Read the Docs build information
Build id: 1760370
Project: icb-anndata
Version: latest
Commit: e5ebff0f925c371251faabf8ab3213fe721afbf5
Date: 2023-10-04T12:13:33.132531Z
State: cancelled
Success: False


[rtd-command-info] start-time: 2023-10-04T12:13:42.175132Z, end-time: 2023-10-04T12:13:42.797155Z, duration: 0, exit-code: 0
git clone --depth 1 https://github.com/scverse/anndata.git .
Cloning into '.'...

[rtd-command-info] start-time: 2023-10-04T12:13:43.229879Z, end-time: 2023-10-04T12:13:44.393300Z, duration: 1, exit-code: 0
git fetch origin --force --prune --prune-tags --depth 50 refs/heads/main:refs/remotes/origin/main
From https://github.com/scverse/anndata
 * [new tag]         0.10.0rc1  -> 0.10.0rc1

[rtd-command-info] start-time: 2023-10-04T12:13:44.911911Z, end-time: 2023-10-04T12:13:44.988018Z, duration: 0, exit-code: 0
git checkout --force origin/main
Note: switching to 'origin/main'.

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 <new-branch-name>

Or undo this operation with:

  git switch -

Turn off this advice by setting config variable advice.detachedHead to false

HEAD is now at e5ebff0 Optimize contiguous sparse slicing (#1131)

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git clean -d -f -f


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git submodule sync


[rtd-command-info] start-time: 2023-10-04T12:13:48.181601Z, end-time: 2023-10-04T12:13:48.931783Z, duration: 0, exit-code: 0
git submodule update --init --force --recursive -- docs/tutorials/notebooks
Submodule 'docs/tutorials/notebooks' (https://github.com/scverse/anndata-tutorials) registered for path 'docs/tutorials/notebooks'
Cloning into '/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/tutorials/notebooks'...
Submodule path 'docs/tutorials/notebooks': checked out '9e186c5c694793bb04ea1397721d154d6e0b7069'

[rtd-command-info] start-time: 2023-10-04T12:13:51.637598Z, end-time: 2023-10-04T12:13:51.707379Z, duration: 0, exit-code: 0
cat .readthedocs.yml
version: 2
build:
  os: ubuntu-20.04
  tools:
    python: "3.11"
sphinx:
  configuration: docs/conf.py
  fail_on_warning: true # do not change or you will be fired
python:
  install:
    - method: pip
      path: .
      extra_requirements:
        - doc
submodules:
  include:
    - "docs/tutorials/notebooks"
  recursive: true

[rtd-command-info] start-time: 2023-10-04T12:14:06.412303Z, end-time: 2023-10-04T12:14:08.790501Z, duration: 2, exit-code: 0
asdf global python 3.11.4


[rtd-command-info] start-time: 2023-10-04T12:14:10.930526Z, end-time: 2023-10-04T12:14:13.466142Z, duration: 2, exit-code: 0
python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH
created virtual environment CPython3.11.4.final.0-64 in 624ms
  creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest, clear=False, no_vcs_ignore=False, global=False)
  seeder FromAppData(download=False, pip=bundle, setuptools=bundle, wheel=bundle, via=copy, app_data_dir=/home/docs/.local/share/virtualenv)
    added seed packages: pip==21.2.3, setuptools==57.4.0, wheel==0.37.0
  activators BashActivator,CShellActivator,FishActivator,PowerShellActivator,PythonActivator

[rtd-command-info] start-time: 2023-10-04T12:14:13.880092Z, end-time: 2023-10-04T12:14:27.802235Z, duration: 13, 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-anndata/envs/latest/lib/python3.11/site-packages (21.2.3)
Collecting pip
  Downloading pip-23.2.1-py3-none-any.whl (2.1 MB)
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.11/site-packages (57.4.0)
Collecting setuptools
  Downloading setuptools-68.2.2-py3-none-any.whl (807 kB)
Installing collected packages: setuptools, pip
  Attempting uninstall: setuptools
    Found existing installation: setuptools 57.4.0
    Uninstalling setuptools-57.4.0:
      Successfully uninstalled setuptools-57.4.0
  Attempting uninstall: pip
    Found existing installation: pip 21.2.3
    Uninstalling pip-21.2.3:
      Successfully uninstalled pip-21.2.3
Successfully installed pip-23.2.1 setuptools-68.2.2

[rtd-command-info] start-time: 2023-10-04T12:14:28.252696Z, end-time: 2023-10-04T12:14:35.650154Z, duration: 7, exit-code: 0
python -m pip install --upgrade --no-cache-dir sphinx readthedocs-sphinx-ext
Collecting sphinx
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Installing collected packages: snowballstemmer, urllib3, sphinxcontrib-jsmath, Pygments, packaging, MarkupSafe, imagesize, idna, docutils, charset-normalizer, certifi, babel, alabaster, requests, Jinja2, readthedocs-sphinx-ext, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, sphinx
Successfully installed Jinja2-3.1.2 MarkupSafe-2.1.3 Pygments-2.16.1 alabaster-0.7.13 babel-2.13.0 certifi-2023.7.22 charset-normalizer-3.3.0 docutils-0.20.1 idna-3.4 imagesize-1.4.1 packaging-23.2 readthedocs-sphinx-ext-2.2.3 requests-2.31.0 snowballstemmer-2.2.0 sphinx-7.2.6 sphinxcontrib-applehelp-1.0.7 sphinxcontrib-devhelp-1.0.5 sphinxcontrib-htmlhelp-2.0.4 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.6 sphinxcontrib-serializinghtml-1.1.9 urllib3-2.0.6

