Read the Docs build information
Build id: 456486
Project: icb-scanpy
Version: latest
Commit: 040e61ff50836d4a6cdd7da7482dcb4ee50d05ae
Date: 2020-10-20T14:40:53.353612Z
State: finished
Success: False


[rtd-command-info] start-time: 2020-10-20T14:40:55.104042Z, end-time: 2020-10-20T14:40:57.422083Z, duration: 2, exit-code: 0
git clone --no-single-branch --depth 50 https://github.com/theislab/scanpy.git .
Cloning into '.'...

[rtd-command-info] start-time: 2020-10-20T14:40:58.020852Z, end-time: 2020-10-20T14:40:58.189896Z, duration: 0, exit-code: 0
git checkout --force origin/master
Note: checking out '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 performing another checkout.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -b with the checkout command again. Example:

  git checkout -b <new-branch-name>

HEAD is now at 040e61f Update ecosystem.rst

[rtd-command-info] start-time: 2020-10-20T14:40:58.676556Z, end-time: 2020-10-20T14:40:58.731395Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2020-10-20T14:41:00.122599Z, end-time: 2020-10-20T14:41:04.275178Z, duration: 4, exit-code: 0
python3.6 -mvirtualenv 
Using base prefix '/home/docs/.pyenv/versions/3.6.8'
New python executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/bin/python3.6
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/bin/python
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2020-10-20T14:41:04.386758Z, end-time: 2020-10-20T14:41:05.164308Z, duration: 0, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip
Requirement already up-to-date: pip in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (20.2.4)

