Read the Docs build information
Build id: 265340
Project: icb-scanpy-tutorials
Version: latest
Commit: 0bc9658492503c14b887ca7ccb387a094f8597d4
Date: 2019-12-03T15:28:20.318931Z
State: finished
Success: True


[rtd-command-info] start-time: 2019-12-03T15:28:21.505431Z, end-time: 2019-12-03T15:28:25.302536Z, duration: 3, exit-code: 0
git clone --no-single-branch --depth 50 https://github.com/theislab/scanpy-tutorials.git .
Cloning into '.'...

[rtd-command-info] start-time: 2019-12-03T15:28:25.527261Z, end-time: 2019-12-03T15:28:25.645019Z, 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 0bc9658 Add rtd theme color, remove nonstandard CSS

[rtd-command-info] start-time: 2019-12-03T15:28:25.721148Z, end-time: 2019-12-03T15:28:25.731468Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2019-12-03T15:28:26.908350Z, end-time: 2019-12-03T15:28:31.072265Z, duration: 4, exit-code: 0
python3.6 -mvirtualenv --no-site-packages --no-download 
Using base prefix '/home/docs/.pyenv/versions/3.6.8'
New python executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/bin/python3.6
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/bin/python
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2019-12-03T15:28:31.161193Z, end-time: 2019-12-03T15:28:33.700748Z, duration: 2, exit-code: 0
python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/.cache/pip pip
Collecting pip
  Downloading https://files.pythonhosted.org/packages/00/b6/9cfa56b4081ad13874b0c6f96af8ce16cfbc1cb06bedf8e9164ce5551ec1/pip-19.3.1-py2.py3-none-any.whl (1.4MB)
Installing collected packages: pip
  Found existing installation: pip 19.1.1
    Uninstalling pip-19.1.1:
      Successfully uninstalled pip-19.1.1
Successfully installed pip-19.3.1

