Read the Docs build information
Build id: 944816
Project: icb-scanpy
Version: 2255
Commit: c0357f3055d96414da176583035944e000d1ab2a
Date: 2022-05-12T14:23:28.768071Z
State: finished
Success: False


[rtd-command-info] start-time: 2022-05-12T14:23:30.730845Z, end-time: 2022-05-12T14:23:34.897183Z, duration: 4, exit-code: 0
git clone --no-single-branch --depth 50 https://github.com/scverse/scanpy.git .
Cloning into '.'...

[rtd-command-info] start-time: 2022-05-12T14:23:35.106767Z, end-time: 2022-05-12T14:23:35.640175Z, duration: 0, exit-code: 0
git fetch origin --force --tags --prune --prune-tags --depth 50 pull/2255/head:external-2255
From https://github.com/scverse/scanpy
 * [new ref]           refs/pull/2255/head -> external-2255

[rtd-command-info] start-time: 2022-05-12T14:23:35.835005Z, end-time: 2022-05-12T14:23:36.058995Z, duration: 0, exit-code: 0
git checkout --force c0357f3055d96414da176583035944e000d1ab2a
Note: switching to 'c0357f3055d96414da176583035944e000d1ab2a'.

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 c0357f30 fix diffmap plot

[rtd-command-info] start-time: 2022-05-12T14:23:36.251151Z, end-time: 2022-05-12T14:23:36.330874Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2022-05-12T14:23:41.557806Z, end-time: 2022-05-12T14:23:41.635199Z, duration: 0, exit-code: 0
asdf global python 3.9.7


[rtd-command-info] start-time: 2022-05-12T14:23:42.176024Z, end-time: 2022-05-12T14:23:43.094755Z, duration: 0, exit-code: 0
python -mvirtualenv 
created virtual environment CPython3.9.7.final.0-64 in 626ms
  creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2255, 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: 2022-05-12T14:23:43.336850Z, end-time: 2022-05-12T14:23:53.853575Z, duration: 10, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip setuptools<58.3.0
Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2255/lib/python3.9/site-packages (21.2.3)
Collecting pip
  Downloading pip-22.1-py3-none-any.whl (2.1 MB)
Requirement already satisfied: setuptools<58.3.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2255/lib/python3.9/site-packages (57.4.0)
Collecting setuptools<58.3.0
  Downloading setuptools-58.2.0-py3-none-any.whl (946 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-22.1 setuptools-58.2.0

