Read the Docs build information Build id: 213791 Project: icb-anndata Version: stable Commit: e91e3bb32b25169fa5eaa93efb58bd967efffccf Date: 2019-06-06T09:05:20.595949Z State: finished Success: True [rtd-command-info] start-time: 2019-06-06T09:05:21.101701Z, end-time: 2019-06-06T09:05:21.108244Z, duration: 0, exit-code: 0 git remote set-url origin https://github.com/theislab/anndata.git [rtd-command-info] start-time: 2019-06-06T09:05:21.168538Z, end-time: 2019-06-06T09:05:21.534441Z, duration: 0, exit-code: 0 git fetch --tags --prune --prune-tags --depth 50 From https://github.com/theislab/anndata - [deleted] (none) -> origin/strings_to_categories 76375e2..e91e3bb master -> origin/master * [new tag] 0.6.21 -> 0.6.21 [rtd-command-info] start-time: 2019-06-06T09:05:21.763475Z, end-time: 2019-06-06T09:05:21.785757Z, duration: 0, exit-code: 0 git checkout --force e91e3bb32b25169fa5eaa93efb58bd967efffccf Previous HEAD position was 6fb0834 Use unpack_index from our code (#151) HEAD is now at e91e3bb removed brief release description [rtd-command-info] start-time: 2019-06-06T09:05:21.847102Z, end-time: 2019-06-06T09:05:21.857550Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2019-06-06T09:05:22.751945Z, end-time: 2019-06-06T09:05:27.338052Z, 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-anndata/envs/stable/bin/python3.6 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/stable/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2019-06-06T09:05:27.400428Z, end-time: 2019-06-06T09:05:28.294609Z, duration: 0, exit-code: 0 python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/.cache/pip pip Requirement already up-to-date: pip in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/stable/lib/python3.6/site-packages (19.1.1) [rtd-command-info] start-time: 2019-06-06T09:05:28.388315Z, end-time: 2019-06-06T09:05:37.745735Z, duration: 9, exit-code: 0 python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/.cache/pip Pygments==2.3.1 setuptools==41.0.1 docutils==0.14 mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.8.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<0.6 Collecting Pygments==2.3.1 Using cached 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2019-06-06T09:05:53.294128Z, duration: 15, exit-code: 0 python -m pip install --exists-action=w --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/.cache/pip -r docs/requires.txt Requirement already satisfied: sphinx>=1.8 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/stable/lib/python3.6/site-packages (from -r docs/requires.txt (line 2)) (1.8.5) Collecting sphinx-autodoc-typehints (from -r docs/requires.txt (line 3)) Using cached https://files.pythonhosted.org/packages/de/57/e90dba6e31db7b5c4cc9eaab69a56f2c93a498febd188d35c8216da18b6f/sphinx_autodoc_typehints-1.6.0-py3-none-any.whl Collecting scanpydoc>=0.3.2 (from -r docs/requires.txt (line 4)) Using cached https://files.pythonhosted.org/packages/50/65/8472fc898d98291aec6f72bff82e872eb42437cd53ad371c2aae3d87a575/scanpydoc-0.3.3-py3-none-any.whl Collecting pandas~=0.21 (from -r docs/requires.txt (line 6)) Using cached 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(1.1.0) Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/stable/lib/python3.6/site-packages (from sphinx>=1.8->-r docs/requires.txt (line 2)) (19.0) Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/stable/lib/python3.6/site-packages (from sphinx>=1.8->-r docs/requires.txt (line 2)) (0.7.12) Requirement already satisfied: docutils>=0.11 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/stable/lib/python3.6/site-packages (from sphinx>=1.8->-r docs/requires.txt (line 2)) (0.14) Requirement already satisfied: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/stable/lib/python3.6/site-packages (from sphinx>=1.8->-r docs/requires.txt (line 2)) (2.7.0) Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/stable/lib/python3.6/site-packages 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get-version, scanpydoc, numpy, python-dateutil, pandas, scipy, h5py, natsort Successfully installed future-fstrings-1.1.0 get-version-2.0.6 h5py-2.9.0 natsort-6.0.0 numpy-1.16.4 pandas-0.24.2 python-dateutil-2.8.0 scanpydoc-0.3.3 scipy-1.3.0 sphinx-autodoc-typehints-1.6.0 [rtd-command-info] start-time: 2019-06-06T09:05:53.824034Z, end-time: 2019-06-06T09:05:54.133584Z, duration: 0, exit-code: 0 cat docs/conf.py import sys import logging from pathlib import Path from datetime import datetime HERE = Path(__file__).parent sys.path.insert(0, str(HERE.parent)) import anndata # noqa logger = logging.getLogger(__name__) for generated in HERE.glob('anndata.*.rst'): generated.unlink() # -- General configuration ------------------------------------------------ needs_sphinx = '1.7' # autosummary bugfix # General information project = 'anndata' author = anndata.__author__ copyright = f'{datetime.now():%Y}, {author}.' version = anndata.