Read the Docs build information
Build id: 172876
Project: icb-scanpy
Version: latest
Commit: a0d8c5839e234eccf1191f11b4800885b007887e
Date: 2019-01-09T10:00:18.548270Z
State: finished
Success: False


[rtd-command-info] start-time: 2019-01-09T10:00:19.043022Z, end-time: 2019-01-09T10:00:20.294322Z, duration: 1, exit-code: 0
git clone --depth 50 --no-single-branch https://github.com/theislab/scanpy.git .
Cloning into '.'...

[rtd-command-info] start-time: 2019-01-09T10:00:20.616693Z, end-time: 2019-01-09T10:00:20.707229Z, 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 a0d8c58 Fix docs badge

[rtd-command-info] start-time: 2019-01-09T10:00:20.768525Z, end-time: 2019-01-09T10:00:20.775596Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2019-01-09T10:00:21.428727Z, end-time: 2019-01-09T10:00:24.812477Z, duration: 3, exit-code: 0
python3.6 -mvirtualenv --no-site-packages --no-download 
Using base prefix '/home/docs/.pyenv/versions/3.6.2'
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: 2019-01-09T10:00:24.877193Z, end-time: 2019-01-09T10:00:27.339084Z, duration: 2, exit-code: 0
python pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/.cache/pip pip
Collecting pip
  Downloading https://files.pythonhosted.org/packages/c2/d7/90f34cb0d83a6c5631cf71dfe64cc1054598c843a92b400e55675cc2ac37/pip-18.1-py2.py3-none-any.whl (1.3MB)
Installing collected packages: pip
  Found existing installation: pip 9.0.3
    Uninstalling pip-9.0.3:
      Successfully uninstalled pip-9.0.3
Successfully installed pip-18.1

