Read the Docs build information Build id: 2949950 Project: icb-scanpy Version: 1.11.x Commit: 80edaf008747191387e5f4a10e12acf2fe93d6ed Date: 2025-04-08T09:08:01.274444Z State: finished Success: False [rtd-command-info] start-time: 2025-04-08T09:08:02.135707Z, end-time: 2025-04-08T09:08:07.624783Z, duration: 5, exit-code: 0 git clone --depth 1 https://github.com/scverse/scanpy.git . Cloning into '.'... [rtd-command-info] start-time: 2025-04-08T09:08:07.684219Z, end-time: 2025-04-08T09:08:08.890927Z, duration: 1, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 refs/heads/1.11.x:refs/remotes/origin/1.11.x From https://github.com/scverse/scanpy * [new branch] 1.11.x -> origin/1.11.x * [new tag] 1.11.0 -> 1.11.0 * [new tag] 1.11.0rc1 -> 1.11.0rc1 * [new tag] 1.11.0rc2 -> 1.11.0rc2 * [new tag] 1.11.1 -> 1.11.1 [rtd-command-info] start-time: 2025-04-08T09:08:08.993209Z, end-time: 2025-04-08T09:08:09.154323Z, duration: 0, exit-code: 0 git checkout --force origin/1.11.x Note: switching to 'origin/1.11.x'. 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 80edaf0 Backport PR #3566: [pre-commit.ci] pre-commit autoupdate (#3569) [rtd-command-info] start-time: 2025-04-08T09:08:09.212067Z, end-time: 2025-04-08T09:08:09.251879Z, duration: 0, exit-code: 0 cat .readthedocs.yml version: 2 submodules: include: all build: os: ubuntu-24.04 tools: python: '3.12' jobs: post_checkout: # unshallow so version can be derived from tag - git fetch --unshallow || true pre_build: # run towncrier to preview the next version’s release notes - ( find docs/release-notes -regex '[^.]+[.][^.]+.md' | grep -q . ) && towncrier build --keep || true sphinx: fail_on_warning: true # do not change or you will be fired configuration: docs/conf.py python: install: - method: pip path: . extra_requirements: - doc - dev # for towncrier - leiden [rtd-command-info] start-time: 2025-04-08T09:08:09.354973Z, end-time: 2025-04-08T09:08:09.412038Z, duration: 0, exit-code: 0 git submodule sync [rtd-command-info] start-time: 2025-04-08T09:08:09.468767Z, end-time: 2025-04-08T09:08:23.781815Z, duration: 14, exit-code: 0 git submodule update --init --force -- Submodule 'notebooks' (https://github.com/scverse/scanpy-tutorials/) registered for path 'notebooks' Cloning into '/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.11.x/notebooks'... Submodule path 'notebooks': checked out '9f6926f87f052603916ee8f222965f654896e0c7' [rtd-command-info] start-time: 2025-04-08T09:08:23.850948Z, end-time: 2025-04-08T09:08:27.961273Z, duration: 4, exit-code: 0 git fetch --unshallow || true From https://github.com/scverse/scanpy * [new tag] 0.0 -> 0.0 * [new tag] 0.1 -> 0.1 * [new tag] 0.2 -> 0.2 * [new tag] 0.2.1 -> 0.2.1 * [new tag] 0.2.3 -> 0.2.3 * [new tag] 0.2.3.5 -> 0.2.3.5 * [new tag] 0.2.4 -> 0.2.4 * [new tag] 0.2.5 -> 0.2.5 * [new tag] 0.2.6 -> 0.2.6 * [new tag] 0.2.7 -> 0.2.7 * [new tag] 0.2.8 -> 0.2.8 * [new tag] 0.2.9 -> 0.2.9 * [new tag] 0.2.9.1 -> 0.2.9.1 * [new tag] 0.3 -> 0.3 * [new tag] 0.3.1 -> 0.3.1 * [new tag] 0.3.2 -> 0.3.2 * [new tag] 0.4 -> 0.4 * [new tag] 0.4.1 -> 0.4.1 * [new tag] 0.4.2 -> 0.4.2 * [new tag] 0.4.2.post1 -> 0.4.2.post1 * [new tag] 0.4.2.post2 -> 0.4.2.post2 * [new tag] 0.4.3 -> 0.4.3 * [new tag] 0.4.4 -> 0.4.4 * [new tag] 1.0 -> 1.0 * [new tag] 1.0.1 -> 1.0.1 * [new tag] 1.0.2 -> 1.0.2 * [new tag] 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tag] 1.8.0 -> 1.8.0 * [new tag] 1.8.0.dev0 -> 1.8.0.dev0 * [new tag] 1.9.0 -> 1.9.0 * [new tag] 1.9.0.dev0 -> 1.9.0.dev0 [rtd-command-info] start-time: 2025-04-08T09:08:32.165357Z, end-time: 2025-04-08T09:08:32.221568Z, duration: 0, exit-code: 0 asdf global python 3.12.7 [rtd-command-info] start-time: 2025-04-08T09:08:32.571790Z, end-time: 2025-04-08T09:08:33.392260Z, duration: 0, exit-code: 0 