Read the Docs build information Build id: 176008 Project: icb-scanpy-tutorials Version: latest Commit: b5342f081747167e7d8d37515ab742bdc5187913 Date: 2019-01-21T12:47:57.564037Z State: finished Success: True [rtd-command-info] start-time: 2019-01-21T12:48:41.156010Z, end-time: 2019-01-21T12:48:41.169072Z, duration: 0, exit-code: 0 git remote set-url origin https://github.com/theislab/scanpy-tutorials.git [rtd-command-info] start-time: 2019-01-21T12:48:41.231535Z, end-time: 2019-01-21T12:48:41.471577Z, duration: 0, exit-code: 0 git fetch --tags --prune --prune-tags --depth 50 [rtd-command-info] start-time: 2019-01-21T12:48:41.639038Z, end-time: 2019-01-21T12:48:41.718716Z, duration: 0, exit-code: 0 git checkout --force origin/master HEAD is now at b5342f0 added note sections in pbmc3k [rtd-command-info] start-time: 2019-01-21T12:48:41.779765Z, end-time: 2019-01-21T12:48:41.786335Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2019-01-21T12:48:42.837658Z, end-time: 2019-01-21T12:48:45.612587Z, duration: 2, exit-code: 0 python3.5 -mvirtualenv --no-site-packages --no-download Using base prefix '/usr' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/bin/python3.5 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/bin/python Installing setuptools, pip, wheel...done. 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bleach->nbconvert!=5.4->nbsphinx==0.3.5->-r requirements.txt (line 3)) Using cached https://files.pythonhosted.org/packages/f4/24/2a3e3df732393fed8b3ebf2ec078f05546de641fe1b667ee316ec1dcf3b7/webencodings-0.5.1-py2.py3-none-any.whl Building wheels for collected packages: tornado, backcall, pandocfilters Running setup.py bdist_wheel for tornado: started Running setup.py bdist_wheel for tornado: finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/.cache/pip/wheels/6d/e1/ce/f4ee2fa420cc6b940123c64992b81047816d0a9fad6b879325 Running setup.py bdist_wheel for backcall: started Running setup.py bdist_wheel for backcall: finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/.cache/pip/wheels/98/b0/dd/29e28ff615af3dda4c67cab719dd51357597eabff926976b45 Running setup.py bdist_wheel for pandocfilters: started Running setup.py bdist_wheel for pandocfilters: finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/.cache/pip/wheels/39/01/56/f1b08a6275acc59e846fa4c1e1b65dbc1919f20157d9e66c20 Successfully built tornado backcall pandocfilters Installing collected packages: pyzmq, tornado, ipython-genutils, decorator, traitlets, jupyter-core, python-dateutil, jupyter-client, pickleshare, wcwidth, prompt-toolkit, ptyprocess, pexpect, backcall, parso, jedi, ipython, ipykernel, mistune, jsonschema, nbformat, pandocfilters, testpath, entrypoints, webencodings, bleach, nbconvert, nbsphinx Successfully installed backcall-0.1.0 bleach-3.1.0 decorator-4.3.0 entrypoints-0.3 ipykernel-5.1.0 ipython-7.2.0 ipython-genutils-0.2.0 jedi-0.13.2 jsonschema-2.6.0 jupyter-client-5.2.4 jupyter-core-4.4.0 mistune-0.8.4 nbconvert-5.3.1 nbformat-4.4.0 nbsphinx-0.3.5 pandocfilters-1.4.2 parso-0.3.1 pexpect-4.6.0 pickleshare-0.7.5 prompt-toolkit-2.0.7 ptyprocess-0.6.0 python-dateutil-2.7.5 pyzmq-17.1.2 testpath-0.4.2 tornado-5.1.1 traitlets-4.3.2 wcwidth-0.1.7 webencodings-0.5.1 [rtd-command-info] start-time: 2019-01-21T12:49:13.110935Z, end-time: 2019-01-21T12:49:13.165192Z, duration: 0, exit-code: 0 cat conf.py project = 'Scanpy' copyright = '2018, Scanpy authors' author = 'Scanpy authors' version = '' release = version extensions = [ 'nbsphinx', ] templates_path = ['_templates'] source_suffix = '.rst' master_doc = 'index' language = None exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', '**.ipynb_checkpoints'] pygments_style = 'sphinx' # -- 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-tutorials', # Repo name github_version='master', # Version conf_py_path='/', # Path in the checkout to the docs root ) html_static_path = ['_static'] def setup(app): app.add_stylesheet('css/custom.css') ########################################################################### # 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') # 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/"), ], 'downloads': [ ("htmlzip", "//readthedocs.com/projects/icb-scanpy-tutorials/downloads/htmlzip/latest/"), ], 'subprojects': [ ], 'slug': 'icb-scanpy-tutorials', 'name': u'scanpy-tutorials', 'rtd_language': u'en', 'programming_language': u'py', 'canonical_url': 'https://icb-scanpy-tutorials.readthedocs-hosted.com/en/latest/', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/', 'api_host': 'https://readthedocs.com', 'github_user': 'theislab', 'github_repo': 'scanpy-tutorials', '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': 'b5342f08', } 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: 2019-01-21T12:49:13.234861Z, end-time: 2019-01-21T12:49:17.661070Z, duration: 4, exit-code: 0 python sphinx-build -T -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html Running Sphinx v1.7.9 loading translations [en]... done making output directory... loading pickled environment... failed: build environment version not current building [mo]: targets for 0 po files that are out of date building [readthedocs]: targets for 4 source files that are out of date updating environment: 4 added, 0 changed, 0 removed reading sources... 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