[rtd-command-info] start-time: 2019-01-09T10:00:27.398983Z, end-time: 2019-01-09T10:00:48.866465Z, duration: 21, exit-code: 0
python pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/.cache/pip Pygments==2.2.0 setuptools<40 docutils==0.13.1 mock==1.0.1 pillow==2.6.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.5.4 recommonmark==0.4.0 sphinx<1.8 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<0.6
Collecting Pygments==2.2.0
  Downloading https://files.pythonhosted.org/packages/02/ee/b6e02dc6529e82b75bb06823ff7d005b141037cb1416b10c6f00fc419dca/Pygments-2.2.0-py2.py3-none-any.whl (841kB)
Collecting setuptools<40
  Downloading https://files.pythonhosted.org/packages/7f/e1/820d941153923aac1d49d7fc37e17b6e73bfbd2904959fffbad77900cf92/setuptools-39.2.0-py2.py3-none-any.whl (567kB)
Collecting docutils==0.13.1
  Downloading https://files.pythonhosted.org/packages/7c/30/8fb30d820c012a6f701a66618ce065b6d61d08ac0a77e47fc7808dbaee47/docutils-0.13.1-py3-none-any.whl (536kB)
Collecting mock==1.0.1
  Downloading https://files.pythonhosted.org/packages/a2/52/7edcd94f0afb721a2d559a5b9aae8af4f8f2c79bc63fdbe8a8a6c9b23bbe/mock-1.0.1.tar.gz (818kB)
Collecting pillow==2.6.1
  Downloading https://files.pythonhosted.org/packages/9f/53/9dafa3a48ffa25f4e22f40df880b58b99ad53648f0990caf09b1824d5db2/Pillow-2.6.1.tar.gz (7.3MB)
Collecting alabaster!=0.7.5,<0.8,>=0.7
  Downloading https://files.pythonhosted.org/packages/10/ad/00b090d23a222943eb0eda509720a404f531a439e803f6538f35136cae9e/alabaster-0.7.12-py2.py3-none-any.whl
Collecting commonmark==0.5.4
  Downloading https://files.pythonhosted.org/packages/4d/93/3808cbcebe94d205f55a9a32857df733a603339d32c46cd32669d808d964/CommonMark-0.5.4.tar.gz (120kB)
Collecting recommonmark==0.4.0
  Downloading https://files.pythonhosted.org/packages/df/a5/8ee4b84af7f997dfdba71254a88008cfc19c49df98983c9a4919e798f8ce/recommonmark-0.4.0-py2.py3-none-any.whl
Collecting sphinx<1.8
  Downloading https://files.pythonhosted.org/packages/90/f9/a0babe32c78480994e4f1b93315558f5ed756104054a7029c672a8d77b72/Sphinx-1.7.9-py2.py3-none-any.whl (1.9MB)
Collecting sphinx-rtd-theme<0.5
  Downloading https://files.pythonhosted.org/packages/ef/0c/e4a462190506bc4bff6ca8cf93da07b2d13e540466d2e8a760352d0c69b0/sphinx_rtd_theme-0.4.2-py2.py3-none-any.whl (6.4MB)
Collecting readthedocs-sphinx-ext<0.6
  Downloading https://files.pythonhosted.org/packages/a5/19/abebb2ac7554119cc56d77ce03abcb17b200d6cc3b04dce05cd31248f06f/readthedocs_sphinx_ext-0.5.16-py2.py3-none-any.whl
Collecting six>=1.5 (from sphinx<1.8)
  Downloading https://files.pythonhosted.org/packages/73/fb/00a976f728d0d1fecfe898238ce23f502a721c0ac0ecfedb80e0d88c64e9/six-1.12.0-py2.py3-none-any.whl
Collecting Jinja2>=2.3 (from sphinx<1.8)
  Downloading https://files.pythonhosted.org/packages/7f/ff/ae64bacdfc95f27a016a7bed8e8686763ba4d277a78ca76f32659220a731/Jinja2-2.10-py2.py3-none-any.whl (126kB)
Collecting packaging (from sphinx<1.8)
  Downloading https://files.pythonhosted.org/packages/89/d1/92e6df2e503a69df9faab187c684585f0136662c12bb1f36901d426f3fab/packaging-18.0-py2.py3-none-any.whl
Collecting imagesize (from sphinx<1.8)
  Downloading https://files.pythonhosted.org/packages/fc/b6/aef66b4c52a6ad6ac18cf6ebc5731ed06d8c9ae4d3b2d9951f261150be67/imagesize-1.1.0-py2.py3-none-any.whl
Collecting requests>=2.0.0 (from sphinx<1.8)
  Downloading https://files.pythonhosted.org/packages/7d/e3/20f3d364d6c8e5d2353c72a67778eb189176f08e873c9900e10c0287b84b/requests-2.21.0-py2.py3-none-any.whl (57kB)
Collecting babel!=2.0,>=1.3 (from sphinx<1.8)
  Downloading https://files.pythonhosted.org/packages/b8/ad/c6f60602d3ee3d92fbed87675b6fb6a6f9a38c223343ababdb44ba201f10/Babel-2.6.0-py2.py3-none-any.whl (8.1MB)
Collecting sphinxcontrib-websupport (from sphinx<1.8)
