Read the Docs build information Build id: 328851 Project: icb-scanpy-tutorials Version: latest Commit: a8df6c4b1f9097a440456e37d532aa2884fdb688 Date: 2020-05-10T18:50:56.794205Z State: finished Success: True [rtd-command-info] start-time: 2020-05-10T18:50:58.832943Z, end-time: 2020-05-10T18:51:02.236826Z, duration: 3, exit-code: 0 git clone --no-single-branch --depth 50 https://github.com/theislab/scanpy-tutorials.git . Cloning into '.'... [rtd-command-info] start-time: 2020-05-10T18:51:02.544376Z, end-time: 2020-05-10T18:51:02.968023Z, 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 a8df6c4 fixed sb to sns [rtd-command-info] start-time: 2020-05-10T18:51:03.099382Z, end-time: 2020-05-10T18:51:03.296443Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2020-05-10T18:51:04.668966Z, end-time: 2020-05-10T18:51:08.548364Z, duration: 3, exit-code: 0 python3.6 -mvirtualenv Using base prefix '/home/docs/.pyenv/versions/3.6.8' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/bin/python3.6 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2020-05-10T18:51:08.660770Z, end-time: 2020-05-10T18:51:09.492313Z, duration: 0, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip Requirement already up-to-date: pip in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (20.1) [rtd-command-info] start-time: 2020-05-10T18:51:09.599356Z, end-time: 2020-05-10T18:51:19.361061Z, duration: 9, exit-code: 0 python -m pip install --upgrade --no-cache-dir 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<1.1 Collecting Pygments==2.3.1 Downloading Pygments-2.3.1-py2.py3-none-any.whl (849 kB) Collecting setuptools==41.0.1 Downloading setuptools-41.0.1-py2.py3-none-any.whl (575 kB) Collecting docutils==0.14 Downloading docutils-0.14-py3-none-any.whl (543 kB) Collecting mock==1.0.1 Downloading mock-1.0.1.tar.gz (818 kB) Collecting pillow==5.4.1 Downloading Pillow-5.4.1-cp36-cp36m-manylinux1_x86_64.whl (2.0 MB) Collecting alabaster!=0.7.5,<0.8,>=0.7 Downloading alabaster-0.7.12-py2.py3-none-any.whl (14 kB) Collecting commonmark==0.8.1 Downloading commonmark-0.8.1-py2.py3-none-any.whl (47 kB) Collecting recommonmark==0.5.0 Downloading recommonmark-0.5.0-py2.py3-none-any.whl (9.8 kB) Collecting sphinx<2 Downloading Sphinx-1.8.5-py2.py3-none-any.whl (3.1 MB) Collecting sphinx-rtd-theme<0.5 Downloading sphinx_rtd_theme-0.4.3-py2.py3-none-any.whl (6.4 MB) Collecting readthedocs-sphinx-ext<1.1 Downloading readthedocs_sphinx_ext-1.0.3-py2.py3-none-any.whl (28 kB) Collecting future Downloading future-0.18.2.tar.gz (829 kB) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.0.0-py2.py3-none-any.whl (97 kB) Collecting requests>=2.0.0 Downloading requests-2.23.0-py2.py3-none-any.whl (58 kB) Collecting sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.2.2-py2.py3-none-any.whl (39 kB) Collecting imagesize Downloading imagesize-1.2.0-py2.py3-none-any.whl (4.8 kB) Collecting six>=1.5 Downloading six-1.14.0-py2.py3-none-any.whl (10 kB) Collecting packaging Downloading packaging-20.3-py2.py3-none-any.whl (37 kB) Collecting babel!=2.0,>=1.3 Downloading Babel-2.8.0-py2.py3-none-any.whl (8.6 MB) Collecting Jinja2>=2.3 Downloading Jinja2-2.11.2-py2.py3-none-any.whl (125 kB) Collecting idna<3,>=2.5 Downloading idna-2.9-py2.py3-none-any.whl (58 kB) Collecting certifi>=2017.4.17 Downloading certifi-2020.4.5.1-py2.py3-none-any.whl (157 kB) Collecting chardet<4,>=3.0.2 Downloading chardet-3.0.4-py2.py3-none-any.whl (133 kB) Collecting urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 Downloading urllib3-1.25.9-py2.py3-none-any.whl (126 kB) Collecting pyparsing>=2.0.2 Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 kB) Collecting pytz>=2015.7 Downloading pytz-2020.1-py2.py3-none-any.whl (510 kB) Collecting