Read the Docs build information Build id: 4167841 Project: icb-scanpy Version: 4188 Commit: b854ca62f76c1359a30cd304d97fda85f7ad02c1 Date: 2026-07-02T08:19:25.530952Z State: finished Success: False [rtd-command-info] start-time: 2026-07-02T08:19:38.313718Z, end-time: 2026-07-02T08:19:39.284726Z, duration: 0, exit-code: 0 git clone --depth 1 https://github.com/scverse/scanpy.git . Cloning into '.'... [rtd-command-info] start-time: 2026-07-02T08:19:39.366333Z, end-time: 2026-07-02T08:19:39.972597Z, duration: 0, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 pull/4188/head:external-4188 From https://github.com/scverse/scanpy * [new ref] refs/pull/4188/head -> external-4188 [rtd-command-info] start-time: 2026-07-02T08:19:40.814100Z, end-time: 2026-07-02T08:19:40.981583Z, duration: 0, exit-code: 0 git checkout --force b854ca62f76c1359a30cd304d97fda85f7ad02c1 Note: switching to 'b854ca62f76c1359a30cd304d97fda85f7ad02c1'. 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 b854ca6 Merge branch 'naked-base' into plotting [rtd-command-info] start-time: 2026-07-02T08:19:41.079099Z, end-time: 2026-07-02T08:19:41.119906Z, duration: 0, exit-code: 0 cat .readthedocs.yml # https://docs.readthedocs.io/en/stable/config-file/v2.html version: 2 submodules: include: all build: os: ubuntu-24.04 tools: python: '3.13' 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 run docs:build - mv docs/_build $READTHEDOCS_OUTPUT [rtd-command-info] start-time: 2026-07-02T08:19:41.241252Z, end-time: 2026-07-02T08:19:41.298123Z, duration: 0, exit-code: 0 git submodule sync [rtd-command-info] start-time: 2026-07-02T08:19:41.376804Z, end-time: 2026-07-02T08:20:02.933180Z, duration: 21, 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/4188/notebooks'... Submodule path 'notebooks': checked out 'ac0e94be9f36977400177dc940cbd8eac1d2297c' [rtd-command-info] start-time: 2026-07-02T08:20:03.014920Z, end-time: 2026-07-02T08:20:07.875418Z, 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] 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] 1.1a1 -> 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 Fetching submodule notebooks From https://github.com/scverse/scanpy-tutorials * branch 26e16f83387caef76abdd42afda3c7c13f7139f1 -> FETCH_HEAD [rtd-command-info] start-time: 2026-07-02T08:20:12.353296Z, end-time: 2026-07-02T08:20:12.413673Z, duration: 0, exit-code: 0 asdf global python 3.13.14 [rtd-command-info] start-time: 2026-07-02T08:20:12.749939Z, end-time: 2026-07-02T08:20:13.841377Z, duration: 1, exit-code: 0 asdf plugin add uv updating plugin repository...From https://github.com/asdf-vm/asdf-plugins 8e311ee..c0369a1 master -> origin/master * [new branch] dependabot/github_actions/actions/checkout-6 -> origin/dependabot/github_actions/actions/checkout-6 * [new branch] 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] dependabot/github_actions/asdf-vm/actions-4 -> origin/dependabot/github_actions/asdf-vm/actions-4 HEAD is now at c0369a1 feat: add yasm plugin (#1087) [rtd-command-info] start-time: 2026-07-02T08:20:13.915258Z, end-time: 2026-07-02T08:20:14.814704Z, duration: 0, exit-code: 0 asdf install uv latest redirect url: https://github.com/astral-sh/uv/releases/tag/0.11.26 * Downloading uv release 0.11.26... uv 0.11.26 installation was successful! [rtd-command-info] start-time: 2026-07-02T08:20:14.891970Z, end-time: 2026-07-02T08:20:15.001175Z, duration: 0, exit-code: 0 asdf global uv latest redirect url: https://github.com/astral-sh/uv/releases/tag/0.11.26 [rtd-command-info] start-time: 2026-07-02T08:20:15.145378Z, end-time: 2026-07-02T08:20:21.861961Z, duration: 6, exit-code: 0 ( find docs/release-notes -regex '[^.]+[.][^.]+.md' | grep -q . ) && uvx hatch run towncrier build --keep || true Downloading uv (25.0MiB) Downloading pygments (1.2MiB) Downloading cryptography (4.5MiB) Downloading virtualenv (4.3MiB) Downloaded uv Downloaded cryptography Downloaded virtualenv Downloaded pygments Installed 43 packages in 20ms 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/4188/docs/release-notes/4126.perf.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/4055.feat.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/4141.perf.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/4178.fix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/4184.fix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/3953.feat.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/4081.feat.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/4052.breaking.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/4037.feat.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/4081.perf.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/4010.chore.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/4013.perf.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/4147.perf.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/3983.feat.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/4142.fix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/4143.perf.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/4192.fix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/4112.fix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/4100.docs.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/4039.breaking.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/4036.perf.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/4079.docs.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/3999.feat.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/4017.feat.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/4062.perf.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/3984.breaking.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4188/docs/release-notes/4076.feat.md Done! [rtd-command-info] start-time: 2026-07-02T08:20:21.943405Z, end-time: 2026-07-02T08:22:39.085884Z, duration: 137, exit-code: 1 uvx hatch run docs:build Creating environment: docs Installing project in development mode Checking dependencies Syncing dependencies × Failed to download `harmonypy==2.0.0` ├─▶ Failed to extract archive: │ harmonypy-2.0.0-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl ├─▶ I/O operation failed during extraction ╰─▶ Failed to download distribution due to network timeout. Try increasing UV_HTTP_TIMEOUT (current value: 30s). hint: `harmonypy` (v2.0.0) was included because `sam-algorithm` (v1.0.2) depends on `harmonypy`