  Downloading https://files.pythonhosted.org/packages/52/69/3c2fbdc3702358c5b34ee25e387b24838597ef099761fc9a42c166796e8f/sphinxcontrib_websupport-1.1.0-py2.py3-none-any.whl
Collecting snowballstemmer>=1.1 (from sphinx<1.8)
  Downloading https://files.pythonhosted.org/packages/d4/6c/8a935e2c7b54a37714656d753e4187ee0631988184ed50c0cf6476858566/snowballstemmer-1.2.1-py2.py3-none-any.whl (64kB)
Collecting MarkupSafe>=0.23 (from Jinja2>=2.3->sphinx<1.8)
  Downloading https://files.pythonhosted.org/packages/08/04/f2191b50fb7f0712f03f064b71d8b4605190f2178ba02e975a87f7b89a0d/MarkupSafe-1.1.0-cp36-cp36m-manylinux1_x86_64.whl
Collecting pyparsing>=2.0.2 (from packaging->sphinx<1.8)
  Downloading https://files.pythonhosted.org/packages/71/e8/6777f6624681c8b9701a8a0a5654f3eb56919a01a78e12bf3c73f5a3c714/pyparsing-2.3.0-py2.py3-none-any.whl (59kB)
Collecting chardet<3.1.0,>=3.0.2 (from requests>=2.0.0->sphinx<1.8)
  Downloading https://files.pythonhosted.org/packages/bc/a9/01ffebfb562e4274b6487b4bb1ddec7ca55ec7510b22e4c51f14098443b8/chardet-3.0.4-py2.py3-none-any.whl (133kB)
Collecting certifi>=2017.4.17 (from requests>=2.0.0->sphinx<1.8)
  Downloading https://files.pythonhosted.org/packages/9f/e0/accfc1b56b57e9750eba272e24c4dddeac86852c2bebd1236674d7887e8a/certifi-2018.11.29-py2.py3-none-any.whl (154kB)
Collecting idna<2.9,>=2.5 (from requests>=2.0.0->sphinx<1.8)
  Downloading https://files.pythonhosted.org/packages/14/2c/cd551d81dbe15200be1cf41cd03869a46fe7226e7450af7a6545bfc474c9/idna-2.8-py2.py3-none-any.whl (58kB)
Collecting urllib3<1.25,>=1.21.1 (from requests>=2.0.0->sphinx<1.8)
  Downloading https://files.pythonhosted.org/packages/62/00/ee1d7de624db8ba7090d1226aebefab96a2c71cd5cfa7629d6ad3f61b79e/urllib3-1.24.1-py2.py3-none-any.whl (118kB)
Collecting pytz>=0a (from babel!=2.0,>=1.3->sphinx<1.8)
  Downloading https://files.pythonhosted.org/packages/61/28/1d3920e4d1d50b19bc5d24398a7cd85cc7b9a75a490570d5a30c57622d34/pytz-2018.9-py2.py3-none-any.whl (510kB)
Building wheels for collected packages: mock, pillow, commonmark
  Running setup.py bdist_wheel for mock: started
  Running setup.py bdist_wheel for mock: finished with status 'done'
  Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/.cache/pip/wheels/7e/72/92/744b532c779242b57aab4bcba80c312b30c069bbd60025e7e6
  Running setup.py bdist_wheel for pillow: started
  Running setup.py bdist_wheel for pillow: finished with status 'done'
  Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/.cache/pip/wheels/de/0e/6b/556798d1ac8762a076ddff5b20f65b2e6cc2ae13b0e683c263
  Running setup.py bdist_wheel for commonmark: started
  Running setup.py bdist_wheel for commonmark: finished with status 'done'
  Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/.cache/pip/wheels/a0/f4/35/019d917f6875107ade3aad634c982f5c6b604c5631cddf20ac
Successfully built mock pillow commonmark
Installing collected packages: Pygments, setuptools, docutils, mock, pillow, alabaster, commonmark, recommonmark, six, MarkupSafe, Jinja2, pyparsing, packaging, imagesize, chardet, certifi, idna, urllib3, requests, pytz, babel, sphinxcontrib-websupport, snowballstemmer, sphinx, sphinx-rtd-theme, readthedocs-sphinx-ext
  Found existing installation: setuptools 39.0.1
    Uninstalling setuptools-39.0.1:
      Successfully uninstalled setuptools-39.0.1
Successfully installed Jinja2-2.10 MarkupSafe-1.1.0 Pygments-2.2.0 alabaster-0.7.12 babel-2.6.0 certifi-2018.11.29 chardet-3.0.4 commonmark-0.5.4 docutils-0.13.1 idna-2.8 imagesize-1.1.0 mock-1.0.1 packaging-18.0 pillow-2.6.1 pyparsing-2.3.0 pytz-2018.9 readthedocs-sphinx-ext-0.5.16 recommonmark-0.4.0 requests-2.21.0 setuptools-39.2.0 six-1.12.0 snowballstemmer-1.2.1 sphinx-1.7.9 sphinx-rtd-theme-0.4.2 sphinxcontrib-websupport-1.1.0 urllib3-1.24.1