[rtd-command-info] start-time: 2019-12-03T15:28:34.707221Z, end-time: 2019-12-03T15:28:47.873179Z, duration: 13, exit-code: 0
python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/.cache/pip Pygments==2.3.1 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 Pygments==2.3.1
  Downloading https://files.pythonhosted.org/packages/13/e5/6d710c9cf96c31ac82657bcfb441df328b22df8564d58d0c4cd62612674c/Pygments-2.3.1-py2.py3-none-any.whl (849kB)
Requirement already up-to-date: setuptools==41.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (41.0.1)
Collecting docutils==0.14
  Downloading https://files.pythonhosted.org/packages/36/fa/08e9e6e0e3cbd1d362c3bbee8d01d0aedb2155c4ac112b19ef3cae8eed8d/docutils-0.14-py3-none-any.whl (543kB)
Collecting mock==1.0.1
  Downloading https://files.pythonhosted.org/packages/a2/52/7edcd94f0afb721a2d559a5b9aae8af4f8f2c79bc63fdbe8a8a6c9b23bbe/mock-1.0.1.tar.gz (818kB)
Collecting pillow==5.4.1
  Downloading https://files.pythonhosted.org/packages/85/5e/e91792f198bbc5a0d7d3055ad552bc4062942d27eaf75c3e2783cf64eae5/Pillow-5.4.1-cp36-cp36m-manylinux1_x86_64.whl (2.0MB)
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==0.8.1
  Downloading https://files.pythonhosted.org/packages/ab/ca/439c88039583a29564a0043186875258e9a4f041fb5c422cd387b8e10175/commonmark-0.8.1-py2.py3-none-any.whl (47kB)
Collecting recommonmark==0.5.0
  Downloading https://files.pythonhosted.org/packages/9b/3d/92ea48401622510e57b4bdaa74dc9db2fb9e9e892324b48f9c02d716a93a/recommonmark-0.5.0-py2.py3-none-any.whl
Collecting sphinx<2
  Downloading https://files.pythonhosted.org/packages/7d/66/a4af242b4348b729b9d46ce5db23943ce9bca7da9bbe2ece60dc27f26420/Sphinx-1.8.5-py2.py3-none-any.whl (3.1MB)
Collecting sphinx-rtd-theme<0.5
  Downloading https://files.pythonhosted.org/packages/60/b4/4df37087a1d36755e3a3bfd2a30263f358d2dea21938240fa02313d45f51/sphinx_rtd_theme-0.4.3-py2.py3-none-any.whl (6.4MB)
Collecting readthedocs-sphinx-ext<1.1
  Downloading https://files.pythonhosted.org/packages/8a/b5/73b740dc7182b4f458de18ab54adaf5698ace3a723569c5e2a748130a314/readthedocs_sphinx_ext-1.0.1-py2.py3-none-any.whl
Collecting future
  Downloading https://files.pythonhosted.org/packages/45/0b/38b06fd9b92dc2b68d58b75f900e97884c45bedd2ff83203d933cf5851c9/future-0.18.2.tar.gz (829kB)
Collecting babel!=2.0,>=1.3
  Downloading https://files.pythonhosted.org/packages/2c/60/f2af68eb046c5de5b1fe6dd4743bf42c074f7141fe7b2737d3061533b093/Babel-2.7.0-py2.py3-none-any.whl (8.4MB)
Collecting sphinxcontrib-websupport
  Downloading https://files.pythonhosted.org/packages/2a/59/d64bda9b7480a84a3569be4dde267c0f6675b255ba63b4c8e84469940457/sphinxcontrib_websupport-1.1.2-py2.py3-none-any.whl
Collecting packaging
  Downloading https://files.pythonhosted.org/packages/cf/94/9672c2d4b126e74c4496c6b3c58a8b51d6419267be9e70660ba23374c875/packaging-19.2-py2.py3-none-any.whl
Collecting requests>=2.0.0
  Downloading https://files.pythonhosted.org/packages/51/bd/23c926cd341ea6b7dd0b2a00aba99ae0f828be89d72b2190f27c11d4b7fb/requests-2.22.0-py2.py3-none-any.whl (57kB)
Collecting snowballstemmer>=1.1
  Downloading https://files.pythonhosted.org/packages/7d/4b/cdf1113a0e88b641893b814e9c36f69a6fda28cd88b62c7f0d858cde3166/snowballstemmer-2.0.0-py2.py3-none-any.whl (97kB)
Collecting six>=1.5
  Downloading https://files.pythonhosted.org/packages/65/26/32b8464df2a97e6dd1b656ed26b2c194606c16fe163c695a992b36c11cdf/six-1.13.0-py2.py3-none-any.whl
Collecting imagesize
  Downloading https://files.pythonhosted.org/packages/fc/b6/aef66b4c52a6ad6ac18cf6ebc5731ed06d8c9ae4d3b2d9951f261150be67/imagesize-1.1.0-py2.py3-none-any.whl
Collecting Jinja2>=2.3
  Downloading https://files.pythonhosted.org/packages/65/e0/eb35e762802015cab1ccee04e8a277b03f1d8e53da3ec3106882ec42558b/Jinja2-2.10.3-py2.py3-none-any.whl (125kB)
Collecting pytz>=2015.7
  Downloading https://files.pythonhosted.org/packages/e7/f9/f0b53f88060247251bf481fa6ea62cd0d25bf1b11a87888e53ce5b7c8ad2/pytz-2019.3-py2.py3-none-any.whl (509kB)
Collecting pyparsing>=2.0.2
  Downloading https://files.pythonhosted.org/packages/c0/0c/fc2e007d9a992d997f04a80125b0f183da7fb554f1de701bbb70a8e7d479/pyparsing-2.4.5-py2.py3-none-any.whl (67kB)
Collecting certifi>=2017.4.17
  Downloading https://files.pythonhosted.org/packages/b9/63/df50cac98ea0d5b006c55a399c3bf1db9da7b5a24de7890bc9cfd5dd9e99/certifi-2019.11.28-py2.py3-none-any.whl (156kB)
Collecting idna<2.9,>=2.5
  Downloading https://files.pythonhosted.org/packages/14/2c/cd551d81dbe15200be1cf41cd03869a46fe7226e7450af7a6545bfc474c9/idna-2.8-py2.py3-none-any.whl (58kB)
Collecting urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1
  Downloading https://files.pythonhosted.org/packages/b4/40/a9837291310ee1ccc242ceb6ebfd9eb21539649f193a7c8c86ba15b98539/urllib3-1.25.7-py2.py3-none-any.whl (125kB)
Collecting chardet<3.1.0,>=3.0.2
  Downloading https://files.pythonhosted.org/packages/bc/a9/01ffebfb562e4274b6487b4bb1ddec7ca55ec7510b22e4c51f14098443b8/chardet-3.0.4-py2.py3-none-any.whl (133kB)
Collecting MarkupSafe>=0.23
  Downloading https://files.pythonhosted.org/packages/b2/5f/23e0023be6bb885d00ffbefad2942bc51a620328ee910f64abe5a8d18dd1/MarkupSafe-1.1.1-cp36-cp36m-manylinux1_x86_64.whl
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-cp36-none-any.whl size=23755 sha256=2fcb85de52f43a8ad8cb8ea38ac024cb32fcff51433c9eb7c27efa120395aaae
  Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/.cache/pip/wheels/7e/72/92/744b532c779242b57aab4bcba80c312b30c069bbd60025e7e6
  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-cp36-none-any.whl size=491058 sha256=3b1b79a10fa6fe2898497d6bd483770797b136e2251d66a82cf9e9bd3c0f402f
  Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/.cache/pip/wheels/8b/99/a0/81daf51dcd359a9377b110a8a886b3895921802d2fc1b2397e
Successfully built mock future
Installing collected packages: Pygments, docutils, mock, pillow, alabaster, future, commonmark, pytz, babel, sphinxcontrib-websupport, six, pyparsing, packaging, certifi, idna, urllib3, chardet, requests, snowballstemmer, imagesize, MarkupSafe, Jinja2, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext
Successfully installed Jinja2-2.10.3 MarkupSafe-1.1.1 Pygments-2.3.1 alabaster-0.7.12 babel-2.7.0 certifi-2019.11.28 chardet-3.0.4 commonmark-0.8.1 docutils-0.14 future-0.18.2 idna-2.8 imagesize-1.1.0 mock-1.0.1 packaging-19.2 pillow-5.4.1 pyparsing-2.4.5 pytz-2019.3 readthedocs-sphinx-ext-1.0.1 recommonmark-0.5.0 requests-2.22.0 six-1.13.0 snowballstemmer-2.0.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-websupport-1.1.2 urllib3-1.25.7

