Read the Docs build information Build id: 2496429 Project: icb-scanpy Version: 3206 Commit: e4c45ed3303616ac06e41b46d329ad6746208685 Date: 2024-09-20T13:13:16.173677Z State: cancelled Success: False [rtd-command-info] start-time: 2024-09-20T13:13:17.313443Z, end-time: 2024-09-20T13:13:18.399022Z, duration: 1, exit-code: 0 git clone --depth 1 https://github.com/scverse/scanpy.git . Cloning into '.'... [rtd-command-info] start-time: 2024-09-20T13:13:18.481859Z, end-time: 2024-09-20T13:13:19.070543Z, duration: 0, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 pull/3206/head:external-3206 From https://github.com/scverse/scanpy * [new ref] refs/pull/3206/head -> external-3206 [rtd-command-info] start-time: 2024-09-20T13:13:19.206574Z, end-time: 2024-09-20T13:13:19.417894Z, duration: 0, exit-code: 0 git checkout --force e4c45ed3303616ac06e41b46d329ad6746208685 Note: switching to 'e4c45ed3303616ac06e41b46d329ad6746208685'. 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 e4c45ed Merge branch 'main' into fix-style [rtd-command-info] start-time: 2024-09-20T13:13:19.484744Z, end-time: 2024-09-20T13:13:19.548435Z, duration: 0, exit-code: 0 cat .readthedocs.yml version: 2 submodules: include: all build: os: ubuntu-24.04 tools: python: '3.12' jobs: post_checkout: # unshallow so version can be derived from tag - git fetch --unshallow || true pre_build: # run towncrier to preview the next version’s release notes - ( find docs/release-notes -regex '[^.]+[.][^.]+.md' | grep -q . ) && towncrier build --keep || true sphinx: fail_on_warning: true # do not change or you will be fired configuration: docs/conf.py python: install: - method: pip path: . extra_requirements: - doc - dev # for towncrier - leiden [rtd-command-info] start-time: 2024-09-20T13:13:19.676610Z, end-time: 2024-09-20T13:13:19.763024Z, duration: 0, exit-code: 0 git submodule sync [rtd-command-info] start-time: 2024-09-20T13:13:19.828990Z, end-time: 2024-09-20T13:13:34.159046Z, duration: 14, 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/3206/notebooks'... Submodule path 'notebooks': checked out '3385df77ce0f63987104bc644562a811c5d1b441' [rtd-command-info] start-time: 2024-09-20T13:13:34.231464Z, end-time: 2024-09-20T13:13:37.845842Z, duration: 3, 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] 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2024-09-20T13:13:52.137983Z, end-time: 2024-09-20T13:14:04.483666Z, duration: 12, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip setuptools Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3206/lib/python3.12/site-packages (23.1) Collecting pip Downloading pip-24.2-py3-none-any.whl (1.8 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.8/1.8 MB 31.4 MB/s eta 0:00:00 Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/3206/lib/python3.12/site-packages (67.6.1) Collecting setuptools Downloading setuptools-75.1.0-py3-none-any.whl (1.