[rtd-command-info] start-time: 2022-05-12T14:23:54.079951Z, end-time: 2022-05-12T14:24:25.328866Z, duration: 31, exit-code: 0
python -m pip install --upgrade --no-cache-dir mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.8.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<2.2 jinja2<3.1.0
Collecting mock==1.0.1
  Downloading mock-1.0.1.zip (861 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 861.9/861.9 kB 25.7 MB/s eta 0:00:00
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting pillow==5.4.1
  Downloading Pillow-5.4.1.tar.gz (16.0 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 16.0/16.0 MB 190.3 MB/s eta 0:00:00
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting alabaster!=0.7.5,<0.8,>=0.7
  Downloading alabaster-0.7.12-py2.py3-none-any.whl (14 kB)
Collecting commonmark==0.8.1
  Downloading commonmark-0.8.1-py2.py3-none-any.whl (47 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 47.4/47.4 kB 182.4 MB/s eta 0:00:00
Collecting recommonmark==0.5.0
  Downloading recommonmark-0.5.0-py2.py3-none-any.whl (9.8 kB)
Collecting sphinx<2
  Downloading Sphinx-1.8.6-py2.py3-none-any.whl (3.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.1/3.1 MB 207.3 MB/s eta 0:00:00
Collecting sphinx-rtd-theme<0.5
  Downloading sphinx_rtd_theme-0.4.3-py2.py3-none-any.whl (6.4 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 6.4/6.4 MB 177.3 MB/s eta 0:00:00
Collecting readthedocs-sphinx-ext<2.2
  Downloading readthedocs_sphinx_ext-2.1.6-py2.py3-none-any.whl (11 kB)
Collecting jinja2<3.1.0
  Downloading Jinja2-3.0.3-py3-none-any.whl (133 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 133.6/133.6 kB 223.8 MB/s eta 0:00:00
Collecting future
  Downloading future-0.18.2.tar.gz (829 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 829.2/829.2 kB 239.3 MB/s eta 0:00:00
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting docutils>=0.11
  Downloading docutils-0.18.1-py2.py3-none-any.whl (570 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 570.0/570.0 kB 252.0 MB/s eta 0:00:00
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2255/lib/python3.9/site-packages (from sphinx<2) (58.2.0)
Collecting Pygments>=2.0
  Downloading Pygments-2.12.0-py3-none-any.whl (1.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 259.6 MB/s eta 0:00:00
Collecting docutils>=0.11
  Downloading docutils-0.17.1-py2.py3-none-any.whl (575 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 575.5/575.5 kB 254.5 MB/s eta 0:00:00
Collecting six>=1.5
  Downloading six-1.16.0-py2.py3-none-any.whl (11 kB)
Collecting babel!=2.0,>=1.3
  Downloading Babel-2.10.1-py3-none-any.whl (9.5 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 9.5/9.5 MB 200.9 MB/s eta 0:00:00
Collecting packaging
  Downloading packaging-21.3-py3-none-any.whl (40 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 40.8/40.8 kB 182.3 MB/s eta 0:00:00
Collecting sphinxcontrib-websupport
  Downloading sphinxcontrib_websupport-1.2.4-py2.py3-none-any.whl (39 kB)
Collecting imagesize
  Downloading imagesize-1.3.0-py2.py3-none-any.whl (5.2 kB)
Collecting snowballstemmer>=1.1
  Downloading snowballstemmer-2.2.0-py2.py3-none-any.whl (93 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 93.0/93.0 kB 219.4 MB/s eta 0:00:00
Collecting requests>=2.0.0
  Downloading requests-2.27.1-py2.py3-none-any.whl (63 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 63.1/63.1 kB 209.6 MB/s eta 0:00:00
Collecting MarkupSafe>=2.0
  Downloading MarkupSafe-2.1.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (25 kB)
Collecting pytz>=2015.7
  Downloading pytz-2022.1-py2.py3-none-any.whl (503 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 503.5/503.5 kB 249.3 MB/s eta 0:00:00
Collecting charset-normalizer~=2.0.0
  Downloading charset_normalizer-2.0.12-py3-none-any.whl (39 kB)
Collecting urllib3<1.27,>=1.21.1
  Downloading urllib3-1.26.9-py2.py3-none-any.whl (138 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 139.0/139.0 kB 235.4 MB/s eta 0:00:00
Collecting idna<4,>=2.5
  Downloading idna-3.3-py3-none-any.whl (61 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 61.2/61.2 kB 210.7 MB/s eta 0:00:00
Collecting certifi>=2017.4.17
  Downloading certifi-2021.10.8-py2.py3-none-any.whl (149 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 149.2/149.2 kB 220.9 MB/s eta 0:00:00
Collecting pyparsing!=3.0.5,>=2.0.2
  Downloading pyparsing-3.0.9-py3-none-any.whl (98 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 98.3/98.3 kB 221.2 MB/s eta 0:00:00
Collecting sphinxcontrib-serializinghtml
  Downloading sphinxcontrib_serializinghtml-1.1.5-py2.py3-none-any.whl (94 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 94.0/94.0 kB 218.5 MB/s eta 0:00:00
Building wheels for collected packages: mock, pillow, future
  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=23772 sha256=704c38b4049833995a6f3c17456c7d0de78035e2d9842353055d432054022ac2
  Stored in directory: /tmp/pip-ephem-wheel-cache-_em4_q51/wheels/44/dc/c7/e89296d3612588db0aa6545ee3305c23b7a48b3a9922916e1f
  Building wheel for pillow (setup.py): started
  Building wheel for pillow (setup.py): finished with status 'done'
  Created wheel for pillow: filename=Pillow-5.4.1-cp39-cp39-linux_x86_64.whl size=1361342 sha256=d4cdc23c658008e7c8cb8473f4541e33fa5839553c322d8bb656d34249a47c62
  Stored in directory: /tmp/pip-ephem-wheel-cache-_em4_q51/wheels/d3/de/21/f0ad1b0453288616d3f4d2ce28431aa7a2adde8f27c9b7a0af
  Building wheel for future (setup.py): started
  Building wheel for future (setup.py): finished with status 'done'
  Created wheel for future: filename=future-0.18.2-py3-none-any.whl size=491070 sha256=5c4dcd1228c2cc52dd96312e8aff026380f20ade30c50dd8d4e49e75efb7dae0
  Stored in directory: /tmp/pip-ephem-wheel-cache-_em4_q51/wheels/2f/a0/d3/4030d9f80e6b3be787f19fc911b8e7aa462986a40ab1e4bb94
Successfully built mock pillow future
Installing collected packages: snowballstemmer, pytz, mock, certifi, alabaster, urllib3, sphinxcontrib-serializinghtml, six, pyparsing, Pygments, pillow, MarkupSafe, imagesize, idna, future, docutils, charset-normalizer, babel, sphinxcontrib-websupport, requests, packaging, jinja2, commonmark, sphinx, readthedocs-sphinx-ext, sphinx-rtd-theme, recommonmark
Successfully installed MarkupSafe-2.1.1 Pygments-2.12.0 alabaster-0.7.12 babel-2.10.1 certifi-2021.10.8 charset-normalizer-2.0.12 commonmark-0.8.1 docutils-0.17.1 future-0.18.2 idna-3.3 imagesize-1.3.0 jinja2-3.0.3 mock-1.0.1 packaging-21.3 pillow-5.4.1 pyparsing-3.0.9 pytz-2022.1 readthedocs-sphinx-ext-2.1.6 recommonmark-0.5.0 requests-2.27.1 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 urllib3-1.26.9