[rtd-command-info] start-time: 2019-12-03T15:28:47.993462Z, end-time: 2019-12-03T15:29:22.042596Z, duration: 34, exit-code: 0
python -m pip install --exists-action=w --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/.cache/pip -r requirements.txt
Requirement already satisfied: sphinx>=1.4 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from -r requirements.txt (line 1)) (1.8.5)
Collecting ipykernel
  Downloading https://files.pythonhosted.org/packages/e1/92/8fec943b5b81078399f969f00557804d884c96fcd0bc296e81a2ed4fd270/ipykernel-5.1.3-py3-none-any.whl (116kB)
Collecting nbsphinx==0.3.5
  Downloading https://files.pythonhosted.org/packages/a2/4a/9cb6871496c823188037018d43d11709776a0b8079eb6f2cff82ca3eebcd/nbsphinx-0.3.5-py2.py3-none-any.whl
Collecting nbclean
  Downloading https://files.pythonhosted.org/packages/ff/f6/c20849f506184cd4a4c732bdebb18da311ab35e9fec54721e32fdc3a69b0/nbclean-0.3.2-py2.py3-none-any.whl
Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from sphinx>=1.4->-r requirements.txt (line 1)) (0.7.12)
Requirement already satisfied: sphinxcontrib-websupport in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from sphinx>=1.4->-r requirements.txt (line 1)) (1.1.2)
Requirement already satisfied: requests>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from sphinx>=1.4->-r requirements.txt (line 1)) (2.22.0)
Requirement already satisfied: docutils>=0.11 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from sphinx>=1.4->-r requirements.txt (line 1)) (0.14)
Requirement already satisfied: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from sphinx>=1.4->-r requirements.txt (line 1)) (1.13.0)
Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from sphinx>=1.4->-r requirements.txt (line 1)) (2.0.0)
Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from sphinx>=1.4->-r requirements.txt (line 1)) (1.1.0)
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from sphinx>=1.4->-r requirements.txt (line 1)) (41.0.1)
Requirement already satisfied: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from sphinx>=1.4->-r requirements.txt (line 1)) (2.3.1)
Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from sphinx>=1.4->-r requirements.txt (line 1)) (19.2)
Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from sphinx>=1.4->-r requirements.txt (line 1)) (2.10.3)
Requirement already satisfied: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from sphinx>=1.4->-r requirements.txt (line 1)) (2.7.0)
Collecting tornado>=4.2
  Downloading https://files.pythonhosted.org/packages/30/78/2d2823598496127b21423baffaa186b668f73cd91887fcef78b6eade136b/tornado-6.0.3.tar.gz (482kB)
Collecting jupyter-client
  Downloading https://files.pythonhosted.org/packages/13/81/fe0eee1bcf949851a120254b1f530ae1e01bdde2d3ab9710c6ff81525061/jupyter_client-5.3.4-py2.py3-none-any.whl (92kB)
Collecting ipython>=5.0.0
  Downloading https://files.pythonhosted.org/packages/00/17/c3e3dd337cc601b47c599441786fd4e888b587a2a512d38ac752274fd0bc/ipython-7.10.1-py3-none-any.whl (778kB)
Collecting traitlets>=4.1.0
  Downloading https://files.pythonhosted.org/packages/ca/ab/872a23e29cec3cf2594af7e857f18b687ad21039c1f9b922fac5b9b142d5/traitlets-4.3.3-py2.py3-none-any.whl (75kB)
Collecting nbformat
  Downloading https://files.pythonhosted.org/packages/da/27/9a654d2b6cc1eaa517d1c5a4405166c7f6d72f04f6e7eea41855fe808a46/nbformat-4.4.0-py2.py3-none-any.whl (155kB)
Collecting nbconvert!=5.4
  Downloading https://files.pythonhosted.org/packages/79/6c/05a569e9f703d18aacb89b7ad6075b404e8a4afde2c26b73ca77bb644b14/nbconvert-5.6.1-py2.py3-none-any.whl (455kB)
Collecting nbgrader
  Downloading https://files.pythonhosted.org/packages/bd/78/35fcf2fdeac19f9afcdd851cba97cade1bf095f55a8065df50094997b478/nbgrader-0.6.1.tar.gz (13.3MB)
Collecting tqdm
  Downloading https://files.pythonhosted.org/packages/a5/13/cd55c23e3e158ed5b87cae415ee3844fc54cb43803fa3a0a064d23ecb883/tqdm-4.40.0-py2.py3-none-any.whl (54kB)
Collecting numpy
  Downloading https://files.pythonhosted.org/packages/d2/ab/43e678759326f728de861edbef34b8e2ad1b1490505f20e0d1f0716c3bf4/numpy-1.17.4-cp36-cp36m-manylinux1_x86_64.whl (20.0MB)
Collecting matplotlib
  Downloading https://files.pythonhosted.org/packages/4e/11/06958a2b895a3853206dea1fb2a5b11bf044f626f90745987612af9c8f2c/matplotlib-3.1.2-cp36-cp36m-manylinux1_x86_64.whl (13.1MB)
Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from requests>=2.0.0->sphinx>=1.4->-r requirements.txt (line 1)) (2019.11.28)
Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from requests>=2.0.0->sphinx>=1.4->-r requirements.txt (line 1)) (1.25.7)
Requirement already satisfied: chardet<3.1.0,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from requests>=2.0.0->sphinx>=1.4->-r requirements.txt (line 1)) (3.0.4)