python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH created virtual environment CPython3.12.7.final.0-64 in 532ms creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1.11.x, 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: 2025-04-08T09:08:33.454169Z, end-time: 2025-04-08T09:08:42.796273Z, duration: 9, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip setuptools Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1.11.x/lib/python3.12/site-packages (23.1) Collecting pip Downloading pip-25.0.1-py3-none-any.whl (1.8 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.8/1.8 MB 8.6 MB/s eta 0:00:00 Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1.11.x/lib/python3.12/site-packages (67.6.1) Collecting setuptools Downloading setuptools-78.1.0-py3-none-any.whl (1.3 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.3/1.3 MB 17.1 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 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sphinxcontrib_devhelp-2.0.0-py3-none-any.whl (82 kB) Downloading sphinxcontrib_htmlhelp-2.1.0-py3-none-any.whl (98 kB) Downloading sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB) Downloading sphinxcontrib_qthelp-2.0.0-py3-none-any.whl (88 kB) Downloading sphinxcontrib_serializinghtml-2.0.0-py3-none-any.whl (92 kB) Downloading certifi-2025.1.31-py3-none-any.whl (166 kB) Downloading charset_normalizer-3.4.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (145 kB) Downloading idna-3.10-py3-none-any.whl (70 kB) Downloading MarkupSafe-3.0.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (23 kB) Downloading urllib3-2.3.0-py3-none-any.whl (128 kB) Installing collected packages: snowballstemmer, urllib3, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, roman-numerals-py, Pygments, packaging, MarkupSafe, imagesize, idna, docutils, charset-normalizer, certifi, babel, alabaster, requests, Jinja2, sphinx Successfully installed Jinja2-3.1.6 MarkupSafe-3.0.2 Pygments-2.19.1 alabaster-1.0.0 babel-2.17.0 certifi-2025.1.31 charset-normalizer-3.4.1 docutils-0.21.2 idna-3.10 imagesize-1.4.1 packaging-24.2 requests-2.32.3 roman-numerals-py-3.1.0 snowballstemmer-2.2.0 sphinx-8.2.3 sphinxcontrib-applehelp-2.0.0 sphinxcontrib-devhelp-2.0.0 sphinxcontrib-htmlhelp-2.1.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-2.0.0 sphinxcontrib-serializinghtml-2.0.0 urllib3-2.3.0 [rtd-command-info] start-time: 2025-04-08T09:08:50.144098Z, end-time: 2025-04-08T09:09:07.328145Z, duration: 17, exit-code: 1 python -m pip install --upgrade --upgrade-strategy only-if-needed --no-cache-dir .[doc,dev,leiden] Processing /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/1.11.x Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'done' Preparing metadata (pyproject.toml): started Preparing metadata (pyproject.toml): finished with status 'done' Collecting anndata>=0.8 (from scanpy==1.12.0.dev6+g80edaf00) Downloading anndata-0.11.4-py3-none-any.whl.metadata (9.3 kB) Collecting h5py>=3.7 (from scanpy==1.12.0.dev6+g80edaf00) Downloading h5py-3.13.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.5 kB) Collecting joblib (from scanpy==1.12.0.dev6+g80edaf00) Downloading joblib-1.4.2-py3-none-any.whl.metadata (5.4 kB) Collecting legacy-api-wrap>=1.4 (from scanpy==1.12.0.dev6+g80edaf00) Downloading legacy_api_wrap-1.4.1-py3-none-any.whl.metadata (2.1 kB) Collecting matplotlib>=3.7 (from scanpy==1.12.0.dev6+g80edaf00) Downloading matplotlib-3.10.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (11 kB) Collecting natsort (from scanpy==1.12.0.dev6+g80edaf00) Downloading natsort-8.4.0-py3-none-any.whl.metadata (21 kB) Collecting networkx>=2.7 (from scanpy==1.12.0.dev6+g80edaf00) Downloading networkx-3.4.2-py3-none-any.whl.metadata (6.3 kB) Collecting numba>=0.57 (from scanpy==1.12.0.dev6+g80edaf00) Downloading numba-0.61.0-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (2.8 kB) Collecting numpy>=1.24 (from scanpy==1.12.0.dev6+g80edaf00) Downloading numpy-2.2.4-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (62 kB) Requirement already satisfied: packaging>=21.