[rtd-command-info] start-time: 2019-01-09T10:00:48.932743Z, end-time: 2019-01-09T10:01:16.234195Z, duration: 27, exit-code: 0
python pip install --exists-action=w --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/.cache/pip -r docs/requirements.txt
Requirement already satisfied: sphinx_rtd_theme>=0.3.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 2)) (0.4.2)
Collecting sphinx>=1.8 (from -r docs/requirements.txt (line 4))
  Downloading https://files.pythonhosted.org/packages/0e/5c/e7d076cf2900b38cba5c7d48545953540d86634d391b702067c00d99cb01/Sphinx-1.8.3-py2.py3-none-any.whl (3.1MB)
Collecting sphinx-autodoc-typehints (from -r docs/requirements.txt (line 5))
  Downloading https://files.pythonhosted.org/packages/de/57/e90dba6e31db7b5c4cc9eaab69a56f2c93a498febd188d35c8216da18b6f/sphinx_autodoc_typehints-1.6.0-py3-none-any.whl
Collecting scanpydoc (from -r docs/requirements.txt (line 6))
  Downloading https://files.pythonhosted.org/packages/16/5f/b3957132d2932c80b1c2ed218953bcbb8321b6813dde722206cfaede7799/scanpydoc-0.1.2-py3-none-any.whl (50kB)
Collecting anndata>=0.6.16 (from -r docs/requirements.txt (line 8))
  Downloading https://files.pythonhosted.org/packages/2c/6f/2174c43d4e55ba2324ecc1735f1eb066dbe302b4d25337e149342cf50f6d/anndata-0.6.16.tar.gz (53kB)
Collecting matplotlib>=2.2 (from -r docs/requirements.txt (line 9))
  Downloading https://files.pythonhosted.org/packages/71/07/16d781df15be30df4acfd536c479268f1208b2dfbc91e9ca5d92c9caf673/matplotlib-3.0.2-cp36-cp36m-manylinux1_x86_64.whl (12.9MB)
Collecting pandas>=0.21 (from -r docs/requirements.txt (line 10))
  Downloading https://files.pythonhosted.org/packages/e1/d8/feeb346d41f181e83fba45224ab14a8d8af019b48af742e047f3845d8cff/pandas-0.23.4-cp36-cp36m-manylinux1_x86_64.whl (8.9MB)
Collecting scipy (from -r docs/requirements.txt (line 11))
  Downloading https://files.pythonhosted.org/packages/67/e6/6d4edaceee6a110ecf6f318482f5229792f143e468b34a631f5a0899f56d/scipy-1.2.0-cp36-cp36m-manylinux1_x86_64.whl (26.6MB)
Collecting seaborn (from -r docs/requirements.txt (line 12))
  Downloading https://files.pythonhosted.org/packages/a8/76/220ba4420459d9c4c9c9587c6ce607bf56c25b3d3d2de62056efe482dadc/seaborn-0.9.0-py3-none-any.whl (208kB)
Collecting h5py (from -r docs/requirements.txt (line 13))
  Downloading https://files.pythonhosted.org/packages/30/99/d7d4fbf2d02bb30fb76179911a250074b55b852d34e98dd452a9f394ac06/h5py-2.9.0-cp36-cp36m-manylinux1_x86_64.whl (2.8MB)
Collecting tables (from -r docs/requirements.txt (line 14))
  Downloading https://files.pythonhosted.org/packages/d7/1b/21f4c7f296b718575c17ef25e61c05742a283c45077b4c8d5a190b3e0b59/tables-3.4.4-cp36-cp36m-manylinux1_x86_64.whl (3.8MB)
Collecting scikit-learn>=0.19.1 (from -r docs/requirements.txt (line 15))
  Downloading https://files.pythonhosted.org/packages/0d/3a/b92670f5c368c20329ecc4c255993fae7934564d485c3ed7ea7b8da7f741/scikit_learn-0.20.2-cp36-cp36m-manylinux1_x86_64.whl (5.4MB)
Collecting networkx (from -r docs/requirements.txt (line 17))
  Downloading https://files.pythonhosted.org/packages/f3/f4/7e20ef40b118478191cec0b58c3192f822cace858c19505c7670961b76b2/networkx-2.2.zip (1.7MB)
Collecting natsort (from -r docs/requirements.txt (line 18))
  Downloading https://files.pythonhosted.org/packages/d8/67/9f795649f1173b18851941e288035695386ee44c33bb0960832550f8a236/natsort-5.5.0-py2.py3-none-any.whl
Collecting joblib (from -r docs/requirements.txt (line 19))
  Downloading https://files.pythonhosted.org/packages/0d/1b/995167f6c66848d4eb7eabc386aebe07a1571b397629b2eac3b7bebdc343/joblib-0.13.0-py2.py3-none-any.whl (276kB)
Collecting numba (from -r docs/requirements.txt (line 20))
  Downloading https://files.pythonhosted.org/packages/d4/49/6cbbec05bcbd3502872c3f164df92f7f7a7bfdcb6139c7293d73275b029b/numba-0.42.0-cp36-cp36m-manylinux1_x86_64.whl (3.2MB)
Requirement already satisfied: requests>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=1.8->-r docs/requirements.txt (line 4)) (2.21.0)
Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=1.8->-r docs/requirements.txt (line 4)) (18.0)
Requirement already satisfied: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=1.8->-r docs/requirements.txt (line 4)) (1.12.0)
Requirement already satisfied: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=1.8->-r docs/requirements.txt (line 4)) (2.2.0)
Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=1.8->-r docs/requirements.txt (line 4)) (0.7.12)
Requirement already satisfied: sphinxcontrib-websupport in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=1.8->-r docs/requirements.txt (line 4)) (1.1.0)
Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=1.8->-r docs/requirements.txt (line 4)) (1.2.1)
Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=1.8->-r docs/requirements.txt (line 4)) (1.1.0)
Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=1.8->-r docs/requirements.txt (line 4)) (2.10)
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=1.8->-r docs/requirements.txt (line 4)) (39.2.0)