Requirement already satisfied: idna<2.9,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from requests>=2.0.0->sphinx>=1.4->-r requirements.txt (line 1)) (2.8)
Requirement already satisfied: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from packaging->sphinx>=1.4->-r requirements.txt (line 1)) (2.4.5)
Requirement already satisfied: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from Jinja2>=2.3->sphinx>=1.4->-r requirements.txt (line 1)) (1.1.1)
Requirement already satisfied: pytz>=2015.7 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from babel!=2.0,>=1.3->sphinx>=1.4->-r requirements.txt (line 1)) (2019.3)
Collecting pyzmq>=13
  Downloading https://files.pythonhosted.org/packages/94/07/cee3d328a2e13f9de1c2b62cced7a389b61ac81424f2e377f3dc9d668282/pyzmq-18.1.1-cp36-cp36m-manylinux1_x86_64.whl (1.1MB)
Collecting python-dateutil>=2.1
  Downloading https://files.pythonhosted.org/packages/d4/70/d60450c3dd48ef87586924207ae8907090de0b306af2bce5d134d78615cb/python_dateutil-2.8.1-py2.py3-none-any.whl (227kB)
Collecting jupyter-core>=4.6.0
  Downloading https://files.pythonhosted.org/packages/fb/82/86437f661875e30682e99d04c13ba6c216f86f5f6ca6ef212d3ee8b6ca11/jupyter_core-4.6.1-py2.py3-none-any.whl (82kB)
Collecting prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0
  Downloading https://files.pythonhosted.org/packages/7f/1f/e145dd467dc9b0e6f1e64232c03119498dfec497e383f1e8be9f83eaa97e/prompt_toolkit-3.0.2-py3-none-any.whl (344kB)
Collecting backcall
  Downloading https://files.pythonhosted.org/packages/84/71/c8ca4f5bb1e08401b916c68003acf0a0655df935d74d93bf3f3364b310e0/backcall-0.1.0.tar.gz
Collecting pickleshare
  Downloading https://files.pythonhosted.org/packages/9a/41/220f49aaea88bc6fa6cba8d05ecf24676326156c23b991e80b3f2fc24c77/pickleshare-0.7.5-py2.py3-none-any.whl
Collecting jedi>=0.10
  Downloading https://files.pythonhosted.org/packages/55/54/da994f359e4e7da4776a200e76dbc85ba5fc319eefc22e33d55296d95a1d/jedi-0.15.1-py2.py3-none-any.whl (1.0MB)
Collecting pexpect; sys_platform != "win32"
  Downloading https://files.pythonhosted.org/packages/0e/3e/377007e3f36ec42f1b84ec322ee12141a9e10d808312e5738f52f80a232c/pexpect-4.7.0-py2.py3-none-any.whl (58kB)
Collecting decorator
  Downloading https://files.pythonhosted.org/packages/8f/b7/f329cfdc75f3d28d12c65980e4469e2fa373f1953f5df6e370e84ea2e875/decorator-4.4.1-py2.py3-none-any.whl
Collecting ipython-genutils
  Downloading https://files.pythonhosted.org/packages/fa/bc/9bd3b5c2b4774d5f33b2d544f1460be9df7df2fe42f352135381c347c69a/ipython_genutils-0.2.0-py2.py3-none-any.whl
Collecting jsonschema!=2.5.0,>=2.4
  Downloading https://files.pythonhosted.org/packages/c5/8f/51e89ce52a085483359217bc72cdbf6e75ee595d5b1d4b5ade40c7e018b8/jsonschema-3.2.0-py2.py3-none-any.whl (56kB)
Collecting pandocfilters>=1.4.1
  Downloading https://files.pythonhosted.org/packages/4c/ea/236e2584af67bb6df960832731a6e5325fd4441de001767da328c33368ce/pandocfilters-1.4.2.tar.gz
Collecting defusedxml
  Downloading https://files.pythonhosted.org/packages/06/74/9b387472866358ebc08732de3da6dc48e44b0aacd2ddaa5cb85ab7e986a2/defusedxml-0.6.0-py2.py3-none-any.whl
Collecting entrypoints>=0.2.2
  Downloading https://files.pythonhosted.org/packages/ac/c6/44694103f8c221443ee6b0041f69e2740d89a25641e62fb4f2ee568f2f9c/entrypoints-0.3-py2.py3-none-any.whl
Collecting mistune<2,>=0.8.1
  Downloading https://files.pythonhosted.org/packages/09/ec/4b43dae793655b7d8a25f76119624350b4d65eb663459eb9603d7f1f0345/mistune-0.8.4-py2.py3-none-any.whl
Collecting bleach
  Downloading https://files.pythonhosted.org/packages/ab/05/27e1466475e816d3001efb6e0a85a819be17411420494a1e602c36f8299d/bleach-3.1.0-py2.py3-none-any.whl (157kB)
Collecting testpath
  Downloading https://files.pythonhosted.org/packages/1b/9e/1a170feaa54f22aeb5a5d16c9015e82234275a3c8ab630b552493f9cb8a9/testpath-0.4.4-py2.py3-none-any.whl (163kB)
Collecting sqlalchemy
  Downloading https://files.pythonhosted.org/packages/34/5c/0e1d7ad0ca52544bb12f9cb8d5cc454af45821c92160ffedd38db0a317f6/SQLAlchemy-1.3.11.tar.gz (6.0MB)
Collecting jupyter
  Downloading https://files.pythonhosted.org/packages/83/df/0f5dd132200728a86190397e1ea87cd76244e42d39ec5e88efd25b2abd7e/jupyter-1.0.0-py2.py3-none-any.whl
Collecting notebook>=4.2
  Downloading https://files.pythonhosted.org/packages/f5/69/d2ffaf7efc20ce47469187e3a41e6e03e17b45de5a6559f4e7ab3eace5e1/notebook-6.0.2-py3-none-any.whl (9.7MB)
Collecting alembic
  Downloading https://files.pythonhosted.org/packages/84/64/493c45119dce700a4b9eeecc436ef9e8835ab67bae6414f040cdc7b58f4b/alembic-1.3.1.tar.gz (1.1MB)
Collecting fuzzywuzzy
  Downloading https://files.pythonhosted.org/packages/d8/f1/5a267addb30ab7eaa1beab2b9323073815da4551076554ecc890a3595ec9/fuzzywuzzy-0.17.0-py2.py3-none-any.whl
