Read the Docs build information
Build id: 234401
Project: icb-scanpy
Version: latest
Commit: 0c30b3f759cf31eaecfa7bd2a21074f79d00c9a4
Date: 2019-08-21T16:04:43.688716Z
State: finished
Success: False
[rtd-command-info] start-time: 2019-08-21T16:04:44.183587Z, end-time: 2019-08-21T16:04:44.196728Z, duration: 0, exit-code: 0
git remote set-url origin https://github.com/theislab/scanpy.git
[rtd-command-info] start-time: 2019-08-21T16:04:44.277762Z, end-time: 2019-08-21T16:04:44.772129Z, duration: 0, exit-code: 0
git fetch origin --tags --prune --prune-tags --depth 50
From https://github.com/theislab/scanpy
85b03e2..0c30b3f master -> origin/master
[rtd-command-info] start-time: 2019-08-21T16:04:45.075860Z, end-time: 2019-08-21T16:04:45.098196Z, duration: 0, exit-code: 0
git checkout --force origin/master
Previous HEAD position was 85b03e2 More param type fixes
HEAD is now at 0c30b3f Don’t let broken docs compile
[rtd-command-info] start-time: 2019-08-21T16:04:45.203849Z, end-time: 2019-08-21T16:04:45.220065Z, duration: 0, exit-code: 0
git clean -d -f -f
[rtd-command-info] start-time: 2019-08-21T16:04:46.260519Z, end-time: 2019-08-21T16:04:50.540070Z, duration: 4, exit-code: 0
python3.6 -mvirtualenv --no-site-packages --no-download
Using base prefix '/home/docs/.pyenv/versions/3.6.4'
New python executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/bin/python3.6
Not overwriting existing python script /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/bin/python (you must use /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/bin/python3.6)
Installing setuptools, pip, wheel...
done.
[rtd-command-info] start-time: 2019-08-21T16:04:50.631607Z, end-time: 2019-08-21T16:04:51.873415Z, duration: 1, exit-code: 0
python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/.cache/pip pip
Requirement already up-to-date: pip in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (19.2.2)
[rtd-command-info] start-time: 2019-08-21T16:04:51.957698Z, end-time: 2019-08-21T16:05:00.283545Z, duration: 8, exit-code: 0
python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/.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
Requirement already up-to-date: Pygments==2.3.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (2.3.1)
Requirement already up-to-date: setuptools==41.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (41.0.1)
Requirement already up-to-date: docutils==0.14 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (0.14)
Collecting mock==1.0.1
Requirement already up-to-date: pillow==5.4.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (5.4.1)
Requirement already up-to-date: alabaster!=0.7.5,<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (0.7.12)
Requirement already up-to-date: commonmark==0.8.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (0.8.1)
Requirement already up-to-date: recommonmark==0.5.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (0.5.0)
Collecting sphinx<2
Using cached https://files.pythonhosted.org/packages/7d/66/a4af242b4348b729b9d46ce5db23943ce9bca7da9bbe2ece60dc27f26420/Sphinx-1.8.5-py2.py3-none-any.whl
Requirement already up-to-date: sphinx-rtd-theme<0.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (0.4.3)
Requirement already up-to-date: readthedocs-sphinx-ext<1.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (1.0.0)
Requirement already satisfied, skipping upgrade: future in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from commonmark==0.8.1) (0.17.1)
Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx<2) (1.9.0)
Requirement already satisfied, skipping upgrade: sphinxcontrib-websupport in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx<2) (1.1.2)
Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx<2) (2.10.1)
Requirement already satisfied, skipping upgrade: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx<2) (1.12.0)
Requirement already satisfied, skipping upgrade: packaging in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx<2) (19.1)
Requirement already satisfied, skipping upgrade: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx<2) (1.1.0)
Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx<2) (2.7.0)
Requirement already satisfied, skipping upgrade: requests>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx<2) (2.22.0)
Requirement already satisfied, skipping upgrade: 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<2) (1.1.1)
Requirement already satisfied, skipping upgrade: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from packaging->sphinx<2) (2.4.2)
Requirement already satisfied, skipping upgrade: attrs in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from packaging->sphinx<2) (19.1.0)
Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from babel!=2.0,>=1.3->sphinx<2) (2019.2)
Requirement already satisfied, skipping upgrade: 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>=2.0.0->sphinx<2) (1.25.3)
Requirement already satisfied, skipping upgrade: 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<2) (3.0.4)
Requirement already satisfied, skipping upgrade: 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<2) (2.8)
Requirement already satisfied, skipping upgrade: 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<2) (2019.6.16)
tables 3.5.2 has requirement mock>=2.0, but you'll have mock 1.0.1 which is incompatible.
sphinx-autodoc-typehints 1.7.0 has requirement Sphinx>=2.1, but you'll have sphinx 1.8.5 which is incompatible.