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 141.9 MB/s eta 0:00:00 Installing collected packages: setuptools, pip Attempting uninstall: setuptools Found existing installation: setuptools 67.6.1 Uninstalling setuptools-67.6.1: Successfully uninstalled setuptools-67.6.1 Attempting uninstall: pip Found existing installation: 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requests, Jinja2, sphinx, readthedocs-sphinx-ext Successfully installed Jinja2-3.1.4 MarkupSafe-2.1.5 Pygments-2.18.0 alabaster-1.0.0 babel-2.16.0 certifi-2024.8.30 charset-normalizer-3.3.2 docutils-0.21.2 idna-3.10 imagesize-1.4.1 packaging-24.1 readthedocs-sphinx-ext-2.2.5 requests-2.32.3 snowballstemmer-2.2.0 sphinx-8.0.2 sphinxcontrib-applehelp-2.0.0 sphinxcontrib-devhelp-2.0.0 sphinxcontrib-htmlhelp-2.1.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-2.0.0 sphinxcontrib-serializinghtml-2.0.0 urllib3-2.2.3 [rtd-command-info] start-time: 2024-09-20T13:14:13.516569Z, end-time: 2024-09-20T13:16:03.401236Z, duration: 109, exit-code: 0 python -m pip install --upgrade --upgrade-strategy only-if-needed --no-cache-dir .[doc,dev,leiden] Processing /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/3206 Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to 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0:00:00 Downloading distlib-0.3.8-py2.py3-none-any.whl (468 kB) Downloading executing-2.1.0-py2.py3-none-any.whl (25 kB) Downloading fastjsonschema-2.20.0-py3-none-any.whl (23 kB) Downloading filelock-3.16.1-py3-none-any.whl (16 kB) Downloading jsonschema-4.23.0-py3-none-any.whl (88 kB) Downloading attrs-24.2.0-py3-none-any.whl (63 kB) Downloading jupyter_client-8.6.3-py3-none-any.whl (106 kB) Downloading jupyter_core-5.7.2-py3-none-any.whl (28 kB) Downloading latexcodec-3.0.0-py3-none-any.whl (18 kB) Downloading mdurl-0.1.2-py3-none-any.whl (10.0 kB) Downloading mistune-3.0.2-py3-none-any.whl (47 kB) Downloading pandocfilters-1.5.1-py2.py3-none-any.whl (8.7 kB) Downloading parso-0.8.4-py2.py3-none-any.whl (103 kB) Downloading platformdirs-4.3.6-py3-none-any.whl (18 kB) Downloading ptyprocess-0.7.0-py2.py3-none-any.whl (13 kB) Downloading pyzmq-26.2.0-cp312-cp312-manylinux_2_28_x86_64.whl (860 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 860.6/860.6 kB 391.9 MB/s eta 0:00:00 Downloading SQLAlchemy-2.0.35-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.2/3.2 MB 378.6 MB/s eta 0:00:00 Downloading tornado-6.4.1-cp38-abi3-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (436 kB) Downloading zipp-3.20.2-py3-none-any.whl (9.2 kB) Downloading accessible_pygments-0.0.5-py3-none-any.whl (1.4 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.4/1.4 MB 490.8 MB/s eta 0:00:00 Downloading beautifulsoup4-4.12.3-py3-none-any.whl (147 kB) Downloading defusedxml-0.7.1-py2.py3-none-any.whl (25 kB) Downloading jupyterlab_pygments-0.3.0-py3-none-any.whl (15 kB) Downloading locket-1.0.0-py2.py3-none-any.whl (4.4 kB) Downloading nest_asyncio-1.6.0-py3-none-any.whl (5.2 kB) Downloading psutil-6.0.0-cp36-abi3-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (290 kB) Downloading pure_eval-0.2.3-py3-none-any.whl (11 kB) Downloading tabulate-0.9.0-py3-none-any.whl (35 kB) Downloading tinycss2-1.3.0-py3-none-any.whl (22 kB) Downloading wcwidth-0.2.13-py2.py3-none-any.whl (34 kB) Downloading greenlet-3.1.0-cp312-cp312-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (626 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 626.7/626.7 kB 450.7 MB/s eta 0:00:00 Downloading jsonschema_specifications-2023.12.1-py3-none-any.whl (18 kB) Downloading referencing-0.35.1-py3-none-any.whl (26 kB) Downloading rpds_py-0.20.