[rtd-command-info] start-time: 2023-10-04T12:14:36.898660Z, end-time: 2023-10-04T12:15:17.196595Z, duration: 40, exit-code: 0
python -m pip install --upgrade --upgrade-strategy only-if-needed --no-cache-dir .[doc]
Processing /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest
  Installing build dependencies: started
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Building wheels for collected packages: anndata, asciitree
  Building wheel for anndata (pyproject.toml): started
  Building wheel for anndata (pyproject.toml): finished with status 'done'
  Created wheel for anndata: filename=anndata-0.10.0rc2.dev5+ge5ebff0-py3-none-any.whl size=117664 sha256=227d811ab8c77556f1a78580ec24b265f672ff865e5bd0343e6fd19c324221b8
  Stored in directory: /tmp/pip-ephem-wheel-cache-mqm8hv_h/wheels/ac/78/17/d6beb4bb5885bedd4df2dd7b9cf80e3cd148368110ea659730
  Building wheel for asciitree (setup.py): started
  Building wheel for asciitree (setup.py): finished with status 'done'
  Created wheel for asciitree: filename=asciitree-0.3.3-py3-none-any.whl size=5033 sha256=7cc83c044ddf6beb3e8357423e652ff2bd83bee331f979a1755f449bdc0c9a94
  Stored in directory: /tmp/pip-ephem-wheel-cache-mqm8hv_h/wheels/71/c1/da/23077eb3b87d24d6f3852ed1ed1a1ac2d3c885ad6ebd2b4a07
Successfully built anndata asciitree
Installing collected packages: webencodings, wcwidth, pytz, pure-eval, ptyprocess, pickleshare, fastjsonschema, executing, backcall, asciitree, zipp, tzdata, typing-extensions, traitlets, tornado, tinycss2, soupsieve, six, rpds-py, pyzmq, pyyaml, pyparsing, prompt-toolkit, platformdirs, pillow, pexpect, parso, pandocfilters, numpy, natsort, mistune, mdurl, kiwisolver, jupyterlab-pygments, fonttools, fasteners, entrypoints, docutils, defusedxml, decorator, cycler, attrs, array-api-compat, accessible-pygments, scipy, referencing, python-dateutil, numcodecs, matplotlib-inline, markdown-it-py, jupyter-core, jedi, importlib-metadata, h5py, contourpy, bleach, beautifulsoup4, awkward-cpp, asttokens, zarr, stack-data, pandas, mdit-py-plugins, matplotlib, jupyter-client, jsonschema-specifications, awkward, jsonschema, ipython, anndata, nbformat, nbclient, nbconvert, sphinx, pydata-sphinx-theme, sphinxext-opengraph, sphinx-issues, sphinx-copybutton, sphinx-book-theme, sphinx-autodoc-typehints, scanpydoc, nbsphinx, myst-parser
  Attempting uninstall: docutils
    Found existing installation: docutils 0.20.1
    Uninstalling docutils-0.20.1:
      Successfully uninstalled docutils-0.20.1
  Attempting uninstall: sphinx
    Found existing installation: Sphinx 7.2.6
    Uninstalling Sphinx-7.2.6:
      Successfully uninstalled Sphinx-7.2.6
Successfully installed accessible-pygments-0.0.4 anndata-0.10.0rc2.dev5+ge5ebff0 array-api-compat-1.4 asciitree-0.3.3 asttokens-2.4.0 attrs-23.1.0 awkward-2.4.4 awkward-cpp-24 backcall-0.2.0 beautifulsoup4-4.12.2 bleach-6.0.0 contourpy-1.1.1 cycler-0.12.0 decorator-5.1.1 defusedxml-0.7.1 docutils-0.19 entrypoints-0.4 executing-2.0.0 fasteners-0.19 fastjsonschema-2.18.1 fonttools-4.43.0 h5py-3.9.0 importlib-metadata-6.8.0 ipython-8.16.1 jedi-0.19.1 jsonschema-4.19.1 jsonschema-specifications-2023.7.1 jupyter-client-8.3.1 jupyter-core-5.3.2 jupyterlab-pygments-0.2.2 kiwisolver-1.4.5 markdown-it-py-3.0.0 matplotlib-3.8.0 matplotlib-inline-0.1.6 mdit-py-plugins-0.4.0 mdurl-0.1.2 mistune-3.0.2 myst-parser-2.0.0 natsort-8.4.0 nbclient-0.8.0 nbconvert-7.9.0 nbformat-5.9.2 nbsphinx-0.9.3 numcodecs-0.11.0 numpy-1.26.0 pandas-2.1.1 pandocfilters-1.5.0 parso-0.8.3 pexpect-4.8.0 pickleshare-0.7.5 pillow-10.0.1 platformdirs-3.11.0 prompt-toolkit-3.0.39 ptyprocess-0.7.0 pure-eval-0.2.2 pydata-sphinx-theme-0.14.1 pyparsing-3.1.1 python-dateutil-2.8.2 pytz-2023.3.post1 pyyaml-6.0.1 pyzmq-25.1.1 referencing-0.30.2 rpds-py-0.10.3 scanpydoc-0.9.5 scipy-1.11.3 six-1.16.0 soupsieve-2.5 sphinx-6.2.1 sphinx-autodoc-typehints-1.23.0 sphinx-book-theme-1.0.1 sphinx-copybutton-0.5.2 sphinx-issues-3.0.1 sphinxext-opengraph-0.8.2 stack-data-0.6.3 tinycss2-1.2.1 tornado-6.3.3 traitlets-5.11.2 typing-extensions-4.8.0 tzdata-2023.3 wcwidth-0.2.8 webencodings-0.5.1 zarr-2.16.1 zipp-3.17.0