Read the Docs build information Build id: 251240 Project: icb-scanpy Version: latest Commit: 172a1a423ed004e418eef2ef08e881f99ca6dc24 Date: 2019-10-18T15:15:55.924933Z State: finished Success: False [rtd-command-info] start-time: 2019-10-18T15:15:56.375589Z, end-time: 2019-10-18T15:15:58.350655Z, 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: 2019-10-18T15:15:58.718779Z, end-time: 2019-10-18T15:15:58.816705Z, 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 172a1a4 Fixed scvelo inventory URL [rtd-command-info] start-time: 2019-10-18T15:15:58.893726Z, end-time: 2019-10-18T15:15:58.901709Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2019-10-18T15:15:59.991719Z, end-time: 2019-10-18T15:16:04.736734Z, 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. [rtd-command-info] start-time: 2019-10-18T15:16:04.831000Z, end-time: 2019-10-18T15:16:07.407102Z, duration: 2, exit-code: 0 python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/.cache/pip pip Collecting pip Downloading https://files.pythonhosted.org/packages/00/b6/9cfa56b4081ad13874b0c6f96af8ce16cfbc1cb06bedf8e9164ce5551ec1/pip-19.3.1-py2.py3-none-any.whl (1.4MB) Installing collected packages: pip Found existing installation: pip 19.1.1 Uninstalling pip-19.1.1: Successfully uninstalled pip-19.1.1 Successfully installed pip-19.3.1 [rtd-command-info] start-time: 2019-10-18T15:16:07.505682Z, end-time: 2019-10-18T15:16:18.117081Z, duration: 10, 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 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https://files.pythonhosted.org/packages/b2/5f/23e0023be6bb885d00ffbefad2942bc51a620328ee910f64abe5a8d18dd1/MarkupSafe-1.1.1-cp36-cp36m-manylinux1_x86_64.whl Collecting pyparsing>=2.0.2 Downloading https://files.pythonhosted.org/packages/11/fa/0160cd525c62d7abd076a070ff02b2b94de589f1a9789774f17d7c54058e/pyparsing-2.4.2-py2.py3-none-any.whl (65kB) Building wheels for collected packages: mock, future Building wheel for mock (setup.py): started Building wheel for mock (setup.py): finished with status 'done' Created wheel for mock: filename=mock-1.0.1-cp36-none-any.whl size=23755 sha256=5054740826b157e478b85fa9e75642d87a19a8e0d32ab77263ff8f73229d1c79 Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/.cache/pip/wheels/7e/72/92/744b532c779242b57aab4bcba80c312b30c069bbd60025e7e6 Building wheel for future (setup.py): started Building wheel for future (setup.py): finished with status 'done' Created wheel for future: filename=future-0.18.1-cp36-none-any.whl 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https://files.pythonhosted.org/packages/1d/70/97966deebaeeda0b81d3cd63ba9f8ec929b838871ed17476de9d8159db3e/setuptools_scm-3.3.3-py2.py3-none-any.whl Collecting umap-learn Downloading https://files.pythonhosted.org/packages/ad/92/36bac74962b424870026cb0b42cec3d5b6f4afa37d81818475d8762f9255/umap-learn-0.3.10.tar.gz (40kB) 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: 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) Collecting sphinxcontrib-qthelp Downloading https://files.pythonhosted.org/packages/ce/5b/4747c3ba98b3a3e21a66faa183d8f79b9ded70e74212a7988d236a6eb78a/sphinxcontrib_qthelp-1.0.2-py2.py3-none-any.whl (90kB) Requirement already satisfied: packaging in 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Collecting zipp>=0.5 Downloading https://files.pythonhosted.org/packages/74/3d/1ee25a26411ba0401b43c6376d2316a71addcc72ef8690b101b4ea56d76a/zipp-0.6.0-py2.py3-none-any.whl 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: 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)) (2019.9.11) 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)) (1.25.6) 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: 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) Collecting more-itertools Downloading https://files.pythonhosted.org/packages/45/dc/3241eef99eb45f1def35cf93af35d1cf9ef4c0991792583b8f33ea41b092/more_itertools-7.2.0-py3-none-any.whl (57kB) Building wheels for collected packages: umap-learn Building wheel for umap-learn (setup.py): started Building wheel for umap-learn (setup.py): finished with status 'done' Created wheel for umap-learn: filename=umap_learn-0.3.10-cp36-none-any.whl size=38881 sha256=1925f076a27961348d3cddcd1aab3f7a35a3830422d6cba98b8fb2dfb783dc4e Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/.cache/pip/wheels/d0/f8/d5/8e3af3ee957feb9b403a060ebe72f7561887fef9dea658326e Successfully built umap-learn Installing collected packages: sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-serializinghtml, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, sphinx, sphinx-autodoc-typehints, get-version, scanpydoc, natsort, numpy, python-dateutil, pandas, h5py, scipy, anndata, cycler, kiwisolver, matplotlib, seaborn, numexpr, tables, joblib, scikit-learn, decorator, networkx, llvmlite, numba, tqdm, more-itertools, zipp, importlib-metadata, setuptools-scm, umap-learn Found existing installation: Sphinx 1.8.5 Uninstalling Sphinx-1.8.5: Successfully uninstalled Sphinx-1.8.5 Successfully installed anndata-0.6.22.post1 cycler-0.10.0 decorator-4.4.0 get-version-2.1 h5py-2.10.0 importlib-metadata-0.23 joblib-0.14.0 kiwisolver-1.1.0 llvmlite-0.30.0 matplotlib-3.1.1 more-itertools-7.2.0 natsort-6.0.0 networkx-2.4 numba-0.46.0 numexpr-2.7.0 numpy-1.17.3 pandas-0.25.1 python-dateutil-2.8.0 scanpydoc-0.4.2 scikit-learn-0.21.3 scipy-1.3.1 seaborn-0.9.0 setuptools-scm-3.3.3 sphinx-2.2.0 sphinx-autodoc-typehints-1.8.0 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-3.6.0 tqdm-4.36.1 