Collecting cycler>=0.10
  Downloading https://files.pythonhosted.org/packages/f7/d2/e07d3ebb2bd7af696440ce7e754c59dd546ffe1bbe732c8ab68b9c834e61/cycler-0.10.0-py2.py3-none-any.whl
Collecting kiwisolver>=1.0.1
  Downloading https://files.pythonhosted.org/packages/f8/a1/5742b56282449b1c0968197f63eae486eca2c35dcd334bab75ad524e0de1/kiwisolver-1.1.0-cp36-cp36m-manylinux1_x86_64.whl (90kB)
Collecting wcwidth
  Downloading https://files.pythonhosted.org/packages/7e/9f/526a6947247599b084ee5232e4f9190a38f398d7300d866af3ab571a5bfe/wcwidth-0.1.7-py2.py3-none-any.whl
Collecting parso>=0.5.0
  Downloading https://files.pythonhosted.org/packages/a3/bd/bf4e5bd01d79906e5b945a7af033154da49fd2b0d5b5c705a21330323305/parso-0.5.1-py2.py3-none-any.whl (95kB)
Collecting ptyprocess>=0.5
  Downloading https://files.pythonhosted.org/packages/d1/29/605c2cc68a9992d18dada28206eeada56ea4bd07a239669da41674648b6f/ptyprocess-0.6.0-py2.py3-none-any.whl
Collecting importlib-metadata; python_version < "3.8"
  Downloading https://files.pythonhosted.org/packages/ed/82/ebece33bc20b9097683d09e47563d487e411e2cf3a37789d7ec0a88c4ce4/importlib_metadata-1.1.0-py2.py3-none-any.whl
Collecting pyrsistent>=0.14.0
  Downloading https://files.pythonhosted.org/packages/6c/6f/c1a2e8da80a0029f6b618d7e20e1a6f2a61dd04e2e54225309c2cc4268f7/pyrsistent-0.15.6.tar.gz (107kB)
Collecting attrs>=17.4.0
  Downloading https://files.pythonhosted.org/packages/a2/db/4313ab3be961f7a763066401fb77f7748373b6094076ae2bda2806988af6/attrs-19.3.0-py2.py3-none-any.whl
Collecting webencodings
  Downloading https://files.pythonhosted.org/packages/f4/24/2a3e3df732393fed8b3ebf2ec078f05546de641fe1b667ee316ec1dcf3b7/webencodings-0.5.1-py2.py3-none-any.whl
Collecting qtconsole
  Downloading https://files.pythonhosted.org/packages/7c/57/3528b84ffa753e2089908bbf74bb5ae60653eb7a63797b6234e88b847d67/qtconsole-4.6.0-py2.py3-none-any.whl (121kB)
Collecting ipywidgets
  Downloading https://files.pythonhosted.org/packages/56/a0/dbcf5881bb2f51e8db678211907f16ea0a182b232c591a6d6f276985ca95/ipywidgets-7.5.1-py2.py3-none-any.whl (121kB)
Collecting jupyter-console
  Downloading https://files.pythonhosted.org/packages/cb/ee/6374ae8c21b7d0847f9c3722dcdfac986b8e54fa9ad9ea66e1eb6320d2b8/jupyter_console-6.0.0-py2.py3-none-any.whl
Collecting prometheus-client
  Downloading https://files.pythonhosted.org/packages/b3/23/41a5a24b502d35a4ad50a5bb7202a5e1d9a0364d0c12f56db3dbf7aca76d/prometheus_client-0.7.1.tar.gz
Collecting terminado>=0.8.1
  Downloading https://files.pythonhosted.org/packages/ff/96/1d9a2c23990aea8f8e0b5c3b6627d03196a73771a17a2d9860bbe9823ab6/terminado-0.8.3-py2.py3-none-any.whl
Collecting Send2Trash
  Downloading https://files.pythonhosted.org/packages/49/46/c3dc27481d1cc57b9385aff41c474ceb7714f7935b1247194adae45db714/Send2Trash-1.5.0-py3-none-any.whl
Collecting Mako
  Downloading https://files.pythonhosted.org/packages/b0/3c/8dcd6883d009f7cae0f3157fb53e9afb05a0d3d33b3db1268ec2e6f4a56b/Mako-1.1.0.tar.gz (463kB)
Collecting python-editor>=0.3
  Downloading https://files.pythonhosted.org/packages/c6/d3/201fc3abe391bbae6606e6f1d598c15d367033332bd54352b12f35513717/python_editor-1.0.4-py3-none-any.whl
Collecting zipp>=0.5
  Downloading https://files.pythonhosted.org/packages/74/3d/1ee25a26411ba0401b43c6376d2316a71addcc72ef8690b101b4ea56d76a/zipp-0.6.0-py2.py3-none-any.whl
Collecting widgetsnbextension~=3.5.0
  Downloading https://files.pythonhosted.org/packages/6c/7b/7ac231c20d2d33c445eaacf8a433f4e22c60677eb9776c7c5262d7ddee2d/widgetsnbextension-3.5.1-py2.py3-none-any.whl (2.2MB)
Collecting more-itertools
  Downloading https://files.pythonhosted.org/packages/5c/1d/3df99de956abb96305956e09e6a1fa955883295e1f28808f9c97b3d5364d/more_itertools-8.0.0-py3-none-any.whl (40kB)
Building wheels for collected packages: tornado, nbgrader, backcall, pandocfilters, sqlalchemy, alembic, pyrsistent, prometheus-client, Mako
  Building wheel for tornado (setup.py): started
  Building wheel for tornado (setup.py): finished with status 'done'
  Created wheel for tornado: filename=tornado-6.0.3-cp36-cp36m-linux_x86_64.whl size=423203 sha256=e697d4315fe722359bedad0e61301b84937362cbd5ea3e0615f30bea12ee7327
  Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/.cache/pip/wheels/84/bf/40/2f6ef700f48401ca40e5e3dd7d0e3c0a90e064897b7fe5fc08
  Building wheel for nbgrader (setup.py): started
  Building wheel for nbgrader (setup.py): finished with status 'done'
  Created wheel for nbgrader: filename=nbgrader-0.6.1-cp36-none-any.whl size=13507857 sha256=f1661e7f1a73576da27a1ff4990b7e6d5f1efbfaf1b6d8b55ce02c5cd67befdd
  Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/.cache/pip/wheels/22/00/61/991b052f161819b207471e4d9b22418010530681be8b6dc35c
