Read the Docs build information Build id: 561045 Project: icb-anndata Version: 0.4.1 Commit: 562954b43a9b8faa969e0ec01707bc56cbc021b0 Date: 2021-02-14T12:35:17.831816Z State: finished Success: False [rtd-command-info] start-time: 2021-02-14T12:35:19.329022Z, end-time: 2021-02-14T12:35:20.913381Z, duration: 1, exit-code: 0 git clone --no-single-branch --depth 50 https://github.com/theislab/anndata.git . Cloning into '.'... [rtd-command-info] start-time: 2021-02-14T12:35:21.198466Z, end-time: 2021-02-14T12:35:21.255995Z, duration: 0, exit-code: 0 git checkout --force 562954b43a9b8faa969e0ec01707bc56cbc021b0 Note: checking out '562954b43a9b8faa969e0ec01707bc56cbc021b0'. 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 HEAD is now at 562954b updated docs [rtd-command-info] start-time: 2021-02-14T12:35:21.537923Z, end-time: 2021-02-14T12:35:21.591552Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2021-02-14T12:35:22.773553Z, end-time: 2021-02-14T12:35:26.649160Z, duration: 3, exit-code: 0 python3.7 -mvirtualenv Using base prefix '/home/docs/.pyenv/versions/3.7.9' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/0.4.1/bin/python3.7 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/0.4.1/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2021-02-14T12:35:26.760283Z, end-time: 2021-02-14T12:35:27.570493Z, duration: 0, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/0.4.1/lib/python3.7/site-packages (21.0.1) [rtd-command-info] start-time: 2021-02-14T12:35:27.698369Z, end-time: 2021-02-14T12:35:36.486201Z, duration: 8, exit-code: 0 python -m pip install --upgrade --no-cache-dir setuptools==41.0.1 docutils==0.14 mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 six commonmark==0.8.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<2.2 Collecting setuptools==41.0.1 Downloading setuptools-41.0.1-py2.py3-none-any.whl (575 kB) Collecting docutils==0.14 Downloading docutils-0.14-py3-none-any.whl (543 kB) Collecting mock==1.0.1 Downloading mock-1.0.1.zip (861 kB) Collecting pillow==5.4.1 Downloading Pillow-5.4.1-cp37-cp37m-manylinux1_x86_64.whl (2.0 MB) Collecting alabaster!=0.7.5,<0.8,>=0.7 Downloading alabaster-0.7.12-py2.py3-none-any.whl (14 kB) Collecting six Downloading six-1.15.0-py2.py3-none-any.whl (10 kB) Collecting commonmark==0.8.1 Downloading commonmark-0.8.1-py2.py3-none-any.whl (47 kB) Collecting recommonmark==0.5.0 Downloading recommonmark-0.5.0-py2.py3-none-any.whl (9.8 kB) Collecting sphinx<2 Downloading Sphinx-1.8.5-py2.py3-none-any.whl (3.1 MB) Collecting sphinx-rtd-theme<0.5 Downloading sphinx_rtd_theme-0.4.3-py2.py3-none-any.whl (6.4 MB) Collecting readthedocs-sphinx-ext<2.2 Downloading readthedocs_sphinx_ext-2.1.3-py2.py3-none-any.whl (11 kB) Collecting future Downloading future-0.18.2.tar.gz (829 kB) Collecting requests Downloading requests-2.25.1-py2.py3-none-any.whl (61 kB) Collecting Jinja2>=2.9 Downloading Jinja2-2.11.3-py2.py3-none-any.whl (125 kB) Collecting babel!=2.0,>=1.3 Downloading Babel-2.9.0-py2.py3-none-any.whl (8.8 MB) Collecting Pygments>=2.0 Downloading Pygments-2.7.4-py3-none-any.whl (950 kB) Collecting sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.2.4-py2.py3-none-any.whl (39 kB) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.1.0-py2.py3-none-any.whl (93 kB) Collecting packaging Downloading packaging-20.9-py2.py3-none-any.whl (40 kB) Collecting imagesize Downloading imagesize-1.2.0-py2.py3-none-any.whl (4.8 kB) Collecting pytz>=2015.7 Downloading pytz-2021.1-py2.py3-none-any.whl (510 kB) Collecting MarkupSafe>=0.23 Downloading MarkupSafe-1.1.1-cp37-cp37m-manylinux2010_x86_64.whl (33 kB) Collecting certifi>=2017.4.17 Downloading certifi-2020.12.5-py2.py3-none-any.whl (147 kB) Collecting chardet<5,>=3.0.2 Downloading chardet-4.0.0-py2.py3-none-any.whl (178 kB) Collecting idna<3,>=2.5 Downloading idna-2.10-py2.py3-none-any.whl (58 kB) Collecting urllib3<1.27,>=1.21.1 Downloading urllib3-1.26.3-py2.py3-none-any.whl (137 kB) Collecting pyparsing>=2.0.2 Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 kB) Collecting sphinxcontrib-serializinghtml Downloading sphinxcontrib_serializinghtml-1.1.4-py2.py3-none-any.whl (89 kB) Building wheels for collected packages: mock, future