Read the Docs build information
Build id: 1548762
Project: icb-scanpy-tutorials
Version: latest
Commit: f7f678c99fab8bcc1db5c91d16e8eb49996389b7
Date: 2023-06-20T09:50:07.203639Z
State: finished
Success: True


[rtd-command-info] start-time: 2023-06-20T09:52:08.989622Z, end-time: 2023-06-20T09:52:21.265700Z, duration: 12, exit-code: 0
git clone --no-single-branch --depth 50 https://github.com/scverse/scanpy-tutorials.git .
Cloning into '.'...

[rtd-command-info] start-time: 2023-06-20T09:52:21.563506Z, end-time: 2023-06-20T09:52:21.986215Z, 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 f7f678c Fix RTD config (#70)

[rtd-command-info] start-time: 2023-06-20T09:52:22.191256Z, end-time: 2023-06-20T09:52:22.261315Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2023-06-20T09:52:29.076168Z, end-time: 2023-06-20T09:52:29.173564Z, duration: 0, exit-code: 0
asdf global python 3.11.0


[rtd-command-info] start-time: 2023-06-20T09:52:30.196939Z, end-time: 2023-06-20T09:52:31.181628Z, duration: 0, exit-code: 0
python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH
created virtual environment CPython3.11.0.final.0-64 in 594ms
  creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/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: 2023-06-20T09:52:31.445776Z, end-time: 2023-06-20T09:52:41.589663Z, duration: 10, 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-tutorials/envs/latest/lib/python3.11/site-packages (21.2.3)
Collecting pip
  Downloading pip-23.1.2-py3-none-any.whl (2.1 MB)
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.11/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-23.1.2 setuptools-68.0.0

[rtd-command-info] start-time: 2023-06-20T09:52:41.871458Z, end-time: 2023-06-20T09:52:49.279048Z, duration: 7, exit-code: 0
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
Collecting pillow
  Downloading Pillow-9.5.0-cp311-cp311-manylinux_2_28_x86_64.whl (3.4 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.4/3.4 MB 14.7 MB/s eta 0:00:00
Collecting mock==1.0.1
  Downloading mock-1.0.1.zip (861 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 861.9/861.9 kB 35.3 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-0.7.13-py3-none-any.whl (13 kB)
Collecting commonmark==0.9.1
  Downloading commonmark-0.9.1-py2.py3-none-any.whl (51 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 51.1/51.1 kB 226.0 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 46.7 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 78.8 MB/s eta 0:00:00
Collecting readthedocs-sphinx-ext<2.3
  Downloading readthedocs_sphinx_ext-2.2.1-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 264.3 MB/s eta 0:00:00
Collecting docutils>=0.11 (from recommonmark==0.5.0)
  Downloading docutils-0.20.1-py3-none-any.whl (572 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 572.7/572.7 kB 237.5 MB/s eta 0:00:00
Collecting six>=1.5 (from sphinx<2)
  Downloading six-1.16.0-py2.py3-none-any.whl (11 kB)
Collecting Pygments>=2.0 (from sphinx<2)
  Downloading Pygments-2.15.1-py3-none-any.whl (1.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 136.2 MB/s eta 0:00:00
Collecting docutils>=0.11 (from recommonmark==0.5.0)
  Downloading docutils-0.17.1-py2.py3-none-any.whl (575 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 575.5/575.5 kB 231.6 MB/s eta 0:00:00
Collecting snowballstemmer>=1.1 (from sphinx<2)
  Downloading snowballstemmer-2.2.0-py2.py3-none-any.whl (93 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 93.0/93.0 kB 259.3 MB/s eta 0:00:00
Collecting babel!=2.0,>=1.3 (from sphinx<2)
  Downloading Babel-2.12.1-py3-none-any.whl (10.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 10.1/10.1 MB 145.7 MB/s eta 0:00:00
Collecting imagesize (from sphinx<2)
  Downloading imagesize-1.4.1-py2.py3-none-any.whl (8.8 kB)
Collecting requests>=2.0.0 (from sphinx<2)
  Downloading requests-2.31.0-py3-none-any.whl (62 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.6/62.6 kB 246.9 MB/s eta 0:00:00
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.11/site-packages (from sphinx<2) (68.0.0)
Collecting packaging (from sphinx<2)
  Downloading packaging-23.1-py3-none-any.whl (48 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 48.9/48.9 kB 240.4 MB/s eta 0:00:00
Collecting sphinxcontrib-websupport (from sphinx<2)
  Downloading sphinxcontrib_websupport-1.2.4-py2.py3-none-any.whl (39 kB)
Collecting MarkupSafe>=2.0 (from jinja2<3.1.0)
  Downloading MarkupSafe-2.1.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (28 kB)
Collecting charset-normalizer<4,>=2 (from requests>=2.0.0->sphinx<2)
  Downloading charset_normalizer-3.1.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (197 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 197.3/197.3 kB 268.9 MB/s eta 0:00:00
Collecting idna<4,>=2.5 (from requests>=2.0.0->sphinx<2)
  Downloading idna-3.4-py3-none-any.whl (61 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 61.5/61.5 kB 242.3 MB/s eta 0:00:00
Collecting urllib3<3,>=1.21.1 (from requests>=2.0.0->sphinx<2)
  Downloading urllib3-2.0.3-py3-none-any.whl (123 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 123.6/123.6 kB 253.5 MB/s eta 0:00:00
Collecting certifi>=2017.4.17 (from requests>=2.0.0->sphinx<2)
  Downloading certifi-2023.5.7-py3-none-any.whl (156 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 157.0/157.0 kB 287.8 MB/s eta 0:00:00
Collecting sphinxcontrib-serializinghtml (from sphinxcontrib-websupport->sphinx<2)
  Downloading sphinxcontrib_serializinghtml-1.1.5-py2.py3-none-any.whl (94 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 94.0/94.0 kB 263.3 MB/s eta 0:00:00
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=74634ba5b1594fe927b69c3f252672c450514527708ecc2ab26c00ee903ba012
  Stored in directory: /tmp/pip-ephem-wheel-cache-wxu4s5mh/wheels/80/c2/c8/630c9eb889f0be0202cb11bf30b47aa54bf7588e8d50b70005
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-3.1.0 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-9.5.0 readthedocs-sphinx-ext-2.2.1 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 urllib3-2.0.3