  Building wheel for backcall (setup.py): started
  Building wheel for backcall (setup.py): finished with status 'done'
  Created wheel for backcall: filename=backcall-0.1.0-cp36-none-any.whl size=10414 sha256=4505fb4cb83f6de5e65e49c347a89a0a9570b36c3971d5130bf2da714973c006
  Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/.cache/pip/wheels/98/b0/dd/29e28ff615af3dda4c67cab719dd51357597eabff926976b45
  Building wheel for pandocfilters (setup.py): started
  Building wheel for pandocfilters (setup.py): finished with status 'done'
  Created wheel for pandocfilters: filename=pandocfilters-1.4.2-cp36-none-any.whl size=7857 sha256=e8a8c17245bfcf301c87d909d74869c0669b712752fafd8c79c8a66d3957ac55
  Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/.cache/pip/wheels/39/01/56/f1b08a6275acc59e846fa4c1e1b65dbc1919f20157d9e66c20
  Building wheel for sqlalchemy (setup.py): started
  Building wheel for sqlalchemy (setup.py): finished with status 'done'
  Created wheel for sqlalchemy: filename=SQLAlchemy-1.3.11-cp36-cp36m-linux_x86_64.whl size=1212245 sha256=0b5a7fd73bd621f3f40aa3c7f15ca7ff21e48bca9baf8ece0c0572abaa0a452f
  Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/.cache/pip/wheels/a3/67/7d/6c41104a1a08ff1a25e260d3edec3ac19203141d1aaa2f0975
  Building wheel for alembic (setup.py): started
  Building wheel for alembic (setup.py): finished with status 'done'
  Created wheel for alembic: filename=alembic-1.3.1-py2.py3-none-any.whl size=144524 sha256=8083600afa87a255181e481150833f0a2b797b183f1f0fffcd052f8072de5a70
  Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/.cache/pip/wheels/b2/d4/19/5ab879d30af7cbc79e6dcc1d421795b1aa9d78f455b0412ef7
  Building wheel for pyrsistent (setup.py): started
  Building wheel for pyrsistent (setup.py): finished with status 'done'
  Created wheel for pyrsistent: filename=pyrsistent-0.15.6-cp36-cp36m-linux_x86_64.whl size=114944 sha256=3f79e449bf7ff1a2015a10f8b30505efc19c87cf6a69b7d3b4dc2a6441cbf88d
  Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/.cache/pip/wheels/83/89/d3/1712b9c33c9b9c0911b188a86aeff2a9a05e113f986cf79d92
  Building wheel for prometheus-client (setup.py): started
  Building wheel for prometheus-client (setup.py): finished with status 'done'
  Created wheel for prometheus-client: filename=prometheus_client-0.7.1-cp36-none-any.whl size=41406 sha256=4e7fe0614b0bcde8badabc2a9f5b54f67956a4ea024cccba2d8d0572951cc3ff
  Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/.cache/pip/wheels/1c/54/34/fd47cd9b308826cc4292b54449c1899a30251ef3b506bc91ea
  Building wheel for Mako (setup.py): started
  Building wheel for Mako (setup.py): finished with status 'done'
  Created wheel for Mako: filename=Mako-1.1.0-cp36-none-any.whl size=75361 sha256=23d6c088cbd1e4b69f9b6f12c2565f19631bddfed8fc43e7ae8898ebd3ca1030
  Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/.cache/pip/wheels/98/32/7b/a291926643fc1d1e02593e0d9e247c5a866a366b8343b7aa27
Successfully built tornado nbgrader backcall pandocfilters sqlalchemy alembic pyrsistent prometheus-client Mako
ERROR: jupyter-console 6.0.0 has requirement prompt-toolkit<2.1.0,>=2.0.0, but you'll have prompt-toolkit 3.0.2 which is incompatible.
Installing collected packages: tornado, pyzmq, python-dateutil, decorator, ipython-genutils, traitlets, jupyter-core, jupyter-client, wcwidth, prompt-toolkit, backcall, pickleshare, parso, jedi, ptyprocess, pexpect, ipython, ipykernel, more-itertools, zipp, importlib-metadata, pyrsistent, attrs, jsonschema, nbformat, pandocfilters, defusedxml, entrypoints, mistune, webencodings, bleach, testpath, nbconvert, nbsphinx, sqlalchemy, qtconsole, prometheus-client, terminado, Send2Trash, notebook, widgetsnbextension, ipywidgets, jupyter-console, jupyter, Mako, python-editor, alembic, fuzzywuzzy, nbgrader, tqdm, numpy, cycler, kiwisolver, matplotlib, nbclean
Successfully installed Mako-1.1.0 Send2Trash-1.5.0 alembic-1.3.1 attrs-19.3.0 backcall-0.1.0 bleach-3.1.0 cycler-0.10.0 decorator-4.4.1 defusedxml-0.6.0 entrypoints-0.3 fuzzywuzzy-0.17.0 importlib-metadata-1.1.0 ipykernel-5.1.3 ipython-7.10.1 ipython-genutils-0.2.0 ipywidgets-7.5.1 jedi-0.15.1 jsonschema-3.2.0 jupyter-1.0.0 jupyter-client-5.3.4 jupyter-console-6.0.0 jupyter-core-4.6.1 kiwisolver-1.1.0 matplotlib-3.1.2 mistune-0.8.4 more-itertools-8.0.0 nbclean-0.3.2 nbconvert-5.6.1 nbformat-4.4.0 nbgrader-0.6.1 nbsphinx-0.3.5 notebook-6.0.2 numpy-1.17.4 pandocfilters-1.4.2 parso-0.5.1 pexpect-4.7.0 pickleshare-0.7.5 prometheus-client-0.7.1 prompt-toolkit-3.0.2 ptyprocess-0.6.0 pyrsistent-0.15.6 python-dateutil-2.8.1 python-editor-1.0.4 pyzmq-18.1.1 qtconsole-4.6.0 sqlalchemy-1.3.11 terminado-0.8.3 testpath-0.4.4 tornado-6.0.3 tqdm-4.40.0 traitlets-4.3.3 wcwidth-0.1.7 webencodings-0.5.1 widgetsnbextension-3.5.1 zipp-0.6.0

