Read the Docs build information Build id: 4603603 Project: icb-scanpy Version: 4427 Commit: a9dd54be9de6f659cf4670ee40ee19848117c54c Date: 2026-10-21T09:23:31.275444Z State: cancelled Success: False [rtd-command-info] start-time: 2026-10-21T09:23:32.088040Z, end-time: 2026-10-21T09:23:34.751992Z, duration: 2, exit-code: 0 git clone --depth 1 https://github.com/scverse/scanpy.git . Cloning into '.'... [rtd-command-info] start-time: 2026-10-21T09:23:34.867440Z, end-time: 2026-10-21T09:23:37.427119Z, duration: 2, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 pull/4427/head:external-4427 From https://github.com/scverse/scanpy * [new ref] refs/pull/4427/head -> external-4427 * [new tag] 1.13.0a2 -> 1.13.0a2 [rtd-command-info] start-time: 2026-10-21T09:23:38.182790Z, end-time: 2026-10-21T09:23:38.473147Z, duration: 0, exit-code: 0 git checkout --force a9dd54be9de6f659cf4670ee40ee19848117c54c Note: switching to 'a9dd54be9de6f659cf4670ee40ee19848117c54c'. 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 a9dd54b perf: sample discarded counts in downsample_counts when keeping most of the data [rtd-command-info] start-time: 2026-10-21T09:23:38.609036Z, end-time: 2026-10-21T09:23:38.644950Z, duration: 0, exit-code: 0 cat .readthedocs.yml # https://docs.readthedocs.io/page/config-file/v2.html version: 2 build: os: ubuntu-26.04 tools: python: '3.14' jobs: post_checkout: # unshallow so version can be derived from tag - git fetch --unshallow || true create_environment: - asdf plugin add uv - asdf install uv latest - asdf global uv latest pre_build: # run towncrier to preview the next version’s release notes - ( find docs/release-notes -regex '[^.]+[.][^.]+.md' | grep -q . ) && uvx hatch run towncrier build --keep || true build: html: - uvx hatch -v env create docs - uvx hatch run docs:build -T - mv docs/_build $READTHEDOCS_OUTPUT [rtd-command-info] start-time: 2026-10-21T09:23:38.731511Z, end-time: 2026-10-21T09:23:41.595260Z, duration: 2, 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] 1.0.3 -> 1.0.3 * [new tag] 1.0.4 -> 1.0.4 * [new tag] 1.1 -> 1.1 * [new tag] 1.10.0.dev0 -> 1.10.0.dev0 * [new tag] 1.10.0rc1 -> 1.10.0rc1 * [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] 1.12.0 -> 1.12.0 * [new tag] 1.12.0rc1 -> 1.12.0rc1 * [new tag] 1.13.0a1 -> 1.13.0a1 * [new tag] 1.1a1 -> 1.1a1 * [new tag] 1.1a2 -> 1.1a2 * [new tag] 1.2.0 -> 1.2.0 * [new tag] 1.2.1 -> 1.2.1 * [new tag] 1.2.2 -> 1.2.2 * [new tag] 1.3 -> 1.3 * [new tag] 1.3.1 -> 1.3.1 * [new tag] 1.3.2 -> 1.3.2 * [new tag] 1.3.3 -> 1.3.3 * [new tag] 1.3.4 -> 1.3.4 * [new tag] 1.3.5 -> 1.3.5 * [new tag] 1.3.6 -> 1.3.6 * [new tag] 1.3.7 -> 1.3.7 * [new tag] 1.3.8 -> 1.3.8 * [new tag] 1.4 -> 1.4 * [new tag] 1.4.1 -> 1.4.1 * [new tag] 1.4.2 -> 1.4.2 * [new tag] 1.4.3 -> 1.4.3 * [new tag] 1.4.4 -> 1.4.4 * [new tag] 1.4.5 -> 1.4.5 * [new tag] 1.4.5.1 -> 1.4.5.1 * [new tag] 1.4.5.post1 -> 1.4.5.post1 * [new tag] 1.4.5.post2 -> 1.4.5.post2 * [new tag] 1.4.5.post3 -> 1.4.5.post3 * [new tag] 1.4.6 -> 1.4.6 * [new tag] 1.5.0 -> 1.5.0 * [new tag] 1.5.0a1 -> 1.5.0a1 * [new tag] 1.5.1 -> 1.5.1 * [new tag] 1.6.0 -> 1.6.0 * [new tag] 1.7.0rc1 -> 1.7.0rc1 * [new 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: 2026-10-21T09:23:46.022984Z, end-time: 2026-10-21T09:23:46.089581Z, duration: 0, exit-code: 0 asdf global python 3.14.6 [rtd-command-info] start-time: 2026-10-21T09:23:46.706813Z, end-time: 2026-10-21T09:23:47.921122Z, duration: 1, exit-code: 0 asdf plugin add uv updating plugin repository...From https://github.com/asdf-vm/asdf-plugins c0369a1..3715919 master -> origin/master 8f55a19..035221f dependabot/github_actions/actions/checkout-6 -> origin/dependabot/github_actions/actions/checkout-6 26de994..a1633cc dependabot/github_actions/amannn/action-semantic-pull-request-6.1.1 -> origin/dependabot/github_actions/amannn/action-semantic-pull-request-6.1.1 * [new branch] tb/remove-deleted-plugins -> origin/tb/remove-deleted-plugins HEAD is now at 3715919 feat: add elp plugin (#1089) [rtd-command-info] start-time: 2026-10-21T09:23:48.030510Z, end-time: 2026-10-21T09:23:49.350285Z, duration: 1, exit-code: 0 asdf install uv latest redirect url: https://github.com/astral-sh/uv/releases/tag/0.13.4 * Downloading uv release 0.13.4... uv 0.13.4 installation was successful! [rtd-command-info] start-time: 2026-10-21T09:23:49.428800Z, end-time: 2026-10-21T09:23:49.566404Z, duration: 0, exit-code: 0 asdf global uv latest redirect url: https://github.com/astral-sh/uv/releases/tag/0.13.4 [rtd-command-info] start-time: 2026-10-21T09:23:49.724841Z, end-time: 2026-10-21T09:23:54.469721Z, duration: 4, exit-code: 0 ( find docs/release-notes -regex '[^.]+[.][^.]+.md' | grep -q . ) && uvx hatch run towncrier build --keep || true Downloading virtualenv (5.3MiB) Downloading uv (16.4MiB) Downloading cryptography (4.5MiB) Downloading pygments (1.2MiB) Downloaded pygments Downloaded virtualenv Downloaded cryptography Downloaded uv Installed 43 packages in 18ms Creating environment: default Installing project in development mode Checking dependencies Syncing dependencies Loading template... Finding news fragments... Rendering news fragments... Writing to newsfile... Staging newsfile... Keeping the following files: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4427/docs/release-notes/4329.fix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4427/docs/release-notes/4390.chore.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4427/docs/release-notes/4333.feat.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4427/docs/release-notes/4389.fix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4427/docs/release-notes/4298.fix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4427/docs/release-notes/4325.feat.md Done! [rtd-command-info] start-time: 2026-10-21T09:23:54.612027Z, end-time: 2026-10-21T09:23:59.743712Z, duration: 5, exit-code: 0 uvx hatch -v env create docs Creating environment: docs Using CPython 3.14.6 interpreter at: /home/docs/.cache/uv/archive-v0/2gZFC8iF4uXVCOBU/bin/python Creating virtual environment at: /home/docs/.local/share/hatch/env/virtual/scanpy/_Vc6WOIU/docs Installing project in development mode Using Python 3.14.6 environment at: /home/docs/.local/share/hatch/env/virtual/scanpy/_Vc6WOIU/docs Resolved 59 packages