[rtd-command-info] start-time: 2023-06-20T09:52:49.571387Z, end-time: 2023-06-20T09:53:22.560134Z, duration: 32, exit-code: 0
python -m pip install --exists-action=w --no-cache-dir -r requirements.txt
Requirement already satisfied: sphinx>=1.4 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.11/site-packages (from -r requirements.txt (line 1)) (1.8.6)
Collecting ipykernel (from -r requirements.txt (line 2))
  Downloading ipykernel-6.23.2-py3-none-any.whl (152 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 152.8/152.8 kB 4.2 MB/s eta 0:00:00
Collecting nbsphinx>=0.4 (from -r requirements.txt (line 3))
  Downloading nbsphinx-0.9.2-py3-none-any.whl (30 kB)
Collecting nbclean (from -r requirements.txt (line 4))
  Downloading nbclean-0.3.2-py2.py3-none-any.whl (21 kB)
Requirement already satisfied: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.11/site-packages (from sphinx>=1.4->-r requirements.txt (line 1)) (1.16.0)
Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.11/site-packages (from sphinx>=1.4->-r requirements.txt (line 1)) (3.0.3)
Requirement already satisfied: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.11/site-packages (from sphinx>=1.4->-r requirements.txt (line 1)) (2.15.1)
Requirement already satisfied: docutils<0.18,>=0.11 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.11/site-packages (from sphinx>=1.4->-r requirements.txt (line 1)) (0.17.1)
Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.11/site-packages (from sphinx>=1.4->-r requirements.txt (line 1)) (2.2.0)
Requirement already satisfied: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.11/site-packages (from sphinx>=1.4->-r requirements.txt (line 1)) (2.12.1)
Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.11/site-packages (from sphinx>=1.4->-r requirements.txt (line 1)) (0.7.13)
Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.11/site-packages (from sphinx>=1.4->-r requirements.txt (line 1)) (1.4.1)
Requirement already satisfied: requests>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.11/site-packages (from sphinx>=1.4->-r requirements.txt (line 1)) (2.31.0)
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.11/site-packages (from sphinx>=1.4->-r requirements.txt (line 1)) (68.0.0)
Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.11/site-packages (from sphinx>=1.4->-r requirements.txt (line 1)) (23.1)
Requirement already satisfied: sphinxcontrib-websupport in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.11/site-packages (from sphinx>=1.4->-r requirements.txt (line 1)) (1.2.4)
Collecting comm>=0.1.1 (from ipykernel->-r requirements.txt (line 2))
  Downloading comm-0.1.3-py3-none-any.whl (6.6 kB)
Collecting debugpy>=1.6.5 (from ipykernel->-r requirements.txt (line 2))
  Downloading debugpy-1.6.7-py2.py3-none-any.whl (4.9 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.9/4.9 MB 18.6 MB/s eta 0:00:00
Collecting ipython>=7.23.1 (from ipykernel->-r requirements.txt (line 2))
  Downloading ipython-8.14.0-py3-none-any.whl (798 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 798.7/798.7 kB 48.4 MB/s eta 0:00:00
Collecting jupyter-client>=6.1.12 (from ipykernel->-r requirements.txt (line 2))
  Downloading jupyter_client-8.2.0-py3-none-any.whl (103 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 103.2/103.2 kB 258.2 MB/s eta 0:00:00
Collecting jupyter-core!=5.0.*,>=4.12 (from ipykernel->-r requirements.txt (line 2))
  Downloading jupyter_core-5.3.1-py3-none-any.whl (93 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 93.7/93.7 kB 258.7 MB/s eta 0:00:00
Collecting matplotlib-inline>=0.1 (from ipykernel->-r requirements.txt (line 2))
  Downloading matplotlib_inline-0.1.6-py3-none-any.whl (9.4 kB)
Collecting nest-asyncio (from ipykernel->-r requirements.txt (line 2))
  Downloading nest_asyncio-1.5.6-py3-none-any.whl (5.2 kB)
Collecting psutil (from ipykernel->-r requirements.txt (line 2))
  Downloading psutil-5.9.5-cp36-abi3-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (282 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 282.1/282.1 kB 106.9 MB/s eta 0:00:00
Collecting pyzmq>=20 (from ipykernel->-r requirements.txt (line 2))
  Downloading pyzmq-25.1.0-cp311-cp311-manylinux_2_28_x86_64.whl (1.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 50.2 MB/s eta 0:00:00
Collecting tornado>=6.1 (from ipykernel->-r requirements.txt (line 2))
  Downloading tornado-6.3.2-cp38-abi3-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (426 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 426.9/426.9 kB 63.8 MB/s eta 0:00:00
Collecting traitlets>=5.4.0 (from ipykernel->-r requirements.txt (line 2))
  Downloading traitlets-5.9.0-py3-none-any.whl (117 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 117.4/117.4 kB 242.7 MB/s eta 0:00:00
Collecting nbconvert!=5.4 (from nbsphinx>=0.4->-r requirements.txt (line 3))
  Downloading nbconvert-7.6.0-py3-none-any.whl (290 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 290.4/290.4 kB 135.6 MB/s eta 0:00:00
Collecting nbformat (from nbsphinx>=0.4->-r requirements.txt (line 3))
  Downloading nbformat-5.9.0-py3-none-any.whl (77 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 77.6/77.6 kB 255.5 MB/s eta 0:00:00
Collecting numpy (from nbclean->-r requirements.txt (line 4))
  Downloading numpy-1.25.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (17.6 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 17.6/17.6 MB 144.0 MB/s eta 0:00:00
Collecting nbgrader (from nbclean->-r requirements.txt (line 4))
  Downloading nbgrader-0.8.4-py3-none-any.whl (10.8 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 10.8/10.8 MB 212.9 MB/s eta 0:00:00
Collecting matplotlib (from nbclean->-r requirements.txt (line 4))
  Downloading matplotlib-3.7.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.6 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.6/11.6 MB 208.1 MB/s eta 0:00:00
Collecting tqdm (from nbclean->-r requirements.txt (line 4))
  Downloading tqdm-4.65.0-py3-none-any.whl (77 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 77.1/77.1 kB 258.4 MB/s eta 0:00:00
Collecting backcall (from ipython>=7.23.1->ipykernel->-r requirements.txt (line 2))
  Downloading backcall-0.2.0-py2.py3-none-any.whl (11 kB)
Collecting decorator (from ipython>=7.23.1->ipykernel->-r requirements.txt (line 2))
  Downloading decorator-5.1.1-py3-none-any.whl (9.1 kB)
Collecting jedi>=0.16 (from ipython>=7.23.1->ipykernel->-r requirements.txt (line 2))
  Downloading jedi-0.18.2-py2.py3-none-any.whl (1.6 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.6/1.6 MB 243.8 MB/s eta 0:00:00
Collecting pickleshare (from ipython>=7.23.1->ipykernel->-r requirements.txt (line 2))
  Downloading pickleshare-0.7.5-py2.py3-none-any.whl (6.9 kB)
Collecting prompt-toolkit!=3.0.37,<3.1.0,>=3.0.30 (from ipython>=7.23.1->ipykernel->-r requirements.txt (line 2))
  Downloading prompt_toolkit-3.0.38-py3-none-any.whl (385 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 385.8/385.8 kB 272.2 MB/s eta 0:00:00
Collecting stack-data (from ipython>=7.23.1->ipykernel->-r requirements.txt (line 2))
  Downloading stack_data-0.6.2-py3-none-any.whl (24 kB)
Collecting pexpect>4.3 (from ipython>=7.23.1->ipykernel->-r requirements.txt (line 2))
  Downloading pexpect-4.8.0-py2.py3-none-any.whl (59 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 59.0/59.0 kB 241.9 MB/s eta 0:00:00
Requirement already satisfied: MarkupSafe>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.11/site-packages (from Jinja2>=2.3->sphinx>=1.4->-r requirements.txt (line 1)) (2.1.3)
Collecting python-dateutil>=2.8.2 (from jupyter-client>=6.1.12->ipykernel->-r requirements.txt (line 2))
  Downloading python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 247.7/247.7 kB 285.1 MB/s eta 0:00:00
Collecting platformdirs>=2.5 (from jupyter-core!=5.0.*,>=4.12->ipykernel->-r requirements.txt (line 2))
  Downloading platformdirs-3.6.0-py3-none-any.whl (16 kB)
Collecting beautifulsoup4 (from nbconvert!=5.4->nbsphinx>=0.4->-r requirements.txt (line 3))
  Downloading beautifulsoup4-4.12.2-py3-none-any.whl (142 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 143.0/143.0 kB 275.9 MB/s eta 0:00:00
Collecting bleach!=5.0.0 (from nbconvert!=5.4->nbsphinx>=0.4->-r requirements.txt (line 3))
  Downloading bleach-6.0.0-py3-none-any.whl (162 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 162.5/162.5 kB 282.1 MB/s eta 0:00:00
Collecting defusedxml (from nbconvert!=5.4->nbsphinx>=0.4->-r requirements.txt (line 3))
  Downloading defusedxml-0.7.1-py2.py3-none-any.whl (25 kB)
Collecting jupyterlab-pygments (from nbconvert!=5.4->nbsphinx>=0.4->-r requirements.txt (line 3))
  Downloading jupyterlab_pygments-0.2.2-py2.py3-none-any.whl (21 kB)
Collecting mistune<4,>=2.0.3 (from nbconvert!=5.4->nbsphinx>=0.4->-r requirements.txt (line 3))
  Downloading mistune-3.0.1-py3-none-any.whl (47 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 48.0/48.0 kB 230.0 MB/s eta 0:00:00
Collecting nbclient>=0.5.0 (from nbconvert!=5.4->nbsphinx>=0.4->-r requirements.txt (line 3))