[rtd-command-info] start-time: 2020-10-20T14:41:05.273228Z, end-time: 2020-10-20T14:41:14.092558Z, duration: 8, exit-code: 0
python -m pip install --upgrade --no-cache-dir setuptools==41.0.1 docutils==0.14 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<1.1
Collecting setuptools==41.0.1
  Downloading setuptools-41.0.1-py2.py3-none-any.whl (575 kB)
Collecting docutils==0.14
  Downloading docutils-0.14-py3-none-any.whl (543 kB)
Collecting mock==1.0.1
  Downloading mock-1.0.1.tar.gz (818 kB)
Collecting pillow==5.4.1
  Downloading Pillow-5.4.1-cp36-cp36m-manylinux1_x86_64.whl (2.0 MB)
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)
Collecting recommonmark==0.5.0
  Downloading recommonmark-0.5.0-py2.py3-none-any.whl (9.8 kB)
Collecting sphinx<2
  Downloading Sphinx-1.8.5-py2.py3-none-any.whl (3.1 MB)
Collecting sphinx-rtd-theme<0.5
  Downloading sphinx_rtd_theme-0.4.3-py2.py3-none-any.whl (6.4 MB)
Collecting readthedocs-sphinx-ext<1.1
  Downloading readthedocs_sphinx_ext-1.0.4-py2.py3-none-any.whl (28 kB)
Collecting future
  Downloading future-0.18.2.tar.gz (829 kB)
Collecting requests>=2.0.0
  Downloading requests-2.24.0-py2.py3-none-any.whl (61 kB)
Collecting snowballstemmer>=1.1
  Downloading snowballstemmer-2.0.0-py2.py3-none-any.whl (97 kB)
Collecting babel!=2.0,>=1.3
  Downloading Babel-2.8.0-py2.py3-none-any.whl (8.6 MB)
Collecting six>=1.5
  Downloading six-1.15.0-py2.py3-none-any.whl (10 kB)
Collecting Pygments>=2.0
  Downloading Pygments-2.7.1-py3-none-any.whl (944 kB)
Collecting packaging
  Downloading packaging-20.4-py2.py3-none-any.whl (37 kB)
Collecting imagesize
  Downloading imagesize-1.2.0-py2.py3-none-any.whl (4.8 kB)
Collecting sphinxcontrib-websupport
  Downloading sphinxcontrib_websupport-1.2.4-py2.py3-none-any.whl (39 kB)
Collecting Jinja2>=2.3
  Downloading Jinja2-2.11.2-py2.py3-none-any.whl (125 kB)
Collecting urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1
  Downloading urllib3-1.25.11-py2.py3-none-any.whl (127 kB)
Collecting chardet<4,>=3.0.2
  Downloading chardet-3.0.4-py2.py3-none-any.whl (133 kB)
Collecting certifi>=2017.4.17
  Downloading certifi-2020.6.20-py2.py3-none-any.whl (156 kB)
Collecting idna<3,>=2.5
  Downloading idna-2.10-py2.py3-none-any.whl (58 kB)
Collecting pytz>=2015.7
  Downloading pytz-2020.1-py2.py3-none-any.whl (510 kB)
Collecting pyparsing>=2.0.2
  Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 kB)
Collecting sphinxcontrib-serializinghtml
  Downloading sphinxcontrib_serializinghtml-1.1.4-py2.py3-none-any.whl (89 kB)
Collecting MarkupSafe>=0.23
  Downloading MarkupSafe-1.1.1-cp36-cp36m-manylinux1_x86_64.whl (27 kB)
Building wheels for collected packages: mock, 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=23754 sha256=a666082e982cf740cef953f77c18a9684bbd025e5a34b6b77949a030c84e7fd7
  Stored in directory: /tmp/pip-ephem-wheel-cache-yxcg15u_/wheels/15/fd/39/f238f155700d6d5e6231e82ae3ccf3aa7490a1b17d2073251b
  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=491059 sha256=cbb5953fd1f03c34091d4d473892cff34be8e9b36a7d1e77174b8ea9acf45856
  Stored in directory: /tmp/pip-ephem-wheel-cache-yxcg15u_/wheels/6e/9c/ed/4499c9865ac1002697793e0ae05ba6be33553d098f3347fb94
Successfully built mock future
Installing collected packages: setuptools, docutils, mock, pillow, alabaster, future, commonmark, urllib3, chardet, certifi, idna, requests, snowballstemmer, pytz, babel, six, Pygments, pyparsing, packaging, imagesize, sphinxcontrib-serializinghtml, sphinxcontrib-websupport, MarkupSafe, Jinja2, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext
  Attempting uninstall: setuptools
    Found existing installation: setuptools 50.3.2
    Uninstalling setuptools-50.3.2:
      Successfully uninstalled setuptools-50.3.2
Successfully installed Jinja2-2.11.2 MarkupSafe-1.1.1 Pygments-2.7.1 alabaster-0.7.12 babel-2.8.0 certifi-2020.6.20 chardet-3.0.4 commonmark-0.8.1 docutils-0.14 future-0.18.2 idna-2.10 imagesize-1.2.0 mock-1.0.1 packaging-20.4 pillow-5.4.1 pyparsing-2.4.7 pytz-2020.1 readthedocs-sphinx-ext-1.0.4 recommonmark-0.5.0 requests-2.24.0 setuptools-41.0.1 six-1.15.0 snowballstemmer-2.0.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.4 sphinxcontrib-websupport-1.2.4 urllib3-1.25.11

