Read the Docs build information
Build id: 1613005
Project: icb-scanpy
Version: latest
Commit: 9f27fc9bbd9630458d6f11eab9d8243f29483c37
Date: 2023-07-21T10:51:42.809822Z
State: cancelled
Success: False


[rtd-command-info] start-time: 2023-07-21T10:51:47.111535Z, end-time: 2023-07-21T10:51:50.034722Z, duration: 2, exit-code: 0
git clone --no-single-branch --depth 50 https://github.com/scverse/scanpy.git .
Cloning into '.'...

[rtd-command-info] start-time: 2023-07-21T10:51:50.273306Z, end-time: 2023-07-21T10:51:50.396899Z, duration: 0, exit-code: 0
git checkout --force origin/master
Note: switching to 'origin/master'.

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 9f27fc9b Fix library_id types (#2541)

[rtd-command-info] start-time: 2023-07-21T10:51:50.652014Z, end-time: 2023-07-21T10:51:50.716853Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2023-07-21T10:51:50.946121Z, end-time: 2023-07-21T10:51:51.026965Z, duration: 0, exit-code: 0
git submodule sync


[rtd-command-info] start-time: 2023-07-21T10:51:51.266979Z, end-time: 2023-07-21T10:52:02.065948Z, duration: 10, exit-code: 0
git submodule update --init --force docs/tutorials
Submodule 'docs/tutorials' (https://github.com/scverse/scanpy-tutorials.git) registered for path 'docs/tutorials'
Cloning into '/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/tutorials'...
Submodule path 'docs/tutorials': checked out 'ba8e433ea7c0fc3b1e1e482ecc2e1dd5f59a9d9d'

[rtd-command-info] start-time: 2023-07-21T10:52:02.285177Z, end-time: 2023-07-21T10:52:02.385163Z, duration: 0, exit-code: 0
cat .readthedocs.yml
version: 2
build:
  os: ubuntu-20.04
  tools:
    python: '3.9'
sphinx:
  configuration: docs/conf.py
python:
  install:
  - method: pip
    path: .
    extra_requirements:
    - doc
    - leiden
submodules:
  include:
     - "docs/tutorials"

[rtd-command-info] start-time: 2023-07-21T10:52:08.426230Z, end-time: 2023-07-21T10:52:08.509613Z, duration: 0, exit-code: 0
asdf global python 3.9.17


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python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH
created virtual environment CPython3.9.17.final.0-64 in 717ms
  creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/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: 2023-07-21T10:52:10.293581Z, end-time: 2023-07-21T10:52:20.070760Z, duration: 9, 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/latest/lib/python3.9/site-packages (21.2.3)
Collecting pip
  Downloading pip-23.2-py3-none-any.whl (2.1 MB)
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.9/site-packages (57.4.0)
Collecting setuptools
  Downloading setuptools-68.0.0-py3-none-any.whl (804 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 setuptools-68.0.0

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python -m pip install --upgrade --no-cache-dir pillow mock==1.0.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.9.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<2.3 jinja2<3.1.0
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Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.9/site-packages (from sphinx<2) (68.0.0)
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Building wheels for collected packages: mock
  Building wheel for mock (setup.py): started
  Building wheel for mock (setup.py): finished with status 'done'
  Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23753 sha256=d08bebcc2a2eaff5360d9e42551aa5ba757b0c7b7255b071b3b265c02a26b3d7
  Stored in directory: /tmp/pip-ephem-wheel-cache-xzxnsyej/wheels/44/dc/c7/e89296d3612588db0aa6545ee3305c23b7a48b3a9922916e1f
Successfully built mock
Installing collected packages: snowballstemmer, mock, commonmark, urllib3, sphinxcontrib-serializinghtml, six, Pygments, pillow, packaging, MarkupSafe, imagesize, idna, docutils, charset-normalizer, certifi, babel, alabaster, sphinxcontrib-websupport, requests, jinja2, sphinx, readthedocs-sphinx-ext, sphinx-rtd-theme, recommonmark
Successfully installed MarkupSafe-2.1.3 Pygments-2.15.1 alabaster-0.7.13 babel-2.12.1 certifi-2023.5.7 charset-normalizer-3.2.0 commonmark-0.9.1 docutils-0.17.1 idna-3.4 imagesize-1.4.1 jinja2-3.0.3 mock-1.0.1 packaging-23.1 pillow-10.0.0 readthedocs-sphinx-ext-2.2.2 recommonmark-0.5.0 requests-2.31.0 six-1.16.0 snowballstemmer-2.2.0 sphinx-1.8.6 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.5 sphinxcontrib-websupport-1.2.4 urllib3-2.0.4