  Downloading nbclient-0.8.0-py3-none-any.whl (73 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 73.1/73.1 kB 250.7 MB/s eta 0:00:00
Collecting pandocfilters>=1.4.1 (from nbconvert!=5.4->nbsphinx>=0.4->-r requirements.txt (line 3))
  Downloading pandocfilters-1.5.0-py2.py3-none-any.whl (8.7 kB)
Collecting tinycss2 (from nbconvert!=5.4->nbsphinx>=0.4->-r requirements.txt (line 3))
  Downloading tinycss2-1.2.1-py3-none-any.whl (21 kB)
Collecting fastjsonschema (from nbformat->nbsphinx>=0.4->-r requirements.txt (line 3))
  Downloading fastjsonschema-2.17.1-py3-none-any.whl (23 kB)
Collecting jsonschema>=2.6 (from nbformat->nbsphinx>=0.4->-r requirements.txt (line 3))
  Downloading jsonschema-4.17.3-py3-none-any.whl (90 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 90.4/90.4 kB 245.2 MB/s eta 0:00:00
Requirement already satisfied: charset-normalizer<4,>=2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.11/site-packages (from requests>=2.0.0->sphinx>=1.4->-r requirements.txt (line 1)) (3.1.0)
Requirement already satisfied: idna<4,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.11/site-packages (from requests>=2.0.0->sphinx>=1.4->-r requirements.txt (line 1)) (3.4)
Requirement already satisfied: urllib3<3,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.11/site-packages (from requests>=2.0.0->sphinx>=1.4->-r requirements.txt (line 1)) (2.0.3)
Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.11/site-packages (from requests>=2.0.0->sphinx>=1.4->-r requirements.txt (line 1)) (2023.5.7)
Collecting contourpy>=1.0.1 (from matplotlib->nbclean->-r requirements.txt (line 4))
  Downloading contourpy-1.1.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (300 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 300.4/300.4 kB 288.8 MB/s eta 0:00:00
Collecting cycler>=0.10 (from matplotlib->nbclean->-r requirements.txt (line 4))
  Downloading cycler-0.11.0-py3-none-any.whl (6.4 kB)
Collecting fonttools>=4.22.0 (from matplotlib->nbclean->-r requirements.txt (line 4))
  Downloading fonttools-4.40.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.3 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.3/4.3 MB 218.0 MB/s eta 0:00:00
Collecting kiwisolver>=1.0.1 (from matplotlib->nbclean->-r requirements.txt (line 4))
  Downloading kiwisolver-1.4.4-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.4 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.4/1.4 MB 248.5 MB/s eta 0:00:00
Requirement already satisfied: pillow>=6.2.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.11/site-packages (from matplotlib->nbclean->-r requirements.txt (line 4)) (9.5.0)
Collecting pyparsing>=2.3.1 (from matplotlib->nbclean->-r requirements.txt (line 4))
  Downloading pyparsing-3.1.0-py3-none-any.whl (102 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 102.6/102.6 kB 245.8 MB/s eta 0:00:00
Collecting alembic>=1.7 (from nbgrader->nbclean->-r requirements.txt (line 4))
  Downloading alembic-1.11.1-py3-none-any.whl (224 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 224.5/224.5 kB 266.6 MB/s eta 0:00:00
Collecting ipywidgets>=7.6 (from nbgrader->nbclean->-r requirements.txt (line 4))
  Downloading ipywidgets-8.0.6-py3-none-any.whl (138 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 138.3/138.3 kB 276.3 MB/s eta 0:00:00
Collecting jupyter-server<2,>=1.12 (from nbgrader->nbclean->-r requirements.txt (line 4))
  Downloading jupyter_server-1.24.0-py3-none-any.whl (347 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 347.5/347.5 kB 289.7 MB/s eta 0:00:00
Collecting jupyterlab-server (from nbgrader->nbclean->-r requirements.txt (line 4))
  Downloading jupyterlab_server-2.23.0-py3-none-any.whl (57 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 57.3/57.3 kB 236.0 MB/s eta 0:00:00
Collecting jupyterlab<4 (from nbgrader->nbclean->-r requirements.txt (line 4))
  Downloading jupyterlab-3.6.4-py3-none-any.whl (8.9 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 8.9/8.9 MB 219.0 MB/s eta 0:00:00
Collecting notebook<7,>=6.4 (from nbgrader->nbclean->-r requirements.txt (line 4))
  Downloading notebook-6.5.4-py3-none-any.whl (529 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 529.8/529.8 kB 278.6 MB/s eta 0:00:00
Collecting rapidfuzz>=1.8 (from nbgrader->nbclean->-r requirements.txt (line 4))
  Downloading rapidfuzz-3.1.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.1/3.1 MB 229.8 MB/s eta 0:00:00
Collecting sqlalchemy<3,>=1.4 (from nbgrader->nbclean->-r requirements.txt (line 4))
  Downloading SQLAlchemy-2.0.16-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (2.8 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.8/2.8 MB 226.2 MB/s eta 0:00:00
Requirement already satisfied: sphinxcontrib-serializinghtml in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.11/site-packages (from sphinxcontrib-websupport->sphinx>=1.4->-r requirements.txt (line 1)) (1.1.5)
Collecting Mako (from alembic>=1.7->nbgrader->nbclean->-r requirements.txt (line 4))
  Downloading Mako-1.2.4-py3-none-any.whl (78 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 78.7/78.7 kB 252.5 MB/s eta 0:00:00
Collecting typing-extensions>=4 (from alembic>=1.7->nbgrader->nbclean->-r requirements.txt (line 4))
  Downloading typing_extensions-4.6.3-py3-none-any.whl (31 kB)
Collecting webencodings (from bleach!=5.0.0->nbconvert!=5.4->nbsphinx>=0.4->-r requirements.txt (line 3))
  Downloading webencodings-0.5.1-py2.py3-none-any.whl (11 kB)
Collecting widgetsnbextension~=4.0.7 (from ipywidgets>=7.6->nbgrader->nbclean->-r requirements.txt (line 4))
  Downloading widgetsnbextension-4.0.7-py3-none-any.whl (2.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.1/2.1 MB 246.1 MB/s eta 0:00:00
Collecting jupyterlab-widgets~=3.0.7 (from ipywidgets>=7.6->nbgrader->nbclean->-r requirements.txt (line 4))
  Downloading jupyterlab_widgets-3.0.7-py3-none-any.whl (198 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 198.2/198.2 kB 288.9 MB/s eta 0:00:00
Collecting parso<0.9.0,>=0.8.0 (from jedi>=0.16->ipython>=7.23.1->ipykernel->-r requirements.txt (line 2))
  Downloading parso-0.8.3-py2.py3-none-any.whl (100 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100.8/100.8 kB 265.1 MB/s eta 0:00:00
Collecting attrs>=17.4.0 (from jsonschema>=2.6->nbformat->nbsphinx>=0.4->-r requirements.txt (line 3))
  Downloading attrs-23.1.0-py3-none-any.whl (61 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 61.2/61.2 kB 242.3 MB/s eta 0:00:00
Collecting pyrsistent!=0.17.0,!=0.17.1,!=0.17.2,>=0.14.0 (from jsonschema>=2.6->nbformat->nbsphinx>=0.4->-r requirements.txt (line 3))
  Downloading pyrsistent-0.19.3-py3-none-any.whl (57 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 57.5/57.5 kB 230.0 MB/s eta 0:00:00
Collecting anyio<4,>=3.1.0 (from jupyter-server<2,>=1.12->nbgrader->nbclean->-r requirements.txt (line 4))
  Downloading anyio-3.7.0-py3-none-any.whl (80 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 80.9/80.9 kB 235.7 MB/s eta 0:00:00
Collecting argon2-cffi (from jupyter-server<2,>=1.12->nbgrader->nbclean->-r requirements.txt (line 4))
  Downloading argon2_cffi-21.3.0-py3-none-any.whl (14 kB)
Collecting prometheus-client (from jupyter-server<2,>=1.12->nbgrader->nbclean->-r requirements.txt (line 4))
  Downloading prometheus_client-0.17.0-py3-none-any.whl (60 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 60.6/60.6 kB 240.5 MB/s eta 0:00:00
Collecting Send2Trash (from jupyter-server<2,>=1.12->nbgrader->nbclean->-r requirements.txt (line 4))
  Downloading Send2Trash-1.8.2-py3-none-any.whl (18 kB)
Collecting terminado>=0.8.3 (from jupyter-server<2,>=1.12->nbgrader->nbclean->-r requirements.txt (line 4))
  Downloading terminado-0.17.1-py3-none-any.whl (17 kB)
Collecting websocket-client (from jupyter-server<2,>=1.12->nbgrader->nbclean->-r requirements.txt (line 4))
  Downloading websocket_client-1.6.0-py3-none-any.whl (56 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 56.9/56.9 kB 205.6 MB/s eta 0:00:00
Collecting jupyter-ydoc~=0.2.4 (from jupyterlab<4->nbgrader->nbclean->-r requirements.txt (line 4))
  Downloading jupyter_ydoc-0.2.4-py3-none-any.whl (5.9 kB)
Collecting jupyter-server-ydoc~=0.8.0 (from jupyterlab<4->nbgrader->nbclean->-r requirements.txt (line 4))
  Downloading jupyter_server_ydoc-0.8.0-py3-none-any.whl (11 kB)
Collecting nbclassic (from jupyterlab<4->nbgrader->nbclean->-r requirements.txt (line 4))
  Downloading nbclassic-1.0.0-py3-none-any.whl (10.0 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 10.0/10.0 MB 218.5 MB/s eta 0:00:00
Collecting json5>=0.9.0 (from jupyterlab-server->nbgrader->nbclean->-r requirements.txt (line 4))
  Downloading json5-0.9.14-py2.py3-none-any.whl (19 kB)
Collecting ipython-genutils (from notebook<7,>=6.4->nbgrader->nbclean->-r requirements.txt (line 4))
  Downloading ipython_genutils-0.2.0-py2.py3-none-any.whl (26 kB)
Collecting ptyprocess>=0.5 (from pexpect>4.3->ipython>=7.23.1->ipykernel->-r requirements.txt (line 2))
  Downloading ptyprocess-0.7.0-py2.py3-none-any.whl (13 kB)
Collecting wcwidth (from prompt-toolkit!=3.0.37,<3.1.0,>=3.0.30->ipython>=7.23.1->ipykernel->-r requirements.txt (line 2))
