Read the Docs build information Build id: 173971 Project: icb-anndata Version: latest Commit: a0cd0c62bc0ae792955cd90a9f5f55d093a08743 Date: 2019-01-12T01:57:47.948940Z State: finished Success: True [rtd-command-info] start-time: 2019-01-12T01:57:48.453462Z, end-time: 2019-01-12T01:57:48.460744Z, duration: 0, exit-code: 0 git remote set-url origin https://github.com/theislab/anndata.git [rtd-command-info] start-time: 2019-01-12T01:57:48.521226Z, end-time: 2019-01-12T01:57:48.756850Z, duration: 0, exit-code: 0 git fetch --depth 50 --tags --prune --prune-tags From https://github.com/theislab/anndata - [deleted] (none) -> origin/sparse_dense_test 622503a..a0cd0c6 master -> origin/master * [new tag] 0.6.17 -> 0.6.17 [rtd-command-info] start-time: 2019-01-12T01:57:49.067698Z, end-time: 2019-01-12T01:57:49.075853Z, duration: 0, exit-code: 0 git checkout --force origin/master Previous HEAD position was 622503a Sparse dense test (#95) HEAD is now at a0cd0c6 added test for strings_to_categoricals [rtd-command-info] start-time: 2019-01-12T01:57:49.141775Z, end-time: 2019-01-12T01:57:49.149477Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2019-01-12T01:57:49.790326Z, end-time: 2019-01-12T01:57:54.740001Z, duration: 4, 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-anndata/envs/latest/bin/python3.6 Not overwriting existing python script /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/bin/python (you must use /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/bin/python3.6) Installing setuptools, pip, wheel...done. [rtd-command-info] start-time: 2019-01-12T01:57:54.802758Z, end-time: 2019-01-12T01:57:55.467916Z, duration: 0, exit-code: 0 python pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/.cache/pip pip Cache entry deserialization failed, entry ignored Requirement already up-to-date: pip in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages [rtd-command-info] start-time: 2019-01-12T01:57:55.526524Z, end-time: 2019-01-12T01:58:05.597357Z, duration: 10, exit-code: 0 python pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/.cache/pip Pygments==2.2.0 setuptools<40 docutils==0.13.1 mock==1.0.1 pillow==2.6.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.5.4 recommonmark==0.4.0 sphinx<1.8 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<0.6 Cache entry deserialization failed, entry ignored Requirement already up-to-date: Pygments==2.2.0 in 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deserialization failed, entry ignored Requirement already up-to-date: packaging in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx<1.8) Cache entry deserialization failed, entry ignored Requirement already up-to-date: requests>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx<1.8) Cache entry deserialization failed, entry ignored Requirement already up-to-date: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx<1.8) Cache entry deserialization failed, entry ignored Requirement already up-to-date: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx<1.8) Cache entry deserialization failed, entry ignored Requirement already up-to-date: babel!=2.0,>=1.3 in 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/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from requests>=2.0.0->sphinx<1.8) Cache entry deserialization failed, entry ignored Requirement already up-to-date: chardet<3.1.0,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from requests>=2.0.0->sphinx<1.8) Cache entry deserialization failed, entry ignored Requirement already up-to-date: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from Jinja2>=2.3->sphinx<1.8) Cache entry deserialization failed, entry ignored Requirement already up-to-date: pytz>=0a in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from babel!=2.0,>=1.3->sphinx<1.8) Installing collected packages: sphinx Found existing installation: Sphinx 1.8.3 Uninstalling Sphinx-1.8.3: Successfully uninstalled Sphinx-1.8.3 Successfully installed sphinx-1.7.9 [rtd-command-info] start-time: 2019-01-12T01:58:05.661306Z, end-time: 2019-01-12T01:58:08.472720Z, duration: 2, exit-code: 0 python pip install --exists-action=w --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/.cache/pip -r docs/requires.txt Collecting sphinx>=1.8 (from -r docs/requires.txt (line 2)) Cache entry deserialization failed, entry ignored Downloading https://files.pythonhosted.org/packages/0e/5c/e7d076cf2900b38cba5c7d48545953540d86634d391b702067c00d99cb01/Sphinx-1.8.3-py2.py3-none-any.whl (3.1MB) Requirement already satisfied: sphinx-autodoc-typehints in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from -r docs/requires.txt (line 3)) Requirement already satisfied: scanpydoc in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from -r docs/requires.txt (line 4)) Requirement already satisfied: pandas~=0.21 in 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satisfied: pytz>=2011k in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from pandas~=0.21->-r docs/requires.txt (line 6)) Requirement already satisfied: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from packaging->sphinx>=1.8->-r docs/requires.txt (line 2)) Requirement already satisfied: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from Jinja2>=2.3->sphinx>=1.8->-r docs/requires.txt (line 2)) Requirement already satisfied: chardet<3.1.0,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from requests>=2.0.0->sphinx>=1.8->-r docs/requires.txt (line 2)) Requirement already satisfied: idna<2.9,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from requests>=2.0.0->sphinx>=1.8->-r docs/requires.txt (line 2)) Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from requests>=2.0.0->sphinx>=1.8->-r docs/requires.txt (line 2)) Requirement already satisfied: urllib3<1.25,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from requests>=2.0.0->sphinx>=1.8->-r docs/requires.txt (line 2)) Installing collected packages: sphinx Found existing installation: Sphinx 1.7.9 Uninstalling Sphinx-1.7.9: Successfully uninstalled Sphinx-1.7.9 Successfully installed sphinx-1.8.3 [rtd-command-info] start-time: 2019-01-12T01:58:08.953884Z, end-time: 2019-01-12T01:58:09.014248Z, 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 intersphinx_mapping = dict( h5py=('http://docs.h5py.org/en/latest/', 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'] 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 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 = ( ( '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/"), ], 'downloads': [ ("htmlzip", "//readthedocs.com/projects/icb-anndata/downloads/htmlzip/latest/"), ], 'subprojects': [ ], 'slug': 'icb-anndata', 'name': u'anndata', 'rtd_language': u'en', 'programming_language': u'py', 'canonical_url': 'https://icb-anndata.readthedocs-hosted.com/en/latest/', 'analytics_code': '', 'single_version': False, 'conf_py_path': '/docs/', 'api_host': 'https://readthedocs.com', 'github_user': 'theislab', 'github_repo': 'anndata', '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': 'a0cd0c62', } 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: 2019-01-12T01:58:09.084119Z, end-time: 2019-01-12T01:58:24.334707Z, duration: 15, exit-code: 0 python sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html Running Sphinx v1.8.3 loading translations [en]... done making output directory... loading intersphinx inventory from http://docs.h5py.org/en/latest/objects.inv... loading intersphinx inventory from https://docs.scipy.org/doc/numpy/objects.inv... loading intersphinx inventory from http://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://scikit-learn.org/stable/objects.inv... [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/latest/docs/anndata.AnnData.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.write.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.write_csvs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.write_loom.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.write_zarr.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.read_csv.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.read_excel.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.read_h5ad.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.read_hdf.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.read_loom.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.read_mtx.