Building wheel for mock (setup.py): started Building wheel for mock (setup.py): finished with status 'done' Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23755 sha256=c6fa532d287eb74468813c33568e0287702d8c3bc3906c24fb238b463a81415e Stored in directory: /tmp/pip-ephem-wheel-cache-lozrs9y_/wheels/7a/94/b1/0fdc5339a5bd487a5cc15421ec200d9ba3e2aa7190e4a727f1 Building wheel for future (setup.py): started Building wheel for future (setup.py): finished with status 'done' Created wheel for future: filename=future-0.18.2-py3-none-any.whl size=491059 sha256=ca195ba585aa713dc15abf6933efe99e7db3f1146d087039c1a3335cdc10b93b Stored in directory: /tmp/pip-ephem-wheel-cache-lozrs9y_/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0 Successfully built mock future Installing collected packages: urllib3, sphinxcontrib-serializinghtml, pytz, pyparsing, MarkupSafe, idna, chardet, certifi, sphinxcontrib-websupport, snowballstemmer, six, setuptools, requests, Pygments, packaging, Jinja2, imagesize, future, docutils, babel, alabaster, sphinx, commonmark, sphinx-rtd-theme, recommonmark, readthedocs-sphinx-ext, pillow, mock Attempting uninstall: setuptools Found existing installation: setuptools 53.0.0 Uninstalling setuptools-53.0.0: Successfully uninstalled setuptools-53.0.0 Successfully installed Jinja2-2.11.3 MarkupSafe-1.1.1 Pygments-2.7.4 alabaster-0.7.12 babel-2.9.0 certifi-2020.12.5 chardet-4.0.0 commonmark-0.8.1 docutils-0.14 future-0.18.2 idna-2.10 imagesize-1.2.0 mock-1.0.1 packaging-20.9 pillow-5.4.1 pyparsing-2.4.7 pytz-2021.1 readthedocs-sphinx-ext-2.1.3 recommonmark-0.5.0 requests-2.25.1 setuptools-41.0.1 six-1.15.0 snowballstemmer-2.1.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.4 sphinxcontrib-websupport-1.2.4 urllib3-1.26.3 [rtd-command-info] start-time: 2021-02-14T12:35:36.633581Z, end-time: 2021-02-14T12:35:46.627822Z, duration: 9, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r docs/requires.txt Collecting numpydoc Downloading numpydoc-1.1.0-py3-none-any.whl (47 kB) Collecting pandas>=0.21.0 Downloading pandas-1.2.2-cp37-cp37m-manylinux1_x86_64.whl (9.9 MB) Collecting scipy Downloading scipy-1.6.0-cp37-cp37m-manylinux1_x86_64.whl (27.4 MB) Collecting h5py Downloading h5py-3.1.0-cp37-cp37m-manylinux1_x86_64.whl (4.0 MB) Collecting python-dateutil>=2.7.3 Downloading python_dateutil-2.8.1-py2.py3-none-any.whl (227 kB) Requirement already satisfied: pytz>=2017.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/0.4.1/lib/python3.7/site-packages (from pandas>=0.21.0->-r docs/requires.txt (line 4)) (2021.1) Collecting numpy>=1.16.5 Downloading numpy-1.20.1-cp37-cp37m-manylinux2010_x86_64.whl (15.3 MB) Requirement already satisfied: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/0.4.1/lib/python3.7/site-packages (from python-dateutil>=2.7.3->pandas>=0.21.0->-r docs/requires.txt (line 4)) (1.15.0) Collecting cached-property Downloading cached_property-1.5.2-py2.py3-none-any.whl (7.6 kB) Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/0.4.1/lib/python3.7/site-packages (from numpydoc->-r docs/requires.txt (line 2)) (2.11.3) Requirement already satisfied: sphinx>=1.6.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/0.4.1/lib/python3.7/site-packages (from numpydoc->-r docs/requires.txt (line 2)) (1.8.5) Requirement already satisfied: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/0.4.1/lib/python3.7/site-packages (from Jinja2>=2.3->numpydoc->-r docs/requires.txt (line 2)) (1.1.1) Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/0.4.1/lib/python3.7/site-packages (from sphinx>=1.6.5->numpydoc->-r docs/requires.txt (line 2)) (2.1.0) Requirement already satisfied: docutils>=0.11 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/0.4.1/lib/python3.7/site-packages (from sphinx>=1.6.5->numpydoc->-r docs/requires.txt (line 2)) (0.14) Requirement already satisfied: requests>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/0.4.1/lib/python3.7/site-packages (from sphinx>=1.6.5->numpydoc->-r docs/requires.txt (line 2)) (2.25.1) Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/0.4.1/lib/python3.7/site-packages (from sphinx>=1.6.5->numpydoc->-r docs/requires.txt (line 2)) (0.7.12) Requirement already