__version__.replace('.dirty', '') release = version # default settings templates_path = ['_templates'] source_suffix = '.rst' master_doc = 'index' default_role = 'literal' exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] pygments_style = 'sphinx' extensions = [ 'sphinx.ext.autodoc', 'sphinx.ext.intersphinx', 'sphinx.ext.doctest', 'sphinx.ext.coverage', 'sphinx.ext.mathjax', 'sphinx.ext.napoleon', 'sphinx.ext.autosummary', # 'plot_generator', # 'plot_directive', 'sphinx_autodoc_typehints', # needs to be after napoleon # 'ipython_directive', # 'ipython_console_highlighting', 'scanpydoc', ] # Generate the API documentation when building autosummary_generate = True autodoc_member_order = 'bysource' # autodoc_default_flags = ['members'] napoleon_google_docstring = False napoleon_numpy_docstring = True napoleon_include_init_with_doc = False napoleon_use_rtype = True # having a separate entry generally helps readability napoleon_use_param = True napoleon_custom_sections = [('Params', 'Parameters')] todo_include_todos = False nitpicky = True # Report broken links intersphinx_mapping = dict( h5py=('http://docs.h5py.org/en/latest/', None), loompy=('https://linnarssonlab.org/loompy/', None), numpy=('https://docs.scipy.org/doc/numpy/', None), pandas=('http://pandas.pydata.org/pandas-docs/stable/', None), python=('https://docs.python.org/3', None), scipy=('https://docs.scipy.org/doc/scipy/reference/', None), sklearn=('https://scikit-learn.org/stable/', None), ) # -- Options for HTML output ---------------------------------------------- html_theme = 'sphinx_rtd_theme' html_theme_options = dict( navigation_depth=2, ) html_context = dict( display_github=True, # Integrate GitHub github_user='theislab', # Username github_repo='anndata', # Repo name github_version='master', # Version conf_py_path='/docs/', # Path in the checkout to the docs root ) html_static_path = ['_static'] html_show_sphinx = False def setup(app): app.add_stylesheet('css/custom.css') # -- Options for other output formats ------------------------------------------ htmlhelp_basename = f'{project}doc' doc_title = f'{project} Documentation' latex_documents = [ (master_doc, f'{project}.tex', doc_title, author, 'manual'), ] man_pages = [ (master_doc, project, doc_title, [author], 1) ] texinfo_documents = [ (master_doc, project, doc_title, author, project, 'One line description of project.', 'Miscellaneous'), ] ########################################################################### # auto-created readthedocs.org specific configuration # ########################################################################### # # The following code was added during an automated build on readthedocs.org # It is auto created and injected for every build. The result is based on the # conf.py.tmpl file found in the readthedocs.org codebase: # https://github.com/rtfd/readthedocs.org/blob/master/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl # import importlib import sys import os.path from six import string_types from sphinx import version_info # Get suffix for proper linking to GitHub # This is deprecated in Sphinx 1.3+, # as each page can have its own suffix if globals().get('source_suffix', False): if isinstance(source_suffix, string_types): SUFFIX = source_suffix elif isinstance(source_suffix, (list, tuple)): # Sphinx >= 1.3 supports list/tuple to define multiple suffixes SUFFIX = source_suffix[0] elif isinstance(source_suffix, dict): # Sphinx >= 1.8 supports a mapping dictionary for mulitple 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': "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': [ ("html", "//readthedocs.com/projects/icb-anndata/downloads/htmlzip/stable/"), ], 'subprojects': [ ], 'slug': 'icb-anndata', 'name': u'anndata', 'rtd_language': u'en', 'programming_language': u'py', 'canonical_url': 'https://icb-anndata.readthedocs-hosted.com/en/stable/', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/docs/', 'api_host': 'https://readthedocs.com', 'github_user': 'theislab', 'github_repo': 'anndata', 'github_version': 'e91e3bb32b25169fa5eaa93efb58bd967efffccf', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'e91e3bb32b25169fa5eaa93efb58bd967efffccf', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'e91e3bb32b25169fa5eaa93efb58bd967efffccf', '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': 'e91e3bb3', } 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"] 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: 2019-06-06T09:05:54.235116Z, end-time: 2019-06-06T09:06:04.773117Z, duration: 10, exit-code: 0 python sphinx-build -T -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html Running Sphinx v1.8.5 loading translations [en]... done making output directory... loading pickled environment... done [autosummary] generating autosummary for: api.rst, benchmarks.rst, index.rst, references.rst, release_notes.rst [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.write.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.write_csvs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.write_loom.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.write_zarr.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.h5py.