[rtd-command-info] start-time: 2020-10-20T14:41:14.310997Z, end-time: 2020-10-20T14:41:46.604377Z, duration: 32, exit-code: 0
python -m pip install --upgrade --upgrade-strategy eager --no-cache-dir .[doc]
Processing /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest
  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'
    Preparing wheel metadata: started
    Preparing wheel metadata: finished with status 'done'
Collecting legacy-api-wrap
  Downloading legacy_api_wrap-1.2-py3-none-any.whl (37 kB)
Collecting matplotlib>=3.1.2
  Downloading matplotlib-3.3.2-cp36-cp36m-manylinux1_x86_64.whl (11.6 MB)
Collecting scikit-learn>=0.21.2
  Downloading scikit_learn-0.23.2-cp36-cp36m-manylinux1_x86_64.whl (6.8 MB)
Collecting patsy
  Downloading patsy-0.5.1-py2.py3-none-any.whl (231 kB)
Collecting networkx>=2.3
  Downloading networkx-2.5-py3-none-any.whl (1.6 MB)
Collecting h5py>=2.10.0
  Downloading h5py-2.10.0-cp36-cp36m-manylinux1_x86_64.whl (2.9 MB)
Collecting pandas>=0.21
  Downloading pandas-1.1.3-cp36-cp36m-manylinux1_x86_64.whl (9.5 MB)
Collecting tables
  Downloading tables-3.6.1-cp36-cp36m-manylinux1_x86_64.whl (4.3 MB)
Collecting statsmodels>=0.10.0rc2
  Downloading statsmodels-0.12.0-cp36-cp36m-manylinux1_x86_64.whl (9.5 MB)
Collecting natsort
  Downloading natsort-7.0.1-py3-none-any.whl (33 kB)
Collecting seaborn
  Downloading seaborn-0.11.0-py3-none-any.whl (283 kB)
Collecting importlib-metadata>=0.7; python_version < "3.8"
  Downloading importlib_metadata-2.0.0-py2.py3-none-any.whl (31 kB)
Collecting anndata>=0.7
  Downloading anndata-0.7.4-py3-none-any.whl (118 kB)
Collecting joblib
  Downloading joblib-0.17.0-py3-none-any.whl (301 kB)
Collecting numpy>=1.17.0
  Downloading numpy-1.19.2-cp36-cp36m-manylinux2010_x86_64.whl (14.5 MB)
Collecting sinfo
  Downloading sinfo-0.3.1.tar.gz (23 kB)
Collecting tqdm
  Downloading tqdm-4.50.2-py2.py3-none-any.whl (70 kB)
Collecting umap-learn>=0.3.10
  Downloading umap-learn-0.4.6.tar.gz (69 kB)
Requirement already up-to-date: packaging in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from scanpy==1.6.1.dev46+g040e61f) (20.4)
Collecting scipy>=1.4
  Downloading scipy-1.5.3-cp36-cp36m-manylinux1_x86_64.whl (25.9 MB)
Collecting numba>=0.41.0
  Downloading numba-0.51.2-cp36-cp36m-manylinux2014_x86_64.whl (3.1 MB)
Collecting sphinx<3.1,>3; extra == "doc"
  Downloading Sphinx-3.0.4-py3-none-any.whl (2.8 MB)
Collecting scanpydoc>=0.5; extra == "doc"
  Downloading scanpydoc-0.5.3-py3-none-any.whl (28 kB)
Collecting sphinx-rtd-theme>=0.3.1; extra == "doc"
  Downloading sphinx_rtd_theme-0.5.0-py2.py3-none-any.whl (10.8 MB)
Collecting typing-extensions; python_version < "3.8" and extra == "doc"
  Downloading typing_extensions-3.7.4.3-py3-none-any.whl (22 kB)
Collecting sphinx-autodoc-typehints; extra == "doc"
  Downloading sphinx_autodoc_typehints-1.11.1-py3-none-any.whl (8.7 kB)
Collecting setuptools
  Downloading setuptools-50.3.2-py3-none-any.whl (785 kB)
Collecting get-version>=2.0.4
  Downloading get_version-2.1-py3-none-any.whl (43 kB)
Requirement already up-to-date: certifi>=2020.06.20 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from matplotlib>=3.1.2->scanpy==1.6.1.dev46+g040e61f) (2020.6.20)
Collecting python-dateutil>=2.1
  Downloading python_dateutil-2.8.1-py2.py3-none-any.whl (227 kB)
Collecting pillow>=6.2.0
  Downloading Pillow-8.0.0-cp36-cp36m-manylinux1_x86_64.whl (2.2 MB)
Collecting kiwisolver>=1.0.1
  Downloading kiwisolver-1.2.0-cp36-cp36m-manylinux1_x86_64.whl (88 kB)
