Read the Docs build information Build id: 156104 Project: icb-scanpy Version: stable Commit: 9937451581287929a7db126fe05f73aac124dda1 Date: 2018-11-05T06:08:25.667454Z State: finished Success: True [rtd-command-info] start-time: 2018-11-05T12:08:26.107111Z, end-time: 2018-11-05T12:08:27.834098Z, duration: 1, exit-code: 0 git clone https://github.com/theislab/scanpy.git . Cloning into '.'... [rtd-command-info] start-time: 2018-11-05T12:08:27.891900Z, end-time: 2018-11-05T12:08:27.989738Z, duration: 0, exit-code: 0 git checkout --force 9937451581287929a7db126fe05f73aac124dda1 Note: checking out '9937451581287929a7db126fe05f73aac124dda1'. 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 9937451 release 1.3.3 [rtd-command-info] start-time: 2018-11-05T12:08:28.053343Z, end-time: 2018-11-05T12:08:28.060697Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2018-11-05T12:08:28.142965Z, end-time: 2018-11-05T12:08:28.148610Z, duration: 0, exit-code: 0 git branch -r origin/HEAD -> origin/master origin/VolkerBergen-patch-1 origin/hvg origin/master origin/version0 [rtd-command-info] start-time: 2018-11-05T12:08:28.959536Z, end-time: 2018-11-05T12:08:31.733181Z, duration: 2, exit-code: 0 python3.6 -mvirtualenv --no-site-packages --no-download Using base prefix '/home/docs/.pyenv/versions/3.6.2' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/bin/python3.6 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/bin/python Installing setuptools, pip, wheel...done. 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You should consider upgrading via the 'pip install --upgrade pip' command. 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started Running setup.py bdist_wheel for anndata: finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/.cache/pip/wheels/f1/f0/02/ea67db3107825884bae91e3806e425718f10062c631e2b1367 Successfully built anndata Installing collected packages: sphinx-autodoc-typehints, python-dateutil, numpy, pandas, scipy, h5py, natsort, anndata, kiwisolver, cycler, matplotlib, seaborn, numexpr, tables, scikit-learn, decorator, networkx, joblib, llvmlite, numba Successfully installed anndata-0.6.13 cycler-0.10.0 decorator-4.3.0 h5py-2.8.0 joblib-0.12.5 kiwisolver-1.0.1 llvmlite-0.25.0 matplotlib-3.0.1 natsort-5.4.1 networkx-2.2 numba-0.40.1 numexpr-2.6.8 numpy-1.15.4 pandas-0.23.4 python-dateutil-2.7.5 scikit-learn-0.20.0 scipy-1.1.0 seaborn-0.9.0 sphinx-autodoc-typehints-1.3.0 tables-3.4.4 You are using pip version 9.0.3, however version 18.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command. [rtd-command-info] start-time: 2018-11-05T12:09:10.786584Z, end-time: 2018-11-05T12:09:10.871093Z, duration: 0, exit-code: 0 cat docs/conf.py import sys import inspect import logging from pathlib import Path from datetime import datetime from typing import Optional from sphinx.application import Sphinx from sphinx.ext import autosummary # remove PyCharm’s old six module if 'six' in sys.modules: print(*sys.path, sep='\n') for pypath in list(sys.path): if any(p in pypath for p in ['PyCharm', 'pycharm']) and 'helpers' in pypath: sys.path.remove(pypath) del sys.modules['six'] 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.api # noqa logger = logging.getLogger(__name__) # -- General configuration ------------------------------------------------ needs_sphinx = '1.7' # autosummary bugfix extensions = [ 'sphinx.ext.autodoc', 'sphinx.ext.doctest', 'sphinx.ext.coverage', 'sphinx.ext.mathjax', 'sphinx.ext.autosummary', # 'plot_generator', # 'plot_directive', 'sphinx.ext.napoleon', 'sphinx_autodoc_typehints', 'sphinx.ext.intersphinx', # 'ipython_directive', # 'ipython_console_highlighting', ] # Generate the API documentation when building autosummary_generate = True # both of the following two lines don't work # see falexwolf's issue for numpydoc # 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 = False napoleon_custom_sections = [('Params', 'Parameters')] intersphinx_mapping = dict( python=('https://docs.python.org/3', None), numpy=('https://docs.scipy.org/doc/numpy/', None), scipy=('https://docs.scipy.org/doc/scipy/reference/', None), pandas=('http://pandas.pydata.org/pandas-docs/stable/', None), matplotlib=('https://matplotlib.org/', None), anndata=('https://anndata.readthedocs.io/en/latest/', None), ) templates_path = ['_templates'] source_suffix = '.rst' master_doc = 'index' project = 'Scanpy' author = 'Alex Wolf, Philipp Angerer, Fidel Ramirez, Isaac Virshup, Davide Cittaro, Gokcen Eraslan, Tom White, Tobias Callies, Andrés R. Muñoz-Rojas.' copyright = f'{datetime.now():%Y}, {author}' version = scanpy.