in 482ms Building scanpy @ file:///home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4427 Built scanpy @ file:///home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4427 Prepared 1 package in 182ms Installed 59 packages in 98ms + anndata==0.13.4 + annotated-types==0.8.0 + array-api-compat==1.15.0 + certifi==2026.10.19 + charset-normalizer==3.5.2 + cloudpickle==3.1.2 + contourpy==1.4.0 + cycler==0.12.1 + donfig==0.8.1.post1 + fast-array-utils==1.5.1 + fonttools==4.67.0 + formulaic==1.2.2 + google-crc32c==1.9.0 + h5py==3.16.0 + idna==3.20 + interface-meta==2.0.1 + joblib==1.6.0 + kiwisolver==1.5.1 + legacy-api-wrap==1.5 + llvmlite==0.50.0 + matplotlib==3.11.2 + msgspec==0.22.0 + narwhals==2.27.1 + natsort==8.4.0 + networkx==3.7 + numba==0.68.0 + numcodecs==0.17.1 + numpy==2.5.4 + packaging==26.3 + pandas==3.0.6 + patsy==1.0.3 + pillow==13.0.0 + platformdirs==4.13.5 + pooch==1.9.0 + pydantic==2.14.1 + pydantic-core==2.50.1 + pydantic-settings==2.16.1 + pynndescent==0.6.0 + pyparsing==3.3.3 + python-dateutil==2.9.0.post0 + python-dotenv==1.2.4 + pyyaml==6.0.3 + requests==2.34.2 + scanpy==1.14.0.dev32+ga9dd54be9.d20261021 (from file:///home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4427) + scikit-learn==1.9.1 + scipy==1.18.1 + scverse-misc==0.1.7 + seaborn==0.13.2 + session-info2==0.4.2 + six==1.17.0 + statsmodels==0.15.0 + threadpoolctl==3.7.0 + tqdm==4.70.1 + typing-extensions==4.16.0 + typing-inspection==0.4.4 + umap-learn==0.5.12 + urllib3==2.8.0 + wrapt==2.5.1 + zarr==3.4.1 Checking dependencies Syncing dependencies Using Python 3.14.6 environment at: /home/docs/.local/share/hatch/env/virtual/scanpy/_Vc6WOIU/docs Updating https://github.com/scverse/anndata.git (HEAD) Updated https://github.com/scverse/anndata.git (1ec7ba8a9e44ee1eb9fe6756e01ee542666272f8) Resolved 182 packages in 1.95s Building scanpy @ file:///home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4427 Building anndata @ git+https://github.com/scverse/anndata.git@1ec7ba8a9e44ee1eb9fe6756e01ee542666272f8 Downloading jedi (4.7MiB) Downloading babel (9.7MiB) Downloading dask (1.4MiB) Downloading plotly (9.2MiB) Downloading pyarrow (51.5MiB) Downloading scikit-image (13.1MiB) Downloading bokeh (6.1MiB) Downloading sqlalchemy (4.4MiB) Downloading igraph (5.4MiB) Downloading sphinx-design (2.1MiB) Downloading colour-science (8.6MiB) Downloading holoviews (5.7MiB) Downloading debugpy (3.8MiB) Downloading panel-material-ui (1.7MiB) Downloading panel (28.9MiB) Downloading sphinx (3.7MiB) Downloading accessible-pygments (1.3MiB) Downloading leidenalg (2.6MiB) Downloading pydata-sphinx-theme (5.9MiB) Built scanpy @ file:///home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4427 Built anndata @ git+https://github.com/scverse/anndata.git@1ec7ba8a9e44ee1eb9fe6756e01ee542666272f8 Downloaded accessible-pygments Downloaded dask Downloaded panel-material-ui Downloaded sphinx-design Downloaded leidenalg Downloaded sphinx Downloaded debugpy Downloaded sqlalchemy Downloaded igraph Downloaded holoviews Downloaded pydata-sphinx-theme Downloaded jedi Downloaded bokeh Downloaded plotly Downloaded babel Downloaded