Read the Docs build information Build id: 4314617 Project: icb-scanpy Version: 4293 Commit: ff691713028c45a1ae3aebbd91662070ea14abe1 Date: 2026-08-13T11:39:14.009161Z State: finished Success: False [rtd-command-info] start-time: 2026-08-13T11:39:14.746221Z, end-time: 2026-08-13T11:39:18.736088Z, duration: 3, exit-code: 0 git clone --depth 1 https://github.com/scverse/scanpy.git . Cloning into '.'... [rtd-command-info] start-time: 2026-08-13T11:39:18.813231Z, end-time: 2026-08-13T11:39:20.223668Z, duration: 1, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 pull/4293/head:external-4293 From https://github.com/scverse/scanpy * [new ref] refs/pull/4293/head -> external-4293 * [new tag] 1.13.0a1 -> 1.13.0a1 [rtd-command-info] start-time: 2026-08-13T11:39:20.880925Z, end-time: 2026-08-13T11:39:21.199786Z, duration: 0, exit-code: 0 git checkout --force ff691713028c45a1ae3aebbd91662070ea14abe1 Note: switching to 'ff691713028c45a1ae3aebbd91662070ea14abe1'. 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 ff69171 docs: use working hatch version [rtd-command-info] start-time: 2026-08-13T11:39:21.282043Z, end-time: 2026-08-13T11:39:21.320551Z, duration: 0, exit-code: 0 cat .readthedocs.yml # https://docs.readthedocs.io/en/stable/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 --from=hatch!=1.18.0 hatch run docs:build -T - mv docs/_build $READTHEDOCS_OUTPUT [rtd-command-info] start-time: 2026-08-13T11:39:21.414647Z, end-time: 2026-08-13T11:39:24.369009Z, 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] 1.1a1 -> 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: 2026-08-13T11:39:29.105440Z, end-time: 2026-08-13T11:39:29.172124Z, duration: 0, exit-code: 0 asdf global python 3.14.6 [rtd-command-info] start-time: 2026-08-13T11:39:29.710876Z, end-time: 2026-08-13T11:39:31.352557Z, duration: 1, 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: 2026-08-13T11:39:31.432123Z, end-time: 2026-08-13T11:39:32.573295Z, duration: 1, exit-code: 0 asdf install uv latest redirect url: https://github.com/astral-sh/uv/releases/tag/0.12.3 * Downloading uv release 0.12.3... uv 0.12.3 installation was successful! [rtd-command-info] start-time: 2026-08-13T11:39:32.651438Z, end-time: 2026-08-13T11:39:32.771327Z, duration: 0, exit-code: 0 asdf global uv latest redirect url: https://github.com/astral-sh/uv/releases/tag/0.12.3 [rtd-command-info] start-time: 2026-08-13T11:39:32.901828Z, end-time: 2026-08-13T11:39:39.949251Z, duration: 7, exit-code: 0 ( find docs/release-notes -regex '[^.]+[.][^.]+.md' | grep -q . ) && uvx hatch run towncrier build --keep || true Downloading pygments (1.2MiB) Downloading uv (21.3MiB) Downloading virtualenv (5.1MiB) Downloading cryptography (4.5MiB) Downloaded virtualenv Downloaded cryptography Downloaded pygments Downloaded uv Installed 42 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/4293/docs/release-notes/4260.fix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4293/docs/release-notes/4263.fix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4293/docs/release-notes/4231.fix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4293/docs/release-notes/4232.feat.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4293/docs/release-notes/4252.fix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4293/docs/release-notes/4256.fix.md /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/4293/docs/release-notes/4269.feat.md Done! [rtd-command-info] start-time: 2026-08-13T11:39:40.030353Z, end-time: 2026-08-13T11:39:53.180571Z, duration: 13, exit-code: 1 uvx --from=hatch!=1.18.0 hatch run docs:build -T Installed 42 packages in 17ms Creating environment: docs Installing project in development mode Checking dependencies Syncing dependencies × Failed to build `harmonypy==2.0.0` ├─▶ The build backend returned an error ╰─▶ Call to `scikit_build_core.build.build_wheel` failed (exit status: 1) [stdout] *** scikit-build-core 1.0.3 using CMake 4.4.2 (wheel) *** Configuring CMake... loading initial cache file /tmp/harmonypy-build/cp314-cp314-linux_x86_64/CMakeInit.txt -- The CXX compiler identification is GNU 15.2.0 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Python: /home/docs/.cache/uv/builds-v0/.tmpfQh6U1/bin/python (found suitable version "3.14.6", minimum required is "3.9") found components: Interpreter Development.Module Development.SABIModule -- Performing Test NB_HAS_MTLS_GNU2 -- Performing Test NB_HAS_MTLS_GNU2 - Success -- System Armadillo not found, fetching headers... -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Configuring incomplete, errors occurred! [stderr] CMake Warning (author) at /home/docs/.cache/uv/builds-v0/.tmpfQh6U1/lib/python3.14/site-packages/cmake/data/share/cmake-4.4/Modules/FetchContent.cmake:1968 (message): Calling FetchContent_Populate(armadillo) is deprecated, call FetchContent_MakeAvailable(armadillo) instead. Policy CMP0169 can be set to OLD to allow FetchContent_Populate(armadillo) to be called directly for now, but the ability to call it with declared details will be removed completely in a future version. Call Stack (most recent call first): CMakeLists.txt:33 (FetchContent_Populate) This warning is for project developers. Use -Wno-author to suppress it. CMake Error at /home/docs/.cache/uv/builds-v0/.tmpfQh6U1/lib/python3.14/site-packages/cmake/data/share/cmake-4.4/Modules/FindPackageHandleStandardArgs.cmake:290 (message): Could NOT find BLAS (missing: BLAS_LIBRARIES) Call Stack (most recent call first): /home/docs/.cache/uv/builds-v0/.tmpfQh6U1/lib/python3.14/site-packages/cmake/data/share/cmake-4.4/Modules/FindPackageHandleStandardArgs.cmake:654 (_FPHSA_FAILURE_MESSAGE) /home/docs/.cache/uv/builds-v0/.tmpfQh6U1/lib/python3.14/site-packages/cmake/data/share/cmake-4.4/Modules/FindBLAS.cmake:1509 (find_package_handle_standard_args) CMakeLists.txt:65 (find_package) *** CMake configuration failed hint: `harmonypy` (v2.0.0) was included because `sam-algorithm` (v1.0.2) depends on `harmonypy` hint: Build failures usually indicate a problem with the package or the build environment