Requirement already up-to-date: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from matplotlib>=3.1.2->scanpy==1.6.1.dev46+g040e61f) (2.4.7)
Collecting cycler>=0.10
  Downloading cycler-0.10.0-py2.py3-none-any.whl (6.5 kB)
Collecting threadpoolctl>=2.0.0
  Downloading threadpoolctl-2.1.0-py3-none-any.whl (12 kB)
Requirement already up-to-date: six in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from patsy->scanpy==1.6.1.dev46+g040e61f) (1.15.0)
Collecting decorator>=4.3.0
  Downloading decorator-4.4.2-py2.py3-none-any.whl (9.2 kB)
Requirement already up-to-date: pytz>=2017.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from pandas>=0.21->scanpy==1.6.1.dev46+g040e61f) (2020.1)
Collecting numexpr>=2.6.2
  Downloading numexpr-2.7.1-cp36-cp36m-manylinux1_x86_64.whl (162 kB)
Collecting zipp>=0.5
  Downloading zipp-3.3.1-py3-none-any.whl (5.3 kB)
Collecting stdlib_list
  Downloading stdlib_list-0.7.0-py3-none-any.whl (60 kB)
Collecting llvmlite<0.35,>=0.34.0.dev0
  Downloading llvmlite-0.34.0-cp36-cp36m-manylinux2010_x86_64.whl (24.6 MB)
Requirement already up-to-date: requests>=2.5.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx<3.1,>3; extra == "doc"->scanpy==1.6.1.dev46+g040e61f) (2.24.0)
Requirement already up-to-date: sphinxcontrib-serializinghtml in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx<3.1,>3; extra == "doc"->scanpy==1.6.1.dev46+g040e61f) (1.1.4)
Collecting sphinxcontrib-devhelp
  Downloading sphinxcontrib_devhelp-1.0.2-py2.py3-none-any.whl (84 kB)
Collecting sphinxcontrib-applehelp
  Downloading sphinxcontrib_applehelp-1.0.2-py2.py3-none-any.whl (121 kB)
Collecting docutils>=0.12
  Downloading docutils-0.16-py2.py3-none-any.whl (548 kB)
Collecting sphinxcontrib-qthelp
  Downloading sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl (90 kB)
Requirement already up-to-date: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx<3.1,>3; extra == "doc"->scanpy==1.6.1.dev46+g040e61f) (2.7.1)
Requirement already up-to-date: babel>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx<3.1,>3; extra == "doc"->scanpy==1.6.1.dev46+g040e61f) (2.8.0)
Collecting sphinxcontrib-jsmath
  Downloading sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB)
Requirement already up-to-date: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx<3.1,>3; extra == "doc"->scanpy==1.6.1.dev46+g040e61f) (2.0.0)
Collecting sphinxcontrib-htmlhelp
  Downloading sphinxcontrib_htmlhelp-1.0.3-py2.py3-none-any.whl (96 kB)
Requirement already up-to-date: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx<3.1,>3; extra == "doc"->scanpy==1.6.1.dev46+g040e61f) (2.11.2)
Requirement already up-to-date: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx<3.1,>3; extra == "doc"->scanpy==1.6.1.dev46+g040e61f) (1.2.0)
Requirement already up-to-date: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx<3.1,>3; extra == "doc"->scanpy==1.6.1.dev46+g040e61f) (0.7.12)
Requirement already up-to-date: chardet<4,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from requests>=2.5.0->sphinx<3.1,>3; extra == "doc"->scanpy==1.6.1.dev46+g040e61f) (3.0.4)
Requirement already up-to-date: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from requests>=2.5.0->sphinx<3.1,>3; extra == "doc"->scanpy==1.6.1.dev46+g040e61f) (1.25.11)
Requirement already up-to-date: idna<3,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from requests>=2.5.0->sphinx<3.1,>3; extra == "doc"->scanpy==1.6.1.dev46+g040e61f) (2.10)
Requirement already up-to-date: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from Jinja2>=2.3->sphinx<3.1,>3; extra == "doc"->scanpy==1.6.1.dev46+g040e61f) (1.1.1)