Installing collected packages: mock, sphinx
Found existing installation: mock 3.0.5
Uninstalling mock-3.0.5:
Successfully uninstalled mock-3.0.5
Found existing installation: Sphinx 2.2.0
Uninstalling Sphinx-2.2.0:
Successfully uninstalled Sphinx-2.2.0
Successfully installed mock-1.0.1 sphinx-1.8.5
[rtd-command-info] start-time: 2019-08-21T16:05:00.374528Z, end-time: 2019-08-21T16:05:03.905766Z, duration: 3, exit-code: 0
python -m 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)) (0.4.3)
Collecting sphinx>=2.0.1 (from -r docs/requirements.txt (line 5))
Using cached https://files.pythonhosted.org/packages/8e/4c/95a21788db2e1653e931420f561015a0bbc9bd4660c4520467ab9e733eb2/Sphinx-2.2.0-py3-none-any.whl
Requirement already satisfied: sphinx-autodoc-typehints in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 6)) (1.7.0)
Collecting scanpydoc>=0.3.8 (from -r docs/requirements.txt (line 7))
Downloading https://files.pythonhosted.org/packages/bd/c2/6f5fdf1e57a4bfcafac9b3571156e098d83867023fc0eff374eecdda4f32/scanpydoc-0.3.8-py3-none-any.whl (54kB)
Requirement already satisfied: anndata>=0.6.18 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 9)) (0.6.22.post1)
Requirement already satisfied: matplotlib>=2.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 10)) (3.1.1)
Requirement already satisfied: pandas>=0.21 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 11)) (0.25.0)
Requirement already satisfied: scipy in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 12)) (1.3.1)
Requirement already satisfied: seaborn in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 13)) (0.9.0)
Requirement already satisfied: h5py in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 14)) (2.9.0)
Requirement already satisfied: tables in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 15)) (3.5.2)
Requirement already satisfied: scikit-learn>=0.19.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 16)) (0.21.3)
Requirement already satisfied: networkx in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 18)) (2.3)
Requirement already satisfied: natsort in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 19)) (6.0.0)
Requirement already satisfied: joblib in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 20)) (0.13.2)
Requirement already satisfied: numba in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 21)) (0.45.1)
Requirement already satisfied: tqdm in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 22)) (4.34.0)
Requirement already satisfied: importlib_metadata in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 23)) (0.19)
Requirement already satisfied: umap-learn in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from -r docs/requirements.txt (line 24)) (0.3.10)
Requirement already satisfied: requests>=2.5.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (2.22.0)
Requirement already satisfied: sphinxcontrib-applehelp in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (1.0.1)
Requirement already satisfied: sphinxcontrib-serializinghtml in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (1.1.3)
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>=2.0.1->-r docs/requirements.txt (line 5)) (2.10.1)
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (41.0.1)
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>=2.0.1->-r docs/requirements.txt (line 5)) (0.7.12)
Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (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>=2.0.1->-r docs/requirements.txt (line 5)) (1.9.0)
Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (19.1)
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>=2.0.1->-r docs/requirements.txt (line 5)) (2.3.1)
Requirement already satisfied: docutils>=0.12 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (0.14)
Requirement already satisfied: sphinxcontrib-devhelp in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (1.0.1)
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>=2.0.1->-r docs/requirements.txt (line 5)) (2.7.0)
Requirement already satisfied: sphinxcontrib-qthelp in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (1.0.2)
Requirement already satisfied: sphinxcontrib-jsmath in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (1.0.1)
Requirement already satisfied: sphinxcontrib-htmlhelp in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (1.0.2)
Requirement already satisfied: get_version in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from scanpydoc>=0.3.8->-r docs/requirements.txt (line 7)) (2.0.6)
Requirement already satisfied: numpy~=1.14 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from anndata>=0.6.18->-r docs/requirements.txt (line 9)) (1.17.0)
Requirement already satisfied: python-dateutil>=2.1 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 10)) (2.8.0)
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 10)) (2.4.2)
Requirement already satisfied: kiwisolver>=1.0.1 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 10)) (1.1.0)
Requirement already satisfied: cycler>=0.10 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 10)) (0.10.0)
Requirement already satisfied: pytz>=2017.2 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 11)) (2019.2)
Requirement already satisfied: six in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from h5py->-r docs/requirements.txt (line 14)) (1.12.0)
