Read the Docs build information Build id: 4598925 Project: icb-scanpy Version: 4160 Commit: d9611e21cb3057d60fd5ee105bf1f970210437e7 Date: 2026-10-20T16:21:27.148424Z State: cancelled Success: False [rtd-command-info] start-time: 2026-10-20T16:22:59.821041Z, end-time: 2026-10-20T16:23:02.596837Z, duration: 2, exit-code: 0 git clone --depth 1 https://github.com/scverse/scanpy.git . Cloning into '.'... [rtd-command-info] start-time: 2026-10-20T16:23:02.732873Z, end-time: 2026-10-20T16:23:05.297979Z, duration: 2, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 pull/4160/head:external-4160 From https://github.com/scverse/scanpy * [new ref] refs/pull/4160/head -> external-4160 * [new tag] 1.13.0a2 -> 1.13.0a2 [rtd-command-info] start-time: 2026-10-20T16:23:06.461527Z, end-time: 2026-10-20T16:23:06.724883Z, duration: 0, exit-code: 0 git checkout --force d9611e21cb3057d60fd5ee105bf1f970210437e7 Note: switching to 'd9611e21cb3057d60fd5ee105bf1f970210437e7'. 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 d9611e2 Merge branch 'main' into feature/normalize_clr [rtd-command-info] start-time: 2026-10-20T16:23:06.858340Z, end-time: 2026-10-20T16:23:06.890710Z, 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: 2026-10-20T16:23:07.049218Z, end-time: 2026-10-20T16:23:09.989649Z, 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: 2026-10-20T16:23:20.084016Z, end-time: 2026-10-20T16:23:20.215792Z, duration: 0, exit-code: 0 asdf global python 3.14.6 [rtd-command-info] start-time: 2026-10-20T16:23:20.846182Z, end-time: 2026-10-20T16:23:23.449094Z, duration: 2, 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: 2026-10-20T16:23:23.551397Z, end-time: 2026-10-20T16:23:24.313955Z, duration: 0, 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: 2026-10-20T16:23:24.399233Z, end-time: 2026-10-20T16:23:24.513516Z, 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: 2026-10-20T16:23:24.646693Z, end-time: 2026-10-20T16:23:31.290124Z, duration: 6, exit-code: 0 ( find docs/release-notes -regex '[^.]+[.][^.]+.md' | grep -q . ) && uvx hatch run towncrier build --keep || true Downloading pygments (1.2MiB) Downloading uv (16.4MiB) Downloading virtualenv (5.2MiB) Downloading cryptography (4.5MiB) Downloaded pygments Downloaded cryptography Downloaded virtualenv Downloaded uv Installed 43 packages in 15ms 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/4160/docs/release-notes/4329.fix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4160/docs/release-notes/4390.chore.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4160/docs/release-notes/4333.feat.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4160/docs/release-notes/4389.fix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4160/docs/release-notes/4298.fix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4160/docs/release-notes/4160.feat.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4160/docs/release-notes/4325.feat.md Done! [rtd-command-info] start-time: 2026-10-20T16:23:31.359642Z, end-time: 2026-10-20T16:23:36.546660Z, 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/zP4Y5Q_Y7_CXXvh6/bin/python Creating virtual environment at: /home/docs/.local/share/hatch/env/virtual/scanpy/bWgWxp9-/docs Installing project in development mode Using Python 3.14.6 environment at: /home/docs/.local/share/hatch/env/virtual/scanpy/bWgWxp9-/docs Resolved 59 packages in 428ms Building scanpy @ file:///home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4160 Built scanpy @ file:///home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4160 Prepared 1 package in 161ms Installed 59 packages in 87ms + 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==0.17.0 + 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.dev71+gd9611e21c.d20261020 (from file:///home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4160) + 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/bWgWxp9-/docs Updating https://github.com/scverse/anndata.git (HEAD) Updated https://github.com/scverse/anndata.git (1ec7ba8a9e44ee1eb9fe6756e01ee542666272f8) Resolved 182 packages in 2.27s Building scanpy @ file:///home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4160 Building anndata @ git+https://github.com/scverse/anndata.git@1ec7ba8a9e44ee1eb9fe6756e01ee542666272f8 Downloading debugpy (3.8MiB) Downloading accessible-pygments (1.3MiB) Downloading jedi (4.7MiB) Downloading babel (9.7MiB) Downloading sphinx-design (2.1MiB) Downloading plotly (9.2MiB) Downloading pyarrow (51.5MiB) Downloading dask (1.4MiB) Downloading pydata-sphinx-theme (5.9MiB) Downloading scikit-image (13.1MiB) Downloading holoviews (5.7MiB) Downloading sqlalchemy (4.4MiB) Downloading igraph (5.4MiB) Downloading colour-science (8.6MiB) Downloading bokeh (6.1MiB) Downloading panel-material-ui (1.7MiB) Downloading panel (28.9MiB) Downloading leidenalg (2.6MiB) Downloading sphinx (3.7MiB) Built scanpy @ file:///home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4160 Downloaded dask Downloaded accessible-pygments Downloaded panel-material-ui Built anndata @ git+https://github.com/scverse/anndata.git@1ec7ba8a9e44ee1eb9fe6756e01ee542666272f8 Downloaded sphinx-design Downloaded leidenalg Downloaded debugpy Downloaded sphinx Downloaded sqlalchemy Downloaded jedi Downloaded igraph Downloaded pydata-sphinx-theme Downloaded holoviews Downloaded bokeh Downloaded plotly Downloaded colour-science Downloaded babel Downloaded scikit-image Downloaded panel Downloaded pyarrow Prepared 117 packages in 1.04s Uninstalled 2 packages in 1ms Installed 125 packages in 396ms + 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.dev71+gd9611e21c.d20261020 (from file:///home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4160) + 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==9.1.1 + 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==1.0.1 + 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