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.read_csv.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.read_excel.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.read_h5ad.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.read_hdf.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.read_loom.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.read_mtx.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.read_text.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.read_umi_tools.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.read_zarr.rst [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.T.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.chunk_X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.chunked_X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.concatenate.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.copy.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.filename.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.isbacked.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.isview.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.layers.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.var_names.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.var_names_make_unique.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.var_vector.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.varm.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.varm_keys.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.write_h5ad.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.h5py.Dataset.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.h5py.File.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.h5py.Group.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.h5py.SparseDataset.rst [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.h5py.Dataset.astype.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.h5py.Dataset.attrs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.h5py.Dataset.chunks.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.h5py.Dataset.compression.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.h5py.Dataset.compression_opts.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.h5py.Dataset.dims.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.h5py.Dataset.dtype.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.h5py.Dataset.external.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.h5py.Dataset.file.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.h5py.Dataset.fillvalue.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.h5py.File.filename.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.h5py.File.id.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.h5py.File.keys.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.h5py.Group.create_dataset.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.h5py.Group.keys.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.h5py.SparseDataset.append.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.h5py.SparseDataset.dtype.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.h5py.SparseDataset.format_str.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.h5py.SparseDataset.shape.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.h5py.SparseDataset.value.rst building [mo]: targets for 0 po files that are out of date building [readthedocs]: targets for 100 source files that are out of date updating environment: 102 added, 0 changed, 0 removed reading sources... 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(code: en) ... done dumping object inventory... done build succeeded, 34 warnings. The HTML pages are in _build/html. [rtd-command-info] start-time: 2019-06-06T09:06:04.915310Z, end-time: 2019-06-06T09:06:12.213699Z, duration: 7, exit-code: 0 python sphinx-build -T -b readthedocssinglehtmllocalmedia -d _build/doctrees-readthedocssinglehtmllocalmedia -D language=en . _build/localmedia Running Sphinx v1.8.5 loading translations [en]... done making output directory... loading pickled environment... done [autosummary] generating autosummary for: api.rst, benchmarks.rst, index.rst, references.rst, release_notes.rst [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.write.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.write_csvs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.write_loom.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.write_zarr.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.h5py.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.read_csv.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.read_excel.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.read_h5ad.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.read_hdf.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.read_loom.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.read_mtx.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.read_text.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.read_umi_tools.