umap-learn-0.3.10 zipp-0.6.0 [rtd-command-info] start-time: 2019-10-18T15:16:47.660834Z, end-time: 2019-10-18T15:16:47.978755Z, duration: 0, exit-code: 0 cat docs/conf.py import os 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 on_rtd = os.environ.get('READTHEDOCS') == 'True' # -- General configuration ------------------------------------------------ nitpicky = True # Warn about broken links needs_sphinx = '2.0' # Nicer param docs 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/stable/', None), bbknn=('https://bbknn.readthedocs.io/en/latest/', None), cycler=('https://matplotlib.org/cycler/', None), h5py=('http://docs.h5py.org/en/stable/', 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), scvelo=('https://scvelo.readthedocs.io/', 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 = on_rtd app.add_stylesheet('css/custom.css') app.connect('autodoc-process-docstring', insert_function_images) app.connect('build-finished', show_param_warnings) 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 # -- Warn for non-annotated params --------------------------------------------- _format_docutils_params_orig = NumpyDocstring._format_docutils_params param_warnings = {} def scanpy_log_param_types(self, fields, field_role='param', type_role='type'): for _name, _type, _desc in fields: if not _type: continue set_item = r"`'[a-z0-9_.-]+'`" if re.fullmatch(rf"{{{set_item}(, {set_item})*}}", _type): continue param_warnings.setdefault((self._name, self._obj), []).append( (_name, _type) ) return _format_docutils_params_orig(self, fields, field_role, type_role) def show_param_warnings(app, exception): import inspect for (fname, fun), params in param_warnings.items(): _, line = inspect.getsourcelines(fun) file_name = inspect.getsourcefile(fun) params_str = '\n'.join(f'\t{n}: {t}' for n, t in params) warnings.warn_explicit( f'\nParameters in `{fname}` not set-like: {{`elm-1`, `s_el.2`}}.\n' 'Convert to this format or replace with type annotations:\n' + params_str, UserWarning, file_name, line, ) NumpyDocstring._format_docutils_params = scanpy_log_param_types # -- 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 ---------------------------------------------------- qualname_overrides = { "sklearn.neighbors.dist_metrics.DistanceMetric": "sklearn.neighbors.DistanceMetric" } nitpick_ignore = [ # Will probably be documented ('py:class', 'scanpy._settings.Verbosity'), # Currently undocumented: https://github.com/mwaskom/seaborn/issues/1810 ('py:class', 'seaborn.ClusterGrid'), # Won’t be documented ('py:class', 'scanpy.readwrite.Empty'), ] 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': '172a1a42', } 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: 2019-10-18T15:16:48.080613Z, end-time: 2019-10-18T15:18:14.983264Z, duration: 86, 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/stable/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 http://docs.h5py.org/en/stable/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://scvelo.readthedocs.io/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: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy.Neighbors.compute_eigen.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy.Neighbors.compute_neighbors.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy.Neighbors.compute_transitions.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy.Neighbors.connectivities.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy.Neighbors.distances.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy.Neighbors.distances_dpt.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy.Neighbors.eigen_basis.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy.Neighbors.eigen_values.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy.Neighbors.getdoc.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy.Neighbors.rp_forest.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy._settings.ScanpyConfig.file_format_data.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy._settings.ScanpyConfig.file_format_figs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy._settings.ScanpyConfig.logfile.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy._settings.ScanpyConfig.logpath.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy._settings.ScanpyConfig.max_memory.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy._settings.ScanpyConfig.n_jobs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy._settings.ScanpyConfig.plot_suffix.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy._settings.ScanpyConfig.set_figure_params.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy._settings.ScanpyConfig.verbosity.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/scanpy._settings.ScanpyConfig.writedir.rst building [mo]: targets for 0 po files that are out of date building [readthedocs]: targets for 13 source files that are out of date updating environment: [new config] 154 added, 0 changed, 0 removed reading sources... 