Requirement already satisfied: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=1.8->-r docs/requirements.txt (line 4)) (2.6.0)
Requirement already satisfied: docutils>=0.11 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=1.8->-r docs/requirements.txt (line 4)) (0.13.1)
Collecting get_version (from scanpydoc->-r docs/requirements.txt (line 6))
  Downloading https://files.pythonhosted.org/packages/2d/27/610ef458455cb1bcc4b454cebab43de3579e43d080af872727b9ac3146c8/get_version-2.0.6-py3-none-any.whl (43kB)
Collecting future-fstrings (from scanpydoc->-r docs/requirements.txt (line 6))
  Downloading https://files.pythonhosted.org/packages/90/32/6bb42916d91cf9e548f90b95f15c5d951c691c29b97d4a7ec9385d6c1700/future_fstrings-0.4.4-py2.py3-none-any.whl
Collecting numpy~=1.14 (from anndata>=0.6.16->-r docs/requirements.txt (line 8))
  Downloading https://files.pythonhosted.org/packages/ff/7f/9d804d2348471c67a7d8b5f84f9bc59fd1cefa148986f2b74552f8573555/numpy-1.15.4-cp36-cp36m-manylinux1_x86_64.whl (13.9MB)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from matplotlib>=2.2->-r docs/requirements.txt (line 9)) (2.3.0)
Collecting cycler>=0.10 (from matplotlib>=2.2->-r docs/requirements.txt (line 9))
  Downloading https://files.pythonhosted.org/packages/f7/d2/e07d3ebb2bd7af696440ce7e754c59dd546ffe1bbe732c8ab68b9c834e61/cycler-0.10.0-py2.py3-none-any.whl
Collecting kiwisolver>=1.0.1 (from matplotlib>=2.2->-r docs/requirements.txt (line 9))
  Downloading https://files.pythonhosted.org/packages/69/a7/88719d132b18300b4369fbffa741841cfd36d1e637e1990f27929945b538/kiwisolver-1.0.1-cp36-cp36m-manylinux1_x86_64.whl (949kB)
Collecting python-dateutil>=2.1 (from matplotlib>=2.2->-r docs/requirements.txt (line 9))
  Downloading https://files.pythonhosted.org/packages/74/68/d87d9b36af36f44254a8d512cbfc48369103a3b9e474be9bdfe536abfc45/python_dateutil-2.7.5-py2.py3-none-any.whl (225kB)
Requirement already satisfied: pytz>=2011k in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from pandas>=0.21->-r docs/requirements.txt (line 10)) (2018.9)
Collecting numexpr>=2.5.2 (from tables->-r docs/requirements.txt (line 14))
  Downloading https://files.pythonhosted.org/packages/0e/13/d38d56c4c49e50b35b6912c80d89f856d50aff605c9e3a4dbba91fc3df44/numexpr-2.6.9-cp36-cp36m-manylinux1_x86_64.whl (163kB)
Collecting decorator>=4.3.0 (from networkx->-r docs/requirements.txt (line 17))
  Downloading https://files.pythonhosted.org/packages/bc/bb/a24838832ba35baf52f32ab1a49b906b5f82fb7c76b2f6a7e35e140bac30/decorator-4.3.0-py2.py3-none-any.whl
Collecting llvmlite>=0.27.0dev0 (from numba->-r docs/requirements.txt (line 20))
  Downloading https://files.pythonhosted.org/packages/17/2f/e7f053e8f2616eae980a9a5d352f6cfeff2abb5f88cc0530b23c61713afa/llvmlite-0.27.0-cp36-cp36m-manylinux1_x86_64.whl (16.8MB)
Requirement already satisfied: chardet<3.1.0,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from requests>=2.0.0->sphinx>=1.8->-r docs/requirements.txt (line 4)) (3.0.4)
Requirement already satisfied: urllib3<1.25,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from requests>=2.0.0->sphinx>=1.8->-r docs/requirements.txt (line 4)) (1.24.1)
Requirement already satisfied: idna<2.9,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from requests>=2.0.0->sphinx>=1.8->-r docs/requirements.txt (line 4)) (2.8)
Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from requests>=2.0.0->sphinx>=1.8->-r docs/requirements.txt (line 4)) (2018.11.29)
Requirement already satisfied: 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>=1.8->-r docs/requirements.txt (line 4)) (1.1.0)
Building wheels for collected packages: anndata, networkx
  Running setup.py bdist_wheel for anndata: started
  Running setup.py bdist_wheel for anndata: finished with status 'done'
  Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/.cache/pip/wheels/e2/3f/f7/330ca05f91cbd72aadefc8f43f7b15710431c78f73659afa9c
  Running setup.py bdist_wheel for networkx: started
  Running setup.py bdist_wheel for networkx: finished with status 'done'
  Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/.cache/pip/wheels/68/f8/29/b53346a112a07d30a5a84d53f19aeadaa1a474897c0423af91
Successfully built anndata networkx
Installing collected packages: sphinx, sphinx-autodoc-typehints, future-fstrings, get-version, scanpydoc, numpy, python-dateutil, pandas, scipy, h5py, natsort, anndata, cycler, kiwisolver, matplotlib, seaborn, numexpr, tables, scikit-learn, decorator, networkx, joblib, llvmlite, numba
  Found existing installation: Sphinx 1.7.9
    Uninstalling Sphinx-1.7.9:
      Successfully uninstalled Sphinx-1.7.9
Successfully installed anndata-0.6.16 cycler-0.10.0 decorator-4.3.0 future-fstrings-0.4.4 get-version-2.0.6 h5py-2.9.0 joblib-0.13.0 kiwisolver-1.0.1 llvmlite-0.27.0 matplotlib-3.0.2 natsort-5.5.0 networkx-2.2 numba-0.42.0 numexpr-2.6.9 numpy-1.15.4 pandas-0.23.4 python-dateutil-2.7.5 scanpydoc-0.1.2 scikit-learn-0.20.2 scipy-1.2.0 seaborn-0.9.0 sphinx-1.8.3 sphinx-autodoc-typehints-1.6.0 tables-3.4.4

