Read the Docs build information Build id: 263504 Project: icb-anndata Version: latest Commit: 4a4e71368e42ab92c1372d7f6728ef9ec4e92694 Date: 2019-11-26T09:08:44.616137Z State: finished Success: True [rtd-command-info] start-time: 2019-11-26T09:08:45.380087Z, end-time: 2019-11-26T09:08:45.395747Z, duration: 0, exit-code: 0 git remote set-url origin https://github.com/theislab/anndata.git [rtd-command-info] start-time: 2019-11-26T09:08:45.475231Z, end-time: 2019-11-26T09:08:46.011327Z, duration: 0, exit-code: 0 git fetch origin --force --tags --prune --prune-tags --depth 50 From https://github.com/theislab/anndata 5c634f2..4a4e713 master -> origin/master [rtd-command-info] start-time: 2019-11-26T09:08:46.279812Z, end-time: 2019-11-26T09:08:46.292971Z, duration: 0, exit-code: 0 git checkout --force origin/master Previous HEAD position was 5c634f2 Modify way write exceptions are raised HEAD is now at 4a4e713 Color handling in uns fix (#259) [rtd-command-info] start-time: 2019-11-26T09:08:46.371098Z, end-time: 2019-11-26T09:08:46.392224Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2019-11-26T09:08:47.381025Z, end-time: 2019-11-26T09:08:52.546792Z, duration: 5, 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-anndata/envs/latest/bin/python3.6 Not overwriting existing python script /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/bin/python (you must use /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/bin/python3.6) Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2019-11-26T09:08:52.636761Z, end-time: 2019-11-26T09:08:53.730734Z, duration: 1, exit-code: 0 python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/.cache/pip pip Requirement already up-to-date: pip in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (19.3.1) [rtd-command-info] start-time: 2019-11-26T09:08:53.812292Z, end-time: 2019-11-26T09:08:57.560150Z, duration: 3, exit-code: 0 python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/.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-anndata/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-anndata/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-anndata/envs/latest/lib/python3.6/site-packages (0.14) Requirement already up-to-date: mock==1.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (1.0.1) Requirement already up-to-date: pillow==5.4.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/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-anndata/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-anndata/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-anndata/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-anndata/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-anndata/envs/latest/lib/python3.6/site-packages (1.0.1) Requirement already satisfied, skipping upgrade: future in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from commonmark==0.8.1) (0.18.2) Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx<2) (2.7.0) Requirement already satisfied, skipping upgrade: packaging in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx<2) (19.2) Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx<2) (2.10.3) Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx<2) (2.0.0) Requirement already satisfied, skipping upgrade: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx<2) (1.1.0) Requirement already satisfied, skipping upgrade: sphinxcontrib-websupport in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx<2) (1.1.2) Requirement already satisfied, skipping upgrade: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx<2) (1.13.0) Requirement already satisfied, skipping upgrade: requests>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx<2) (2.22.0) Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from babel!=2.0,>=1.3->sphinx<2) (2019.3) Requirement already satisfied, skipping upgrade: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from packaging->sphinx<2) (2.4.5) Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from Jinja2>=2.3->sphinx<2) (1.1.1) Requirement already satisfied, skipping upgrade: chardet<3.1.0,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/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-anndata/envs/latest/lib/python3.6/site-packages (from requests>=2.0.0->sphinx<2) (2.8) 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-anndata/envs/latest/lib/python3.6/site-packages (from requests>=2.0.0->sphinx<2) (1.25.7) Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from requests>=2.0.0->sphinx<2) (2019.9.11) ERROR: sphinx-autodoc-typehints 1.10.3 has requirement Sphinx>=2.1, but you'll have sphinx 1.8.5 which is incompatible. Installing collected packages: sphinx Found existing installation: Sphinx 2.2.1 Uninstalling Sphinx-2.2.1: Successfully uninstalled Sphinx-2.2.1 Successfully installed sphinx-1.8.5 [rtd-command-info] start-time: 2019-11-26T09:08:57.638297Z, end-time: 2019-11-26T09:09:00.313086Z, duration: 2, exit-code: 0 python -m pip install --exists-action=w --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/.cache/pip -r docs/requires.txt Requirement already satisfied: setuptools_scm in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from -r docs/requires.txt (line 2)) (3.3.3) Requirement already satisfied: importlib_metadata>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from -r docs/requires.txt (line 3)) (0.23) Requirement already satisfied: typing_extensions in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from -r docs/requires.txt (line 4)) (3.7.4.1) Collecting sphinx>=2.0.1 (from -r docs/requires.txt (line 6)) Using cached https://files.pythonhosted.org/packages/1d/58/a547b02946af1cf337c701cafcf3267065c1c83d6e701f540961f4907b5d/Sphinx-2.2.1-py3-none-any.whl Requirement already satisfied: sphinx-autodoc-typehints in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from -r docs/requires.txt (line 7)) (1.10.3) Requirement already satisfied: scanpydoc>=0.4.