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[100%] tutorials /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/setuptools_scm/git.py:68: UserWarning: "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest" is shallow and may cause errors warnings.warn('"%s" is shallow and may cause errors' % (wd.path,)) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/preprocessing/_simple.py:714: UserWarning: Parameters in `scanpy.pp.regress_out` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: adata: :class:`~anndata.AnnData` keys: `str` or list of `str` n_jobs: `int` or `None`, optional. If None is given, then the n_jobs seting is used (default: `None`) copy: `bool`, optional (default: `False`) adata: :class:`~anndata.AnnData` keys: `str` or list of `str` n_jobs: `int` or `None`, optional. If None is given, then the n_jobs seting is used (default: `None`) copy: `bool`, optional (default: `False`) def regress_out(adata, keys, n_jobs=None, copy=False) -> Optional[AnnData]: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/preprocessing/_simple.py:842: UserWarning: Parameters in `scanpy.pp.scale` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: data: :class:`~anndata.AnnData`, `np.ndarray`, `sp.sparse` zero_center: `bool`, optional (default: `True`) max_value: `float` or `None`, optional (default: `None`) copy: `bool`, optional (default: `False`) data: :class:`~anndata.AnnData`, `np.ndarray`, `sp.sparse` zero_center: `bool`, optional (default: `True`) max_value: `float` or `None`, optional (default: `None`) copy: `bool`, optional (default: `False`) def scale(data, zero_center=True, max_value=None, copy=False) -> Optional[AnnData]: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/preprocessing/_simple.py:898: UserWarning: Parameters in `scanpy.pp.subsample` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: data: :class:`~anndata.AnnData`, `np.ndarray`, `sp.sparse` fraction: `float` in [0, 1] or `None`, optional (default: `None`) n_obs: `int` or `None`, optional (default: `None`) random_state: `int` or `None`, optional (default: 0) copy: `bool`, optional (default: `False`) data: :class:`~anndata.AnnData`, `np.ndarray`, `sp.sparse` fraction: `float` in [0, 1] or `None`, optional (default: `None`) n_obs: `int` or `None`, optional (default: `None`) random_state: `int` or `None`, optional (default: 0) copy: `bool`, optional (default: `False`) def subsample(data, fraction=None, n_obs=None, random_state=0, copy=False) -> Optional[AnnData]: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/preprocessing/_recipes.py:75: UserWarning: Parameters in `scanpy.pp.recipe_zheng17` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: adata: :class:`~anndata.AnnData` n_top_genes: `int`, optional (default: 1000) log: `bool`, optional (default: `True`) plot: `bool`, optional (default: `True`) copy: `bool`, optional (default: `False`) adata: :class:`~anndata.AnnData` n_top_genes: `int`, optional (default: 1000) log: `bool`, optional (default: `True`) plot: `bool`, optional (default: `True`) copy: `bool`, optional (default: `False`) def recipe_zheng17(adata, n_top_genes=1000, log=True, plot=False, copy=False): /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/preprocessing/_combat.py:135: UserWarning: Parameters in `scanpy.pp.combat` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: adata: :class:`~anndata.AnnData` key: `str`, optional (default: `"batch"`) inplace: bool, optional (default: `True`) adata: :class:`~anndata.AnnData` key: `str`, optional (default: `"batch"`) inplace: bool, optional (default: `True`) def combat(adata: AnnData, key: str = 'batch', covariates: Optional[Collection[str]] = None, inplace: bool = True): /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/neighbors/__init__.py:35: UserWarning: Parameters in `scanpy.pp.neighbors` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: n_pcs: `int` or `None`, optional (default: `None`) use_rep: {`None`, 'X'} or any key for `.obsm`, optional (default: `None`) n_pcs: `int` or `None`, optional (default: `None`) use_rep: {`None`, 'X'} or any key for `.obsm`, optional (default: `None`) @_doc_params(n_pcs=doc_n_pcs, use_rep=doc_use_rep) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/tools/_tsne.py:7: UserWarning: Parameters in `scanpy.tl.tsne` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: adata: :class:`~anndata.AnnData` n_pcs: `int` or `None`, optional (default: `None`) use_rep: {`None`, 'X'} or any key for `.obsm`, optional (default: `None`) perplexity: `float`, optional (default: 30) early_exaggeration: `float`, optional (default: 12.0) learning_rate: `float`, optional (default: 1000) random_state: `int` or `None`, optional (default: 0) use_fast_tsne: `bool`, optional (default: `True`) n_jobs: `int` or `None` (default: `sc.settings.n_jobs`) copy: `bool` (default: `False`) adata: :class:`~anndata.AnnData` n_pcs: `int` or `None`, optional (default: `None`) use_rep: {`None`, 'X'} or any key for `.obsm`, optional (default: `None`) perplexity: `float`, optional (default: 30) early_exaggeration: `float`, optional (default: 12.0) learning_rate: `float`, optional (default: 1000) random_state: `int` or `None`, optional (default: 0) use_fast_tsne: `bool`, optional (default: `True`) n_jobs: `int` or `None` (default: `sc.settings.n_jobs`) copy: `bool` (default: `False`) @_doc_params(doc_n_pcs=doc_n_pcs, use_rep=doc_use_rep) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/tools/_diffmap.py:4: UserWarning: Parameters in `scanpy.tl.diffmap` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: adata: :class:`~anndata.AnnData` n_comps: `int`, optional (default: 15) copy: `bool` (default: `False`) adata: :class:`~anndata.AnnData` n_comps: `int`, optional (default: 15) copy: `bool` (default: `False`) def diffmap(adata, n_comps=15, copy=False): /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/tools/_dendrogram.py:16: UserWarning: Parameters in `scanpy.tl.dendrogram` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: n_pcs: `int` or `None`, optional (default: `None`) use_rep: {`None`, 'X'} or any key