0.6.3-py3-none-any.whl (24 kB) Downloading asttokens-2.4.1-py2.py3-none-any.whl (27 kB) Downloading bleach-6.1.0-py3-none-any.whl (162 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 162.8/162.8 kB 257.5 MB/s eta 0:00:00 Downloading executing-2.0.1-py2.py3-none-any.whl (24 kB) Downloading jsonschema-4.21.1-py3-none-any.whl (85 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 85.5/85.5 kB 219.7 MB/s eta 0:00:00 Downloading jupyter_core-5.7.1-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) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 48.0/48.0 kB 222.5 MB/s eta 0:00:00 Downloading nbclient-0.9.0-py3-none-any.whl (24 kB) Downloading pandocfilters-1.5.1-py2.py3-none-any.whl (8.7 kB) Downloading parso-0.8.3-py2.py3-none-any.whl (100 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100.8/100.8 kB 238.5 MB/s eta 0:00:00 Downloading ptyprocess-0.7.0-py2.py3-none-any.whl (13 kB) Downloading six-1.16.0-py2.py3-none-any.whl (11 kB) Downloading accessible_pygments-0.0.4-py2.py3-none-any.whl (29 kB) Downloading beautifulsoup4-4.12.3-py3-none-any.whl (147 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 147.9/147.9 kB 228.2 MB/s eta 0:00:00 Downloading defusedxml-0.7.1-py2.py3-none-any.whl (25 kB) Downloading fastjsonschema-2.19.1-py3-none-any.whl (23 kB) Downloading jupyterlab_pygments-0.3.0-py3-none-any.whl (15 kB) Downloading pure_eval-0.2.2-py3-none-any.whl (11 kB) Downloading tinycss2-1.2.1-py3-none-any.whl (21 kB) Downloading typing_extensions-4.10.0-py3-none-any.whl (33 kB) Downloading wcwidth-0.2.13-py2.py3-none-any.whl (34 kB) Downloading attrs-23.2.0-py3-none-any.whl (60 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 60.8/60.8 kB 232.5 MB/s eta 0:00:00 Downloading jsonschema_specifications-2023.12.1-py3-none-any.whl (18 kB) Downloading jupyter_client-8.6.0-py3-none-any.whl (105 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 105.9/105.9 kB 249.6 MB/s eta 0:00:00 Downloading platformdirs-4.2.0-py3-none-any.whl (17 kB) Downloading referencing-0.33.0-py3-none-any.whl (26 kB) Downloading rpds_py-0.18.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 263.9 MB/s eta 0:00:00 Downloading soupsieve-2.5-py3-none-any.whl (36 kB) Downloading webencodings-0.5.1-py2.py3-none-any.whl (11 kB) Downloading pyzmq-25.1.2-cp312-cp312-manylinux_2_28_x86_64.whl (1.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 263.4 MB/s eta 0:00:00 Downloading tornado-6.4-cp38-abi3-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (435 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 435.4/435.4 kB 258.2 MB/s eta 0:00:00 Building wheels for collected packages: anndata, asciitree Building wheel for anndata (pyproject.toml): started Building wheel for anndata (pyproject.toml): finished with status 'done' Created wheel for anndata: filename=anndata-0.1.dev50+ga3a0425-py3-none-any.whl size=125484 sha256=6bac69fbf12dcfe0f5d48382a8ba9e8bedeb95c04e0cb23fafafb326abb61f49 Stored in directory: /tmp/pip-ephem-wheel-cache-1e9wqv93/wheels/f6/58/af/e7a2082370c25fd5bdb9c1c756381f15f6c017f72b78a43413 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=5034 sha256=e799d862fa8bdd95114aee9f501b5500e394755d0823a41d728bfa50c746fba6 Stored in directory: /tmp/pip-ephem-wheel-cache-1e9wqv93/wheels/a5/d7/98/f56ae733748cd0fa577172bda0e73e0b1f1793c98e09b9e458 Successfully built anndata asciitree Installing collected packages: webencodings, wcwidth, pytz, pure-eval, ptyprocess, fastjsonschema, asciitree, tzdata, typing-extensions, traitlets, tornado, tinycss2, soupsieve, six, rpds-py, readthedocs-sphinx-search, pyzmq, pyyaml, prompt-toolkit, platformdirs, pexpect, parso, pandocfilters, numpy, natsort, mistune, mdurl, jupyterlab-pygments, fsspec, fasteners, executing, defusedxml, decorator, attrs, array-api-compat, accessible-pygments, scipy, referencing, python-dateutil, numcodecs, matplotlib-inline, markdown-it-py, jupyter-core, jedi, h5py, bleach, beautifulsoup4, awkward-cpp, asttokens, zarr, stack-data, sphinxext-opengraph, sphinx-issues, sphinx-design, sphinx-copybutton, sphinx-autodoc-typehints, scanpydoc, pydata-sphinx-theme, pandas, mdit-py-plugins, jupyter-client, jsonschema-specifications, awkward, sphinx-book-theme, myst-parser, jsonschema, ipython, anndata, nbformat, nbclient, nbconvert, nbsphinx Successfully installed accessible-pygments-0.0.4 anndata-0.1.dev50+ga3a0425 array-api-compat-1.4.1 asciitree-0.3.3 asttokens-2.4.1 attrs-23.2.0 awkward-2.6.2 awkward-cpp-30 beautifulsoup4-4.12.3 bleach-6.1.0 decorator-5.1.1 defusedxml-0.7.1 executing-2.0.1 fasteners-0.19 fastjsonschema-2.19.1 fsspec-2024.2.0 h5py-3.10.0 