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (357 kB) Downloading soupsieve-2.6-py3-none-any.whl (36 kB) Downloading webencodings-0.5.1-py2.py3-none-any.whl (11 kB) Building wheels for collected packages: scanpy, sam-algorithm, session-info, hnswlib Building wheel for scanpy (pyproject.toml): started Building wheel for scanpy (pyproject.toml): finished with status 'done' Created wheel for scanpy: filename=scanpy-1.11.0.dev138+ge4c45ed3-py3-none-any.whl size=2086366 sha256=f30d4e00ad0a7bbab56c92601f7803fdf77e14e62ceac442bb0f724f0b922cf0 Stored in directory: /tmp/pip-ephem-wheel-cache-z0smism_/wheels/a2/e2/c4/8bd02383b93d1bf99c9767e113884fbf0190701531dfe3a24e Building wheel for sam-algorithm (setup.py): started Building wheel for sam-algorithm (setup.py): finished with status 'done' Created wheel for sam-algorithm: filename=sam_algorithm-1.0.2-py3-none-any.whl size=34579 sha256=34deeb03828ee69458bb6f45ecc3edffc67ea26c1d9aed2fb3172dd0b6b57682 Stored in directory: /tmp/pip-ephem-wheel-cache-z0smism_/wheels/57/54/be/ca87c5831826023e1d64b77d6680c582ff898a13844a7ed4ed Building wheel for session-info (setup.py): started Building wheel for session-info (setup.py): finished with status 'done' Created wheel for session-info: filename=session_info-1.0.0-py3-none-any.whl size=8023 sha256=65bebeb65f7759583e0ef7adf15a561edcc79cff3a4a9a234d9b83b69cfe64b0 Stored in directory: /tmp/pip-ephem-wheel-cache-z0smism_/wheels/23/da/7c/868424f4a5845ab58cd8686e0eb405e9e1e2d4152bf702c39d Building wheel for hnswlib (pyproject.toml): started Building wheel for hnswlib (pyproject.toml): finished with status 'done' Created wheel for hnswlib: filename=hnswlib-0.8.0-cp312-cp312-linux_x86_64.whl size=2288949 sha256=bcfc414d7756a21083dfc0e9aad8826ac11e4d2ae98914b2b1f78ca6d8e04725 Stored in directory: /tmp/pip-ephem-wheel-cache-z0smism_/wheels/ac/39/b3/cbd7f9cbb76501d2d5fbc84956e70d0b94e788aac87bda465e Successfully built scanpy sam-algorithm session-info hnswlib Installing collected packages: webencodings, wcwidth, texttable, pytz, pure-eval, ptyprocess, fastjsonschema, distlib, array-api-compat, zipp, tzdata, typing-extensions, traitlets, tqdm, tornado, toolz, tinycss2, threadpoolctl, tabulate, stdlib_list, soupsieve, six, setuptools-scm, rpds-py, readthedocs-sphinx-search, pyzmq, pyyaml, pyparsing, psutil, prompt-toolkit, platformdirs, pillow, pexpect, parso, pandocfilters, numpy, nodeenv, networkx, nest-asyncio, natsort, mistune, mdurl, locket, llvmlite, legacy-api-wrap, latexcodec, kiwisolver, jupyterlab-pygments, joblib, igraph, identify, greenlet, fsspec, fonttools, filelock, executing, dill, defusedxml, decorator, debugpy, cycler, cloudpickle, click, cfgv, attrs, accessible-pygments, virtualenv, towncrier, sqlalchemy, session-info, scipy, referencing, python-dateutil, pybtex, patsy, partd, numba, matplotlib-inline, markdown-it-py, leidenalg, jupyter-core, jedi, importlib_metadata, hnswlib, h5py, contourpy, comm, bleach, beautifulsoup4, asttokens, stack-data, sphinxext-opengraph, sphinx-tabs, sphinx-design, sphinx-copybutton, sphinx-autodoc-typehints, scikit-learn, scanpydoc, pydata-sphinx-theme, pybtex-docutils, pre-commit, pandas, mdit-py-plugins, matplotlib, jupyter-client, jsonschema-specifications, dask, statsmodels, sphinxcontrib-bibtex, sphinx-book-theme, seaborn, pynndescent, myst-parser, jsonschema, ipython, harmonypy, anndata, umap-learn, nbformat, ipykernel, scanpy, sam-algorithm, nbclient, nbconvert, jupyter-cache, nbsphinx, myst-nb Successfully installed accessible-pygments-0.0.5 anndata-0.10.9 array-api-compat-1.8 asttokens-2.4.1 attrs-24.2.0 beautifulsoup4-4.12.3 bleach-6.1.0 cfgv-3.4.0 click-8.1.7 cloudpickle-3.0.0 comm-0.2.2 contourpy-1.3.0 cycler-0.12.1 dask-2024.9.0 debugpy-1.8.5 decorator-5.1.1 defusedxml-0.7.1 dill-0.3.8 distlib-0.3.8 executing-2.1.0 fastjsonschema-2.20.0 filelock-3.16.1 fonttools-4.53.1 fsspec-2024.9.0 greenlet-3.1.0 h5py-3.11.0 harmonypy-0.0.10 hnswlib-0.8.0 identify-2.6.1 igraph-0.11.6 importlib_metadata-8.5.0 ipykernel-6.29.5 ipython-8.27.0 jedi-0.19.1 joblib-1.4.2 jsonschema-4.23.0 jsonschema-specifications-2023.12.1 jupyter-cache-1.0.0 jupyter-client-8.6.3 jupyter-core-5.7.2 jupyterlab-pygments-0.3.0 kiwisolver-1.4.7 latexcodec-3.0.0 legacy-api-wrap-1.4 leidenalg-0.10.2 llvmlite-0.43.0 locket-1.0.0 markdown-it-py-3.0.0 matplotlib-3.9.2 matplotlib-inline-0.1.7 mdit-py-plugins-0.4.2 mdurl-0.1.2 mistune-3.0.2 myst-nb-1.1.1 myst-parser-4.0.0 natsort-8.4.0 nbclient-0.10.0 nbconvert-7.16.4 nbformat-5.10.4 nbsphinx-0.9.5 nest-asyncio-1.6.0 networkx-3.3 nodeenv-1.9.1 numba-0.60.0 numpy-2.0.2 pandas-2.2.3 pandocfilters-1.5.1 parso-0.8.4 partd-1.4.2 patsy-0.5.6 pexpect-4.9.0 pillow-10.4.0 platformdirs-4.3.6 pre-commit-3.8.0 prompt-toolkit-3.0.47 psutil-6.0.0 ptyprocess-0.7.0 pure-eval-0.2.3 pybtex-0.24.0 pybtex-docutils-1.0.3 pydata-sphinx-theme-0.15.4 pynndescent-0.5.13 pyparsing-3.1.4 python-dateutil-2.9.0.post0 pytz-2024.2 pyyaml-6.0.2 pyzmq-26.2.0 readthedocs-sphinx-search-0.3.2 referencing-0.35.1 rpds-py-0.20.0 sam-algorithm-1.0.2 scanpy-1.11.0.dev138+ge4c45ed3 scanpydoc-0.14.1 scikit-learn-1.5.2 scipy-1.14.1 seaborn-0.13.2 session-info-1.0.0 setuptools-scm-8.1.0 six-1.16.0 soupsieve-2.6 sphinx-autodoc-typehints-2.4.4 sphinx-book-theme-1.1.3 sphinx-copybutton-0.5.2 sphinx-design-0.6.1 sphinx-tabs-3.4.5 sphinxcontrib-bibtex-2.6.3 sphinxext-opengraph-0.9.1 sqlalchemy-2.0.35 stack-data-0.6.3 statsmodels-0.14.3 stdlib_list-0.10.0 tabulate-0.9.0 texttable-1.7.0 threadpoolctl-3.5.0 tinycss2-1.3.0 toolz-0.12.1 tornado-6.4.1 towncrier-24.8.0 tqdm-4.66.5 traitlets-5.14.3 typing-extensions-4.12.2 tzdata-2024.1 umap-learn-0.5.6 virtualenv-20.26.5 wcwidth-0.2.13 webencodings-0.5.1 zipp-3.20.2