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.read_text.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.read_umi_tools.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.read_zarr.rst [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.T.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.chunk_X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.chunked_X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.concatenate.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.copy.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.filename.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.isbacked.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.isview.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.layers.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.var_keys.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.var_names.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.var_names_make_unique.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.varm.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.varm_keys.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.write_h5ad.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.Dataset.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.File.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.Group.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.SparseDataset.rst [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.Dataset.astype.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.Dataset.attrs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.Dataset.chunks.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.Dataset.compression.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.Dataset.compression_opts.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.Dataset.dims.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.Dataset.dtype.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.Dataset.external.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.Dataset.file.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.Dataset.fillvalue.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.File.filename.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.File.id.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.File.keys.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.Group.create_dataset.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.Group.keys.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.SparseDataset.append.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.SparseDataset.dtype.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.SparseDataset.format_str.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.SparseDataset.shape.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.SparseDataset.value.rst building [mo]: targets for 0 po files that are out of date building [readthedocs]: targets for 5 source files that are out of date updating environment: 100 added, 0 changed, 0 removed reading sources... [ 1%] anndata.AnnData reading sources... [ 2%] anndata.AnnData.T reading sources... [ 3%] anndata.AnnData.X reading sources... [ 4%] anndata.AnnData.chunk_X reading sources... [ 5%] anndata.AnnData.chunked_X reading sources... [ 6%] anndata.AnnData.concatenate reading sources... [ 7%] anndata.AnnData.copy reading sources... [ 8%] anndata.AnnData.filename reading sources... [ 9%] anndata.AnnData.isbacked reading sources... [ 10%] anndata.AnnData.isview reading sources... [ 11%] anndata.AnnData.layers reading sources... [ 12%] anndata.AnnData.n_obs reading sources... [ 13%] anndata.AnnData.n_vars reading sources... [ 14%] anndata.AnnData.obs reading sources... [ 15%] anndata.AnnData.obs_keys reading sources... [ 16%] anndata.AnnData.obs_names reading sources... [ 17%] anndata.AnnData.obs_names_make_unique reading sources... [ 18%] anndata.AnnData.obsm reading sources... [ 19%] anndata.AnnData.obsm_keys reading sources... [ 20%] anndata.AnnData.raw reading sources... 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WARNING: Missing searchtools.js_t done copying extra files... done dumping search index in English (code: en) ... done dumping object inventory... done build succeeded, 3 warnings. The HTML pages are in _build/html. [rtd-command-info] start-time: 2019-01-12T01:58:24.545817Z, end-time: 2019-01-12T01:58:30.062338Z, duration: 5, exit-code: 0 python sphinx-build -T -b readthedocssinglehtmllocalmedia -d _build/doctrees-readthedocssinglehtmllocalmedia -D language=en . _build/localmedia Running Sphinx v1.8.3 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/latest/docs/anndata.AnnData.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.write.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.write_csvs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.write_loom.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.write_zarr.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.read_csv.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.read_excel.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.read_h5ad.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.read_hdf.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.read_loom.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.read_mtx.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.read_text.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.read_umi_tools.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.read_zarr.rst [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.T.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.chunk_X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.chunked_X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.concatenate.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.copy.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.filename.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.isbacked.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.isview.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.layers.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.var_keys.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.var_names.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.var_names_make_unique.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.varm.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.varm_keys.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.write_h5ad.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.Dataset.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.File.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.Group.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.SparseDataset.rst [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.Dataset.astype.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.Dataset.attrs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.Dataset.chunks.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.Dataset.compression.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.Dataset.compression_opts.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.Dataset.dims.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.Dataset.dtype.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.Dataset.external.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.Dataset.file.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.Dataset.fillvalue.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.File.filename.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.File.id.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.File.keys.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.Group.create_dataset.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.Group.keys.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.SparseDataset.append.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.SparseDataset.dtype.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.SparseDataset.format_str.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.SparseDataset.shape.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.SparseDataset.value.rst building [mo]: targets for 0 po files that are out of date building [readthedocssinglehtmllocalmedia]: all documents updating environment: 100 added, 0 changed, 0 removed reading sources... 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