  Downloading wcwidth-0.2.6-py2.py3-none-any.whl (29 kB)
Collecting greenlet!=0.4.17 (from sqlalchemy<3,>=1.4->nbgrader->nbclean->-r requirements.txt (line 4))
  Downloading greenlet-2.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (618 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 618.8/618.8 kB 281.8 MB/s eta 0:00:00
Collecting soupsieve>1.2 (from beautifulsoup4->nbconvert!=5.4->nbsphinx>=0.4->-r requirements.txt (line 3))
  Downloading soupsieve-2.4.1-py3-none-any.whl (36 kB)
Collecting executing>=1.2.0 (from stack-data->ipython>=7.23.1->ipykernel->-r requirements.txt (line 2))
  Downloading executing-1.2.0-py2.py3-none-any.whl (24 kB)
Collecting asttokens>=2.1.0 (from stack-data->ipython>=7.23.1->ipykernel->-r requirements.txt (line 2))
  Downloading asttokens-2.2.1-py2.py3-none-any.whl (26 kB)
Collecting pure-eval (from stack-data->ipython>=7.23.1->ipykernel->-r requirements.txt (line 2))
  Downloading pure_eval-0.2.2-py3-none-any.whl (11 kB)
Collecting sniffio>=1.1 (from anyio<4,>=3.1.0->jupyter-server<2,>=1.12->nbgrader->nbclean->-r requirements.txt (line 4))
  Downloading sniffio-1.3.0-py3-none-any.whl (10 kB)
Collecting jupyter-server-fileid<1,>=0.6.0 (from jupyter-server-ydoc~=0.8.0->jupyterlab<4->nbgrader->nbclean->-r requirements.txt (line 4))
  Downloading jupyter_server_fileid-0.9.0-py3-none-any.whl (15 kB)
Collecting ypy-websocket<0.9.0,>=0.8.2 (from jupyter-server-ydoc~=0.8.0->jupyterlab<4->nbgrader->nbclean->-r requirements.txt (line 4))
  Downloading ypy_websocket-0.8.4-py3-none-any.whl (10 kB)
Collecting y-py<0.6.0,>=0.5.3 (from jupyter-ydoc~=0.2.4->jupyterlab<4->nbgrader->nbclean->-r requirements.txt (line 4))
  Downloading y_py-0.5.9-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.6 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.6/1.6 MB 218.1 MB/s eta 0:00:00
Collecting notebook-shim>=0.2.3 (from nbclassic->jupyterlab<4->nbgrader->nbclean->-r requirements.txt (line 4))
  Downloading notebook_shim-0.2.3-py3-none-any.whl (13 kB)
Collecting argon2-cffi-bindings (from argon2-cffi->jupyter-server<2,>=1.12->nbgrader->nbclean->-r requirements.txt (line 4))
  Downloading argon2_cffi_bindings-21.2.0-cp36-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (86 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 86.2/86.2 kB 258.5 MB/s eta 0:00:00
Collecting jupyter-events>=0.5.0 (from jupyter-server-fileid<1,>=0.6.0->jupyter-server-ydoc~=0.8.0->jupyterlab<4->nbgrader->nbclean->-r requirements.txt (line 4))
  Downloading jupyter_events-0.6.3-py3-none-any.whl (18 kB)
Collecting aiofiles<23,>=22.1.0 (from ypy-websocket<0.9.0,>=0.8.2->jupyter-server-ydoc~=0.8.0->jupyterlab<4->nbgrader->nbclean->-r requirements.txt (line 4))
  Downloading aiofiles-22.1.0-py3-none-any.whl (14 kB)
Collecting aiosqlite<1,>=0.17.0 (from ypy-websocket<0.9.0,>=0.8.2->jupyter-server-ydoc~=0.8.0->jupyterlab<4->nbgrader->nbclean->-r requirements.txt (line 4))
  Downloading aiosqlite-0.19.0-py3-none-any.whl (15 kB)
INFO: pip is looking at multiple versions of ypy-websocket to determine which version is compatible with other requirements. This could take a while.
Collecting ypy-websocket<0.9.0,>=0.8.2 (from jupyter-server-ydoc~=0.8.0->jupyterlab<4->nbgrader->nbclean->-r requirements.txt (line 4))
  Downloading ypy_websocket-0.8.3-py3-none-any.whl (10 kB)
  Downloading ypy_websocket-0.8.2-py3-none-any.whl (10 kB)
Collecting cffi>=1.0.1 (from argon2-cffi-bindings->argon2-cffi->jupyter-server<2,>=1.12->nbgrader->nbclean->-r requirements.txt (line 4))
  Downloading cffi-1.15.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (462 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 462.6/462.6 kB 297.4 MB/s eta 0:00:00
Collecting pycparser (from cffi>=1.0.1->argon2-cffi-bindings->argon2-cffi->jupyter-server<2,>=1.12->nbgrader->nbclean->-r requirements.txt (line 4))
  Downloading pycparser-2.21-py2.py3-none-any.whl (118 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 118.7/118.7 kB 262.5 MB/s eta 0:00:00
Collecting python-json-logger>=2.0.4 (from jupyter-events>=0.5.0->jupyter-server-fileid<1,>=0.6.0->jupyter-server-ydoc~=0.8.0->jupyterlab<4->nbgrader->nbclean->-r requirements.txt (line 4))
  Downloading python_json_logger-2.0.7-py3-none-any.whl (8.1 kB)
Collecting pyyaml>=5.3 (from jupyter-events>=0.5.0->jupyter-server-fileid<1,>=0.6.0->jupyter-server-ydoc~=0.8.0->jupyterlab<4->nbgrader->nbclean->-r requirements.txt (line 4))
  Downloading PyYAML-6.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (757 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 757.9/757.9 kB 283.7 MB/s eta 0:00:00
Collecting rfc3339-validator (from jupyter-events>=0.5.0->jupyter-server-fileid<1,>=0.6.0->jupyter-server-ydoc~=0.8.0->jupyterlab<4->nbgrader->nbclean->-r requirements.txt (line 4))
  Downloading rfc3339_validator-0.1.4-py2.py3-none-any.whl (3.5 kB)
Collecting rfc3986-validator>=0.1.1 (from jupyter-events>=0.5.0->jupyter-server-fileid<1,>=0.6.0->jupyter-server-ydoc~=0.8.0->jupyterlab<4->nbgrader->nbclean->-r requirements.txt (line 4))
  Downloading rfc3986_validator-0.1.1-py2.py3-none-any.whl (4.2 kB)
Collecting fqdn (from jsonschema>=2.6->nbformat->nbsphinx>=0.4->-r requirements.txt (line 3))
  Downloading fqdn-1.5.1-py3-none-any.whl (9.1 kB)
Collecting isoduration (from jsonschema>=2.6->nbformat->nbsphinx>=0.4->-r requirements.txt (line 3))
  Downloading isoduration-20.11.0-py3-none-any.whl (11 kB)
Collecting jsonpointer>1.13 (from jsonschema>=2.6->nbformat->nbsphinx>=0.4->-r requirements.txt (line 3))
  Downloading jsonpointer-2.4-py2.py3-none-any.whl (7.8 kB)
Collecting uri-template (from jsonschema>=2.6->nbformat->nbsphinx>=0.4->-r requirements.txt (line 3))
  Downloading uri_template-1.2.0-py3-none-any.whl (10 kB)
Collecting webcolors>=1.11 (from jsonschema>=2.6->nbformat->nbsphinx>=0.4->-r requirements.txt (line 3))
  Downloading webcolors-1.13-py3-none-any.whl (14 kB)
Collecting arrow>=0.15.0 (from isoduration->jsonschema>=2.6->nbformat->nbsphinx>=0.4->-r requirements.txt (line 3))
  Downloading arrow-1.2.3-py3-none-any.whl (66 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 66.4/66.4 kB 236.2 MB/s eta 0:00:00
Installing collected packages: y-py, webencodings, wcwidth, pure-eval, ptyprocess, pickleshare, json5, ipython-genutils, fastjsonschema, executing, backcall, widgetsnbextension, websocket-client, webcolors, uri-template, typing-extensions, traitlets, tqdm, tornado, tinycss2, soupsieve, sniffio, Send2Trash, rfc3986-validator, rfc3339-validator, rapidfuzz, pyzmq, pyyaml, python-json-logger, python-dateutil, pyrsistent, pyparsing, pycparser, psutil, prompt-toolkit, prometheus-client, platformdirs, pexpect, parso, pandocfilters, numpy, nest-asyncio, mistune, Mako, kiwisolver, jupyterlab-widgets, jupyterlab-pygments, jupyter-ydoc, jsonpointer, greenlet, fqdn, fonttools, defusedxml, decorator, debugpy, cycler, bleach, attrs, asttokens, aiosqlite, aiofiles, ypy-websocket, terminado, stack-data, sqlalchemy, matplotlib-inline, jupyter-core, jsonschema, jedi, contourpy, comm, cffi, beautifulsoup4, arrow, anyio, nbformat, matplotlib, jupyter-client, isoduration, ipython, argon2-cffi-bindings, alembic, nbclient, ipykernel, argon2-cffi, nbconvert, jupyter-events, ipywidgets, nbsphinx, jupyter-server, notebook-shim, jupyterlab-server, jupyter-server-fileid, nbclassic, jupyter-server-ydoc, notebook, jupyterlab, nbgrader, nbclean
Successfully installed Mako-1.2.4 Send2Trash-1.8.2 aiofiles-22.1.0 aiosqlite-0.19.0 alembic-1.11.1 anyio-3.7.0 argon2-cffi-21.3.0 argon2-cffi-bindings-21.2.0 arrow-1.2.3 asttokens-2.2.1 attrs-23.1.0 backcall-0.2.0 beautifulsoup4-4.12.2 bleach-6.0.0 cffi-1.15.1 comm-0.1.3 contourpy-1.1.0 cycler-0.11.0 debugpy-1.6.7 decorator-5.1.1 defusedxml-0.7.1 executing-1.2.0 fastjsonschema-2.17.1 fonttools-4.40.0 fqdn-1.5.1 greenlet-2.0.2 ipykernel-6.23.2 ipython-8.14.0 ipython-genutils-0.2.0 ipywidgets-8.0.6 isoduration-20.11.0 jedi-0.18.2 json5-0.9.14 jsonpointer-2.4 jsonschema-4.17.3 jupyter-client-8.2.0 jupyter-core-5.3.1 jupyter-events-0.6.3 jupyter-server-1.24.0 jupyter-server-fileid-0.9.0 jupyter-server-ydoc-0.8.0 jupyter-ydoc-0.2.4 jupyterlab-3.6.4 jupyterlab-pygments-0.2.2 jupyterlab-server-2.23.0 jupyterlab-widgets-3.0.7 kiwisolver-1.4.4 matplotlib-3.7.1 matplotlib-inline-0.1.6 mistune-3.0.1 nbclassic-1.0.0 nbclean-0.3.2 nbclient-0.8.0 nbconvert-7.6.0 nbformat-5.9.0 nbgrader-0.8.4 nbsphinx-0.9.2 nest-asyncio-1.5.6 notebook-6.5.4 notebook-shim-0.2.3 numpy-1.25.0 pandocfilters-1.5.0 parso-0.8.3 pexpect-4.8.0 pickleshare-0.7.5 platformdirs-3.6.0 prometheus-client-0.17.0 prompt-toolkit-3.0.38 psutil-5.9.5 ptyprocess-0.7.0 pure-eval-0.2.2 pycparser-2.21 pyparsing-3.1.0 pyrsistent-0.19.3 python-dateutil-2.8.2 python-json-logger-2.0.7 pyyaml-6.0 pyzmq-25.1.0 rapidfuzz-3.1.1 rfc3339-validator-0.1.4 rfc3986-validator-0.1.1 sniffio-1.3.0 soupsieve-2.4.1 sqlalchemy-2.0.16 stack-data-0.6.2 terminado-0.17.1 tinycss2-1.2.1 tornado-6.3.2 tqdm-4.65.0 traitlets-5.9.0 typing-extensions-4.6.3 uri-template-1.2.0 wcwidth-0.2.6 webcolors-1.13 webencodings-0.5.1 websocket-client-1.6.0 widgetsnbextension-4.0.7 y-py-0.5.9 ypy-websocket-0.8.2