colour-science Downloaded scikit-image Downloaded panel Downloaded pyarrow Prepared 117 packages in 1.01s Uninstalled 2 packages in 2ms Installed 125 packages in 475ms + accessible-pygments==0.0.5 + alabaster==1.0.0 - anndata==0.13.4 + anndata==0.14.0.dev79+g1ec7ba8a9 (from git+https://github.com/scverse/anndata.git@1ec7ba8a9e44ee1eb9fe6756e01ee542666272f8) + asttokens==3.0.2 + attrs==26.1.0 + babel==2.18.0 + beautifulsoup4==4.15.0 + bleach==6.4.0 + bokeh==3.9.2 + click==8.5.0 + colorcet==3.2.1 + colour-science==0.4.7 + comm==0.2.3 + dask==2026.8.0 + dask-glm==0.4.0 + dask-ml==2025.1.0 + debugpy==1.8.22 + defusedxml==0.7.1 + distributed==2026.8.0 + docutils==0.22.4 + executing==2.3.0 + fastjsonschema==2.22.2 + fsspec==2026.9.0 + holoviews==1.23.2 + hv-anndata==0.1.2 + igraph==1.0.0 + illico==0.6.0 + imageio==2.38.1 + imagesize==2.0.1 + importlib-metadata==9.0.1 + ipykernel==7.4.0 + ipython==9.17.1 + ipython-pygments-lexers==1.1.1 + jedi==0.20.1 + jinja2==3.1.6 + jsonschema==4.26.0 + jsonschema-specifications==2025.9.1 + jupyter-cache==1.0.1 + jupyter-client==8.10.0 + jupyter-core==5.9.1 + jupyterlab-pygments==0.3.0 + latexcodec==3.0.1 + lazy-loader==0.6 + leidenalg==0.12.0 + linkify-it-py==2.2.0 + locket==1.0.0 + loguru==0.7.3 + markdown==3.11.2 + markdown-it-py==4.2.0 + markupsafe==3.0.4 + matplotlib-inline==0.2.2 + mdit-py-plugins==0.6.1 + mdurl==0.1.2 + mistune==3.4.0 + msgpack==1.2.3 + multipledispatch==1.0.0 + myst-nb==1.4.0 + myst-parser==5.1.0 + nbclient==0.11.0 + nbconvert==7.17.2 + nbformat==5.11.1 + nbsphinx==0.9.8 + nest-asyncio2==1.7.4 + nh3==0.3.7 + pandocfilters==1.5.1 + panel==1.9.4 + panel-material-ui==0.16.5 + param==2.4.2 + parso==0.8.7 + partd==1.4.2 + pexpect==4.9.0 + plotly==7.1.0 + prompt-toolkit==3.0.53 + psutil==7.2.2 + ptyprocess==0.7.0 + pure-eval==0.2.4 + pyarrow==26.0.0 + pybtex==0.26.1 + pybtex-docutils==1.0.3 + pydata-sphinx-theme==0.23.0 + pydocstring-rs==0.4.1 + pygments==2.21.0 + pyviz-comms==3.0.6 + pyzmq==27.2.0 + referencing==0.37.0 + roman-numerals==4.1.0 + rpds-py==2026.9.1 ~ scanpy==1.14.0.dev32+ga9dd54be9.d20261021 (from file:///home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4427) + scikit-image==0.26.0 + scikit-misc==0.5.3 + scverse-doc==0.2.3 + snowballstemmer==3.1.1 + sortedcontainers==2.4.0 + soupsieve==3.0.3 + sparse==0.19.2 + sphinx==9.2.0 + sphinx-autodoc-typehints==3.17.2 + sphinx-copybutton==0.5.2 + sphinx-design==0.7.0 + sphinx-exec-jupyter==0.4.3 + sphinx-issues==6.0.0 + sphinxcontrib-applehelp==2.0.0 + sphinxcontrib-bibtex==2.7.0 + sphinxcontrib-devhelp==2.0.0 + sphinxcontrib-htmlhelp==2.1.0 + sphinxcontrib-jsmath==2.0.0 + sphinxcontrib-katex==0.9.11 + sphinxcontrib-qthelp==2.0.0 + sphinxcontrib-serializinghtml==2.0.0 + sphinxext-opengraph==0.13.0 + sqlalchemy==2.1.5 + stack-data==0.6.3 + tabulate==0.10.0 + tblib==3.2.2 + texttable==1.7.2 + tifffile==2026.10.15 + tinycss2==1.5.1 + toolz==1.2.0 + tornado==6.5.10 + traitlets==5.16.1 + wcwidth==0.9.3 + webencodings==0.6.1 + xyzservices==2026.9.1 + zict==3.0.0 + zipp==4.1.1 [rtd-command-info] start-time: None, end-time: None, duration: None, exit-code: None uvx hatch run docs:build -T