Read the Docs build information Build id: 4609591 Project: icb-scanpy Version: latest Commit: bae52db8a4e01682c0b73cb3568ab47f1981327c Date: 2026-10-22T05:49:57.461969Z State: cancelled Success: False [rtd-command-info] start-time: 2026-10-22T05:49:58.315039Z, end-time: 2026-10-22T05:50:00.689634Z, duration: 2, exit-code: 0 git clone --depth 1 https://github.com/scverse/scanpy.git . Cloning into '.'... [rtd-command-info] start-time: 2026-10-22T05:50:00.777889Z, end-time: 2026-10-22T05:50:02.618774Z, duration: 1, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 HEAD From https://github.com/scverse/scanpy * branch HEAD -> FETCH_HEAD [rtd-command-info] start-time: 2026-10-22T05:50:03.248635Z, end-time: 2026-10-22T05:50:03.284328Z, 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: 2026-10-22T05:50:03.712971Z, end-time: 2026-10-22T05:50:06.333028Z, duration: 2, exit-code: 0 git fetch --unshallow || true From https://github.com/scverse/scanpy * [new tag] 1.13.0a2 -> 1.13.0a2 * [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: 2026-10-22T05:50:10.521418Z, end-time: 2026-10-22T05:50:10.583229Z, duration: 0, exit-code: 0 asdf global python 3.14.6 [rtd-command-info] start-time: 2026-10-22T05:50:11.071978Z, end-time: 2026-10-22T05:50:11.939248Z, 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: 2026-10-22T05:50:12.010119Z, end-time: 2026-10-22T05:50:12.901076Z, duration: 0, 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: 2026-10-22T05:50:12.981409Z, end-time: 2026-10-22T05:50:13.222005Z, 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: 2026-10-22T05:50:13.360747Z, end-time: 2026-10-22T05:50:18.711392Z, duration: 5, exit-code: 0 ( find docs/release-notes -regex '[^.]+[.][^.]+.md' | grep -q . ) && uvx hatch run towncrier build --keep || true Downloading pygments (1.2MiB) Downloading virtualenv (5.3MiB) Downloading uv (16.4MiB) Downloading cryptography (4.5MiB) Downloaded pygments Downloaded virtualenv Downloaded cryptography Downloaded uv Installed 43 packages in 19ms 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/latest/docs/release-notes/4329.fix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/release-notes/4390.chore.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/release-notes/4333.feat.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/release-notes/4389.fix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/release-notes/4298.fix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/release-notes/4325.feat.md Done! [rtd-command-info] start-time: 2026-10-22T05:50:18.788745Z, end-time: 2026-10-22T05:50:24.400414Z, 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/kxuHAfitgnQkNy6x/bin/python Creating virtual environment at: /home/docs/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs Installing project in development mode Using Python 3.14.6 environment at: /home/docs/.local/share/hatch/env/virtual/scanpy/T0JdXacZ/docs Resolved 60 packages in 499ms Building scanpy @ file:///home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest Built scanpy @ file:///home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest Prepared 1 package in 189ms Installed 60 packages in 77ms + 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==3.0.0 + python-dotenv==1.2.4 + pyyaml==6.0.3 + requests==2.34.2 + scanpy==1.14.0.dev32+gbae52db8a.d20261022 (from file:///home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest) + 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/T0JdXacZ/docs Updating https://github.com/scverse/anndata.git (HEAD) Updated https://github.com/scverse/anndata.git (1f3abab80926d8be7f1b4944bcf6f46ed9ee3291) Resolved 183 packages in 2.24s Building scanpy @ file:///home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest Building anndata @ git+https://github.com/scverse/anndata.git@1f3abab80926d8be7f1b4944bcf6f46ed9ee3291 Downloading pyarrow (51.5MiB) Downloading accessible-pygments (1.3MiB) Downloading plotly (9.2MiB) Downloading panel-material-ui (1.7MiB) Downloading babel (9.7MiB) Downloading colour-science (8.6MiB) Downloading leidenalg (2.6MiB) Downloading sphinx-design (2.1MiB) Downloading holoviews (5.7MiB) Downloading jedi (4.7MiB) Downloading igraph (5.4MiB) Downloading sphinx (3.7MiB) Downloading dask (1.4MiB) Downloading panel (28.9MiB) Downloading pydata-sphinx-theme (5.9MiB) Downloading bokeh (6.1MiB) Downloading scikit-image (13.1MiB) Downloading debugpy (3.8MiB) Downloading sqlalchemy (4.4MiB) Downloaded accessible-pygments Downloaded dask Downloaded panel-material-ui Built anndata @ git+https://github.com/scverse/anndata.git@1f3abab80926d8be7f1b4944bcf6f46ed9ee3291 Built scanpy @ file:///home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest Downloaded sphinx-design Downloaded leidenalg Downloaded sphinx Downloaded debugpy Downloaded sqlalchemy Downloaded igraph Downloaded holoviews Downloaded jedi Downloaded pydata-sphinx-theme Downloaded bokeh Downloaded plotly Downloaded colour-science Downloaded babel Downloaded scikit-image Downloaded panel Downloaded pyarrow Prepared 117 packages in 1.34s Uninstalled 2 packages in 1ms Installed 125 packages in 403ms + accessible-pygments==0.0.5 + alabaster==1.0.0 - anndata==0.13.4 + anndata==0.14.0.dev80+g1f3abab80 (from git+https://github.com/scverse/anndata.git@1f3abab80926d8be7f1b4944bcf6f46ed9ee3291) + 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+gbae52db8a.d20261022 (from file:///home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest) + scikit-image==0.26.0 + scikit-misc==0.5.3 + scverse-doc==0.2.4 + 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