Read the Docs build information Build id: 4613130 Project: icb-scanpy Version: 4431 Commit: 519d578e86d969ef1c5d2aa42c661aaf968f538a Date: 2026-10-22T17:53:50.776173Z State: cancelled Success: False [rtd-command-info] start-time: 2026-10-22T17:54:11.951884Z, end-time: 2026-10-22T17:54:14.622090Z, duration: 2, exit-code: 0 git clone --depth 1 https://github.com/scverse/scanpy.git . Cloning into '.'... [rtd-command-info] start-time: 2026-10-22T17:54:14.695268Z, end-time: 2026-10-22T17:54:17.211440Z, duration: 2, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 pull/4431/head:external-4431 From https://github.com/scverse/scanpy * [new ref] refs/pull/4431/head -> external-4431 * [new tag] 1.13.0a2 -> 1.13.0a2 [rtd-command-info] start-time: 2026-10-22T17:54:17.944439Z, end-time: 2026-10-22T17:54:18.319419Z, duration: 0, exit-code: 0 git checkout --force 519d578e86d969ef1c5d2aa42c661aaf968f538a Note: switching to '519d578e86d969ef1c5d2aa42c661aaf968f538a'. 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 519d578 Name the release note after the PR number [rtd-command-info] start-time: 2026-10-22T17:54:18.445681Z, end-time: 2026-10-22T17:54:18.484392Z, 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: 2026-10-22T17:54:18.583233Z, end-time: 2026-10-22T17:54:21.381390Z, 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: 2026-10-22T17:54:25.593027Z, end-time: 2026-10-22T17:54:25.660640Z, duration: 0, exit-code: 0 asdf global python 3.14.6 [rtd-command-info] start-time: 2026-10-22T17:54:26.188211Z, end-time: 2026-10-22T17:54:27.146732Z, duration: 0, exit-code: 0 asdf plugin add uv updating plugin repository...HEAD is now at 3715919 feat: add elp plugin (#1089) [rtd-command-info] start-time: 2026-10-22T17:54:27.230090Z, end-time: 2026-10-22T17:54:28.242615Z, duration: 1, exit-code: 0 asdf install uv latest redirect url: https://github.com/astral-sh/uv/releases/tag/0.13.5 * Downloading uv release 0.13.5... uv 0.13.5 installation was successful! [rtd-command-info] start-time: 2026-10-22T17:54:28.339155Z, end-time: 2026-10-22T17:54:28.478552Z, duration: 0, exit-code: 0 asdf global uv latest redirect url: https://github.com/astral-sh/uv/releases/tag/0.13.5 [rtd-command-info] start-time: 2026-10-22T17:54:28.640513Z, end-time: 2026-10-22T17:54:33.942753Z, duration: 5, 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 pygments (1.2MiB) Downloading cryptography (4.5MiB) Downloaded pygments Downloaded virtualenv Downloaded cryptography Downloaded uv Installed 43 packages in 17ms 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/4431/docs/release-notes/4329.fix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4431/docs/release-notes/4390.chore.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4431/docs/release-notes/4431.fix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4431/docs/release-notes/4333.feat.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4431/docs/release-notes/4389.fix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4431/docs/release-notes/4298.fix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4431/docs/release-notes/4325.feat.md Done! [rtd-command-info] start-time: 2026-10-22T17:54:34.028529Z, end-time: 2026-10-22T17:54:39.858276Z, 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/sl7NJ6NT_ZIEihJp/bin/python Creating virtual environment at: /home/docs/.local/share/hatch/env/virtual/scanpy/1Ik9Aq1v/docs Installing project in development mode Using Python 3.14.6 environment at: /home/docs/.local/share/hatch/env/virtual/scanpy/1Ik9Aq1v/docs Resolved 60 packages in 522ms Building scanpy @ file:///home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4431 Built scanpy @ file:///home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4431 Prepared 1 package in 201ms Installed 60 packages in 84ms + 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==3.1.0 + 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==3.0.0 + python-dotenv==1.2.4 + pyyaml==6.0.3 + requests==2.34.2 + scanpy==1.14.0.dev35+g519d578e8.d20261022 (from file:///home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4431) + 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 + tzdata==2026.5 + 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/1Ik9Aq1v/docs Updating https://github.com/scverse/anndata.git (HEAD) Updated https://github.com/scverse/anndata.git (4783f4f1f521604103899c5e12cb228cc0689e67) Resolved 183 packages in 2.23s Building scanpy @ file:///home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4431 Building anndata @ git+https://github.com/scverse/anndata.git@4783f4f1f521604103899c5e12cb228cc0689e67 Downloading accessible-pygments (1.3MiB) Downloading dask (1.4MiB) Downloading igraph (5.4MiB) Downloading leidenalg (2.6MiB) Downloading jedi (4.7MiB) Downloading sphinx (3.7MiB) Downloading pyarrow (51.5MiB) Downloading debugpy (3.8MiB) Downloading plotly (9.2MiB) Downloading babel (9.7MiB) Downloading sqlalchemy (4.4MiB) Downloading holoviews (5.7MiB) Downloading scikit-image (13.1MiB) Downloading colour-science (8.6MiB) Downloading sphinx-design (2.1MiB) Downloading panel (28.9MiB) Downloading bokeh (6.1MiB) Downloading pydata-sphinx-theme (5.9MiB) Downloading panel-material-ui (1.7MiB) Built scanpy @ file:///home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4431 Built anndata @ git+https://github.com/scverse/anndata.git@4783f4f1f521604103899c5e12cb228cc0689e67 Downloaded dask Downloaded accessible-pygments Downloaded panel-material-ui Downloaded sphinx-design Downloaded leidenalg Downloaded debugpy Downloaded sqlalchemy Downloaded sphinx Downloaded igraph Downloaded pydata-sphinx-theme Downloaded holoviews Downloaded bokeh Downloaded jedi Downloaded colour-science Downloaded plotly Downloaded babel Downloaded scikit-image Downloaded panel Downloaded pyarrow Prepared 117 packages in 1.39s Uninstalled 2 packages in 1ms Installed 125 packages in 418ms + accessible-pygments==0.0.5 + alabaster==1.0.0 - anndata==0.13.4 + anndata==0.14.0.dev81+g4783f4f1f (from git+https://github.com/scverse/anndata.git@4783f4f1f521604103899c5e12cb228cc0689e67) + 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==0.16.6 + 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.dev35+g519d578e8.d20261022 (from file:///home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4431) + scikit-image==0.26.0 + scikit-misc==0.5.3 + scverse-doc==0.3.0 + snowballstemmer==3.1.1 + sortedcontainers==2.4.0 + soupsieve==3.0.4 + 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==2.1.6 + 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==6.6 + traitlets==5.16.1 + wcwidth==0.9.3 + webencodings==0.6.1 + xyzservices==2026.9.1 + zict==3.0.0 + zipp==4.1.2 [rtd-command-info] start-time: None, end-time: None, duration: None, exit-code: None uvx hatch run docs:build -T