__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' html_theme_options = dict( navigation_depth=2, ) 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'] def setup(app): app.add_stylesheet('css/custom.css') # -- Options for other output formats ------------------------------------------ htmlhelp_basename = 'Scanpydoc' latex_documents = [ (master_doc, 'Scanpy.tex', 'Scanpy Documentation', 'Alex Wolf, Philipp Angerer', 'manual'), ] man_pages = [ (master_doc, 'scanpy', 'Scanpy Documentation', [author], 1) ] texinfo_documents = [ (master_doc, 'Scanpy', 'Scanpy Documentation', author, 'Scanpy', 'One line description of project.', 'Miscellaneous'), ] # -- generate_options override ------------------------------------------ # TODO: why? def process_generate_options(app: Sphinx): genfiles = app.config.autosummary_generate if genfiles and not hasattr(genfiles, '__len__'): env = app.builder.env genfiles = [ env.doc2path(x, base=None) for x in env.found_docs if Path(env.doc2path(x)).is_file() ] if not genfiles: return from sphinx.ext.autosummary.generate import generate_autosummary_docs ext = app.config.source_suffix genfiles = [ genfile + (not genfile.endswith(tuple(ext)) and ext[0] or '') for genfile in genfiles ] suffix = autosummary.get_rst_suffix(app) if suffix is None: return generate_autosummary_docs( genfiles, builder=app.builder, warn=logger.warning, info=logger.info, suffix=suffix, base_path=app.srcdir, imported_members=True, app=app, ) autosummary.process_generate_options = process_generate_options # -- GitHub URLs for class and method pages ------------------------------------------ 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: str) -> str: """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 = f'#L{start}-L{end}' if start and end else '' return f'{github_url}/{path}{fragment}' def api_image(qualname: str) -> Optional[str]: # I’d like to make this a contextfilter, but the jinja context doesn’t contain the path, # so no chance to not hardcode “api/” here. path = Path(__file__).parent / 'api' / f'{qualname}.png' print(path, path.is_file()) return f'.. image:: {path.name}\n :width: 200\n :align: right' if path.is_file() else '' # 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.update(modurl=modurl, api_image=api_image) # -- Prettier Param docs -------------------------------------------- from typing import Dict, List, Tuple from docutils import nodes from sphinx import addnodes from sphinx.domains.python import PyTypedField, PyObject from sphinx.environment import BuildEnvironment class PrettyTypedField(PyTypedField): list_type = nodes.definition_list def make_field( self, types: Dict[str, List[nodes.Node]], domain: str, items: Tuple[str, List[nodes.inline]], env: BuildEnvironment = None ) -> nodes.field: def makerefs(rolename, name, node): return self.make_xrefs(rolename, domain, name, node, env=env) def handle_item(fieldarg: str, content: List[nodes.inline]) -> nodes.definition_list_item: head = nodes.term() head += makerefs(self.rolename, fieldarg, addnodes.literal_strong) fieldtype = types.pop(fieldarg, None) if fieldtype is not None: head += nodes.Text(' : ') if len(fieldtype) == 1 and isinstance(fieldtype[0], nodes.Text): typename = ''.join(n.astext() for n in fieldtype) head += makerefs(self.typerolename, typename, addnodes.literal_emphasis) else: head += fieldtype body_content = nodes.paragraph('', '', *content) body = nodes.definition('', body_content) return nodes.definition_list_item('', head, body) fieldname = nodes.field_name('', self.label) if len(items) == 1 and self.can_collapse: fieldarg, content = items[0] bodynode = handle_item(fieldarg, content) else: bodynode = self.list_type() for fieldarg, content in items: bodynode += handle_item(fieldarg, content) fieldbody = nodes.field_body('', bodynode) return nodes.field('', fieldname, fieldbody) # replace matching field types with ours PyObject.doc_field_types = [ PrettyTypedField( ft.name, names=ft.names, typenames=ft.typenames, label=ft.label, rolename=ft.rolename, typerolename=ft.typerolename, can_collapse=ft.can_collapse, ) if isinstance(ft, PyTypedField) else ft for ft in PyObject.doc_field_types ] ########################################################################### # 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 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 else: SUFFIX = source_suffix[0] 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') html_static_path.append('/home/docs/checkouts/readthedocs.org/readthedocs/templates/sphinx/_static') # Add RTD Theme only if they aren't overriding it already using_rtd_theme = False if 'html_theme' in globals(): if html_theme in ['default']: # Allow people to bail with a hack of having an html_style if not 'html_style' in globals(): import sphinx_rtd_theme html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} if 'html_theme_path' in globals(): html_theme_path.append(sphinx_rtd_theme.get_html_theme_path()) else: html_theme_path = [sphinx_rtd_theme.get_html_theme_path()] using_rtd_theme = True else: import sphinx_rtd_theme html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} if 'html_theme_path' in globals(): html_theme_path.append(sphinx_rtd_theme.get_html_theme_path()) else: html_theme_path = [sphinx_rtd_theme.get_html_theme_path()] using_rtd_theme = True 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': "stable", 'version_slug': "stable", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://media.