Requirement already satisfied: numexpr>=2.6.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from tables->-r docs/requirements.txt (line 15)) (2.7.0)
Collecting mock>=2.0 (from tables->-r docs/requirements.txt (line 15))
Using cached https://files.pythonhosted.org/packages/05/d2/f94e68be6b17f46d2c353564da56e6fb89ef09faeeff3313a046cb810ca9/mock-3.0.5-py2.py3-none-any.whl
Requirement already satisfied: decorator>=4.3.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from networkx->-r docs/requirements.txt (line 18)) (4.4.0)
Requirement already satisfied: llvmlite>=0.29.0dev0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from numba->-r docs/requirements.txt (line 21)) (0.29.0)
Requirement already satisfied: zipp>=0.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from importlib_metadata->-r docs/requirements.txt (line 23)) (0.5.2)
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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>=2.5.0->sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (3.0.4)
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>=2.5.0->sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (2.8)
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/envs/latest/lib/python3.6/site-packages (from requests>=2.5.0->sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (1.25.3)
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>=2.0.1->-r docs/requirements.txt (line 5)) (1.1.1)
Requirement already satisfied: attrs in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from packaging->sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (19.1.0)
Requirement already satisfied: future-fstrings in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from get_version->scanpydoc>=0.3.8->-r docs/requirements.txt (line 7)) (1.2.0)
Installing collected packages: sphinx, scanpydoc, mock
Found existing installation: Sphinx 1.8.5
Uninstalling Sphinx-1.8.5:
Successfully uninstalled Sphinx-1.8.5
Found existing installation: scanpydoc 0.3.4
Uninstalling scanpydoc-0.3.4:
Successfully uninstalled scanpydoc-0.3.4
Found existing installation: mock 1.0.1
Uninstalling mock-1.0.1:
Successfully uninstalled mock-1.0.1
Successfully installed mock-3.0.5 scanpydoc-0.3.8 sphinx-2.2.0
[rtd-command-info] start-time: 2019-08-21T16:05:04.637255Z, end-time: 2019-08-21T16:05:04.952105Z, duration: 0, exit-code: 0
cat docs/conf.py
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.insert(0, str(HERE.parent))
import scanpy # noqa
with warnings.catch_warnings():
warnings.filterwarnings('ignore', category=FutureWarning)
import scanpy.api
# -- General configuration ------------------------------------------------
nitpicky = True # Warn about broken links
needs_sphinx = '1.7' # autosummary bugfix
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',
]
# 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),
cycler=('https://matplotlib.org/cycler/', 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),
seaborn=('https://seaborn.pydata.org/', None),
sklearn=('https://scikit-learn.org/stable/', None),
scanpy_tutorials=('https://scanpy-tutorials.readthedocs.io/en/latest', None),
)
# -- Options for HTML output ----------------------------------------------
html_theme = 'sphinx_rtd_theme'
html_theme_options = dict(
navigation_depth=4,
logo_only=True, # Only show the logo
)
html_context = dict(
display_github=True, # Integrate GitHub
github_user='theislab', # Username
github_repo='scanpy', # 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_RGB.png'
gh_url = 'https://github.com/{github_user}/{github_repo}'.format_map(html_context)
def setup(app):
app.warningiserror = True
app.add_stylesheet('css/custom.css')
app.connect('autodoc-process-docstring', insert_function_images)
app.add_role('pr', autolink(f'{gh_url}/pull/{{}}', 'PR {}'))
# -- 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 insert_function_images(app, what, name, obj, options, lines):
path = Path(__file__).parent / 'api' / f'{name}.png'
if what != 'function' or not path.is_file(): return
lines[0:0] = [f'.. image:: {path.name}', ' :width: 200', ' :align: right', '']
# -- GitHub links --------------------------------------------------------------
def autolink(url_template, title_template='{}'):
from docutils import nodes
def role(name, rawtext, text, lineno, inliner, options={}, content=[]):
url = url_template.format(text)
title = title_template.format(text)
node = nodes.reference(rawtext, title, refuri=url, **options)
return [node], []
return role
# -- Test for new scanpydoc functionality --------------------------------------
import re
from sphinx.ext.napoleon import NumpyDocstring
def process_return(lines):
for line in lines:
m = re.fullmatch(r'(?P\w+)\s+:\s+(?P[\w.]+)', line)
if m:
# Once this is in scanpydoc, we can use the fancy hover stuff
yield f'**{m["param"]}** : :class:`~{m["type"]}`'
else:
yield line
def scanpy_parse_returns_section(self, section):
lines_raw = list(process_return(self._dedent(self._consume_to_next_section())))
lines = self._format_block(':returns: ', lines_raw)
if lines and lines[-1]:
lines.append('')
return lines
NumpyDocstring._parse_returns_section = scanpy_parse_returns_section
# -- Debug code ----------------------------------------------------------------
# Just do the following to see the rst of a function:
# rm -f _build/doctrees/api/scanpy..doctree; DEBUG=1 make html
import os
if os.environ.get('DEBUG') is not None:
import sphinx.ext.napoleon
pd = sphinx.ext.napoleon._process_docstring
def pd_new(app, what, name, obj, options, lines):
pd(app, what, name, obj, options, lines)
print(*lines, sep='\n')
sphinx.ext.napoleon._process_docstring = pd_new
# -- Suppress link warnings ----------------------------------------------------
nitpick_ignore = [
# Will probably be documented
('py:class', 'scanpy._settings.Verbosity'),
# Will probably be removed: https://github.com/theislab/scanpy/issues/792
('py:func', 'scanpy.tl.rna_velocity'),
# Currently undocumented: https://github.com/mwaskom/seaborn/issues/1810
('py:class', 'seaborn.ClusterGrid'),
# Bug: https://github.com/agronholm/sphinx-autodoc-typehints/issues/96
('py:class', 'typing.Textio'),
]
for mod_name in [
'pp', 'tl', 'pl',
'queries', 'logging', 'datasets', 'export_to',
None,
]:
if mod_name is None:
mod = scanpy.api
mod_name = 'scanpy.api'
else:
mod = getattr(scanpy.api, mod_name)
mod_name = f'scanpy.api.{mod_name}'
for name, item in vars(mod).items():
if not callable(item):
continue
for kind in ['func', 'obj']:
nitpick_ignore.append((f'py:{kind}', f'{mod_name}.{name}'))
###########################################################################
# 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/"),
("stable", "/en/stable/"),
("contributors", "/en/contributors/"),
],
'downloads': [
("html", "//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/stable/',
'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': '0c30b3f7',
}
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: 2019-08-21T16:05:05.082044Z, end-time: 2019-08-21T16:06:38.999758Z, duration: 93, exit-code: 2
python sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html
Running Sphinx v2.2.0
loading translations [en]... done
making output directory... done
loading intersphinx inventory from https://anndata.readthedocs.io/en/latest/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 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...
loading intersphinx inventory from https://docs.scipy.org/doc/scipy/reference/objects.inv...
loading intersphinx inventory from https://seaborn.pydata.org/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...
[autosummary] generating autosummary for: api/index.rst, api/plotting.rst, api/scanpy.Neighbors.compute_eigen.rst, api/scanpy.Neighbors.compute_neighbors.rst, api/scanpy.Neighbors.compute_transitions.rst, api/scanpy.Neighbors.connectivities.rst, api/scanpy.Neighbors.distances.rst, api/scanpy.Neighbors.distances_dpt.rst, api/scanpy.Neighbors.eigen_basis.rst, api/scanpy.Neighbors.eigen_values.rst, ..., external/scanpy.external.tl.cyclone.rst, external/scanpy.external.tl.palantir.rst, external/scanpy.external.tl.phate.rst, external/scanpy.external.tl.phenograph.rst, external/scanpy.external.tl.sandbag.rst, index.rst, installation.rst, references.rst, release_notes.rst, tutorials.rst
[autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy.pl.rank_genes_groups_tracksplot.rst
building [mo]: targets for 0 po files that are out of date
building [readthedocs]: targets for 224 source files that are out of date
updating environment: [new config] 225 added, 0 changed, 0 removed
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looking for now-outdated files... none found
pickling environment... done
checking consistency... failed
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 276, in build_main
app.build(args.force_all, filenames)
File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/application.py", line 346, in build
self.builder.build_update()
File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/builders/__init__.py", line 299, in build_update
len(to_build))
File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/builders/__init__.py", line 333, in build
self.env.check_consistency()
File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/environment/__init__.py", line 639, in check_consistency
location=docname)
File "/home/docs/.pyenv/versions/3.6.4/lib/python3.6/logging/__init__.py", line 1640, 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 124, in log
super().log(level, msg, *args, **kwargs)
File "/home/docs/.pyenv/versions/3.6.4/lib/python3.6/logging/__init__.py", line 1672, in log
self.logger.log(level, msg, *args, **kwargs)
File "/home/docs/.pyenv/versions/3.6.4/lib/python3.6/logging/__init__.py", line 1372, in log
self._log(level, msg, args, **kwargs)
File "/home/docs/.pyenv/versions/3.6.4/lib/python3.6/logging/__init__.py", line 1442, in _log
self.handle(record)
File "/home/docs/.pyenv/versions/3.6.4/lib/python3.6/logging/__init__.py", line 1452, in handle
self.callHandlers(record)
File "/home/docs/.pyenv/versions/3.6.4/lib/python3.6/logging/__init__.py", line 1514, in callHandlers
hdlr.handle(record)
File "/home/docs/.pyenv/versions/3.6.4/lib/python3.6/logging/__init__.py", line 859, in handle
rv = self.filter(record)
File "/home/docs/.pyenv/versions/3.6.4/lib/python3.6/logging/__init__.py", line 718, 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 404, in filter
raise SphinxWarning(location + ":" + message)
sphinx.errors.SphinxWarning: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy.api.Neighbors.rst:document isn't included in any toctree
Warning, treated as error:
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy.api.Neighbors.rst:document isn't included in any toctree