[rtd-command-info] start-time: 2019-12-03T15:29:23.385663Z, end-time: 2019-12-03T15:29:23.721050Z, duration: 0, exit-code: 0
cat conf.py
from datetime import datetime
project = 'Scanpy'
author = 'Alex Wolf, Fidel Ramirez'
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']
pygments_style = 'sphinx'

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

html_theme = 'sphinx_rtd_theme'
html_theme_options = dict(
    navigation_depth=2,
)
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']

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/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://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/"),
    ],
    'downloads': [ 
    ("html", "//readthedocs.com/projects/icb-scanpy-tutorials/downloads/htmlzip/latest/"),
    ],
    'subprojects': [ 
    ],
    'slug': 'icb-scanpy-tutorials',
    'name': u'scanpy-tutorials',
    'rtd_language': u'en',
    'programming_language': u'py',
    'canonical_url': 'https://icb-scanpy-tutorials.readthedocs-hosted.com/en/latest/',
    'analytics_code': 'None',
    'single_version': False,
    'conf_py_path': '/',
    'api_host': 'https://readthedocs.com',
    'proxied_api_host': 'https://readthedocs.com',
    'github_user': 'theislab',
    '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,
    'user_analytics_code': '',
    'global_analytics_code': 'UA-17997319-2',
    'commit': '0bc96584',
}




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'

[rtd-command-info] start-time: 2019-12-03T15:29:23.802337Z, end-time: 2019-12-03T15:29:32.072000Z, duration: 8, exit-code: 0
python sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html
Running Sphinx v1.8.5
loading translations [en]... done
making output directory...
building [mo]: targets for 0 po files that are out of date
building [readthedocs]: targets for 5 source files that are out of date
updating environment: 5 added, 0 changed, 0 removed
reading sources... [ 20%] README
reading sources... [ 40%] index
reading sources... [ 60%] paga-paul15
reading sources... [ 80%] pbmc3k
reading sources... [100%] visualizing-marker-genes

looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
writing output... [ 20%] README
writing output... [ 40%] index
writing output... [ 60%] paga-paul15
writing output... [ 80%] pbmc3k
writing output... [100%] visualizing-marker-genes

generating indices... genindex
writing additional pages... search
copying images... [  1%] _build/doctrees-readthedocs/nbsphinx/paga-paul15_13_0.png
copying images... [  2%] _build/doctrees-readthedocs/nbsphinx/paga-paul15_19_0.png
copying images... [  4%] _build/doctrees-readthedocs/nbsphinx/paga-paul15_26_1.png
copying images... [  5%] _build/doctrees-readthedocs/nbsphinx/paga-paul15_27_1.png
copying images... [  6%] _build/doctrees-readthedocs/nbsphinx/paga-paul15_34_1.png
copying images... [  8%] _build/doctrees-readthedocs/nbsphinx/paga-paul15_39_0.png
copying images... [  9%] _build/doctrees-readthedocs/nbsphinx/paga-paul15_41_0.png
copying images... [ 11%] _build/doctrees-readthedocs/nbsphinx/paga-paul15_46_1.png
copying images... [ 12%] _build/doctrees-readthedocs/nbsphinx/paga-paul15_55_0.png
copying images... [ 13%] _build/doctrees-readthedocs/nbsphinx/paga-paul15_61_0.png
copying images... [ 15%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_12_0.png
copying images... [ 16%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_19_0.png
copying images... [ 18%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_21_0.png
copying images... [ 19%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_21_1.png
copying images... [ 20%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_33_0.png
copying images... [ 22%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_44_0.png
copying images... [ 23%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_46_0.png
copying images... [ 25%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_56_0.png
copying images... [ 26%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_58_0.png
copying images... [ 27%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_63_0.png
copying images... [ 29%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_68_1.png
copying images... [ 30%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_71_1.png
copying images... [ 31%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_75_1.png
copying images... [ 33%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_86_1.png
copying images... [ 34%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_88_0.png
copying images... [ 36%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_91_0.png
copying images... [ 37%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_93_0.png
copying images... [ 38%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_96_1.png
copying images... [ 40%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_98_0.png
copying images... [ 41%] _build/doctrees-readthedocs/nbsphinx/pbmc3k_100_0.png
copying images... [ 43%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_8_0.png
copying images... [ 44%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_13_0.png
copying images... [ 45%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_15_1.png
copying images... [ 47%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_19_0.png
copying images... [ 48%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_21_0.png
copying images... [ 50%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_23_1.png
copying images... [ 51%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_25_1.png
copying images... [ 52%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_28_0.png
copying images... [ 54%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_30_1.png
copying images... [ 55%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_33_0.png
copying images... [ 56%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_36_0.png
copying images... [ 58%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_38_1.png
copying images... [ 59%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_42_0.png
copying images... [ 61%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_47_0.png
copying images... [ 62%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_49_0.png
copying images... [ 63%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_51_1.png
copying images... [ 65%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_53_1.png
copying images... [ 66%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_55_0.png
copying images... [ 68%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_57_0.png
copying images... [ 69%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_59_0.png
copying images... [ 70%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_60_0.png
copying images... [ 72%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_62_0.png
copying images... [ 73%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_64_0.png
copying images... [ 75%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_65_0.png
copying images... [ 76%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_67_0.png
copying images... [ 77%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_69_0.png
copying images... [ 79%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_75_0.png
copying images... [ 80%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_77_1.png
copying images... [ 81%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_82_0.png
copying images... [ 83%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_84_0.png
copying images... [ 84%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_85_0.png
copying images... [ 86%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_87_0.png
copying images... [ 87%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_88_0.png
copying images... [ 88%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_91_0.png
copying images... [ 90%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_91_1.png
copying images... [ 91%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_91_2.png
copying images... [ 93%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_91_3.png
copying images... [ 94%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_91_4.png
copying images... [ 95%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_91_5.png
copying images... [ 97%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_93_0.png
copying images... [ 98%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_96_0.png
copying images... [100%] _build/doctrees-readthedocs/nbsphinx/visualizing-marker-genes_100_1.png