satisfied: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/0.4.1/lib/python3.7/site-packages (from 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/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/0.4.1/lib/python3.7/site-packages (from sphinx>=1.6.5->numpydoc->-r docs/requires.txt (line 2)) (1.2.0) Requirement already satisfied: idna<3,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/0.4.1/lib/python3.7/site-packages (from requests>=2.0.0->sphinx>=1.6.5->numpydoc->-r docs/requires.txt (line 2)) (2.10) Requirement already satisfied: urllib3<1.27,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/0.4.1/lib/python3.7/site-packages (from requests>=2.0.0->sphinx>=1.6.5->numpydoc->-r docs/requires.txt (line 2)) (1.26.3) Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/0.4.1/lib/python3.7/site-packages (from requests>=2.0.0->sphinx>=1.6.5->numpydoc->-r docs/requires.txt (line 2)) (2020.12.5) Requirement already satisfied: chardet<5,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/0.4.1/lib/python3.7/site-packages (from requests>=2.0.0->sphinx>=1.6.5->numpydoc->-r docs/requires.txt (line 2)) (4.0.0) Requirement already satisfied: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/0.4.1/lib/python3.7/site-packages (from packaging->sphinx>=1.6.5->numpydoc->-r docs/requires.txt (line 2)) (2.4.7) Requirement already satisfied: sphinxcontrib-serializinghtml in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/0.4.1/lib/python3.7/site-packages (from sphinxcontrib-websupport->sphinx>=1.6.5->numpydoc->-r docs/requires.txt (line 2)) (1.1.4) Installing collected packages: python-dateutil, numpy, cached-property, scipy, pandas, numpydoc, h5py Successfully installed cached-property-1.5.2 h5py-3.1.0 numpy-1.20.1 numpydoc-1.1.0 pandas-1.2.2 python-dateutil-2.8.1 scipy-1.6.0 [rtd-command-info] start-time: 2021-02-14T12:35:47.637851Z, end-time: 2021-02-14T12:35:47.691070Z, duration: 0, exit-code: 0 cat docs/conf.py #!/usr/bin/env python3 # -*- coding: utf-8 -*- # # Scanpy documentation build configuration file, created by # sphinx-quickstart on Sun Aug 20 00:29:31 2017. # # This file is execfile()d with the current directory set to its # containing dir. # # Note that not all possible configuration values are present in this # autogenerated file. # # All configuration values have a default; values that are commented out # serve to show the default. # If extensions (or modules to document with autodoc) are in another directory, # add these directories to sys.path here. If the directory is relative to the # documentation root, use os.path.abspath to make it absolute, like shown here. # import os import sys import time import inspect from pathlib import Path sys.path.insert(0, os.path.abspath(os.path.pardir)) # -- General configuration ------------------------------------------------ # If your documentation needs a minimal Sphinx version, state it here. # # needs_sphinx = '1.0' # Add any Sphinx extension module names here, as strings. They can be # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. extensions = ['sphinx.ext.autodoc', 'sphinx.ext.doctest', 'sphinx.ext.coverage', 'sphinx.ext.mathjax', 'sphinx.ext.autosummary', # 'plot_generator', # 'plot_directive', 'numpydoc', # 'ipython_directive', # 'ipython_console_highlighting', ] # Generate the API documentation when building autosummary_generate = True autodoc_mock_imports = ['_tkinter'] # both of the following two lines don't work # see falexwolf's issue for numpydoc # autodoc_member_order = 'bysource' # autodoc_default_flags = ['members'] numpydoc_show_class_members = True # we would like to document the class members as well # but they are not clickable, why? # so, to avoid all these warnings, set this to False numpydoc_class_members_toctree = False templates_path = ['_templates'] source_suffix = '.rst' master_doc = 'index' project = 'anndata' copyright = '{}, Alex Wolf, Philipp Angerer'.format(time.strftime("%Y")) author = 'Alex Wolf, Philipp Angerer' import anndata version = anndata.