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.read_zarr.rst [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.T.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.chunk_X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.chunked_X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.concatenate.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.copy.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.filename.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.isbacked.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.isview.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.layers.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.var_names.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.var_names_make_unique.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.var_vector.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.varm.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.varm_keys.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.write_h5ad.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.h5py.Dataset.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.h5py.File.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.h5py.Group.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.h5py.SparseDataset.rst [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.h5py.Dataset.astype.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.h5py.Dataset.attrs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.h5py.Dataset.chunks.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.h5py.Dataset.compression.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.h5py.Dataset.compression_opts.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.h5py.Dataset.dims.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.h5py.Dataset.dtype.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.h5py.Dataset.external.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.h5py.Dataset.file.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.h5py.Dataset.fillvalue.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.h5py.File.filename.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.h5py.File.id.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.h5py.File.keys.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.h5py.Group.create_dataset.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.h5py.Group.keys.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.h5py.SparseDataset.append.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.h5py.SparseDataset.dtype.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.h5py.SparseDataset.format_str.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.h5py.SparseDataset.shape.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.h5py.SparseDataset.value.rst building [mo]: targets for 0 po files that are out of date building [readthedocssinglehtmllocalmedia]: all documents updating environment: 102 added, 0 changed, 0 removed reading sources... 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anndata.AnnData.rename_categories anndata.AnnData.strings_to_categoricals anndata.AnnData.to_df anndata.AnnData.transpose anndata.AnnData.uns_keys anndata.AnnData.var_keys anndata.AnnData.var_names_make_unique anndata.AnnData.var_vector anndata.AnnData.varm_keys anndata.AnnData.write anndata.AnnData.write_csvs anndata.AnnData.write_h5ad anndata.AnnData.write_loom anndata.AnnData.write_zarr anndata.read_h5ad anndata.read_csv anndata.read_excel anndata.read_hdf anndata.read_loom anndata.read_mtx anndata.read_text anndata.read_umi_tools anndata.read_zarr anndata.h5py anndata.h5py.File anndata.h5py.File.filename anndata.h5py.File.id anndata.h5py.File.close anndata.h5py.File.create_dataset anndata.h5py.File.keys anndata.h5py.Group anndata.h5py.Group.create_dataset anndata.h5py.Group.keys anndata.h5py.Dataset anndata.h5py.Dataset.attrs anndata.h5py.Dataset.chunks anndata.h5py.Dataset.compression anndata.h5py.Dataset.compression_opts anndata.h5py.Dataset.dims anndata.h5py.Dataset.dtype anndata.h5py.Dataset.external anndata.h5py.Dataset.file anndata.h5py.Dataset.fillvalue anndata.h5py.Dataset.fletcher32 anndata.h5py.Dataset.flush anndata.h5py.Dataset.id anndata.h5py.Dataset.is_virtual anndata.h5py.Dataset.maxshape anndata.h5py.Dataset.name anndata.h5py.Dataset.ndim anndata.h5py.Dataset.parent anndata.h5py.Dataset.ref anndata.h5py.Dataset.refresh anndata.h5py.Dataset.regionref anndata.h5py.Dataset.scaleoffset anndata.h5py.Dataset.shape anndata.h5py.Dataset.shuffle anndata.h5py.Dataset.size anndata.h5py.Dataset.value anndata.h5py.Dataset.astype anndata.h5py.Dataset.len anndata.h5py.Dataset.read_direct anndata.h5py.Dataset.resize anndata.h5py.Dataset.virtual_sources anndata.h5py.Dataset.write_direct anndata.h5py.SparseDataset anndata.h5py.SparseDataset.dtype anndata.h5py.SparseDataset.format_str anndata.h5py.SparseDataset.shape anndata.h5py.SparseDataset.value anndata.h5py.SparseDataset.append benchmarks references 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