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

The HTML pages are in _build/html.

[rtd-command-info] start-time: 2019-12-03T15:29:32.224287Z, end-time: 2019-12-03T15:29:40.829267Z, duration: 8, exit-code: 0
python sphinx-build -T -b readthedocssinglehtmllocalmedia -d _build/doctrees-readthedocssinglehtmllocalmedia -D language=en . _build/localmedia
Running Sphinx v1.8.5
loading translations [en]... done
making output directory...
building [mo]: targets for 0 po files that are out of date
building [readthedocssinglehtmllocalmedia]: all documents
updating environment: 5 added, 0 changed, 0 removed
reading sources... [ 20%] README
reading sources... [ 40%] index
reading sources... [ 60%] paga-paul15
reading sources... [ 80%] pbmc3k
reading sources... [100%] visualizing-marker-genes

looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
assembling single document... pbmc3k paga-paul15 visualizing-marker-genes 
writing... done
writing additional files...
copying images... [  1%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_12_0.png
copying images... [  2%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_19_0.png
copying images... [  4%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_21_0.png
copying images... [  5%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_21_1.png
copying images... [  6%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_33_0.png
copying images... [  8%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_44_0.png
copying images... [  9%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_46_0.png
copying images... [ 11%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_56_0.png
copying images... [ 12%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_58_0.png
copying images... [ 13%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_63_0.png
copying images... [ 15%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_68_1.png
copying images... [ 16%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_71_1.png
copying images... [ 18%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_75_1.png
copying images... [ 19%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_86_1.png
copying images... [ 20%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_88_0.png
copying images... [ 22%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_91_0.png
copying images... [ 23%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_93_0.png
copying images... [ 25%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_96_1.png
copying images... [ 26%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_98_0.png
copying images... [ 27%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/pbmc3k_100_0.png
copying images... [ 29%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/paga-paul15_13_0.png
copying images... [ 30%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/paga-paul15_19_0.png
copying images... [ 31%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/paga-paul15_26_1.png
copying images... [ 33%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/paga-paul15_27_1.png
copying images... [ 34%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/paga-paul15_34_1.png
copying images... [ 36%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/paga-paul15_39_0.png
copying images... [ 37%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/paga-paul15_41_0.png
copying images... [ 38%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/paga-paul15_46_1.png
copying images... [ 40%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/paga-paul15_55_0.png
copying images... [ 41%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/paga-paul15_61_0.png
copying images... [ 43%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_8_0.png
copying images... [ 44%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_13_0.png
copying images... [ 45%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_15_1.png
copying images... [ 47%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_19_0.png
copying images... [ 48%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_21_0.png
copying images... [ 50%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_23_1.png
copying images... [ 51%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_25_1.png
copying images... [ 52%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_28_0.png
copying images... [ 54%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_30_1.png
copying images... [ 55%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_33_0.png
copying images... [ 56%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_36_0.png
copying images... [ 58%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_38_1.png
copying images... [ 59%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_42_0.png
copying images... [ 61%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_47_0.png
copying images... [ 62%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_49_0.png
copying images... [ 63%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_51_1.png
copying images... [ 65%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_53_1.png
copying images... [ 66%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_55_0.png
copying images... [ 68%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_57_0.png
copying images... [ 69%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_59_0.png
copying images... [ 70%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_60_0.png
copying images... [ 72%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_62_0.png
copying images... [ 73%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_64_0.png
copying images... [ 75%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_65_0.png
copying images... [ 76%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_67_0.png
copying images... [ 77%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_69_0.png
copying images... [ 79%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_75_0.png
copying images... [ 80%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_77_1.png
copying images... [ 81%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_82_0.png
copying images... [ 83%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_84_0.png
copying images... [ 84%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_85_0.png
copying images... [ 86%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_87_0.png
copying images... [ 87%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_88_0.png
copying images... [ 88%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_91_0.png
copying images... [ 90%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_91_1.png
copying images... [ 91%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_91_2.png
copying images... [ 93%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_91_3.png
copying images... [ 94%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_91_4.png
copying images... [ 95%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_91_5.png
copying images... [ 97%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_93_0.png
copying images... [ 98%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_96_0.png
copying images... [100%] _build/doctrees-readthedocssinglehtmllocalmedia/nbsphinx/visualizing-marker-genes_100_1.png

copying static files... done
copying readthedocs static files... done
copying extra files... done
dumping object inventory... done
build succeeded.

The HTML page is in _build/localmedia.