Read the Docs build information Build id: 177321 Project: icb-scanpy-tutorials Version: latest Commit: 3a0bc24e1574329ec15520f795f339cbe6cdbff2 Date: 2019-01-24T20:43:47.220891Z State: finished Success: True [rtd-command-info] start-time: 2019-01-24T20:43:47.652643Z, end-time: 2019-01-24T20:43:49.888661Z, duration: 2, exit-code: 0 git clone --no-single-branch --depth 50 https://github.com/theislab/scanpy-tutorials.git . Cloning into '.'... [rtd-command-info] start-time: 2019-01-24T20:43:50.083083Z, end-time: 2019-01-24T20:43:50.172053Z, 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 3a0bc24 added paga notebook [rtd-command-info] start-time: 2019-01-24T20:43:50.230890Z, end-time: 2019-01-24T20:43:50.237650Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2019-01-24T20:43:50.821543Z, end-time: 2019-01-24T20:43:53.298244Z, 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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https://files.pythonhosted.org/packages/d1/29/605c2cc68a9992d18dada28206eeada56ea4bd07a239669da41674648b6f/ptyprocess-0.6.0-py2.py3-none-any.whl Collecting webencodings (from bleach->nbconvert!=5.4->nbsphinx==0.3.5->-r requirements.txt (line 3)) Downloading 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 Building wheel for tornado (setup.py): started Building wheel for tornado (setup.py): finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/.cache/pip/wheels/6d/e1/ce/f4ee2fa420cc6b940123c64992b81047816d0a9fad6b879325 Building wheel for backcall (setup.py): started Building wheel for backcall (setup.py): finished with status 'done' Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/.cache/pip/wheels/98/b0/dd/29e28ff615af3dda4c67cab719dd51357597eabff926976b45 Building wheel for pandocfilters (setup.py): started Building wheel for pandocfilters (setup.py): 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: tornado, decorator, ipython-genutils, traitlets, jupyter-core, pyzmq, python-dateutil, jupyter-client, parso, jedi, pickleshare, wcwidth, prompt-toolkit, ptyprocess, pexpect, backcall, ipython, ipykernel, jsonschema, nbformat, pandocfilters, mistune, entrypoints, webencodings, bleach, testpath, nbconvert, nbsphinx Successfully installed backcall-0.1.0 bleach-3.1.0 decorator-4.3.2 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-0.3.2 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: 2019-01-24T20:44:23.753537Z, end-time: 2019-01-24T20:44:23.811597Z, 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': '3a0bc24e', } 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: 2019-01-24T20:44:23.875398Z, end-time: 2019-01-24T20:44:29.757022Z, duration: 5, exit-code: 0 python sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html Running Sphinx v1.7.9 loading translations [en]... done making output directory... 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: 5 added, 0 changed, 0 removed reading sources... 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