Read the Docs build information Build id: 3968676 Project: icb-scanpy Version: 4096 Commit: d51930c70cb8ba47c53f3c794cb18d7a6fd774d2 Date: 2026-04-28T14:19:36.292202Z State: finished Success: False [rtd-command-info] start-time: 2026-04-28T14:19:37.057619Z, end-time: 2026-04-28T14:19:38.786799Z, duration: 1, exit-code: 0 git clone --depth 1 https://github.com/scverse/scanpy.git . Cloning into '.'... [rtd-command-info] start-time: 2026-04-28T14:19:38.873444Z, end-time: 2026-04-28T14:19:39.483378Z, duration: 0, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 pull/4096/head:external-4096 From https://github.com/scverse/scanpy * [new ref] refs/pull/4096/head -> external-4096 [rtd-command-info] start-time: 2026-04-28T14:19:40.136011Z, end-time: 2026-04-28T14:19:40.273813Z, duration: 0, exit-code: 0 git checkout --force d51930c70cb8ba47c53f3c794cb18d7a6fd774d2 Note: switching to 'd51930c70cb8ba47c53f3c794cb18d7a6fd774d2'. 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 d51930c chore: use scverse-misc’s `@deprecated` [rtd-command-info] start-time: 2026-04-28T14:19:40.364276Z, end-time: 2026-04-28T14:19:40.398405Z, 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: 2026-04-28T14:19:40.515412Z, end-time: 2026-04-28T14:19:40.622494Z, duration: 0, exit-code: 0 git submodule sync [rtd-command-info] start-time: 2026-04-28T14:19:40.707884Z, end-time: 2026-04-28T14:20:01.359826Z, duration: 20, 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/4096/notebooks'... Submodule path 'notebooks': checked out '33dcb2d93b4686f313019f52705d5c752b37fc4e' [rtd-command-info] start-time: 2026-04-28T14:20:01.457454Z, end-time: 2026-04-28T14:20:05.801352Z, 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: 2026-04-28T14:20:10.799050Z, end-time: 2026-04-28T14:20:10.861786Z, duration: 0, exit-code: 0 asdf global python 3.13.3 [rtd-command-info] start-time: 2026-04-28T14:20:11.261320Z, end-time: 2026-04-28T14:20:12.779389Z, 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: 2026-04-28T14:20:12.868427Z, end-time: 2026-04-28T14:20:13.754609Z, duration: 0, exit-code: 0 asdf install uv latest redirect url: https://github.com/astral-sh/uv/releases/tag/0.11.8 * Downloading uv release 0.11.8... uv 0.11.8 installation was successful! [rtd-command-info] start-time: 2026-04-28T14:20:13.839649Z, end-time: 2026-04-28T14:20:13.955200Z, duration: 0, exit-code: 0 asdf global uv latest redirect url: https://github.com/astral-sh/uv/releases/tag/0.11.8 [rtd-command-info] start-time: 2026-04-28T14:20:14.114727Z, end-time: 2026-04-28T14:20:19.679554Z, duration: 5, exit-code: 0 ( find docs/release-notes -regex '[^.]+[.][^.]+.md' | grep -q . ) && uvx hatch run towncrier build --keep || true Downloading cryptography (4.5MiB) Downloading virtualenv (7.2MiB) Downloading uv (23.7MiB) Downloading pygments (1.2MiB) Downloaded virtualenv Downloaded cryptography Downloaded uv Downloaded pygments Installed 42 packages in 25ms 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/4096/docs/release-notes/4079.docs.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4096/docs/release-notes/4052.breaking.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4096/docs/release-notes/4055.feat.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4096/docs/release-notes/4010.chore.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4096/docs/release-notes/4036.perf.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4096/docs/release-notes/4017.feat.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4096/docs/release-notes/3984.breaking.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4096/docs/release-notes/3983.feat.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4096/docs/release-notes/4039.breaking.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4096/docs/release-notes/4062.perf.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4096/docs/release-notes/3999.feat.md Done! [rtd-command-info] start-time: 2026-04-28T14:20:19.769670Z, end-time: 2026-04-28T14:20:53.031860Z, duration: 33, exit-code: 2 uvx hatch run docs:build Creating environment: docs Installing project in development mode Checking dependencies Syncing dependencies Running Sphinx v9.1.0 loading translations [en]... done /home/docs/.local/share/hatch/env/virtual/scanpy/hOj5ZzCY/docs/lib/python3.13/site-packages/numcodecs/__init__.py:129: UserWarning: NumPy version >= 2.0.0 detected. The zfpy library is incompatible with this version of NumPy. Please downgrade to NumPy < 2.0.0 or wait for an update from zfpy. from numcodecs.zfpy import ZFPY Versions ======== * Platform: linux; (Linux-6.17.0-1007-aws-x86_64-with-glibc2.39) * Python version: 3.13.3 (CPython) * Sphinx version: 9.1.0 * Docutils version: 0.22.4 * Jinja2 version: 3.1.6 * Pygments version: 2.20.0 Last Messages ============= None. Loaded Extensions ================= None. Traceback ========= File "/home/docs/.local/share/hatch/env/virtual/scanpy/hOj5ZzCY/docs/lib/python3.13/site-packages/scverse_misc/_deprecated.py", line 60, in decorate docmsg = f".. version-deprecated:: {msg.version_deprecated}" ^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'str' object has no attribute 'version_deprecated' The full traceback has been saved in: /tmp/sphinx-err-45sifw77.log To report this error to the developers, please open an issue at . Thanks! Please also report this if it was a user error, so that a better error message can be provided next time.