Read the Docs build information Build id: 234403 Project: icb-scanpy Version: latest Commit: 0c30b3f759cf31eaecfa7bd2a21074f79d00c9a4 Date: 2019-08-21T16:08:56.161659Z State: finished Success: True [rtd-command-info] start-time: 2019-08-21T16:08:56.620881Z, end-time: 2019-08-21T16:08:58.303863Z, duration: 1, exit-code: 0 git clone --no-single-branch --depth 50 https://github.com/theislab/scanpy.git . Cloning into '.'... [rtd-command-info] start-time: 2019-08-21T16:08:58.562434Z, end-time: 2019-08-21T16:08:58.659703Z, duration: 0, exit-code: 0 git checkout --force origin/master Note: checking out 'origin/master'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by performing another checkout. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -b with the checkout command again. Example: git checkout -b HEAD is now at 0c30b3f Don’t let broken docs compile [rtd-command-info] start-time: 2019-08-21T16:08:58.749649Z, end-time: 2019-08-21T16:08:58.758677Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2019-08-21T16:08:59.771249Z, end-time: 2019-08-21T16:09:04.368393Z, duration: 4, exit-code: 0 python3.6 -mvirtualenv --no-site-packages --no-download Using base prefix '/home/docs/.pyenv/versions/3.6.8' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/bin/python3.6 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/bin/python Installing setuptools, pip, wheel... done. 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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) Collecting numexpr>=2.6.2 (from tables->-r docs/requirements.txt (line 15)) Using cached https://files.pythonhosted.org/packages/06/5e/ee657b36ce1b6baabaafe485e97a31e7200f918c4b8643ebc4fd4fd07ada/numexpr-2.7.0-cp36-cp36m-manylinux1_x86_64.whl 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 Collecting decorator>=4.3.0 (from networkx->-r docs/requirements.txt (line 18)) Using cached https://files.pythonhosted.org/packages/5f/88/0075e461560a1e750a0dcbf77f1d9de775028c37a19a346a6c565a257399/decorator-4.4.0-py2.py3-none-any.whl Collecting llvmlite>=0.29.0dev0 (from numba->-r docs/requirements.txt (line 21)) Using cached https://files.pythonhosted.org/packages/1f/bf/c9fc3b6d7d46968186ac37a2453639979edd8fa7199bb9f4b820a813e8c8/llvmlite-0.29.0-1-cp36-cp36m-manylinux1_x86_64.whl Collecting zipp>=0.5 (from importlib_metadata->-r docs/requirements.txt (line 23)) Using cached https://files.pythonhosted.org/packages/da/bd/1a5fdf15aa44231fd09f63ecf175b60f057ae37ec65b343bb009364923f3/zipp-0.5.2-py2.py3-none-any.whl 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: 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: certifi>=2017.4.17 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)) (2019.6.16) 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) Collecting future-fstrings (from get_version->scanpydoc>=0.3.8->-r docs/requirements.txt (line 7)) Using cached https://files.pythonhosted.org/packages/ab/6d/ea1d52e9038558dd37f5d30647eb9f07888c164960a5d4daa5f970c6da25/future_fstrings-1.2.0-py2.py3-none-any.whl Installing collected packages: sphinxcontrib-applehelp, sphinxcontrib-htmlhelp, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-devhelp, sphinx, sphinx-autodoc-typehints, future-fstrings, get-version, scanpydoc, numpy, h5py, natsort, scipy, python-dateutil, pandas, anndata, kiwisolver, cycler, matplotlib, seaborn, numexpr, mock, tables, joblib, scikit-learn, decorator, networkx, llvmlite, numba, tqdm, zipp, importlib-metadata, umap-learn Found existing installation: Sphinx 1.8.5 Uninstalling Sphinx-1.8.5: Successfully uninstalled Sphinx-1.8.5 Found existing installation: mock 1.0.1 Uninstalling mock-1.0.1: Successfully uninstalled mock-1.0.1 Successfully installed anndata-0.6.22.post1 cycler-0.10.0 decorator-4.4.0 future-fstrings-1.2.0 get-version-2.0.6 h5py-2.9.0 importlib-metadata-0.19 joblib-0.13.2 kiwisolver-1.1.0 llvmlite-0.29.0 matplotlib-3.1.1 mock-3.0.5 natsort-6.0.0 networkx-2.3 numba-0.45.1 numexpr-2.7.0 numpy-1.17.0 pandas-0.25.0 python-dateutil-2.8.0 scanpydoc-0.3.8 scikit-learn-0.21.3 scipy-1.3.1 seaborn-0.9.0 sphinx-2.2.0 sphinx-autodoc-typehints-1.7.0 sphinxcontrib-applehelp-1.0.1 sphinxcontrib-devhelp-1.0.1 sphinxcontrib-htmlhelp-1.0.2 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.2 sphinxcontrib-serializinghtml-1.1.3 tables-3.5.2 tqdm-4.34.0 umap-learn-0.3.10 zipp-0.5.2 [rtd-command-info] start-time: 2019-08-21T16:09:49.730789Z, end-time: 2019-08-21T16:09:50.042900Z, 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: 2019-08-21T16:09:50.125700Z, end-time: 2019-08-21T16:11:06.948103Z, duration: 76, exit-code: 0 python sphinx-build -T -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.api.rst, api/scanpy.external.rst, api/scanpy.plotting.rst, basic_usage.rst, examples.rst, external/index.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.Neighbors.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy._settings.ScanpyConfig.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy.datasets.blobs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy.datasets.ebi_expression_atlas.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy.datasets.krumsiek11.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy.datasets.moignard15.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy.datasets.paul15.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy.datasets.pbmc3k.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy.datasets.pbmc68k_reduced.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy.datasets.toggleswitch.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/external/scanpy.external.pl.phate.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/external/scanpy.external.pp.bbknn.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/external/scanpy.external.pp.dca.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/external/scanpy.external.pp.magic.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/external/scanpy.external.pp.mnn_correct.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/external/scanpy.external.tl.cyclone.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/external/scanpy.external.tl.palantir.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/external/scanpy.external.tl.phate.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/external/scanpy.external.tl.phenograph.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/external/scanpy.external.tl.sandbag.rst [autosummary] generating autosummary for: 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