[rtd-command-info] start-time: 2023-06-20T09:53:24.099116Z, end-time: 2023-06-20T09:53:24.176635Z, duration: 0, exit-code: 0
cat conf.py
from datetime import datetime
project = 'Scanpy'
author = 'Alex Wolf, Fidel Ramirez, Sergei Rybakov'
copyright = f'{datetime.now():%Y}, {author}'

version = ''
release = version

extensions = [
    'nbsphinx',
]

templates_path = ['_templates']
source_suffix = '.rst'
master_doc = 'index'
language = None
exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', '**.ipynb_checkpoints', 'scanpy_workshop/*']
pygments_style = 'sphinx'

# -- Options for HTML output ----------------------------------------------

html_theme = 'sphinx_rtd_theme'
html_theme_options = dict(
    navigation_depth=4, logo_only=True  # Only show the logo
)
html_context = dict(
    display_github=True,      # Integrate GitHub
    github_user='theislab',   # Username
    github_repo='scanpy-tutorials',     # Repo name
    github_version='master',  # Version
    conf_py_path='/',    # Path in the checkout to the docs root
)
html_static_path = ['_static']
html_show_sphinx = False
html_logo = '_static/img/Scanpy_Logo_BrightFG.svg'

def setup(app):
    app.add_stylesheet('css/custom.css')

# -- Strip output ----------------------------------------------

import nbclean, glob

for filename in glob.glob('**/*.ipynb', recursive=True):
    ntbk = nbclean.NotebookCleaner(filename)
    ntbk.clear('stderr')
    ntbk.save(filename)




###########################################################################
#          auto-created readthedocs.org specific configuration            #
###########################################################################


#
# The following code was added during an automated build on readthedocs.org
# It is auto created and injected for every build. The result is based on the
# conf.py.tmpl file found in the readthedocs.org codebase:
# https://github.com/rtfd/readthedocs.org/blob/main/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl
#
# Note: this file shouldn't rely on extra dependencies.

import importlib
import sys
import os.path

# Borrowed from six.
PY3 = sys.version_info[0] == 3
string_types = str if PY3 else basestring

from sphinx import version_info

# Get suffix for proper linking to GitHub
# This is deprecated in Sphinx 1.3+,
# as each page can have its own suffix
if globals().get('source_suffix', False):
    if isinstance(source_suffix, string_types):
        SUFFIX = source_suffix
    elif isinstance(source_suffix, (list, tuple)):
        # Sphinx >= 1.3 supports list/tuple to define multiple suffixes
        SUFFIX = source_suffix[0]
    elif isinstance(source_suffix, dict):
        # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes
        SUFFIX = list(source_suffix.keys())[0]  # make a ``list()`` for py2/py3 compatibility
    else:
        # default to .rst
        SUFFIX = '.rst'
else:
    SUFFIX = '.rst'

# Add RTD Static Path. Add to the end because it overwrites previous files.
if not 'html_static_path' in globals():
    html_static_path = []
if os.path.exists('_static'):
    html_static_path.append('_static')