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/1.11.x/lib/python3.12/site-packages (from scanpy==1.12.0.dev6+g80edaf00) (24.2) Collecting pandas>=1.5 (from scanpy==1.12.0.dev6+g80edaf00) Downloading pandas-2.2.3-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (89 kB) Collecting patsy!=1.0.0 (from scanpy==1.12.0.dev6+g80edaf00) Downloading patsy-1.0.1-py2.py3-none-any.whl.metadata (3.3 kB) Collecting pynndescent>=0.5 (from scanpy==1.12.0.dev6+g80edaf00) Downloading pynndescent-0.5.13-py3-none-any.whl.metadata (6.8 kB) Collecting scikit-learn<1.6.0,>=1.1 (from scanpy==1.12.0.dev6+g80edaf00) Downloading scikit_learn-1.5.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (13 kB) Collecting scipy>=1.8 (from scanpy==1.12.0.dev6+g80edaf00) Downloading scipy-1.15.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (61 kB) Collecting seaborn>=0.13 (from scanpy==1.12.0.dev6+g80edaf00) Downloading seaborn-0.13.2-py3-none-any.whl.metadata (5.4 kB) Collecting session-info2 (from scanpy==1.12.0.dev6+g80edaf00) Downloading session_info2-0.1.2-py3-none-any.whl.metadata (2.5 kB) Collecting statsmodels>=0.13 (from scanpy==1.12.0.dev6+g80edaf00) Downloading statsmodels-0.14.4-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (9.2 kB) Collecting tqdm (from scanpy==1.12.0.dev6+g80edaf00) Downloading tqdm-4.67.1-py3-none-any.whl.metadata (57 kB) Collecting typing-extensions (from scanpy==1.12.0.dev6+g80edaf00) Downloading typing_extensions-4.13.1-py3-none-any.whl.metadata (3.0 kB) Collecting umap-learn!=0.5.0,>=0.5 (from scanpy==1.12.0.dev6+g80edaf00) Downloading umap_learn-0.5.7-py3-none-any.whl.metadata (21 kB) Collecting hatch-vcs (from scanpy==1.12.0.dev6+g80edaf00) Downloading hatch_vcs-0.4.0-py3-none-any.whl.metadata (8.6 kB) Collecting pre-commit (from scanpy==1.12.0.dev6+g80edaf00) Downloading pre_commit-4.2.0-py2.py3-none-any.whl.metadata (1.3 kB) Collecting towncrier (from scanpy==1.12.0.dev6+g80edaf00) Downloading towncrier-24.8.0-py3-none-any.whl.metadata (4.2 kB) Collecting dask-ml (from scanpy==1.12.0.dev6+g80edaf00) Downloading dask_ml-2025.1.0-py3-none-any.whl.metadata (6.0 kB) Collecting dask<2024.8.0,>=2022.09.2 (from dask[array]<2024.8.0,>=2022.09.2; extra == "doc"->scanpy==1.12.0.dev6+g80edaf00) Downloading dask-2024.7.1-py3-none-any.whl.metadata (3.8 kB) Collecting igraph (from scanpy==1.12.0.dev6+g80edaf00) Downloading igraph-0.11.8-cp39-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.8 kB) Collecting ipython>=7.20 (from scanpy==1.12.0.dev6+g80edaf00) Downloading ipython-9.1.0-py3-none-any.whl.metadata (4.4 kB) Collecting myst-nb>=1 (from scanpy==1.12.0.dev6+g80edaf00) Downloading myst_nb-1.2.0-py3-none-any.whl.metadata (4.7 kB) Collecting myst-parser>=2 (from scanpy==1.12.0.dev6+g80edaf00) Downloading myst_parser-4.0.1-py3-none-any.whl.metadata (5.5 kB) Collecting nbsphinx>=0.9 (from scanpy==1.12.0.dev6+g80edaf00) Downloading nbsphinx-0.9.7-py3-none-any.whl.metadata (2.3 kB) Collecting readthedocs-sphinx-search (from scanpy==1.12.0.dev6+g80edaf00) Downloading readthedocs_sphinx_search-0.3.2-py3-none-any.whl.metadata (2.4 kB) INFO: pip is looking at multiple versions of scanpy[dev,doc,leiden] to determine which version is compatible with other requirements. This could take a while. ERROR: Could not find a version that satisfies the requirement sam-algorithm; extra == "doc" (from scanpy[dev,doc,leiden]) (from versions: none) ERROR: No matching distribution found for sam-algorithm; extra == "doc"