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from -r docs/requires.txt (line 8)) (0.4.4) Requirement already satisfied: pandas~=0.21 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from -r docs/requires.txt (line 10)) (0.25.3) Requirement already satisfied: scipy in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from -r docs/requires.txt (line 11)) (1.3.3) Requirement already satisfied: h5py in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from -r docs/requires.txt (line 12)) (2.10.0) Requirement already satisfied: natsort in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from -r docs/requires.txt (line 13)) (6.2.0) Requirement already satisfied: zarr in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from -r docs/requires.txt (line 14)) (2.3.2) Requirement already satisfied: zipp>=0.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from importlib_metadata>=0.7->-r docs/requires.txt (line 3)) (0.6.0) Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requires.txt (line 6)) (0.7.12) Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requires.txt (line 6)) (1.1.0) Requirement already satisfied: docutils>=0.12 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requires.txt (line 6)) (0.14) Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requires.txt (line 6)) (19.2) Requirement already satisfied: sphinxcontrib-applehelp in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requires.txt (line 6)) (1.0.1) Requirement already satisfied: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requires.txt (line 6)) (2.7.0) Requirement already satisfied: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requires.txt (line 6)) (2.3.1) Requirement already satisfied: requests>=2.5.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requires.txt (line 6)) (2.22.0) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requires.txt (line 6)) (41.0.1) Requirement already satisfied: sphinxcontrib-jsmath in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requires.txt (line 6)) (1.0.1) Requirement already satisfied: sphinxcontrib-devhelp in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requires.txt (line 6)) (1.0.1) Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requires.txt (line 6)) (2.10.3) Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requires.txt (line 6)) (2.0.0) Requirement already satisfied: sphinxcontrib-serializinghtml in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requires.txt (line 6)) (1.1.3) Requirement already satisfied: sphinxcontrib-htmlhelp in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requires.txt (line 6)) (1.0.2) Requirement already satisfied: sphinxcontrib-qthelp in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx>=2.0.1->-r docs/requires.txt (line 6)) (1.0.2) Requirement already satisfied: get_version in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from scanpydoc>=0.4.2->-r docs/requires.txt (line 8)) (2.1) Requirement already satisfied: numpy>=1.13.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from pandas~=0.21->-r docs/requires.txt (line 10)) (1.17.4) Requirement already satisfied: pytz>=2017.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from pandas~=0.21->-r docs/requires.txt (line 10)) (2019.3) Requirement already satisfied: python-dateutil>=2.6.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from pandas~=0.21->-r docs/requires.txt (line 10)) (2.8.1) Requirement already satisfied: six in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from h5py->-r docs/requires.txt (line 12)) (1.13.0) Requirement already satisfied: asciitree in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from zarr->-r docs/requires.txt (line 14)) (0.3.3) Requirement already satisfied: numcodecs>=0.6.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from zarr->-r docs/requires.txt (line 14)) (0.6.4) Requirement already satisfied: fasteners in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from zarr->-r docs/requires.txt (line 14)) (0.15) Requirement already satisfied: more-itertools in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from zipp>=0.5->importlib_metadata>=0.7->-r docs/requires.txt (line 3)) (7.2.0) Requirement already satisfied: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from packaging->sphinx>=2.0.1->-r docs/requires.txt (line 6)) (2.4.5) Requirement already satisfied: idna<2.9,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from requests>=2.5.0->sphinx>=2.0.1->-r docs/requires.txt (line 6)) (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-anndata/envs/latest/lib/python3.6/site-packages (from requests>=2.5.0->sphinx>=2.0.1->-r docs/requires.txt (line 6)) (1.25.7) Requirement already satisfied: chardet<3.1.0,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from requests>=2.5.0->sphinx>=2.0.1->-r docs/requires.txt (line 6)) (3.0.4) Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from requests>=2.5.0->sphinx>=2.0.1->-r docs/requires.txt (line 6)) (2019.9.11) Requirement already satisfied: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from Jinja2>=2.3->sphinx>=2.0.1->-r docs/requires.txt (line 6)) (1.1.1) Requirement already satisfied: monotonic>=0.