# Add RTD Theme only if they aren't overriding it already
using_rtd_theme = (
    (
        'html_theme' in globals() and
        html_theme in ['default'] and
        # Allow people to bail with a hack of having an html_style
        'html_style' not in globals()
    ) or 'html_theme' not in globals()
)
if using_rtd_theme:
    html_theme = 'sphinx_rtd_theme'
    html_style = None
    html_theme_options = {}


# This following legacy behavior will gradually be sliced out until its deprecated and removed.
# Skipped for Sphinx 6+
# Skipped by internal Feature flag SKIP_SPHINX_HTML_THEME_PATH
# Skipped by all new projects since SKIP_SPHINX_HTML_THEME_PATH's introduction (jan 2023)
if (
        using_rtd_theme
        and version_info < (6,0)
        and not False
    ):
    theme = importlib.import_module('sphinx_rtd_theme')
    if 'html_theme_path' in globals():
        html_theme_path.append(theme.get_html_theme_path())
    else:
        html_theme_path = [theme.get_html_theme_path()]

# Define websupport2_base_url and websupport2_static_url
if globals().get('websupport2_base_url', False):
    websupport2_base_url = 'https://readthedocs.com/websupport'
    websupport2_static_url = 'https://assets.readthedocs.com/'


#Add project information to the template context.
context = {
    'using_theme': using_rtd_theme,
    'html_theme': html_theme,
    'current_version': "latest",
    'version_slug': "latest",
    'MEDIA_URL': "https://media.readthedocs.com/media/",
    'STATIC_URL': "https://assets.readthedocs.com/",
    'PRODUCTION_DOMAIN': "readthedocs.com",
    'proxied_static_path': "/_/static/",
    'versions': [
    ("latest", "/en/latest/"),
    ("multiomics", "/en/multiomics/"),
    ],
    'downloads': [ 
    ("html", "//scanpy-tutorials.readthedocs.io/_/downloads/en/latest/htmlzip/"),
    ],
    'subprojects': [ 
    ],
    'slug': 'icb-scanpy-tutorials',
    'name': u'scanpy-tutorials',
    'rtd_language': u'en',
    'programming_language': u'py',
    'canonical_url': '',
    'analytics_code': 'None',
    'single_version': False,
    'conf_py_path': '/',
    'api_host': 'https://readthedocs.com',
    'github_user': 'scverse',
    'proxied_api_host': '/_',
    'github_repo': 'scanpy-tutorials',
    'github_version': 'master',
    'display_github': True,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': 'master',
    'display_bitbucket': False,
    'gitlab_user': 'None',
    'gitlab_repo': 'None',
    'gitlab_version': 'master',
    'display_gitlab': False,
    'READTHEDOCS': True,
    'using_theme': (html_theme == "default"),
    'new_theme': (html_theme == "sphinx_rtd_theme"),
    'source_suffix': SUFFIX,
    'ad_free': False,
    'docsearch_disabled': False,
    'user_analytics_code': '',
    'global_analytics_code': 'UA-17997319-2',
    'commit': 'f7f678c9',
}

# For sphinx >=1.8 we can use html_baseurl to set the canonical URL.
# https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_baseurl
if version_info >= (1, 8):
    if not globals().get('html_baseurl'):
        html_baseurl = context['canonical_url']
    context['canonical_url'] = None





if 'html_context' in globals():
    for key in context:
        if key not in html_context:
            html_context[key] = context[key]
else:
    html_context = context

# Add custom RTD extension
if 'extensions' in globals():
    # Insert at the beginning because it can interfere
    # with other extensions.
    # See https://github.com/rtfd/readthedocs.org/pull/4054
    extensions.insert(0, "readthedocs_ext.readthedocs")
else:
    extensions = ["readthedocs_ext.readthedocs"]

# Add External version warning banner to the external version documentation
if 'branch' == 'external':
    extensions.insert(1, "readthedocs_ext.external_version_warning")
    readthedocs_vcs_url = 'None'
    readthedocs_build_url = 'https://readthedocs.com/projects/icb-scanpy-tutorials/builds/1548762/'

project_language = 'en'

# User's Sphinx configurations
language_user = globals().get('language', None)
latex_engine_user = globals().get('latex_engine', None)
latex_elements_user = globals().get('latex_elements', None)

# Remove this once xindy gets installed in Docker image and XINDYOPS
# env variable is supported
# https://github.com/rtfd/readthedocs-docker-images/pull/98
latex_use_xindy = False

chinese = any([
    language_user in ('zh_CN', 'zh_TW'),
    project_language in ('zh_CN', 'zh_TW'),
])

japanese = any([
    language_user == 'ja',
    project_language == 'ja',
])

if chinese:
    latex_engine = latex_engine_user or 'xelatex'

    latex_elements_rtd = {
        'preamble': '\\usepackage[UTF8]{ctex}\n',
    }
    latex_elements = latex_elements_user or latex_elements_rtd
elif japanese:
    latex_engine = latex_engine_user or 'platex'

# Make sure our build directory is always excluded
exclude_patterns = globals().get('exclude_patterns', [])
exclude_patterns.extend(['_build'])

[rtd-command-info] start-time: 2023-06-20T09:53:24.386679Z, end-time: 2023-06-20T09:53:59.142662Z, duration: 34, exit-code: 0
python -m sphinx -T -E -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html
Running Sphinx v1.8.6
loading translations [en]... done
making output directory...
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 11 source files that are out of date
updating environment: 11 added, 0 changed, 0 removed
reading sources... [  9%] README
reading sources... [ 18%] index
reading sources... [ 27%] integrating-data-using-ingest
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.11/site-packages/nbsphinx/__init__.py:1058: RuntimeWarning: You are using an unsupported version of pandoc (2.9.2.1).
Your version must be at least (2.14.2) but less than (4.0.0).
Refer to https://pandoc.org/installing.html.
Continuing with doubts...
  nbconvert.utils.pandoc.check_pandoc_version()
reading sources... [ 36%] paga-paul15
reading sources... [ 45%] pbmc3k
reading sources... [ 54%] plotting/advanced
reading sources... [ 63%] plotting/core
reading sources... [ 72%] spatial/basic-analysis
reading sources... [ 81%] spatial/integration-scanorama
reading sources... [ 90%] tutorial_pearson_residuals
reading sources... [100%] visualizing-marker-genes

/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/latest/spatial/basic-analysis.ipynb:31: WARNING: Content block expected for the "note" directive; none found.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/latest/spatial/integration-scanorama.ipynb:31: WARNING: Content block expected for the "note" directive; none found.
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/latest/plotting/advanced.ipynb: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/latest/tutorial_pearson_residuals.ipynb: WARNING: document isn't included in any toctree
done
preparing documents... done
writing output... [  9%] README
writing output... [ 18%] index
writing output... [ 27%] integrating-data-using-ingest
writing output... [ 36%] paga-paul15
writing output... [ 45%] pbmc3k
writing output... [ 54%] plotting/advanced
writing output... [ 63%] plotting/core
writing output... [ 72%] spatial/basic-analysis
writing output... [ 81%] spatial/integration-scanorama
writing output... [ 90%] tutorial_pearson_residuals
writing output... [100%] visualizing-marker-genes