Building wheels for collected packages: scanpy, sinfo, umap-learn
  Building wheel for scanpy (PEP 517): started
  Building wheel for scanpy (PEP 517): finished with status 'done'
  Created wheel for scanpy: filename=scanpy-1.6.1.dev46+g040e61f-py3-none-any.whl size=10142161 sha256=5c30931245bfbebf5b03885f3db9a33b8222fd38228cdc7cc4441042c4a1cfa7
  Stored in directory: /tmp/pip-ephem-wheel-cache-3y7wztm5/wheels/6a/28/ba/610230fded3b65346c81f73a542a95e84cc8e81fb8ff25e962
  Building wheel for sinfo (setup.py): started
  Building wheel for sinfo (setup.py): finished with status 'done'
  Created wheel for sinfo: filename=sinfo-0.3.1-py3-none-any.whl size=7016 sha256=c4573baec8662a1f3e672d408b68e6fdb7077aadf96feff841d25c6d2208314e
  Stored in directory: /tmp/pip-ephem-wheel-cache-3y7wztm5/wheels/f3/57/7c/26afb068dd34e984706ae3b99ef4145c76afcdb8070b4f1244
  Building wheel for umap-learn (setup.py): started
  Building wheel for umap-learn (setup.py): finished with status 'done'
  Created wheel for umap-learn: filename=umap_learn-0.4.6-py3-none-any.whl size=67950 sha256=2aacc891ef4c7129ab3be31e6f605eefcd679d9020c58c1cbe5f6ddd7e9f707d
  Stored in directory: /tmp/pip-ephem-wheel-cache-3y7wztm5/wheels/22/ce/3d/75f6600b4d93c851021aceeec51b7b330c0ad4d9692e69be6a
Successfully built scanpy sinfo umap-learn
Installing collected packages: setuptools, get-version, legacy-api-wrap, python-dateutil, pillow, numpy, kiwisolver, cycler, matplotlib, scipy, threadpoolctl, joblib, scikit-learn, patsy, decorator, networkx, h5py, pandas, numexpr, tables, statsmodels, natsort, seaborn, zipp, importlib-metadata, anndata, stdlib-list, sinfo, tqdm, llvmlite, numba, umap-learn, sphinxcontrib-devhelp, sphinxcontrib-applehelp, docutils, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinx, scanpydoc, sphinx-rtd-theme, typing-extensions, sphinx-autodoc-typehints, scanpy
  Attempting uninstall: setuptools
    Found existing installation: setuptools 41.0.1
    Uninstalling setuptools-41.0.1:
      Successfully uninstalled setuptools-41.0.1
  Attempting uninstall: pillow
    Found existing installation: Pillow 5.4.1
    Uninstalling Pillow-5.4.1:
      Successfully uninstalled Pillow-5.4.1
  Attempting uninstall: docutils
    Found existing installation: docutils 0.14
    Uninstalling docutils-0.14:
      Successfully uninstalled docutils-0.14
  Attempting uninstall: sphinx
    Found existing installation: Sphinx 1.8.5
    Uninstalling Sphinx-1.8.5:
      Successfully uninstalled Sphinx-1.8.5
  Attempting uninstall: sphinx-rtd-theme
    Found existing installation: sphinx-rtd-theme 0.4.3
    Uninstalling sphinx-rtd-theme-0.4.3:
      Successfully uninstalled sphinx-rtd-theme-0.4.3
Successfully installed anndata-0.7.4 cycler-0.10.0 decorator-4.4.2 docutils-0.16 get-version-2.1 h5py-2.10.0 importlib-metadata-2.0.0 joblib-0.17.0 kiwisolver-1.2.0 legacy-api-wrap-1.2 llvmlite-0.34.0 matplotlib-3.3.2 natsort-7.0.1 networkx-2.5 numba-0.51.2 numexpr-2.7.1 numpy-1.19.2 pandas-1.1.3 patsy-0.5.1 pillow-8.0.0 python-dateutil-2.8.1 scanpy-1.6.1.dev46+g040e61f scanpydoc-0.5.3 scikit-learn-0.23.2 scipy-1.5.3 seaborn-0.11.0 setuptools-50.3.2 sinfo-0.3.1 sphinx-3.0.4 sphinx-autodoc-typehints-1.11.1 sphinx-rtd-theme-0.5.0 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-1.0.3 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 statsmodels-0.12.0 stdlib-list-0.7.0 tables-3.6.1 threadpoolctl-2.1.0 tqdm-4.50.2 typing-extensions-3.7.4.3 umap-learn-0.4.6 zipp-3.3.1