__version__.replace('.dirty', '') release = version exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] pygments_style = 'sphinx' todo_include_todos = False # -- Options for HTML output ---------------------------------------------- html_theme = 'sphinx_rtd_theme' if html_theme == 'sphinx_rtd_theme': html_theme_options = { 'navigation_depth': 2, } html_context = { "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 } elif html_theme == 'bootstrap': import sphinx_bootstrap_theme html_theme_path = sphinx_bootstrap_theme.get_html_theme_path() html_theme_options = { 'navbar_site_name': "Site", 'navbar_pagenav_name': "Page", 'source_link_position': "footer", 'bootswatch_theme': "paper", 'navbar_pagenav': False, 'navbar_sidebarrel': False, 'bootstrap_version': "3", 'navbar_links': [ ("API", "api"), ], } html_static_path = ['_static'] # -- Options for HTMLHelp output ------------------------------------------ # Output file base name for HTML help builder. htmlhelp_basename = 'anndatadoc' # -- Options for LaTeX output --------------------------------------------- latex_elements = { # The paper size ('letterpaper' or 'a4paper'). # # 'papersize': 'letterpaper', # The font size ('10pt', '11pt' or '12pt'). # # 'pointsize': '10pt', # Additional stuff for the LaTeX preamble. # # 'preamble': '', # Latex figure (float) alignment # # 'figure_align': 'htbp', } # Grouping the document tree into LaTeX files. List of tuples # (source start file, target name, title, # author, documentclass [howto, manual, or own class]). latex_documents = [ (master_doc, 'anndata.tex', 'anndata Documentation', 'Alex Wolf, Philipp Angerer', 'manual'), ] # -- Options for manual page output --------------------------------------- # One entry per manual page. List of tuples # (source start file, name, description, authors, manual section). man_pages = [ (master_doc, 'anndata', 'anndata Documentation', [author], 1) ] # -- Options for Texinfo output ------------------------------------------- # Grouping the document tree into Texinfo files. List of tuples # (source start file, target name, title, author, # dir menu entry, description, category) texinfo_documents = [ (master_doc, 'anndata', 'anndata Documentation', author, 'anndata', 'One line description of project.', 'Miscellaneous'), ] def get_obj_module(qualname): """Get a module/class/attribute and its original module by qualname""" modname = qualname classname = None attrname = None while modname not in sys.modules: attrname = classname modname, classname = modname.rsplit('.', 1) # retrieve object and find original module name if classname: cls = getattr(sys.modules[modname], classname) modname = cls.__module__ obj = getattr(cls, attrname) if attrname else cls else: obj = None return obj, sys.modules[modname] def get_linenos(obj): """Get an object’s line numbers""" try: lines, start = inspect.getsourcelines(obj) except TypeError: return None, None else: return start, start + len(lines) - 1 project_dir = Path(__file__).parent.parent # project/docs/conf.py/../.. → project/ github_url1 = 'https://github.com/{github_user}/{github_repo}/tree/{github_version}'.format_map(html_context) github_url2 = 'https://github.com/theislab/anndata/tree/master' def modurl(qualname): """Get the full GitHub URL for some object’s qualname.""" obj, module = get_obj_module(qualname) github_url = github_url1 try: path = Path(module.__file__).relative_to(project_dir) except ValueError: # trying to document something from another package github_url = github_url2 path = '/'.join(module.__file__.split('/')[-2:]) start, end = get_linenos(obj) fragment = '#L{}-L{}'.format(start, end) if start and end else '' return '{}/{}{}'.format(github_url, path, fragment) # html_context doesn’t apply to autosummary templates ☹ # and there’s no way to insert filters into those templates # so we have to modify the default filters from jinja2.defaults import DEFAULT_FILTERS DEFAULT_FILTERS['modurl'] = modurl ########################################################################### # auto-created readthedocs.org specific configuration # ########################################################################### # # The following code was added during an automated build on readthedocs.org # It is auto created and injected for every build. The result is based on the # conf.py.tmpl file found in the readthedocs.org codebase: # https://github.com/rtfd/readthedocs.org/blob/master/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl # import importlib import sys import os.path from six import string_types from sphinx import version_info # Get suffix for proper linking to GitHub # This is deprecated in Sphinx 1.3+, # as each page can have its own suffix if globals().get('source_suffix', False): if isinstance(source_suffix, string_types): SUFFIX = source_suffix elif isinstance(source_suffix, (list, tuple)): # Sphinx >= 1.3 supports list/tuple to define multiple suffixes SUFFIX = source_suffix[0] elif isinstance(source_suffix, dict): # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes SUFFIX = list(source_suffix.keys())[0] # make a ``list()`` for py2/py3 compatibility else: # default to .rst SUFFIX = '.rst' else: SUFFIX = '.rst' # Add RTD Static Path. Add to the end because it overwrites previous files. if not 'html_static_path' in globals(): html_static_path = [] if os.path.exists('_static'): html_static_path.append('_static') # Add RTD Theme only if they aren't overriding it already using_rtd_theme = ( ( 'html_theme' in globals() and html_theme in ['default'] and # Allow people to bail with a hack of having an html_style 'html_style' not in globals() ) or 'html_theme' not in globals() ) if using_rtd_theme: theme = importlib.import_module('sphinx_rtd_theme') html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} if 'html_theme_path' in globals(): html_theme_path.append(theme.get_html_theme_path()) else: html_theme_path = [theme.get_html_theme_path()] if globals().get('websupport2_base_url', False): websupport2_base_url = 'https://readthedocs.com/websupport' websupport2_static_url = 'https://assets.readthedocs.com/' #Add project information to the template context. context = { 'using_theme': using_rtd_theme, 'html_theme': html_theme, 'current_version': "0.4.1", 'version_slug': "0.4.1", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://assets.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ("latest", "/en/latest/"), ("stable", "/en/stable/"), ("0.4.1", "/en/0.4.1/"), ("0.3", "/en/0.3/"), ("refpaths", "/en/refpaths/"), ], 'downloads': [ ], 'subprojects': [ ], 'slug': 'icb-anndata', 'name': u'anndata', 'rtd_language': u'en', 'programming_language': u'py', 'canonical_url': 'https://anndata.readthedocs.io/en/latest/', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/docs/', 'api_host': 'https://readthedocs.com', 'github_user': 'theislab', 'proxied_api_host': '/_', 'github_repo': 'anndata', 'github_version': '0.4.1', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': '0.4.1', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': '0.4.1', 'display_gitlab': False, 'READTHEDOCS': True, 'using_theme': (html_theme == "default"), 'new_theme': (html_theme == "sphinx_rtd_theme"), 'source_suffix': SUFFIX, 'ad_free': False, 'docsearch_disabled': False, 'user_analytics_code': '', 'global_analytics_code': 'UA-17997319-2', 'commit': '562954b4', } # For sphinx >=1.8 we can use html_baseurl to set the canonical URL. # https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_baseurl if version_info >= (1, 8): if not globals().get('html_baseurl'): html_baseurl = context['canonical_url'] context['canonical_url'] = None 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 'tag' == 'external': extensions.insert(1, "readthedocs_ext.external_version_warning") readthedocs_vcs_url = 'None' readthedocs_build_url = 'https://readthedocs.com/projects/icb-anndata/builds/561045/' project_language = 'en' # User's Sphinx configurations language_user = globals().get('language', None) latex_engine_user = globals().get('latex_engine', None) latex_elements_user = globals().get('latex_elements', None) # Remove this once xindy gets installed in Docker image and XINDYOPS # env variable is supported # https://github.com/rtfd/readthedocs-docker-images/pull/98 latex_use_xindy = False chinese = any([ language_user in ('zh_CN', 'zh_TW'), project_language in ('zh_CN', 'zh_TW'), ]) japanese = any([ language_user == 'ja', project_language == 'ja', ]) if chinese: latex_engine = latex_engine_user or 'xelatex' latex_elements_rtd = { 'preamble': '\\usepackage[UTF8]{ctex}\n', } latex_elements = latex_elements_user or latex_elements_rtd elif japanese: latex_engine = latex_engine_user or 'platex' # Make sure our build directory is always excluded exclude_patterns = globals().get('exclude_patterns', []) exclude_patterns.extend(['_build']) [rtd-command-info] start-time: 2021-02-14T12:35:47.878073Z, end-time: 2021-02-14T12:35:48.506405Z, duration: 0, exit-code: 2 python -m sphinx -T -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html Running Sphinx v1.8.5 /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/0.4.1/anndata/base.py:10: FutureWarning: pandas.core.index is deprecated and will be removed in a future version. The public classes are available in the top-level namespace. from pandas.core.index import RangeIndex Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/0.4.1/lib/python3.7/site-packages/sphinx/config.py", line 368, in eval_config_file execfile_(filename, namespace) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/0.4.1/lib/python3.7/site-packages/sphinx/util/pycompat.py", line 150, in execfile_ exec_(code, _globals) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/0.4.1/docs/conf.py", line 68, in import anndata File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/0.4.1/anndata/__init__.py", line 1, in from .base import AnnData File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/0.4.1/anndata/base.py", line 13, in from scipy.sparse.sputils import IndexMixin ImportError: cannot import name 'IndexMixin' from 'scipy.sparse.sputils' (/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/0.4.1/lib/python3.7/site-packages/scipy/sparse/sputils.py) During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/0.4.1/lib/python3.7/site-packages/sphinx/cmd/build.py", line 303, in build_main args.tags, args.verbosity, args.jobs, args.keep_going) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/0.4.1/lib/python3.7/site-packages/sphinx/application.py", line 201, in __init__ self.config = Config.read(self.confdir, confoverrides or {}, self.tags) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/0.4.1/lib/python3.7/site-packages/sphinx/config.py", line 203, in read namespace = eval_config_file(filename, tags) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/0.4.1/lib/python3.7/site-packages/sphinx/config.py", line 380, in eval_config_file raise ConfigError(msg % traceback.format_exc()) sphinx.errors.ConfigError: There is a programmable error in your configuration file: Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/0.4.1/lib/python3.7/site-packages/sphinx/config.py", line 368, in eval_config_file execfile_(filename, namespace) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/0.4.1/lib/python3.7/site-packages/sphinx/util/pycompat.py", line 150, in execfile_ exec_(code, _globals) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/0.4.1/docs/conf.py", line 68, in import anndata File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/0.4.1/anndata/__init__.py", line 1, in from .base import AnnData File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/0.4.1/anndata/base.py", line 13, in from scipy.sparse.sputils import IndexMixin ImportError: cannot import name 'IndexMixin' from 'scipy.sparse.sputils' (/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/0.4.1/lib/python3.7/site-packages/scipy/sparse/sputils.py) Configuration error: There is a programmable error in your configuration file: Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/0.4.1/lib/python3.7/site-packages/sphinx/config.py", line 368, in eval_config_file execfile_(filename, namespace) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/0.4.1/lib/python3.7/site-packages/sphinx/util/pycompat.py", line 150, in execfile_ exec_(code, _globals) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/0.4.1/docs/conf.py", line 68, in import anndata File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/0.4.1/anndata/__init__.py", line 1, in from .base import AnnData File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/0.4.1/anndata/base.py", line 13, in from scipy.sparse.sputils import IndexMixin ImportError: cannot import name 'IndexMixin' from 'scipy.sparse.sputils' (/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/0.4.1/lib/python3.7/site-packages/scipy/sparse/sputils.py)