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ("latest", "/en/latest/"), ("stable", "/en/stable/"), ], 'downloads': [ ("htmlzip", "//readthedocs.com/projects/icb-scanpy/downloads/htmlzip/stable/"), ], 'subprojects': [ ], 'slug': 'icb-scanpy', 'name': u'scanpy', 'rtd_language': u'en', 'programming_language': u'py', 'canonical_url': 'https://icb-scanpy.readthedocs-hosted.com/en/latest/', 'analytics_code': '', 'single_version': False, 'conf_py_path': '/docs/', 'api_host': 'https://readthedocs.com', 'github_user': 'theislab', 'github_repo': 'scanpy', 'github_version': '9937451581287929a7db126fe05f73aac124dda1', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': '9937451581287929a7db126fe05f73aac124dda1', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': '9937451581287929a7db126fe05f73aac124dda1', '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': '99374515', } 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"] [rtd-command-info] start-time: 2018-11-05T12:09:10.929181Z, end-time: 2018-11-05T12:09:30.182306Z, duration: 19, exit-code: 0 python sphinx-build -T -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html Running Sphinx v1.7.9 /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/bin /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python36.zip /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6 /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/lib-dynload /home/docs/.pyenv/versions/3.6.2/lib/python3.6 /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages loading translations [en]... done making output directory... loading pickled environment... not yet 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[rtd-command-info] start-time: 2018-11-05T12:09:30.307476Z, end-time: 2018-11-05T12:09:41.853727Z, duration: 11, exit-code: 0 python sphinx-build -T -b readthedocssinglehtmllocalmedia -d _build/doctrees-readthedocssinglehtmllocalmedia -D language=en . _build/localmedia Running Sphinx v1.7.9 /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/bin /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python36.zip /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6 /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/lib-dynload /home/docs/.pyenv/versions/3.6.2/lib/python3.6 /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages loading translations [en]... done making output directory... loading pickled environment... not yet created loading intersphinx inventory from https://docs.python.org/3/objects.inv... loading intersphinx inventory from https://docs.scipy.org/doc/numpy/objects.inv... loading intersphinx inventory from https://docs.scipy.org/doc/scipy/reference/objects.inv... loading intersphinx inventory from http://pandas.pydata.org/pandas-docs/stable/objects.inv... loading intersphinx inventory from https://matplotlib.org/objects.inv... loading intersphinx inventory from https://anndata.readthedocs.io/en/latest/objects.inv... building [mo]: targets for 0 po files that are out of date building [readthedocssinglehtmllocalmedia]: all documents updating environment: 108 added, 0 changed, 0 removed reading sources... 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Parameters ---------- /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/scanpy/plotting/anndata.py:docstring of scanpy.api.pl.dotplot:36: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/scanpy/plotting/anndata.py:docstring of scanpy.api.pl.dotplot:43: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/scanpy/plotting/anndata.py:docstring of scanpy.api.pl.dotplot:50: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/scanpy/plotting/anndata.py:docstring of scanpy.api.pl.dotplot:61: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/scanpy/plotting/anndata.py:docstring of scanpy.api.pl.dotplot:62: WARNING: Inline strong start-string without end-string. /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/scanpy/plotting/anndata.py:docstring of scanpy.api.pl.dotplot:65: WARNING: Unexpected section