[rtd-command-info] start-time: 2019-01-09T10:01:16.746407Z, end-time: 2019-01-09T10:01:16.811471Z, duration: 0, exit-code: 0
cat docs/conf.py
import sys
import logging
from pathlib import Path
from datetime import datetime

from jinja2.defaults import DEFAULT_FILTERS

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

HERE = Path(__file__).parent
sys.path.insert(0, str(HERE.parent))
import scanpy  # noqa


logger = logging.getLogger(__name__)


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


needs_sphinx = '1.7'  # autosummary bugfix

# 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',
]

# 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

intersphinx_mapping = dict(
    anndata=('https://anndata.readthedocs.io/en/latest/', None),
    bbknn=('https://bbknn.readthedocs.io/en/latest/', None),
    leidenalg=('https://leidenalg.readthedocs.io/en/latest/', None),
    louvain=('https://louvain-igraph.readthedocs.io/en/latest/', None),
    matplotlib=('https://matplotlib.org/', None),
    numpy=('https://docs.scipy.org/doc/numpy/', None),
    pandas=('http://pandas.pydata.org/pandas-docs/stable/', None),
    python=('https://docs.python.org/3', None),
    scipy=('https://docs.scipy.org/doc/scipy/reference/', None),
    sklearn=('https://scikit-learn.org/stable/', None),
)


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


html_theme = 'sphinx_rtd_theme'
html_theme_options = dict(
    navigation_depth=4,
)
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']