[rtd-command-info] start-time: 2020-10-20T14:41:48.960285Z, end-time: 2020-10-20T14:41:49.036417Z, duration: 0, exit-code: 0
cat docs/conf.py
import os
import sys
import warnings
from pathlib import Path
from datetime import datetime

import matplotlib  # noqa

# Don’t use tkinter agg when importing scanpy → … → matplotlib
matplotlib.use('agg')

HERE = Path(__file__).parent
sys.path[:0] = [str(HERE.parent), str(HERE / 'extensions')]
import scanpy  # noqa

on_rtd = os.environ.get('READTHEDOCS') == 'True'

# -- General configuration ------------------------------------------------


nitpicky = True  # Warn about broken links. This is here for a reason: Do not change.
needs_sphinx = '2.0'  # Nicer param docs
suppress_warnings = ['ref.citation']

# General information
project = 'Scanpy'
author = scanpy.__author__
copyright = f'{datetime.now():%Y}, {author}.'
version = scanpy.__version__.replace('.dirty', '')
release = version

# default settings
templates_path = ['_templates']
source_suffix = '.rst'
master_doc = 'index'
default_role = 'literal'
exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
pygments_style = 'sphinx'

extensions = [
    'sphinx.ext.autodoc',
    'sphinx.ext.intersphinx',
    'sphinx.ext.doctest',
    'sphinx.ext.coverage',
    'sphinx.ext.mathjax',
    'sphinx.ext.napoleon',
    'sphinx.ext.autosummary',
    # 'plot_generator',
    # 'plot_directive',
    'sphinx_autodoc_typehints',  # needs to be after napoleon
    # 'ipython_directive',
    # 'ipython_console_highlighting',
    'scanpydoc',
    *[p.stem for p in (HERE / 'extensions').glob('*.py')],
]

# Generate the API documentation when building
autosummary_generate = True
autodoc_member_order = 'bysource'
# autodoc_default_flags = ['members']
napoleon_google_docstring = False
napoleon_numpy_docstring = True
napoleon_include_init_with_doc = False
napoleon_use_rtype = True  # having a separate entry generally helps readability
napoleon_use_param = True
napoleon_custom_sections = [('Params', 'Parameters')]
todo_include_todos = False
api_dir = HERE / 'api'  # function_images

scanpy_tutorials_url = 'https://scanpy-tutorials.readthedocs.io/en/latest/'

intersphinx_mapping = dict(
    anndata=('https://anndata.readthedocs.io/en/stable/', None),
    bbknn=('https://bbknn.readthedocs.io/en/latest/', None),
    cycler=('https://matplotlib.org/cycler/', None),
    h5py=('http://docs.h5py.org/en/stable/', None),
    ipython=('https://ipython.readthedocs.io/en/stable/', None),
    leidenalg=('https://leidenalg.readthedocs.io/en/latest/', None),
    louvain=('https://louvain-igraph.readthedocs.io/en/latest/', None),
    matplotlib=('https://matplotlib.org/', None),
    networkx=('https://networkx.github.io/documentation/networkx-1.10/', None),
    numpy=('https://docs.scipy.org/doc/numpy/', None),
    pandas=('https://pandas.pydata.org/pandas-docs/stable/', None),
    python=('https://docs.python.org/3', None),
    scipy=('https://docs.scipy.org/doc/scipy/reference/', None),
    scvelo=('https://scvelo.readthedocs.io/', None),
    seaborn=('https://seaborn.pydata.org/', None),
    sklearn=('https://scikit-learn.org/stable/', None),
    scanpy_tutorials=(scanpy_tutorials_url, None),
)


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


html_theme = 'scanpydoc'
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',  # Repo name
    github_version='master',  # Version
    conf_py_path='/docs/',  # 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.warningiserror = on_rtd


# -- Options for other output formats ------------------------------------------

htmlhelp_basename = f'{project}doc'
doc_title = f'{project} Documentation'
latex_documents = [(master_doc, f'{project}.tex', doc_title, author, 'manual')]
man_pages = [(master_doc, project, doc_title, [author], 1)]
texinfo_documents = [
    (
        master_doc,
        project,
        doc_title,
        author,
        project,
        'One line description of project.',
        'Miscellaneous',
    )
]