[rtd-command-info] start-time: 2022-05-12T14:24:25.524484Z, end-time: 2022-05-12T14:24:30.267897Z, duration: 4, exit-code: 2
python -m pip install --upgrade --upgrade-strategy eager --no-cache-dir .[doc]
Processing /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/2255
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
ERROR: Exception:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2255/lib/python3.9/site-packages/pip/_internal/cli/base_command.py", line 167, in exc_logging_wrapper
    status = run_func(*args)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2255/lib/python3.9/site-packages/pip/_internal/cli/req_command.py", line 205, in wrapper
    return func(self, options, args)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2255/lib/python3.9/site-packages/pip/_internal/commands/install.py", line 340, in run
    requirement_set = resolver.resolve(
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2255/lib/python3.9/site-packages/pip/_internal/resolution/resolvelib/resolver.py", line 75, in resolve
    collected = self.factory.collect_root_requirements(root_reqs)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2255/lib/python3.9/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 506, in collect_root_requirements
    req = self._make_requirement_from_install_req(
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2255/lib/python3.9/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 468, in _make_requirement_from_install_req
    cand = self._make_candidate_from_link(
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2255/lib/python3.9/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 215, in _make_candidate_from_link
    self._link_candidate_cache[link] = LinkCandidate(
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2255/lib/python3.9/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 291, in __init__
    super().__init__(
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2255/lib/python3.9/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 161, in __init__
    self.dist = self._prepare()
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2255/lib/python3.9/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 230, in _prepare
    dist = self._prepare_distribution()
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2255/lib/python3.9/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 302, in _prepare_distribution
    return preparer.prepare_linked_requirement(self._ireq, parallel_builds=True)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2255/lib/python3.9/site-packages/pip/_internal/operations/prepare.py", line 421, in prepare_linked_requirement
    return self._prepare_linked_requirement(req, parallel_builds)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2255/lib/python3.9/site-packages/pip/_internal/operations/prepare.py", line 490, in _prepare_linked_requirement
    dist = _get_prepared_distribution(
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2255/lib/python3.9/site-packages/pip/_internal/operations/prepare.py", line 57, in _get_prepared_distribution
    abstract_dist.prepare_distribution_metadata(finder, build_isolation)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2255/lib/python3.9/site-packages/pip/_internal/distributions/sdist.py", line 45, in prepare_distribution_metadata
    self._install_build_reqs(finder)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2255/lib/python3.9/site-packages/pip/_internal/distributions/sdist.py", line 114, in _install_build_reqs
    conflicting, missing = self.req.build_env.check_requirements(build_reqs)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2255/lib/python3.9/site-packages/pip/_internal/build_env.py", line 178, in check_requirements
    if req.marker is not None and not req.marker.evaluate():
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2255/lib/python3.9/site-packages/pip/_vendor/packaging/markers.py", line 304, in evaluate
    return _evaluate_markers(self._markers, current_environment)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2255/lib/python3.9/site-packages/pip/_vendor/packaging/markers.py", line 234, in _evaluate_markers
    lhs_value = _get_env(environment, lhs.value)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/2255/lib/python3.9/site-packages/pip/_vendor/packaging/markers.py", line 215, in _get_env
    raise UndefinedEnvironmentName(
pip._vendor.packaging.markers.UndefinedEnvironmentName: 'extra' does not exist in evaluation environment.