/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/latest/plotting/advanced.ipynb:13: WARNING: undefined label: /plotting/advanced.ipynb#customization (if the link has no caption the label must precede a section header)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/latest/plotting/advanced.ipynb:13: WARNING: undefined label: /plotting/advanced.ipynb#fig-ax (if the link has no caption the label must precede a section header)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/latest/plotting/advanced.ipynb:13: WARNING: undefined label: /plotting/advanced.ipynb#mpl-ax (if the link has no caption the label must precede a section header)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/latest/plotting/advanced.ipynb:13: WARNING: undefined label: /plotting/advanced.ipynb#size (if the link has no caption the label must precede a section header)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/latest/plotting/advanced.ipynb:13: WARNING: undefined label: /plotting/advanced.ipynb#gap (if the link has no caption the label must precede a section header)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/latest/plotting/advanced.ipynb:13: WARNING: undefined label: /plotting/advanced.ipynb#pretty-axes (if the link has no caption the label must precede a section header)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/latest/plotting/advanced.ipynb:13: WARNING: undefined label: /plotting/advanced.ipynb#legends (if the link has no caption the label must precede a section header)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/latest/plotting/advanced.ipynb:13: WARNING: undefined label: /plotting/advanced.ipynb#marks (if the link has no caption the label must precede a section header)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/latest/plotting/advanced.ipynb:13: WARNING: undefined label: /plotting/advanced.ipynb#colors (if the link has no caption the label must precede a section header)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/latest/plotting/advanced.ipynb:14: WARNING: undefined label: /plotting/advanced.ipynb#umap-subset (if the link has no caption the label must precede a section header)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/latest/plotting/advanced.ipynb:14: WARNING: undefined label: /plotting/advanced.ipynb#umap-order (if the link has no caption the label must precede a section header)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/latest/plotting/advanced.ipynb:14: WARNING: undefined label: /plotting/advanced.ipynb#umap-embed (if the link has no caption the label must precede a section header)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/latest/plotting/advanced.ipynb:14: WARNING: undefined label: /plotting/advanced.ipynb#paga-prune (if the link has no caption the label must precede a section header)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/latest/plotting/advanced.ipynb:14: WARNING: undefined label: /plotting/advanced.ipynb#paga-embed (if the link has no caption the label must precede a section header)
generating indices... genindex
copying notebooks ... [ 12%] integrating-data-using-ingest.ipynb
copying notebooks ... [ 25%] paga-paul15.ipynb
copying notebooks ... [ 37%] pbmc3k.ipynb
copying notebooks ... [ 50%] plotting/advanced.ipynb
copying notebooks ... [ 62%] plotting/core.ipynb
copying notebooks ... [ 75%] spatial/basic-analysis.ipynb
copying notebooks ... [ 87%] spatial/integration-scanorama.ipynb
copying notebooks ... [100%] tutorial_pearson_residuals.ipynb