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from fasteners->zarr->-r docs/requires.txt (line 14)) (1.5) Installing collected packages: sphinx Found existing installation: Sphinx 1.8.5 Uninstalling Sphinx-1.8.5: Successfully uninstalled Sphinx-1.8.5 Successfully installed sphinx-2.2.1 [rtd-command-info] start-time: 2019-11-26T09:09:02.269292Z, end-time: 2019-11-26T09:09:02.579386Z, duration: 0, exit-code: 0 cat docs/conf.py import sys import logging from pathlib import Path from datetime import datetime HERE = Path(__file__).parent sys.path.insert(0, str(HERE.parent)) import anndata # noqa logger = logging.getLogger(__name__) for generated in HERE.glob('anndata.*.rst'): generated.unlink() # -- General configuration ------------------------------------------------ needs_sphinx = '1.7' # autosummary bugfix # General information project = 'anndata' author = anndata.__author__ copyright = f'{datetime.now():%Y}, {author}.' version = anndata.__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 nitpicky = True # Report broken links suppress_warnings = ['ref.citation'] def setup(app): # Don’t allow broken links # app.warningiserror = True app.add_stylesheet('css/custom.css') intersphinx_mapping = dict( h5py=('http://docs.h5py.org/en/latest/', None), loompy=('https://linnarssonlab.org/loompy/', 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), sklearn=('https://scikit-learn.org/stable/', None), ) # -- 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='anndata', # 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 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', ) ] ########################################################################### # 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/"), ], 'downloads': [ ("html", "//readthedocs.com/projects/icb-anndata/downloads/htmlzip/latest/"), ], 'subprojects': [ ], 'slug': 'icb-anndata', 'name': u'anndata', 'rtd_language': u'en', 'programming_language': u'py', 'canonical_url': 'https://icb-anndata.readthedocs-hosted.com/en/stable/', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/docs/', 'api_host': 'https://readthedocs.com', 'proxied_api_host': 'https://readthedocs.com', 'github_user': 'theislab', 'github_repo': 'anndata', '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': '4a4e7136', } 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: 2019-11-26T09:09:02.685164Z, end-time: 2019-11-26T09:09:23.523279Z, duration: 20, exit-code: 0 python sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html Running Sphinx v2.2.1 loading translations [en]... done making output directory... done loading intersphinx inventory from http://docs.h5py.org/en/latest/objects.inv... loading intersphinx inventory from https://linnarssonlab.org/loompy/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://scikit-learn.org/stable/objects.inv... [autosummary] generating autosummary for: api.rst, benchmarks.rst, index.rst, references.rst, release_notes.rst /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages/setuptools_scm/git.py:68: UserWarning: "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest" is shallow and may cause errors warnings.warn('"%s" is shallow and may cause errors' % (wd.path,)) WARNING: [autosummary] failed to import 'anndata.h5py': no module named anndata.h5py [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.write.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.write_csvs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.write_loom.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.write_zarr.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.read_csv.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.read_excel.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.read_h5ad.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.read_hdf.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.read_loom.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.read_mtx.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.read_text.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.read_umi_tools.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.read_zarr.rst [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.T.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.chunk_X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.chunked_X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.concatenate.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.copy.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.filename.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.isbacked.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.isview.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.layers.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.uns_keys.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.var.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.var_keys.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.var_names.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.var_names_make_unique.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.var_vector.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.varm.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.varm_keys.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.varp.