MarkupSafe>=0.23 Downloading MarkupSafe-1.1.1-cp36-cp36m-manylinux1_x86_64.whl (27 kB) Building wheels for collected packages: mock, future Building wheel for mock (setup.py): started Building wheel for mock (setup.py): finished with status 'done' Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23754 sha256=75dc693741497e25663119dbf2dd7633c65b5f20157a43da66f3988fc2a4e425 Stored in directory: /tmp/pip-ephem-wheel-cache-lajhtn8k/wheels/15/fd/39/f238f155700d6d5e6231e82ae3ccf3aa7490a1b17d2073251b Building wheel for future (setup.py): started Building wheel for future (setup.py): finished with status 'done' Created wheel for future: filename=future-0.18.2-py3-none-any.whl size=491058 sha256=bdb579b717cd7d5e76800bc0241d8a1430a66d86202d0ef5861bf010a33324dc Stored in directory: /tmp/pip-ephem-wheel-cache-lajhtn8k/wheels/6e/9c/ed/4499c9865ac1002697793e0ae05ba6be33553d098f3347fb94 Successfully built mock future Installing collected packages: Pygments, setuptools, docutils, mock, pillow, alabaster, future, commonmark, snowballstemmer, idna, certifi, chardet, urllib3, requests, sphinxcontrib-websupport, imagesize, six, pyparsing, packaging, pytz, babel, MarkupSafe, Jinja2, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext Attempting uninstall: setuptools Found existing installation: setuptools 46.1.3 Uninstalling setuptools-46.1.3: Successfully uninstalled setuptools-46.1.3 Successfully installed Jinja2-2.11.2 MarkupSafe-1.1.1 Pygments-2.3.1 alabaster-0.7.12 babel-2.8.0 certifi-2020.4.5.1 chardet-3.0.4 commonmark-0.8.1 docutils-0.14 future-0.18.2 idna-2.9 imagesize-1.2.0 mock-1.0.1 packaging-20.3 pillow-5.4.1 pyparsing-2.4.7 pytz-2020.1 readthedocs-sphinx-ext-1.0.3 recommonmark-0.5.0 requests-2.23.0 setuptools-41.0.1 six-1.14.0 snowballstemmer-2.0.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-websupport-1.2.2 urllib3-1.25.9 [rtd-command-info] start-time: 2020-05-10T18:51:19.997556Z, end-time: 2020-05-10T18:51:44.221760Z, duration: 24, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r requirements.txt Requirement already satisfied: sphinx>=1.4 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from -r requirements.txt (line 1)) (1.8.5) Collecting ipykernel Downloading ipykernel-5.2.1-py3-none-any.whl (118 kB) Collecting nbsphinx>=0.4 Downloading nbsphinx-0.7.0-py3-none-any.whl (24 kB) Collecting nbclean Downloading nbclean-0.3.2-py2.py3-none-any.whl (21 kB) Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from sphinx>=1.4->-r requirements.txt (line 1)) (2.0.0) Requirement already satisfied: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.6/site-packages (from sphinx>=1.4->-r requirements.txt (line 1)) (1.14.0) Requirement already satisfied: requests>=2.0.0 in 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(26 kB) Collecting decorator Downloading decorator-4.4.2-py2.py3-none-any.whl (9.2 kB) Collecting prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0 Downloading prompt_toolkit-3.0.5-py3-none-any.whl (351 kB) Collecting pexpect; sys_platform != "win32" Downloading pexpect-4.8.0-py2.py3-none-any.whl (59 kB) Collecting jedi>=0.10 Downloading jedi-0.17.0-py2.py3-none-any.whl (1.1 MB) Collecting pickleshare Downloading pickleshare-0.7.5-py2.py3-none-any.whl (6.9 kB) Collecting backcall Downloading backcall-0.1.0.tar.gz (9.7 kB) Collecting entrypoints>=0.2.2 Downloading entrypoints-0.3-py2.py3-none-any.whl (11 kB) Collecting testpath Downloading testpath-0.4.4-py2.py3-none-any.whl (163 kB) Collecting defusedxml Downloading defusedxml-0.6.0-py2.py3-none-any.whl (23 kB) Collecting mistune<2,>=0.8.1 Downloading mistune-0.8.4-py2.py3-none-any.whl (16 kB) Collecting pandocfilters>=1.4.1 Downloading pandocfilters-1.4.2.tar.gz (14 kB) Collecting bleach Downloading bleach-3.1.5-py2.py3-none-any.whl (151 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wcwidth-0.1.9-py2.py3-none-any.whl (19 kB) Collecting ptyprocess>=0.5 Downloading ptyprocess-0.6.0-py2.py3-none-any.whl (39 kB) Collecting parso>=0.7.0 Downloading parso-0.7.0-py2.py3-none-any.whl (100 kB) Collecting webencodings Downloading webencodings-0.5.1-py2.py3-none-any.whl (11 kB) Collecting pyrsistent>=0.14.0 Downloading pyrsistent-0.16.0.tar.gz (108 kB) Collecting attrs>=17.4.0 Downloading attrs-19.3.0-py2.py3-none-any.whl (39 kB) Collecting importlib-metadata; python_version < "3.8" Downloading importlib_metadata-1.6.0-py2.py3-none-any.whl (30 kB) Collecting ipywidgets Downloading ipywidgets-7.5.1-py2.py3-none-any.whl (121 kB) Collecting qtconsole Downloading qtconsole-4.7.3-py2.py3-none-any.whl (117 kB) Collecting jupyter-console Downloading jupyter_console-6.1.0-py2.py3-none-any.whl (21 kB) Collecting Send2Trash Downloading Send2Trash-1.5.0-py3-none-any.whl (12 kB) Collecting terminado>=0.8.1 Downloading terminado-0.8.3-py2.py3-none-any.whl (33 kB) Collecting prometheus-client Downloading prometheus_client-0.7.1.tar.gz (38 kB) Collecting Mako Downloading Mako-1.1.2-py2.py3-none-any.whl (75 kB) Collecting python-editor>=0.3 Downloading python_editor-1.0.4-py3-none-any.whl (4.9 kB) Collecting zipp>=0.5 Downloading zipp-3.1.0-py3-none-any.whl (4.9 kB) Collecting widgetsnbextension~=3.5.0 Downloading widgetsnbextension-3.5.1-py2.py3-none-any.whl (2.2 MB) Collecting qtpy Downloading QtPy-1.9.0-py2.py3-none-any.whl (54 kB) Building wheels for collected packages: tornado, nbgrader, backcall, pandocfilters, alembic, pyrsistent, prometheus-client Building wheel for tornado (setup.py): started Building wheel for tornado (setup.py): finished with status 'done' Created wheel for tornado: filename=tornado-6.0.4-cp36-cp36m-linux_x86_64.whl size=427647 sha256=31f70df181707726151342edbb5ee30a1924b55d9408c0c8d6e712c32366e589 Stored in directory: /tmp/pip-ephem-wheel-cache-bj1urlez/wheels/37/a7/db/2d592e44029ef817f3ef63ea991db34191cebaef087a96f505 Building 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sha256=a82da636d6970f51c19fcd442b1eb1a50259ce30daa8b235d2459008dbf36c33 Stored in directory: /tmp/pip-ephem-wheel-cache-bj1urlez/wheels/46/c4/40/718c6fd14c2129ccaee10e0cf03ef6c4d01d98cad5dbbfda38 Building wheel for alembic (PEP 517): started Building wheel for alembic (PEP 517): finished with status 'done' Created wheel for alembic: filename=alembic-1.4.2-py2.py3-none-any.whl size=159543 sha256=cb96bf7fec58a9e323dfbd598d5b52a374f61259ddef076137cbdf1ab9ee04b2 Stored in directory: /tmp/pip-ephem-wheel-cache-bj1urlez/wheels/f2/50/61/5cc491b0ca39be60dfb4dce940b389ff91b847d62e0eb2d680 Building wheel for pyrsistent (setup.py): started Building wheel for pyrsistent (setup.py): finished with status 'done' Created wheel for pyrsistent: filename=pyrsistent-0.16.0-cp36-cp36m-linux_x86_64.whl size=115059 sha256=49965a264fc9d4c6cf3baf63f0825ec84bbc8be7965ca16d0a2a11d1558b112b Stored in directory: /tmp/pip-ephem-wheel-cache-bj1urlez/wheels/d1/8a/1c/32ab9017418a2c64e4fbaf503c08648bed2f8eb311b869a464 Building wheel for prometheus-client (setup.py): started Building wheel for prometheus-client (setup.py): finished with status 'done' Created wheel for prometheus-client: filename=prometheus_client-0.7.1-py3-none-any.whl size=41404 sha256=7c27ba049834de31df0a6a3f5d0458217c2a7bf1b5dc41339f8b029df5123b36 Stored in directory: /tmp/pip-ephem-wheel-cache-bj1urlez/wheels/1d/4a/79/a3ad3f74b3495b4555359375ca33ad7b64e77f8b7a53c8894f Successfully built tornado nbgrader backcall pandocfilters alembic pyrsistent prometheus-client Installing collected packages: ipython-genutils, decorator, traitlets, pyzmq, python-dateutil, tornado, jupyter-core, jupyter-client, wcwidth, prompt-toolkit, ptyprocess, pexpect, parso, jedi, pickleshare, backcall, ipython, ipykernel, entrypoints, testpath, defusedxml, pyrsistent, attrs, zipp, importlib-metadata, jsonschema, nbformat, mistune, pandocfilters, webencodings, bleach, nbconvert, nbsphinx, tqdm, numpy, sqlalchemy, Send2Trash, terminado, prometheus-client, notebook, widgetsnbextension, ipywidgets, qtpy, qtconsole, jupyter-console, jupyter, Mako, python-editor, alembic, fuzzywuzzy, nbgrader, kiwisolver, cycler, matplotlib, nbclean Successfully installed Mako-1.1.2 Send2Trash-1.5.0 alembic-1.4.2 attrs-19.3.0 backcall-0.1.0 bleach-3.1.5 cycler-0.10.0 decorator-4.4.2 defusedxml-0.6.0 entrypoints-0.3 fuzzywuzzy-0.18.0 importlib-metadata-1.6.0 ipykernel-5.2.1 ipython-7.14.0 ipython-genutils-0.2.0 ipywidgets-7.5.1 jedi-0.17.0 jsonschema-3.2.0 jupyter-1.0.0 jupyter-client-6.1.3 jupyter-console-6.1.0 jupyter-core-4.6.3 kiwisolver-1.2.0 matplotlib-3.2.1 mistune-0.8.4 nbclean-0.3.2 nbconvert-5.6.1 nbformat-5.0.6 nbgrader-0.6.1 nbsphinx-0.7.0 notebook-6.0.3 numpy-1.18.4 pandocfilters-1.4.2 parso-0.7.0 pexpect-4.8.0 pickleshare-0.7.5 prometheus-client-0.7.1 prompt-toolkit-3.0.5 ptyprocess-0.6.0 pyrsistent-0.16.0 python-dateutil-2.8.1 python-editor-1.0.4 pyzmq-19.0.1 qtconsole-4.7.3 qtpy-1.9.0 sqlalchemy-1.3.16 terminado-0.8.3 testpath-0.4.4 tornado-6.0.4 tqdm-4.46.0 traitlets-4.3.3 wcwidth-0.1.9 webencodings-0.5.1 widgetsnbextension-3.5.1 zipp-3.1.0 [rtd-command-info] start-time: 2020-05-10T18:51:45.434801Z, end-time: 2020-05-10T18:51:45.651099Z, duration: 0, exit-code: 0 cat conf.py from datetime import datetime project = 'Scanpy' author = 'Alex Wolf, Fidel Ramirez, Sergei Rybakov' copyright = f'{datetime.now():%Y}, {author}' 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=4, logo_only=True # Only show the logo ) 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'] html_show_sphinx = False html_logo = '_static/img/Scanpy_Logo_BrightFG.svg' def setup(app): app.add_stylesheet('css/custom.css') # -- Strip output ---------------------------------------------- import nbclean, glob for filename in glob.glob('**/*.ipynb', recursive=True): ntbk = nbclean.NotebookCleaner(filename) ntbk.clear('stderr') ntbk.save(filename) ########################################################################### # 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 multiple 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://assets.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://assets.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ("latest", "/en/latest/"), ("multiomics", "/en/multiomics/"), ], 'downloads': [ ("html", "//scanpy-tutorials.readthedocs.io/_/downloads/en/latest/htmlzip/"), ], 'subprojects': [ ], 'slug': 'icb-scanpy-tutorials', 'name': u'scanpy-tutorials', 'rtd_language': u'en', 'programming_language': u'py', 'canonical_url': 'https://scanpy-tutorials.readthedocs.io/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': 'a8df6c4b', } 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"] # Add External version warning banner to the external version documentation if 'branch' == 'external': extensions.insert(1, "readthedocs_ext.external_version_warning") 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: 2020-05-10T18:51:45.759600Z, end-time: 2020-05-10T18:52:00.547917Z, duration: 14, exit-code: 0 python sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html Running Sphinx v1.8.5 loading translations [en]... done making output directory... building [mo]: targets for 0 po files that are out of date building [readthedocs]: targets for 11 source files that are out of date updating environment: 11 added, 0 changed, 0 removed reading sources... 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