title. Returns ------- /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/scanpy/plotting/anndata.py:docstring of scanpy.api.pl.dotplot:1: WARNING: Unknown target name: "plot". /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/scanpy/tools/umap.py:docstring of scanpy.api.tl.umap:44: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/examples.rst:5: WARNING: Document or section may not begin with a transition. looking for now-outdated files... none found pickling environment... done checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/references.rst:32: WARNING: Citation [Ester96] is not referenced. /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/references.rst:45: WARNING: Citation [Fruchterman91] is not referenced. /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/references.rst:49: WARNING: Citation [Hagberg08] is not referenced. /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/references.rst:53: WARNING: Citation [Hastie09] is not referenced. /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/references.rst:70: WARNING: Citation [Huber15] is not referenced. /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/references.rst:86: WARNING: Citation [Krumsiek10] is not referenced. /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/references.rst:130: WARNING: Citation [Murphy12] is not referenced. done preparing documents... done assembling single document... examples basic_usage installation api/index api/scanpy.api.pp.calculate_qc_metrics api/scanpy.api.pp.filter_cells api/scanpy.api.pp.filter_genes api/scanpy.api.pp.filter_genes_dispersion api/scanpy.api.pp.log1p api/scanpy.api.pp.pca api/scanpy.api.pp.normalize_per_cell api/scanpy.api.pp.regress_out api/scanpy.api.pp.scale api/scanpy.api.pp.subsample api/scanpy.api.pp.downsample_counts api/scanpy.api.pp.recipe_zheng17 api/scanpy.api.pp.recipe_weinreb17 api/scanpy.api.pp.recipe_seurat api/scanpy.api.pp.mnn_correct api/scanpy.api.pp.dca api/scanpy.api.pp.magic api/scanpy.api.pp.neighbors api/scanpy.api.tl.pca api/scanpy.api.tl.tsne api/scanpy.api.tl.umap api/scanpy.api.tl.draw_graph api/scanpy.api.tl.diffmap api/scanpy.api.tl.phate api/scanpy.api.tl.louvain api/scanpy.api.tl.dpt api/scanpy.api.tl.paga api/scanpy.api.tl.rank_genes_groups api/scanpy.api.tl.score_genes api/scanpy.api.tl.score_genes_cell_cycle api/scanpy.api.tl.sandbag api/scanpy.api.tl.cyclone api/scanpy.api.tl.sim api/plotting api/scanpy.api.pl.scatter api/scanpy.api.pl.heatmap api/scanpy.api.pl.dotplot api/scanpy.api.pl.violin api/scanpy.api.pl.stacked_violin api/scanpy.api.pl.matrixplot api/scanpy.api.pl.clustermap api/scanpy.api.pl.ranking api/scanpy.api.pl.highest_expr_genes api/scanpy.api.pl.filter_genes_dispersion api/scanpy.api.pl.pca api/scanpy.api.pl.pca_loadings api/scanpy.api.pl.pca_variance_ratio api/scanpy.api.pl.pca_overview api/scanpy.api.pl.tsne api/scanpy.api.pl.umap api/scanpy.api.pl.diffmap api/scanpy.api.pl.draw_graph api/scanpy.api.pl.phate api/scanpy.api.pl.dpt_groups_pseudotime api/scanpy.api.pl.dpt_timeseries api/scanpy.api.pl.paga api/scanpy.api.pl.paga_path api/scanpy.api.pl.paga_compare api/scanpy.api.pl.rank_genes_groups api/scanpy.api.pl.rank_genes_groups_violin api/scanpy.api.pl.rank_genes_groups_stacked_violin api/scanpy.api.pl.rank_genes_groups_heatmap api/scanpy.api.pl.rank_genes_groups_dotplot api/scanpy.api.pl.rank_genes_groups_matrixplot api/scanpy.api.pl.sim api/scanpy.api.read api/scanpy.api.read_10x_h5 api/scanpy.api.read_10x_mtx api/scanpy.api.read_h5ad api/scanpy.api.read_csv api/scanpy.api.read_excel api/scanpy.api.read_hdf api/scanpy.api.read_loom api/scanpy.api.read_mtx api/scanpy.api.read_text api/scanpy.api.read_umi_tools api/scanpy.api.queries.mitochondrial_genes api/scanpy.api.Neighbors api/scanpy.api.Neighbors.connectivities api/scanpy.api.Neighbors.distances api/scanpy.api.Neighbors.distances_dpt api/scanpy.api.Neighbors.eigen_basis api/scanpy.api.Neighbors.eigen_values api/scanpy.api.Neighbors.getdoc api/scanpy.api.Neighbors.laplacian api/scanpy.api.Neighbors.transitions api/scanpy.api.Neighbors.transitions_sym api/scanpy.api.Neighbors.compute_eigen api/scanpy.api.Neighbors.compute_neighbors api/scanpy.api.Neighbors.compute_transitions api/scanpy.api.Neighbors.to_igraph api/scanpy.api.set_figure_params api/scanpy.api.logging.print_versions api/scanpy.api.datasets.blobs api/scanpy.api.datasets.krumsiek11 api/scanpy.api.datasets.moignard15 api/scanpy.api.datasets.paul15 api/scanpy.api.datasets.toggleswitch api/scanpy.api.datasets.pbmc68k_reduced api/scanpy.api.export_to.spring_project references writing... done writing additional files... copying images... 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