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.write_h5ad.rst 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: [new config] 56 added, 0 changed, 0 removed reading sources... [ 1%] anndata.AnnData reading sources... [ 3%] anndata.AnnData.T reading sources... [ 5%] anndata.AnnData.X reading sources... [ 7%] anndata.AnnData.chunk_X reading sources... [ 8%] anndata.AnnData.chunked_X reading sources... [ 10%] anndata.AnnData.concatenate reading sources... [ 12%] anndata.AnnData.copy reading sources... [ 14%] anndata.AnnData.filename reading sources... [ 16%] anndata.AnnData.isbacked reading sources... [ 17%] anndata.AnnData.isview reading sources... [ 19%] anndata.AnnData.layers reading sources... [ 21%] anndata.AnnData.n_obs reading sources... [ 23%] anndata.AnnData.n_vars reading sources... [ 25%] anndata.AnnData.obs reading sources... [ 26%] anndata.AnnData.obs_keys reading sources... [ 28%] anndata.AnnData.obs_names reading sources... [ 30%] anndata.AnnData.obs_names_make_unique reading sources... [ 32%] anndata.AnnData.obs_vector reading sources... [ 33%] anndata.AnnData.obsm reading sources... [ 35%] anndata.AnnData.obsm_keys reading sources... 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[ 71%] anndata.AnnData.write_h5ad reading sources... [ 73%] anndata.AnnData.write_loom reading sources... [ 75%] anndata.AnnData.write_zarr reading sources... [ 76%] anndata.read_csv reading sources... [ 78%] anndata.read_excel reading sources... [ 80%] anndata.read_h5ad reading sources... [ 82%] anndata.read_hdf reading sources... [ 83%] anndata.read_loom reading sources... [ 85%] anndata.read_mtx reading sources... [ 87%] anndata.read_text reading sources... [ 89%] anndata.read_umi_tools reading sources... [ 91%] anndata.read_zarr reading sources... [ 92%] api reading sources... [ 94%] benchmarks reading sources... [ 96%] index reading sources... [ 98%] references reading sources... [100%] release_notes /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/anndata/__init__.py:docstring of anndata.rst:63: WARNING: autosummary: stub file not found 'h5py'. 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[ 30%] anndata.AnnData.obs_names_make_unique writing output... [ 32%] anndata.AnnData.obs_vector writing output... [ 33%] anndata.AnnData.obsm writing output... [ 35%] anndata.AnnData.obsm_keys writing output... [ 37%] anndata.AnnData.obsp writing output... [ 39%] anndata.AnnData.raw writing output... [ 41%] anndata.AnnData.rename_categories writing output... [ 42%] anndata.AnnData.shape writing output... [ 44%] anndata.AnnData.strings_to_categoricals writing output... [ 46%] anndata.AnnData.to_df writing output... [ 48%] anndata.AnnData.transpose writing output... [ 50%] anndata.AnnData.uns writing output... [ 51%] anndata.AnnData.uns_keys writing output... [ 53%] anndata.AnnData.var writing output... [ 55%] anndata.AnnData.var_keys writing output... [ 57%] anndata.AnnData.var_names writing output... [ 58%] anndata.AnnData.var_names_make_unique writing output... [ 60%] anndata.AnnData.var_vector writing output... [ 62%] anndata.AnnData.varm writing output... [ 64%] anndata.AnnData.varm_keys writing output... [ 66%] anndata.AnnData.varp writing output... [ 67%] anndata.AnnData.write writing output... [ 69%] anndata.AnnData.write_csvs writing output... [ 71%] anndata.AnnData.write_h5ad writing output... [ 73%] anndata.AnnData.write_loom writing output... [ 75%] anndata.AnnData.write_zarr writing output... [ 76%] anndata.read_csv writing output... [ 78%] anndata.read_excel writing output... [ 80%] anndata.read_h5ad writing output... [ 82%] anndata.read_hdf writing output... [ 83%] anndata.read_loom writing output... [ 85%] anndata.read_mtx writing output... [ 87%] anndata.read_text writing output... [ 89%] anndata.read_umi_tools writing output... [ 91%] anndata.read_zarr writing output... [ 92%] api writing output... [ 94%] benchmarks writing output... [ 96%] index writing output... [ 98%] references writing output... [100%] release_notes /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/anndata/core/anndata.py:docstring of anndata.AnnData:40: WARNING: py:class reference target not found: anndata.h5py.File /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/anndata/core/anndata.py:docstring of anndata.AnnData:42: WARNING: py:class reference target not found: anndata.h5py.File /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/anndata/core/anndata.py:docstring of anndata.AnnData.layers:25: WARNING: py:class reference target not found: anndata.core.alignedmapping.Layers /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/anndata/core/anndata.py:docstring of anndata.AnnData.layers:25: WARNING: py:class reference target not found: anndata.core.alignedmapping.LayersView /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/anndata/core/anndata.py:docstring of 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/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/anndata/__init__.py:docstring of anndata:59: WARNING: py:class reference target not found: anndata.h5py /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/anndata/__init__.py:docstring of anndata:67::1: WARNING: py:obj reference target not found: h5py generating indices... genindex py-modindexdone writing additional pages... searchdone 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, 30 warnings. The HTML pages are in _build/html. /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages/sphinx_rtd_theme/search.html:20: RemovedInSphinx30Warning: To modify script_files in the theme is deprecated. Please insert a