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


# -- 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'),
]


# -- Images for plot functions -------------------------------------------------


def api_image(qualname: str) -> str:
    # I’d like to make this a contextfilter, but the jinja context doesn’t contain the path,
    # so no chance to not hardcode “api/” here.
    path = Path(__file__).parent / 'api' / f'{qualname}.png'
    print(path, path.is_file())
    return f'.. image:: {path.name}\n   :width: 200\n   :align: right' if path.is_file() else ''


# html_context doesn’t apply to autosummary templates ☹
# and there’s no way to insert filters into those templates
# so we have to modify the default filters
DEFAULT_FILTERS['api_image'] = api_image




###########################################################################
#          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
    else:
        SUFFIX = source_suffix[0]
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')
html_static_path.append('/home/docs/checkouts/readthedocs.org/readthedocs/templates/sphinx/_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://media.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://media.readthedocs.com/",
    'PRODUCTION_DOMAIN': "readthedocs.com",
    'versions': [
    ("latest", "/en/latest/"),
    ("stable", "/en/stable/"),
    ("beyondapi", "/en/beyondapi/"),
    ],
    'downloads': [ 
    ("htmlzip", "//readthedocs.com/projects/icb-scanpy/downloads/htmlzip/latest/"),
    ],
    'subprojects': [ 
    ],
    'slug': 'icb-scanpy',
    'name': u'scanpy',
    'rtd_language': u'en',
    'programming_language': u'py',
    'canonical_url': 'https://icb-scanpy.readthedocs-hosted.com/en/latest/',
    'analytics_code': 'None',
    'single_version': False,
    'conf_py_path': '/docs/',
    'api_host': 'https://readthedocs.com',
    'github_user': 'theislab',
    '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,
    'user_analytics_code': '',
    'global_analytics_code': 'UA-17997319-2',
    'commit': 'a0d8c583',
}




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"]

[rtd-command-info] start-time: 2019-01-09T10:01:16.874023Z, end-time: 2019-01-09T10:01:18.235322Z, duration: 1, exit-code: 2
python sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html
Running Sphinx v1.8.3

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/config.py", line 368, in eval_config_file
    execfile_(filename, namespace)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/util/pycompat.py", line 150, in execfile_
    exec_(code, _globals)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/conf.py", line 14, in <module>
    import scanpy  # noqa
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/__init__.py", line 31, in <module>
    from . import tools as tl
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/tools/__init__.py", line 1, in <module>
    from ..preprocessing._simple import pca
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/preprocessing/__init__.py", line 7, in <module>
    from ._combat import combat
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/preprocessing/_combat.py", line 6, in <module>
    import patsy
ModuleNotFoundError: No module named 'patsy'

During handling of the above exception, another exception occurred:

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 303, 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 201, in __init__
    self.config = Config.read(self.confdir, confoverrides or {}, self.tags)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/config.py", line 203, in read
    namespace = eval_config_file(filename, tags)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/config.py", line 380, in eval_config_file
    raise ConfigError(msg % traceback.format_exc())
sphinx.errors.ConfigError: There is a programmable error in your configuration file:

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/config.py", line 368, in eval_config_file
    execfile_(filename, namespace)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/util/pycompat.py", line 150, in execfile_
    exec_(code, _globals)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/conf.py", line 14, in <module>
    import scanpy  # noqa
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/__init__.py", line 31, in <module>
    from . import tools as tl
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/tools/__init__.py", line 1, in <module>
    from ..preprocessing._simple import pca
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/preprocessing/__init__.py", line 7, in <module>
    from ._combat import combat
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/preprocessing/_combat.py", line 6, in <module>
    import patsy
ModuleNotFoundError: No module named 'patsy'


Configuration error:
There is a programmable error in your configuration file:

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/config.py", line 368, in eval_config_file
    execfile_(filename, namespace)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/util/pycompat.py", line 150, in execfile_
    exec_(code, _globals)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/conf.py", line 14, in <module>
    import scanpy  # noqa
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/__init__.py", line 31, in <module>
    from . import tools as tl
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/tools/__init__.py", line 1, in <module>
    from ..preprocessing._simple import pca
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/preprocessing/__init__.py", line 7, in <module>
    from ._combat import combat
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/preprocessing/_combat.py", line 6, in <module>
    import patsy
ModuleNotFoundError: No module named 'patsy'