# -- Suppress link warnings ----------------------------------------------------

qualname_overrides = {
    "sklearn.neighbors.dist_metrics.DistanceMetric": "sklearn.neighbors.DistanceMetric",
    # If the docs are built with an old version of numpy, this will make it work:
    "numpy.random.RandomState": "numpy.random.mtrand.RandomState",
    "scanpy.plotting._matrixplot.MatrixPlot": "scanpy.pl.MatrixPlot",
    "scanpy.plotting._dotplot.DotPlot": "scanpy.pl.DotPlot",
    "scanpy.plotting._stacked_violin.StackedViolin": "scanpy.pl.StackedViolin",
}

nitpick_ignore = [
    # Will probably be documented
    ('py:class', 'scanpy._settings.Verbosity'),
    # Currently undocumented: https://github.com/mwaskom/seaborn/issues/1810
    ('py:class', 'seaborn.ClusterGrid'),
    # Won’t be documented
    ('py:class', 'scanpy.plotting._utils._AxesSubplot'),
    ('py:class', 'scanpy._utils.Empty'),
    ('py:class', 'numpy.random.mtrand.RandomState'),
]




###########################################################################
#          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/master/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl
#


import importlib
import sys
import os.path
from six import string_types

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:
    theme = importlib.import_module('sphinx_rtd_theme')
    html_theme = 'sphinx_rtd_theme'
    html_style = None
    html_theme_options = {}
    if 'html_theme_path' in globals():
        html_theme_path.append(theme.get_html_theme_path())
    else:
        html_theme_path = [theme.get_html_theme_path()]

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",
    'versions': [
    ("latest", "/en/latest/"),
    ("stable", "/en/stable/"),
    ("1.4.4.post1", "/en/1.4.4.post1/"),
    ("1.1", "/en/1.1/"),
    ],
    'downloads': [ 
    ],
    'subprojects': [ 
    ],
    'slug': 'icb-scanpy',
    'name': u'scanpy',
    'rtd_language': u'en',
    'programming_language': u'py',
    'canonical_url': 'https://scanpy.readthedocs.io/en/stable/',
    'analytics_code': 'None',
    'single_version': False,
    'conf_py_path': '/docs/',
    'api_host': 'https://readthedocs.com',
    'github_user': 'theislab',
    'proxied_api_host': '/_',
    'github_repo': 'scanpy',
    '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': '040e61ff',
}




if 'html_context' in globals():
    
    html_context.update(context)
    
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")

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: 2020-10-20T14:41:49.432959Z, end-time: 2020-10-20T14:42:06.584530Z, duration: 17, exit-code: 2
python sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html
Running Sphinx v3.0.4
loading translations [en]... done
making output directory... done
loading intersphinx inventory from https://anndata.readthedocs.io/en/stable/objects.inv...
loading intersphinx inventory from https://bbknn.readthedocs.io/en/latest/objects.inv...
loading intersphinx inventory from https://matplotlib.org/cycler/objects.inv...
loading intersphinx inventory from http://docs.h5py.org/en/stable/objects.inv...
loading intersphinx inventory from https://ipython.readthedocs.io/en/stable/objects.inv...
loading intersphinx inventory from https://leidenalg.readthedocs.io/en/latest/objects.inv...
loading intersphinx inventory from https://louvain-igraph.readthedocs.io/en/latest/objects.inv...
loading intersphinx inventory from https://matplotlib.org/objects.inv...
loading intersphinx inventory from https://networkx.github.io/documentation/networkx-1.10/objects.inv...
loading intersphinx inventory from https://docs.scipy.org/doc/numpy/objects.inv...
loading intersphinx inventory from https://pandas.pydata.org/pandas-docs/stable/objects.inv...
loading intersphinx inventory from https://docs.python.org/3/objects.inv...
intersphinx inventory has moved: https://networkx.github.io/documentation/networkx-1.10/objects.inv -> https://networkx.org/documentation/networkx-1.10/objects.inv
loading intersphinx inventory from https://docs.scipy.org/doc/scipy/reference/objects.inv...
loading intersphinx inventory from https://scvelo.readthedocs.io/objects.inv...
loading intersphinx inventory from https://seaborn.pydata.org/objects.inv...
intersphinx inventory has moved: https://docs.scipy.org/doc/numpy/objects.inv -> https://numpy.org/doc/stable/objects.inv
loading intersphinx inventory from https://scikit-learn.org/stable/objects.inv...
loading intersphinx inventory from https://scanpy-tutorials.readthedocs.io/en/latest/objects.inv...
intersphinx inventory has moved: http://docs.h5py.org/en/stable/objects.inv -> https://docs.h5py.org/en/stable/objects.inv