for `.obsm`, optional (default: `None`) n_pcs: `int` or `None`, optional (default: `None`) use_rep: {`None`, 'X'} or any key for `.obsm`, optional (default: `None`) @_doc_params(n_pcs=doc_n_pcs, use_rep=doc_use_rep) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/tools/_dpt.py:30: UserWarning: Parameters in `scanpy.tl.dpt` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: adata: :class:`~anndata.AnnData` n_dcs: `int`, optional (default: 10) n_branchings: `int`, optional (default: 0) min_group_size: [0, 1] or `float`, optional (default: 0.01) allow_kendall_tau_shift: `bool`, optional (default: `True`) copy: `bool`, optional (default: `False`) adata: :class:`~anndata.AnnData` n_dcs: `int`, optional (default: 10) n_branchings: `int`, optional (default: 0) min_group_size: [0, 1] or `float`, optional (default: 0.01) allow_kendall_tau_shift: `bool`, optional (default: `True`) copy: `bool`, optional (default: `False`) def dpt(adata, n_dcs=10, n_branchings=0, min_group_size=0.01, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/tools/_marker_gene_overlap.py:72: UserWarning: Parameters in `scanpy.tl.marker_gene_overlap` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: method: `{'overlap_count', 'overlap_coef', 'jaccard'}`, optional normalize: `{'reference', 'data', 'None'}`, optional (default: `None`) method: `{'overlap_count', 'overlap_coef', 'jaccard'}`, optional normalize: `{'reference', 'data', 'None'}`, optional (default: `None`) def marker_gene_overlap( /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/anndata/readwrite/read.py:416: UserWarning: Parameters in `scanpy.read_h5ad` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: backed: {``None``, ``'r'``, ``'r+'``} backed: {``None``, ``'r'``, ``'r+'``} def read_h5ad(filename, backed: Optional[str] = None, chunk_size: int = 6000): /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/preprocessing/_simple.py:544: UserWarning: Parameters in `scanpy.pp.normalize_per_cell` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: data: :class:`~anndata.AnnData`, `np.ndarray`, `sp.sparse` counts_per_cell_after: `float` or `None`, optional (default: `None`) counts_per_cell: `np.array`, optional (default: `None`) key_n_counts: `str`, optional (default: `'n_counts'`) copy: `bool`, optional (default: `False`) min_counts: `int`, optional (default: 1) data: :class:`~anndata.AnnData`, `np.ndarray`, `sp.sparse` counts_per_cell_after: `float` or `None`, optional (default: `None`) counts_per_cell: `np.array`, optional (default: `None`) key_n_counts: `str`, optional (default: `'n_counts'`) copy: `bool`, optional (default: `False`) min_counts: `int`, optional (default: 1) def normalize_per_cell( /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/neighbors/__init__.py:812: UserWarning: Parameters in `scanpy.Neighbors.compute_eigen` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: n_comps: `int` sym: `bool` matrix: sparse matrix, np.ndarray, optional (default: `.connectivities`) n_comps: `int` sym: `bool` matrix: sparse matrix, np.ndarray, optional (default: `.connectivities`) def compute_eigen(self, n_comps=15, sym=None, sort='decrease'): /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/neighbors/__init__.py:616: UserWarning: Parameters in `scanpy.Neighbors.compute_neighbors` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: n_pcs: `int` or `None`, optional (default: `None`) use_rep: {`None`, 'X'} or any key for `.obsm`, optional (default: `None`) n_pcs: `int` or `None`, optional (default: `None`) use_rep: {`None`, 'X'} or any key for `.obsm`, optional (default: `None`) @_doc_params(n_pcs=doc_n_pcs, use_rep=doc_use_rep) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/neighbors/__init__.py:774: UserWarning: Parameters in `scanpy.Neighbors.compute_transitions` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: density_normalize: `bool` density_normalize: `bool` def compute_transitions(self, density_normalize=True): /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/preprocessing/_simple.py:544: UserWarning: Parameters in `scanpy.api.pp.normalize_per_cell` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: data: :class:`~anndata.AnnData`, `np.ndarray`, `sp.sparse` counts_per_cell_after: `float` or `None`, optional (default: `None`) counts_per_cell: `np.array`, optional (default: `None`) key_n_counts: `str`, optional (default: `'n_counts'`) copy: `bool`, optional (default: `False`) min_counts: `int`, optional (default: 1) def normalize_per_cell( /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/preprocessing/_simple.py:714: UserWarning: Parameters in `scanpy.api.pp.regress_out` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: adata: :class:`~anndata.AnnData` keys: `str` or list of `str` n_jobs: `int` or `None`, optional. If None is given, then the n_jobs seting is used (default: `None`) copy: `bool`, optional (default: `False`) def regress_out(adata, keys, n_jobs=None, copy=False) -> Optional[AnnData]: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/preprocessing/_simple.py:842: UserWarning: Parameters in `scanpy.api.pp.scale` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: data: :class:`~anndata.AnnData`, `np.ndarray`, `sp.sparse` zero_center: `bool`, optional (default: `True`) max_value: `float` or `None`, optional (default: `None`) copy: `bool`, optional (default: `False`) def scale(data, zero_center=True, max_value=None, copy=False) -> Optional[AnnData]: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/preprocessing/_simple.py:898: UserWarning: Parameters in `scanpy.api.pp.subsample` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: data: :class:`~anndata.AnnData`, `np.ndarray`, `sp.sparse` fraction: `float` in [0, 1] or `None`, optional (default: `None`) n_obs: `int` or `None`, optional (default: `None`) random_state: `int` or `None`, optional (default: 0) copy: `bool`, optional (default: `False`) def subsample(data, fraction=None, n_obs=None, random_state=0, copy=False) -> Optional[AnnData]: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/preprocessing/_recipes.py:75: UserWarning: Parameters in `scanpy.api.pp.recipe_zheng17` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: adata: :class:`~anndata.AnnData` n_top_genes: `int`, optional (default: 1000) log: `bool`, optional (default: `True`) plot: `bool`, optional (default: `True`) copy: `bool`, optional (default: `False`) def recipe_zheng17(adata, n_top_genes=1000, log=True, plot=False, copy=False): /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/external/pp/_dca.py:6: UserWarning: Parameters in `scanpy.api.pp.dca` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: mode: `str`, optional. `denoise`(default), or `latent`. ae_type: `str`, optional. `zinb-conddisp`(default), `zinb`, `nb-conddisp` or `nb`. normalize_per_cell: `bool`, optional. Default: `True`. scale: `bool`, optional. Default: `True`. log1p: `bool`, optional. Default: `True`. hidden_size: `tuple` or `list`, optional. Default: (64, 32, 64). hidden_dropout: `float`, `tuple` or `list`, optional. Default: 0.0. batchnorm: `bool`, optional. Default: `True`. activation: `str`, optional. Default: `relu`. init: `str`, optional. Default: `glorot_uniform`. network_kwds: `dict`, optional. epochs: `int`, optional. Default: 300. reduce_lr: `int`, optional. Default: 10. early_stop: `int`, optional. Default: 15. batch_size: `int`, optional. Default: 32. optimizer: `str`, optional. Default: "rmsprop". random_state: `int`, optional. Default: 0. threads: `int` or None, optional. Default: None learning_rate: `float`, optional. Default: None. verbose: `bool`, optional. Default: `False`. training_kwds: `dict`, optional. return_model: `bool`, optional. Default: `False`. return_info: `bool`, optional. Default: `False`. copy: `bool`, optional. Default: `False`. def dca( /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/neighbors/__init__.py:35: UserWarning: Parameters in `scanpy.api.pp.neighbors` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: n_pcs: `int` or `None`, optional (default: `None`) use_rep: {`None`, 'X'} or any key for `.obsm`, optional (default: `None`) @_doc_params(n_pcs=doc_n_pcs, use_rep=doc_use_rep) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/tools/_tsne.py:7: UserWarning: Parameters in `scanpy.api.tl.tsne` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: adata: :class:`~anndata.AnnData` n_pcs: `int` or `None`, optional (default: `None`) use_rep: {`None`, 'X'} or any key for `.obsm`, optional (default: `None`) perplexity: `float`, optional (default: 30) early_exaggeration: `float`, optional (default: 12.0) learning_rate: `float`, optional (default: 1000) random_state: `int` or `None`, optional (default: 0) use_fast_tsne: `bool`, optional (default: `True`) n_jobs: `int` or `None` (default: `sc.settings.n_jobs`) copy: `bool` (default: `False`) @_doc_params(doc_n_pcs=doc_n_pcs, use_rep=doc_use_rep) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/tools/_diffmap.py:4: UserWarning: Parameters in `scanpy.api.tl.diffmap` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: adata: :class:`~anndata.AnnData` n_comps: `int`, optional (default: 15) copy: `bool` (default: `False`) def diffmap(adata, n_comps=15, copy=False): /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/tools/_dpt.py:30: UserWarning: Parameters in `scanpy.api.tl.dpt` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: adata: :class:`~anndata.AnnData` n_dcs: `int`, optional (default: 10) n_branchings: `int`, optional (default: 0) min_group_size: [0, 1] or `float`, optional (default: 0.01) allow_kendall_tau_shift: `bool`, optional (default: `True`) copy: `bool`, optional (default: `False`) def dpt(adata, n_dcs=10, n_branchings=0, min_group_size=0.01, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/anndata/readwrite/read.py:416: UserWarning: Parameters in `scanpy.api.read_h5ad` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: backed: {``None``, ``'r'``, ``'r+'``} def read_h5ad(filename, backed: Optional[str] = None, chunk_size: int = 6000): /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_anndata.py:1364: UserWarning: Parameters in `scanpy.pl.dotplot` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: adata: :class:`~anndata.AnnData` var_names: `str`, list of `str`, dict or OrderedDict groupby: `str` or `None`, optional (default: `None`) log: `bool`, optional (default: `False`) use_raw: `bool`, optional (default: `None`) num_categories: `int`, optional (default: `7`) figsize: (`float`, `float`), optional (default: `None`) dendrogram: `bool` or `str`, optional (default, `False`) gene_symbols: string, optional (default: `None`) var_group_positions: list of `tuples`. var_group_labels: list of `str` var_group_rotation: `float` (default: `None`) layer: `str`, (default `None`) expression_cutoff: `float` (default: `0.