writing additional pages... search
copying images... [  0%] _build/doctrees/nbsphinx/integrating-data-using-ingest_12_0.png
copying images... [  1%] _build/doctrees/nbsphinx/integrating-data-using-ingest_17_0.png
copying images... [  2%] _build/doctrees/nbsphinx/integrating-data-using-ingest_21_0.png
copying images... [  2%] _build/doctrees/nbsphinx/integrating-data-using-ingest_27_0.png
copying images... [  3%] _build/doctrees/nbsphinx/integrating-data-using-ingest_40_0.png
copying images... [  4%] _build/doctrees/nbsphinx/integrating-data-using-ingest_45_0.png
copying images... [  5%] _build/doctrees/nbsphinx/integrating-data-using-ingest_53_0.png
copying images... [  5%] _build/doctrees/nbsphinx/integrating-data-using-ingest_60_0.png
copying images... [  6%] _build/doctrees/nbsphinx/integrating-data-using-ingest_66_0.png
copying images... [  7%] _build/doctrees/nbsphinx/integrating-data-using-ingest_80_0.png
copying images... [  7%] _build/doctrees/nbsphinx/integrating-data-using-ingest_82_0.png
copying images... [  8%] _build/doctrees/nbsphinx/integrating-data-using-ingest_82_1.png
copying images... [  9%] _build/doctrees/nbsphinx/integrating-data-using-ingest_82_2.png
copying images... [ 10%] _build/doctrees/nbsphinx/paga-paul15_13_0.png
copying images... [ 10%] _build/doctrees/nbsphinx/paga-paul15_19_0.png
copying images... [ 11%] _build/doctrees/nbsphinx/paga-paul15_27_1.png
copying images... [ 12%] _build/doctrees/nbsphinx/paga-paul15_28_1.png
copying images... [ 12%] _build/doctrees/nbsphinx/paga-paul15_35_2.png
copying images... [ 13%] _build/doctrees/nbsphinx/paga-paul15_40_0.png
copying images... [ 14%] _build/doctrees/nbsphinx/paga-paul15_42_0.png
copying images... [ 15%] _build/doctrees/nbsphinx/paga-paul15_47_1.png
copying images... [ 15%] _build/doctrees/nbsphinx/paga-paul15_56_0.png
copying images... [ 16%] _build/doctrees/nbsphinx/paga-paul15_62_0.png
copying images... [ 17%] _build/doctrees/nbsphinx/pbmc3k_15_1.png
copying images... [ 17%] _build/doctrees/nbsphinx/pbmc3k_22_0.png
copying images... [ 18%] _build/doctrees/nbsphinx/pbmc3k_24_0.png
copying images... [ 19%] _build/doctrees/nbsphinx/pbmc3k_24_1.png
copying images... [ 20%] _build/doctrees/nbsphinx/pbmc3k_33_0.png
copying images... [ 20%] _build/doctrees/nbsphinx/pbmc3k_48_0.png
copying images... [ 21%] _build/doctrees/nbsphinx/pbmc3k_50_0.png
copying images... [ 22%] _build/doctrees/nbsphinx/pbmc3k_60_0.png
copying images... [ 22%] _build/doctrees/nbsphinx/pbmc3k_62_0.png
copying images... [ 23%] _build/doctrees/nbsphinx/pbmc3k_67_0.png
copying images... [ 24%] _build/doctrees/nbsphinx/pbmc3k_72_1.png
copying images... [ 25%] _build/doctrees/nbsphinx/pbmc3k_75_1.png
copying images... [ 25%] _build/doctrees/nbsphinx/pbmc3k_79_1.png
copying images... [ 26%] _build/doctrees/nbsphinx/pbmc3k_90_1.png
copying images... [ 27%] _build/doctrees/nbsphinx/pbmc3k_92_0.png
copying images... [ 27%] _build/doctrees/nbsphinx/pbmc3k_95_0.png
copying images... [ 28%] _build/doctrees/nbsphinx/pbmc3k_97_0.png
copying images... [ 29%] _build/doctrees/nbsphinx/pbmc3k_100_1.png
copying images... [ 30%] _build/doctrees/nbsphinx/pbmc3k_102_0.png
copying images... [ 30%] _build/doctrees/nbsphinx/pbmc3k_104_0.png
copying images... [ 31%] plotting/../_build/doctrees/nbsphinx/plotting_advanced_10_1.png
copying images... [ 32%] plotting/../_build/doctrees/nbsphinx/plotting_advanced_12_0.png
copying images... [ 32%] plotting/../_build/doctrees/nbsphinx/plotting_advanced_15_0.png
copying images... [ 33%] plotting/../_build/doctrees/nbsphinx/plotting_advanced_17_0.png
copying images... [ 34%] plotting/../_build/doctrees/nbsphinx/plotting_advanced_19_0.png
copying images... [ 35%] plotting/../_build/doctrees/nbsphinx/plotting_advanced_21_0.png
copying images... [ 35%] plotting/../_build/doctrees/nbsphinx/plotting_advanced_23_0.png
copying images... [ 36%] plotting/../_build/doctrees/nbsphinx/plotting_advanced_24_0.png
copying images... [ 37%] plotting/../_build/doctrees/nbsphinx/plotting_advanced_27_0.png
copying images... [ 37%] plotting/../_build/doctrees/nbsphinx/plotting_advanced_28_0.png
copying images... [ 38%] plotting/../_build/doctrees/nbsphinx/plotting_advanced_29_0.png
copying images... [ 39%] plotting/../_build/doctrees/nbsphinx/plotting_advanced_31_1.png
copying images... [ 40%] plotting/../_build/doctrees/nbsphinx/plotting_advanced_34_0.png
copying images... [ 40%] plotting/../_build/doctrees/nbsphinx/plotting_advanced_36_0.png
copying images... [ 41%] plotting/../_build/doctrees/nbsphinx/plotting_advanced_38_0.png
copying images... [ 42%] plotting/../_build/doctrees/nbsphinx/plotting_advanced_41_0.png
copying images... [ 42%] plotting/../_build/doctrees/nbsphinx/plotting_advanced_43_1.png
copying images... [ 43%] plotting/../_build/doctrees/nbsphinx/plotting_advanced_47_0.png
copying images... [ 44%] plotting/../_build/doctrees/nbsphinx/plotting_advanced_51_0.png
copying images... [ 45%] plotting/../_build/doctrees/nbsphinx/plotting_advanced_52_0.png
copying images... [ 45%] plotting/../_build/doctrees/nbsphinx/plotting_advanced_54_0.png
copying images... [ 46%] plotting/../_build/doctrees/nbsphinx/plotting_advanced_55_0.png
copying images... [ 47%] plotting/../_build/doctrees/nbsphinx/plotting_advanced_60_0.png
copying images... [ 47%] plotting/../_build/doctrees/nbsphinx/plotting_advanced_62_0.png
copying images... [ 48%] plotting/../_build/doctrees/nbsphinx/plotting_advanced_64_0.png
copying images... [ 49%] plotting/../_build/doctrees/nbsphinx/plotting_advanced_66_0.png
copying images... [ 50%] plotting/../_build/doctrees/nbsphinx/plotting_advanced_66_1.png
copying images... [ 50%] plotting/../_build/doctrees/nbsphinx/plotting_advanced_66_2.png
copying images... [ 51%] plotting/../_build/doctrees/nbsphinx/plotting_advanced_66_3.png
copying images... [ 52%] plotting/../_build/doctrees/nbsphinx/plotting_advanced_66_4.png
copying images... [ 52%] plotting/../_build/doctrees/nbsphinx/plotting_advanced_66_5.png
copying images... [ 53%] plotting/../_build/doctrees/nbsphinx/plotting_advanced_66_6.png
copying images... [ 54%] plotting/../_build/doctrees/nbsphinx/plotting_advanced_66_7.png
copying images... [ 55%] plotting/../_build/doctrees/nbsphinx/plotting_advanced_66_8.png
copying images... [ 55%] plotting/../_build/doctrees/nbsphinx/plotting_advanced_70_0.png
copying images... [ 56%] plotting/../_build/doctrees/nbsphinx/plotting_advanced_71_0.png
copying images... [ 57%] plotting/../_build/doctrees/nbsphinx/plotting_advanced_74_0.png
copying images... [ 57%] plotting/../_build/doctrees/nbsphinx/plotting_advanced_75_0.png
copying images... [ 58%] plotting/../_build/doctrees/nbsphinx/plotting_core_12_0.png
copying images... [ 59%] plotting/../_build/doctrees/nbsphinx/plotting_core_14_0.png
copying images... [ 60%] plotting/../_build/doctrees/nbsphinx/plotting_core_17_0.png
copying images... [ 60%] plotting/../_build/doctrees/nbsphinx/plotting_core_22_0.png
copying images... [ 61%] plotting/../_build/doctrees/nbsphinx/plotting_core_25_0.png
copying images... [ 62%] plotting/../_build/doctrees/nbsphinx/plotting_core_26_0.png
copying images... [ 62%] plotting/../_build/doctrees/nbsphinx/plotting_core_29_0.png
copying images... [ 63%] plotting/../_build/doctrees/nbsphinx/plotting_core_31_0.png
copying images... [ 64%] plotting/../_build/doctrees/nbsphinx/plotting_core_34_0.png
copying images... [ 65%] plotting/../_build/doctrees/nbsphinx/plotting_core_37_0.png
copying images... [ 65%] plotting/../_build/doctrees/nbsphinx/plotting_core_40_0.png
copying images... [ 66%] plotting/../_build/doctrees/nbsphinx/plotting_core_43_0.png
copying images... [ 67%] plotting/../_build/doctrees/nbsphinx/plotting_core_46_0.png
copying images... [ 67%] plotting/../_build/doctrees/nbsphinx/plotting_core_48_0.png
copying images... [ 68%] plotting/../_build/doctrees/nbsphinx/plotting_core_51_0.png
copying images... [ 69%] plotting/../_build/doctrees/nbsphinx/plotting_core_57_0.png
copying images... [ 70%] plotting/../_build/doctrees/nbsphinx/plotting_core_59_0.png
copying images... [ 70%] plotting/../_build/doctrees/nbsphinx/plotting_core_62_0.png
copying images... [ 71%] plotting/../_build/doctrees/nbsphinx/plotting_core_64_0.png
copying images... [ 72%] plotting/../_build/doctrees/nbsphinx/plotting_core_66_0.png
copying images... [ 72%] plotting/../_build/doctrees/nbsphinx/plotting_core_68_0.png
copying images... [ 73%] plotting/../_build/doctrees/nbsphinx/plotting_core_70_0.png
copying images... [ 74%] plotting/../_build/doctrees/nbsphinx/plotting_core_72_0.png
copying images... [ 75%] plotting/../_build/doctrees/nbsphinx/plotting_core_74_0.png
copying images... [ 75%] plotting/../_build/doctrees/nbsphinx/plotting_core_74_1.png
copying images... [ 76%] plotting/../_build/doctrees/nbsphinx/plotting_core_74_2.png
copying images... [ 77%] plotting/../_build/doctrees/nbsphinx/plotting_core_74_3.png
copying images... [ 77%] plotting/../_build/doctrees/nbsphinx/plotting_core_74_4.png
copying images... [ 78%] plotting/../_build/doctrees/nbsphinx/plotting_core_74_5.png
copying images... [ 79%] plotting/../_build/doctrees/nbsphinx/plotting_core_74_6.png
copying images... [ 80%] plotting/../_build/doctrees/nbsphinx/plotting_core_74_7.png
copying images... [ 80%] plotting/../_build/doctrees/nbsphinx/plotting_core_74_8.png
copying images... [ 81%] plotting/../_build/doctrees/nbsphinx/plotting_core_77_0.png
copying images... [ 82%] plotting/../_build/doctrees/nbsphinx/plotting_core_80_0.png
copying images... [ 82%] spatial/../_build/doctrees/nbsphinx/spatial_basic-analysis_12_1.png
copying images... [ 83%] spatial/../_build/doctrees/nbsphinx/spatial_basic-analysis_20_0.png
copying images... [ 84%] spatial/../_build/doctrees/nbsphinx/spatial_basic-analysis_23_0.png
copying images... [ 85%] spatial/../_build/doctrees/nbsphinx/spatial_basic-analysis_25_0.png
copying images... [ 85%] spatial/../_build/doctrees/nbsphinx/spatial_basic-analysis_28_0.png
copying images... [ 86%] spatial/../_build/doctrees/nbsphinx/spatial_basic-analysis_31_1.png
copying images... [ 87%] spatial/../_build/doctrees/nbsphinx/spatial_basic-analysis_33_0.png
copying images... [ 87%] spatial/../_build/doctrees/nbsphinx/spatial_basic-analysis_43_0.png
copying images... [ 88%] spatial/../_build/doctrees/nbsphinx/spatial_basic-analysis_56_0.png
copying images... [ 89%] spatial/../_build/doctrees/nbsphinx/spatial_basic-analysis_56_1.png
copying images... [ 90%] spatial/../_build/doctrees/nbsphinx/spatial_integration-scanorama_11_0.png
copying images... [ 90%] spatial/../_build/doctrees/nbsphinx/spatial_integration-scanorama_11_1.png
copying images... [ 91%] spatial/../_build/doctrees/nbsphinx/spatial_integration-scanorama_19_1.png
copying images... [ 92%] spatial/../_build/doctrees/nbsphinx/spatial_integration-scanorama_22_1.png
copying images... [ 92%] spatial/../_build/doctrees/nbsphinx/spatial_integration-scanorama_43_0.png
copying images... [ 93%] spatial/../_build/doctrees/nbsphinx/spatial_integration-scanorama_43_1.png
copying images... [ 94%] spatial/../_build/doctrees/nbsphinx/spatial_integration-scanorama_45_0.png
copying images... [ 95%] spatial/../_build/doctrees/nbsphinx/spatial_integration-scanorama_45_1.png
copying images... [ 95%] _build/doctrees/nbsphinx/tutorial_pearson_residuals_19_1.png
copying images... [ 96%] _build/doctrees/nbsphinx/tutorial_pearson_residuals_19_3.png
copying images... [ 97%] _build/doctrees/nbsphinx/tutorial_pearson_residuals_29_1.png
copying images... [ 97%] _build/doctrees/nbsphinx/tutorial_pearson_residuals_49_1.png
copying images... [ 98%] _build/doctrees/nbsphinx/tutorial_pearson_residuals_49_2.png
copying images... [ 99%] _build/doctrees/nbsphinx/tutorial_pearson_residuals_49_4.png
copying images... [100%] _build/doctrees/nbsphinx/tutorial_pearson_residuals_49_5.png

copying static files... done
copying extra files... done
dumping search index in English (code: en) ... done
dumping object inventory... done
build succeeded, 18 warnings.

The HTML pages are in _readthedocs/html.
Updating searchtools for Read the Docs search...