ipython-8.22.2 jedi-0.19.1 jsonschema-4.21.1 jsonschema-specifications-2023.12.1 jupyter-client-8.6.0 jupyter-core-5.7.1 jupyterlab-pygments-0.3.0 markdown-it-py-3.0.0 matplotlib-inline-0.1.6 mdit-py-plugins-0.4.0 mdurl-0.1.2 mistune-3.0.2 myst-parser-2.0.0 natsort-8.4.0 nbclient-0.9.0 nbconvert-7.16.2 nbformat-5.9.2 nbsphinx-0.9.3 numcodecs-0.12.1 numpy-1.26.4 pandas-2.2.1 pandocfilters-1.5.1 parso-0.8.3 pexpect-4.9.0 platformdirs-4.2.0 prompt-toolkit-3.0.43 ptyprocess-0.7.0 pure-eval-0.2.2 pydata-sphinx-theme-0.15.2 python-dateutil-2.9.0.post0 pytz-2024.1 pyyaml-6.0.1 pyzmq-25.1.2 readthedocs-sphinx-search-0.3.2 referencing-0.33.0 rpds-py-0.18.0 scanpydoc-0.13.4 scipy-1.12.0 six-1.16.0 soupsieve-2.5 sphinx-autodoc-typehints-2.0.0 sphinx-book-theme-1.1.2 sphinx-copybutton-0.5.2 sphinx-design-0.5.0 sphinx-issues-4.0.0 sphinxext-opengraph-0.9.1 stack-data-0.6.3 tinycss2-1.2.1 tornado-6.4 traitlets-5.14.1 typing-extensions-4.10.0 tzdata-2024.1 wcwidth-0.2.13 webencodings-0.5.1 zarr-2.17.1 [rtd-command-info] start-time: 2024-03-11T12:37:15.435805Z, end-time: 2024-03-11T12:37:15.497439Z, duration: 0, exit-code: 0 cat docs/conf.py from __future__ import annotations import sys from datetime import datetime from importlib import metadata from pathlib import Path from typing import TYPE_CHECKING 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", ".md"] master_doc = "index" default_role = "literal" exclude_patterns = [ "_build", "Thumbs.db", ".DS_Store", "**.ipynb_checkpoints", "tutorials/notebooks/*.rst", ] pygments_style = "sphinx" extensions = [ "myst_parser", "sphinx_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", ] myst_enable_extensions = [ "html_image", # So README.md can be used on github and sphinx docs ] # Generate the API documentation when building autosummary_generate = True autodoc_member_order = "bysource" issues_github_path = "scverse/anndata" # autodoc_default_flags = ['members'] napoleon_google_docstring = False napoleon_numpy_docstring = True napoleon_include_init_with_doc = False napoleon_use_rtype = True # having a separate entry generally helps readability napoleon_use_param = True napoleon_custom_sections = [("Params", "Parameters")] typehints_defaults = "braces" todo_include_todos = False nitpicky = True # Report broken links nitpick_ignore = [ ("py:class", "scipy.sparse.base.spmatrix"), ("py:meth", "pandas.DataFrame.iloc"), ("py:meth", "pandas.DataFrame.loc"), ("py:class", "anndata._core.views.ArrayView"), ("py:class", "anndata._core.raw.Raw"), *[ ("py:class", f"anndata._core.aligned_mapping.{cls}{kind}") for cls in "Layers AxisArrays PairwiseArrays".split() for kind in ["", "View"] ], ] suppress_warnings = [ "ref.citation", "myst.header", # https://github.com/executablebooks/MyST-Parser/issues/262 ] def setup(app: Sphinx): # Don’t allow broken links. DO NOT CHANGE THIS LINE, fix problems instead. app.warningiserror = True intersphinx_mapping = dict( h5py=("https://docs.h5py.org/en/latest/", None), hdf5plugin=("https://hdf5plugin.readthedocs.io/en/latest/", None), loompy=("https://linnarssonlab.org/loompy/", None), numpy=("https://numpy.org/doc/stable/", None), pandas=("https://pandas.pydata.org/pandas-docs/stable/", None), python=("https://docs.python.org/3", None), scipy=("https://docs.scipy.org/doc/scipy/", None), sklearn=("https://scikit-learn.org/stable/", None), zarr=("https://zarr.readthedocs.io/en/stable/", None), xarray=("https://xarray.pydata.org/en/stable/", None), ) qualname_overrides = { "h5py._hl.group.Group": "h5py.Group", "h5py._hl.files.File": "h5py.File", "h5py._hl.dataset.Dataset": "h5py.Dataset", "anndata._core.anndata.AnnData": "anndata.AnnData", } # -- Social cards --------------------------------------------------------- ogp_site_url = "https://anndata.readthedocs.io/" ogp_image = "https://anndata.readthedocs.io/en/latest/_static/img/anndata_schema.svg" # -- Options for HTML output ---------------------------------------------- # 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': "1411", 'version_slug': "1411", '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': 'a3a042529d71e15bbae27df68073eaaa56d51216', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'a3a042529d71e15bbae27df68073eaaa56d51216', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'a3a042529d71e15bbae27df68073eaaa56d51216', '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': 'a3a04252', } # 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/1411' readthedocs_build_url = 'https://readthedocs.com/projects/icb-anndata/builds/2074855/' 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'])