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/cmd/build.py", line 279, in build_main
    args.tags, args.verbosity, args.jobs, args.keep_going)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/application.py", line 277, in __init__
    self._init_builder()
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/application.py", line 333, in _init_builder
    self.events.emit('builder-inited')
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/events.py", line 107, in emit
    results.append(listener.handler(self.app, *args))
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/ext/intersphinx.py", line 239, in load_mappings
    updated = [f.result() for f in concurrent.futures.as_completed(futures)]
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/ext/intersphinx.py", line 239, in <listcomp>
    updated = [f.result() for f in concurrent.futures.as_completed(futures)]
  File "/home/docs/.pyenv/versions/3.6.8/lib/python3.6/concurrent/futures/_base.py", line 425, in result
    return self.__get_result()
  File "/home/docs/.pyenv/versions/3.6.8/lib/python3.6/concurrent/futures/_base.py", line 384, in __get_result
    raise self._exception
  File "/home/docs/.pyenv/versions/3.6.8/lib/python3.6/concurrent/futures/thread.py", line 56, in run
    result = self.fn(*self.args, **self.kwargs)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/ext/intersphinx.py", line 225, in fetch_inventory_group
    "with the following issues:") + "\n" + issues)
  File "/home/docs/.pyenv/versions/3.6.8/lib/python3.6/logging/__init__.py", line 1642, in warning
    self.log(WARNING, msg, *args, **kwargs)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/util/logging.py", line 125, in log
    super().log(level, msg, *args, **kwargs)
  File "/home/docs/.pyenv/versions/3.6.8/lib/python3.6/logging/__init__.py", line 1674, in log
    self.logger.log(level, msg, *args, **kwargs)
  File "/home/docs/.pyenv/versions/3.6.8/lib/python3.6/logging/__init__.py", line 1374, in log
    self._log(level, msg, args, **kwargs)
  File "/home/docs/.pyenv/versions/3.6.8/lib/python3.6/logging/__init__.py", line 1444, in _log
    self.handle(record)
  File "/home/docs/.pyenv/versions/3.6.8/lib/python3.6/logging/__init__.py", line 1454, in handle
    self.callHandlers(record)
  File "/home/docs/.pyenv/versions/3.6.8/lib/python3.6/logging/__init__.py", line 1516, in callHandlers
    hdlr.handle(record)
  File "/home/docs/.pyenv/versions/3.6.8/lib/python3.6/logging/__init__.py", line 861, in handle
    rv = self.filter(record)
  File "/home/docs/.pyenv/versions/3.6.8/lib/python3.6/logging/__init__.py", line 720, in filter
    result = f.filter(record)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/util/logging.py", line 417, in filter
    raise SphinxWarning(message)
sphinx.errors.SphinxWarning: failed to reach any of the inventories with the following issues:
intersphinx inventory 'https://scvelo.readthedocs.io/objects.inv' not fetchable due to <class 'requests.exceptions.HTTPError'>: 502 Server Error: Bad Gateway for url: https://scvelo.readthedocs.io/objects.inv

Warning, treated as error:
failed to reach any of the inventories with the following issues:
intersphinx inventory 'https://scvelo.readthedocs.io/objects.inv' not fetchable due to <class 'requests.exceptions.HTTPError'>: 502 Server Error: Bad Gateway for url: https://scvelo.readthedocs.io/objects.inv