`) mean_only_expressed: `bool` (default: `False`) color_map: `str`, optional (default: `Reds`) dot_max: `float` optional (default: `None`) dot_min: `float` optional (default: `None`) smallest_dot: `float` optional (default: 0.) adata: :class:`~anndata.AnnData` var_names: `str`, list of `str`, dict or OrderedDict groupby: `str` or `None`, optional (default: `None`) log: `bool`, optional (default: `False`) use_raw: `bool`, optional (default: `None`) num_categories: `int`, optional (default: `7`) figsize: (`float`, `float`), optional (default: `None`) dendrogram: `bool` or `str`, optional (default, `False`) gene_symbols: string, optional (default: `None`) var_group_positions: list of `tuples`. var_group_labels: list of `str` var_group_rotation: `float` (default: `None`) layer: `str`, (default `None`) expression_cutoff: `float` (default: `0.`) mean_only_expressed: `bool` (default: `False`) color_map: `str`, optional (default: `Reds`) dot_max: `float` optional (default: `None`) dot_min: `float` optional (default: `None`) smallest_dot: `float` optional (default: 0.) @_doc_params(show_save_ax=doc_show_save_ax, common_plot_args=doc_common_plot_args) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/scatterplots.py:26: UserWarning: Parameters in `scanpy.pl.draw_graph` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: edges_color: matplotlib color(s), optional (default: `'grey'`) edges_color: matplotlib color(s), optional (default: `'grey'`) @_doc_params(adata_color_etc=doc_adata_color_etc, edges_arrows=doc_edges_arrows, scatter_bulk=doc_scatter_embedding, show_save_ax=doc_show_save_ax) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/scatterplots.py:26: UserWarning: Parameters in `scanpy.pl.embedding` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: edges_color: matplotlib color(s), optional (default: `'grey'`) edges_color: matplotlib color(s), optional (default: `'grey'`) @_doc_params(adata_color_etc=doc_adata_color_etc, edges_arrows=doc_edges_arrows, scatter_bulk=doc_scatter_embedding, show_save_ax=doc_show_save_ax) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_preprocessing.py:69: UserWarning: Parameters in `scanpy.pl.filter_genes_dispersion` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: show: bool, optional (default: `None`) save: `bool` or `str`, optional (default: `None`) show: bool, optional (default: `None`) save: `bool` or `str`, optional (default: `None`) def filter_genes_dispersion( /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_anndata.py:1075: UserWarning: Parameters in `scanpy.pl.heatmap` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: adata: :class:`~anndata.AnnData` var_names: `str`, list of `str`, dict or OrderedDict groupby: `str` or `None`, optional (default: `None`) log: `bool`, optional (default: `False`) use_raw: `bool`, optional (default: `None`) num_categories: `int`, optional (default: `7`) figsize: (`float`, `float`), optional (default: `None`) dendrogram: `bool` or `str`, optional (default, `False`) gene_symbols: string, optional (default: `None`) var_group_positions: list of `tuples`. var_group_labels: list of `str` var_group_rotation: `float` (default: `None`) layer: `str`, (default `None`) adata: :class:`~anndata.AnnData` var_names: `str`, list of `str`, dict or OrderedDict groupby: `str` or `None`, optional (default: `None`) log: `bool`, optional (default: `False`) use_raw: `bool`, optional (default: `None`) num_categories: `int`, optional (default: `7`) figsize: (`float`, `float`), optional (default: `None`) dendrogram: `bool` or `str`, optional (default, `False`) gene_symbols: string, optional (default: `None`) var_group_positions: list of `tuples`. var_group_labels: list of `str` var_group_rotation: `float` (default: `None`) layer: `str`, (default `None`) @_doc_params(show_save_ax=doc_show_save_ax, common_plot_args=doc_common_plot_args) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_preprocessing.py:14: UserWarning: Parameters in `scanpy.pl.highly_variable_genes` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: adata: :class:`~anndata.AnnData`, `np.recarray` log: `bool` show: bool, optional (default: `None`) save: `bool` or `str`, optional (default: `None`) adata: :class:`~anndata.AnnData`, `np.recarray` log: `bool` show: bool, optional (default: `None`) save: `bool` or `str`, optional (default: `None`) def highly_variable_genes(adata_or_result, log=False, show=None, save=None, highly_variable_genes=True): /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_anndata.py:1696: UserWarning: Parameters in `scanpy.pl.matrixplot` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: adata: :class:`~anndata.AnnData` var_names: `str`, list of `str`, dict or OrderedDict groupby: `str` or `None`, optional (default: `None`) log: `bool`, optional (default: `False`) use_raw: `bool`, optional (default: `None`) num_categories: `int`, optional (default: `7`) figsize: (`float`, `float`), optional (default: `None`) dendrogram: `bool` or `str`, optional (default, `False`) gene_symbols: string, optional (default: `None`) var_group_positions: list of `tuples`. var_group_labels: list of `str` var_group_rotation: `float` (default: `None`) layer: `str`, (default `None`) adata: :class:`~anndata.AnnData` var_names: `str`, list of `str`, dict or OrderedDict groupby: `str` or `None`, optional (default: `None`) log: `bool`, optional (default: `False`) use_raw: `bool`, optional (default: `None`) num_categories: `int`, optional (default: `7`) figsize: (`float`, `float`), optional (default: `None`) dendrogram: `bool` or `str`, optional (default, `False`) gene_symbols: string, optional (default: `None`) var_group_positions: list of `tuples`. var_group_labels: list of `str` var_group_rotation: `float` (default: `None`) layer: `str`, (default `None`) @_doc_params(show_save_ax=doc_show_save_ax, common_plot_args=doc_common_plot_args) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/paga.py:243: UserWarning: Parameters in `scanpy.pl.paga` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: normalize_to_color: `bool`, optional (default: `False`) normalize_to_color: `bool`, optional (default: `False`) def paga( /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/paga.py:23: UserWarning: Parameters in `scanpy.pl.paga_compare` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: adata: :class:`~anndata.AnnData` kwds_scatter: `dict` kwds_paga: `dict` adata: :class:`~anndata.AnnData` kwds_scatter: `dict` kwds_paga: `dict` def paga_compare( /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/__init__.py:26: UserWarning: Parameters in `scanpy.pl.pca_overview` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: color: string or list of strings, optional (default: `None`) use_raw: `bool`, optional (default: `True`) show: bool, optional (default: `None`) save: `bool` or `str`, optional (default: `None`) color: string or list of strings, optional (default: `None`) use_raw: `bool`, optional (default: `True`) show: bool, optional (default: `None`) save: `bool` or `str`, optional (default: `None`) @_doc_params(scatter_bulk=doc_scatter_embedding, show_save_ax=doc_show_save_ax) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/__init__.py:104: UserWarning: Parameters in `scanpy.pl.pca_variance_ratio` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: n_pcs: `int`, optional (default: `30`) log: `bool`, optional (default: `False`) show: `bool`, optional (default: `None`) save: `bool` or `str`, optional (default: `None`) n_pcs: `int`, optional (default: `30`) log: `bool`, optional (default: `False`) show: `bool`, optional (default: `None`) save: `bool` or `str`, optional (default: `None`) def pca_variance_ratio(adata, n_pcs=30, log=False, show=None, save=None): /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/__init__.py:395: UserWarning: Parameters in `scanpy.pl.rank_genes_groups_heatmap` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: adata: :class:`~anndata.AnnData` groups: `str` or `list` of `str` adata: :class:`~anndata.AnnData` groups: `str` or `list` of `str` @_doc_params(show_save_ax=doc_show_save_ax) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/__init__.py:512: UserWarning: Parameters in `scanpy.pl.rank_genes_groups_stacked_violin` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: groups: `str` or `list` of `str` n_genes: `int`, optional (default: 10) groupby: `str` or `None`, optional (default: `None`) groups: `str` or `list` of `str` n_genes: `int`, optional (default: 10) groupby: `str` or `None`, optional (default: `None`) @_doc_params(show_save_ax=doc_show_save_ax) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/__init__.py:590: UserWarning: Parameters in `scanpy.pl.rank_genes_groups_violin` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: use_raw: `bool`, optional (default: `None`) use_raw: `bool`, optional (default: `None`) @_doc_params(show_save_ax=doc_show_save_ax) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_anndata.py:733: UserWarning: Parameters in `scanpy.pl.stacked_violin` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: adata: :class:`~anndata.AnnData` var_names: `str`, list of `str`, dict or OrderedDict groupby: `str` or `None`, optional (default: `None`) log: `bool`, optional (default: `False`) use_raw: `bool`, optional (default: `None`) num_categories: `int`, optional (default: `7`) figsize: (`float`, `float`), optional (default: `None`) dendrogram: `bool` or `str`, optional (default, `False`) gene_symbols: string, optional (default: `None`) var_group_positions: list of `tuples`. var_group_labels: list of `str` var_group_rotation: `float` (default: `None`) layer: `str`, (default `None`) adata: :class:`~anndata.AnnData` var_names: `str`, list of `str`, dict or OrderedDict groupby: `str` or `None`, optional (default: `None`) log: `bool`, optional (default: `False`) use_raw: `bool`, optional (default: `None`) num_categories: `int`, optional (default: `7`) figsize: (`float`, `float`), optional (default: `None`) dendrogram: `bool` or `str`, optional (default, `False`) gene_symbols: string, optional (default: `None`) var_group_positions: list of `tuples`. var_group_labels: list of `str` var_group_rotation: `float` (default: `None`) layer: `str`, (default `None`) @_doc_params(show_save_ax=doc_show_save_ax, common_plot_args=doc_common_plot_args) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_anndata.py:1922: UserWarning: Parameters in `scanpy.pl.tracksplot` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: adata: :class:`~anndata.AnnData` var_names: `str`, list of `str`, dict or OrderedDict groupby: `str` or `None`, optional (default: `None`) log: `bool`, optional (default: `False`) use_raw: `bool`, optional (default: `None`) num_categories: `int`, optional (default: `7`) figsize: (`float`, `float`), optional (default: `None`) dendrogram: `bool` or `str`, optional (default, `False`) gene_symbols: string, optional (default: `None`) var_group_positions: list of `tuples`. var_group_labels: list of `str` var_group_rotation: `float` (default: `None`) layer: `str`, (default `None`) adata: :class:`~anndata.AnnData` var_names: `str`, list of `str`, dict or OrderedDict groupby: `str` or `None`, optional (default: `None`) log: `bool`, optional (default: `False`) use_raw: `bool`, optional (default: `None`) num_categories: `int`, optional (default: `7`) figsize: (`float`, `float`), optional (default: `None`) dendrogram: `bool` or `str`, optional (default, `False`) gene_symbols: string, optional (default: `None`) var_group_positions: list of `tuples`. var_group_labels: list of `str` var_group_rotation: `float` (default: `None`) layer: `str`, (default `None`) @_doc_params(show_save_ax=doc_show_save_ax, common_plot_args=doc_common_plot_args) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/scatterplots.py:26: UserWarning: Parameters in `scanpy.pl.tsne` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: edges_color: matplotlib color(s), optional (default: `'grey'`) edges_color: matplotlib color(s), optional (default: `'grey'`) @_doc_params(adata_color_etc=doc_adata_color_etc, edges_arrows=doc_edges_arrows, scatter_bulk=doc_scatter_embedding, show_save_ax=doc_show_save_ax) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/scatterplots.py:26: UserWarning: Parameters in `scanpy.pl.umap` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: edges_color: matplotlib color(s), optional (default: `'grey'`) edges_color: matplotlib color(s), optional (default: `'grey'`) @_doc_params(adata_color_etc=doc_adata_color_etc, edges_arrows=doc_edges_arrows, scatter_bulk=doc_scatter_embedding, show_save_ax=doc_show_save_ax) /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/external/pp/_dca.py:6: UserWarning: Parameters in `scanpy.external.pp.dca` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: mode: `str`, optional. `denoise`(default), or `latent`. ae_type: `str`, optional. `zinb-conddisp`(default), `zinb`, `nb-conddisp` or `nb`. normalize_per_cell: `bool`, optional. Default: `True`. scale: `bool`, optional. Default: `True`. log1p: `bool`, optional. Default: `True`. hidden_size: `tuple` or `list`, optional. Default: (64, 32, 64). hidden_dropout: `float`, `tuple` or `list`, optional. Default: 0.0. batchnorm: `bool`, optional. Default: `True`. activation: `str`, optional. Default: `relu`. init: `str`, optional. Default: `glorot_uniform`. network_kwds: `dict`, optional. epochs: `int`, optional. Default: 300. reduce_lr: `int`, optional. Default: 10. early_stop: `int`, optional. Default: 15. batch_size: `int`, optional. Default: 32. optimizer: `str`, optional. Default: "rmsprop". random_state: `int`, optional. Default: 0. threads: `int` or None, optional. Default: None learning_rate: `float`, optional. Default: None. verbose: `bool`, optional. Default: `False`. training_kwds: `dict`, optional. return_model: `bool`, optional. Default: `False`. return_info: `bool`, optional. Default: `False`. copy: `bool`, optional. Default: `False`. mode: `str`, optional. `denoise`(default), or `latent`. ae_type: `str`, optional. `zinb-conddisp`(default), `zinb`, `nb-conddisp` or `nb`. normalize_per_cell: `bool`, optional. Default: `True`. scale: `bool`, optional. Default: `True`. log1p: `bool`, optional. Default: `True`. hidden_size: `tuple` or `list`, optional. Default: (64, 32, 64). hidden_dropout: `float`, `tuple` or `list`, optional. Default: 0.0. batchnorm: `bool`, optional. Default: `True`. activation: `str`, optional. Default: `relu`. init: `str`, optional. Default: `glorot_uniform`. network_kwds: `dict`, optional. epochs: `int`, optional. Default: 300. reduce_lr: `int`, optional. Default: 10. early_stop: `int`, optional. Default: 15. batch_size: `int`, optional. Default: 32. optimizer: `str`, optional. Default: "rmsprop". random_state: `int`, optional. Default: 0. threads: `int` or None, optional. Default: None learning_rate: `float`, optional. Default: None. verbose: `bool`, optional. Default: `False`. training_kwds: `dict`, optional. return_model: `bool`, optional. Default: `False`. return_info: `bool`, optional. Default: `False`. copy: `bool`, optional. Default: `False`. def dca( /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/plotting/_tools/scatterplots.py:26: UserWarning: Parameters in `scanpy.external.pl.phate` not set-like: {`elm-1`, `s_el.2`}. Convert to this format or replace with type annotations: edges_color: matplotlib color(s), optional (default: `'grey'`) edges_color: matplotlib color(s), optional (default: `'grey'`) @_doc_params(adata_color_etc=doc_adata_color_etc, edges_arrows=doc_edges_arrows, scatter_bulk=doc_scatter_embedding, show_save_ax=doc_show_save_ax) 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 311, in build updated_docnames = set(self.read()) File "/home/docs/.pyenv/versions/3.6.8/lib/python3.6/contextlib.py", line 88, in __exit__ next(self.gen) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/util/logging.py", line 219, in pending_warnings memhandler.flushTo(logger) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/util/logging.py", line 184, in flushTo logger.handle(record) File "/home/docs/.pyenv/versions/3.6.8/lib/python3.6/logging/__init__.py", line 1454, in handle self.callHandlers(record) File "/home/docs/.pyenv/versions/3.6.8/lib/python3.6/logging/__init__.py", line 1516, in callHandlers hdlr.handle(record) File "/home/docs/.pyenv/versions/3.6.8/lib/python3.6/logging/__init__.py", line 861, in handle rv = self.filter(record) File "/home/docs/.pyenv/versions/3.6.8/lib/python3.6/logging/__init__.py", line 720, 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/index.rst:310::1:Unknown target name: "expression atlas". Warning, treated as error: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/index.rst:310::1:Unknown target name: "expression atlas".