Read the Docs build information Build id: 740952 Project: institute-for-disease-modeling-idm Version: latest Commit: 64c6f8c6a36ece9a958224d8a90bc4b52c04724c Date: 2021-10-07T23:15:50.012546Z State: finished Success: True [rtd-command-info] start-time: 2021-10-07T23:15:51.936899Z, end-time: 2021-10-07T23:15:53.184114Z, duration: 1, exit-code: 0 git clone --no-single-branch --depth 50 git@github.com:InstituteforDiseaseModeling/docs.idmod.org.git . Cloning into '.'... Warning: Permanently added 'github.com,192.30.255.112' (RSA) to the list of known hosts. [rtd-command-info] start-time: 2021-10-07T23:15:53.334492Z, end-time: 2021-10-07T23:15:53.406636Z, duration: 0, exit-code: 0 git checkout --force origin/main Note: checking out 'origin/main'. 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 64c6f8c temporary redirect until iframe is allowed [rtd-command-info] start-time: 2021-10-07T23:15:53.520976Z, end-time: 2021-10-07T23:15:53.591900Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2021-10-07T23:15:54.720063Z, end-time: 2021-10-07T23:16:00.189623Z, duration: 5, exit-code: 0 python3.8 -mvirtualenv Using base prefix '/home/docs/.pyenv/versions/3.8.6' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm/envs/latest/bin/python3.8 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm/envs/latest/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2021-10-07T23:16:00.300774Z, end-time: 2021-10-07T23:16:01.436559Z, duration: 1, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip setuptools Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm/envs/latest/lib/python3.8/site-packages (21.2.4) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm/envs/latest/lib/python3.8/site-packages (58.2.0) [rtd-command-info] start-time: 2021-10-07T23:16:01.541258Z, end-time: 2021-10-07T23:16:27.411931Z, duration: 25, exit-code: 0 python -m pip install --upgrade --no-cache-dir 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<2.2 Collecting mock==1.0.1 Downloading mock-1.0.1.zip (861 kB) Collecting pillow==5.4.1 Downloading Pillow-5.4.1.tar.gz (16.0 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<2.2 Downloading readthedocs_sphinx_ext-2.1.4-py2.py3-none-any.whl (29 kB) Collecting future Downloading future-0.18.2.tar.gz (829 kB) Collecting docutils>=0.11 Downloading docutils-0.17.1-py2.py3-none-any.whl (575 kB) Collecting requests>=2.0.0 Downloading requests-2.26.0-py2.py3-none-any.whl (62 kB) Collecting Jinja2>=2.3 Downloading Jinja2-3.0.2-py3-none-any.whl (133 kB) Collecting six>=1.5 Downloading six-1.16.0-py2.py3-none-any.whl (11 kB) Collecting sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.2.4-py2.py3-none-any.whl (39 kB) Collecting babel!=2.0,>=1.3 Downloading Babel-2.9.1-py2.py3-none-any.whl (8.8 MB) Collecting imagesize Downloading imagesize-1.2.0-py2.py3-none-any.whl (4.8 kB) Collecting Pygments>=2.0 Downloading Pygments-2.10.0-py3-none-any.whl (1.0 MB) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.1.0-py2.py3-none-any.whl (93 kB) Collecting packaging Downloading packaging-21.0-py3-none-any.whl (40 kB) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm/envs/latest/lib/python3.8/site-packages (from sphinx<2) (58.2.0) Collecting pytz>=2015.7 Downloading pytz-2021.3-py2.py3-none-any.whl (503 kB) Collecting MarkupSafe>=2.0 Downloading MarkupSafe-2.0.1-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (30 kB) Collecting charset-normalizer~=2.0.0 Downloading charset_normalizer-2.0.6-py3-none-any.whl (37 kB) Collecting idna<4,>=2.5 Downloading idna-3.2-py3-none-any.whl (59 kB) Collecting urllib3<1.27,>=1.21.1 Downloading urllib3-1.26.7-py2.py3-none-any.whl (138 kB) Collecting certifi>=2017.4.17 Downloading certifi-2021.5.30-py2.py3-none-any.whl (145 kB) Collecting pyparsing>=2.0.2 Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 kB) Collecting sphinxcontrib-serializinghtml Downloading sphinxcontrib_serializinghtml-1.1.5-py2.py3-none-any.whl (94 kB) Building wheels for collected packages: mock, pillow, 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=23772 sha256=5526e674fbf3524e51b7493af3554c682125d217af15bdf8bb6c2728715d1943 Stored in directory: /tmp/pip-ephem-wheel-cache-6mi2wl5o/wheels/41/7c/21/90057f91c6ead7c77a90c52d6e85ca48bf82d8b0d3f8dfbb65 Building wheel for pillow (setup.py): started Building wheel for pillow (setup.py): finished with status 'done' Created wheel for pillow: filename=Pillow-5.4.1-cp38-cp38-linux_x86_64.whl size=1260080 sha256=60d088c9a866775d0e2b053e374b6f8d07c43ba283d5a9fb15095a9895f6534d Stored in directory: /tmp/pip-ephem-wheel-cache-6mi2wl5o/wheels/5f/a8/6b/5b7b3f764d879214eb03570f74d2b086201eb514e6ffa68d6d 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=491070 sha256=1174fea8013ed84a43c03c879f9b899ea252e3865b38e6638e52d8268b31f2d8 Stored in directory: /tmp/pip-ephem-wheel-cache-6mi2wl5o/wheels/8e/70/28/3d6ccd6e315f65f245da085482a2e1c7d14b90b30f239e2cf4 Successfully built mock pillow future Installing collected packages: urllib3, sphinxcontrib-serializinghtml, pytz, pyparsing, MarkupSafe, idna, charset-normalizer, certifi, sphinxcontrib-websupport, snowballstemmer, six, requests, Pygments, packaging, Jinja2, imagesize, future, docutils, babel, alabaster, sphinx, commonmark, sphinx-rtd-theme, recommonmark, readthedocs-sphinx-ext, pillow, mock Successfully installed Jinja2-3.0.2 MarkupSafe-2.0.1 Pygments-2.10.0 alabaster-0.7.12 babel-2.9.1 certifi-2021.5.30 charset-normalizer-2.0.6 commonmark-0.8.1 docutils-0.17.1 future-0.18.2 idna-3.2 imagesize-1.2.0 mock-1.0.1 packaging-21.0 pillow-5.4.1 pyparsing-2.4.7 pytz-2021.3 readthedocs-sphinx-ext-2.1.4 recommonmark-0.5.0 requests-2.26.0 six-1.16.0 snowballstemmer-2.1.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.5 sphinxcontrib-websupport-1.2.4 urllib3-1.26.7 [rtd-command-info] start-time: 2021-10-07T23:16:27.516912Z, end-time: 2021-10-07T23:16:28.284715Z, duration: 0, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r requirements.txt Requirement already satisfied: sphinx in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm/envs/latest/lib/python3.8/site-packages (from -r requirements.txt (line 1)) (1.8.5) Requirement 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/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm/envs/latest/lib/python3.8/site-packages (from sphinx->-r requirements.txt (line 1)) (2.9.1) Requirement already satisfied: requests>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm/envs/latest/lib/python3.8/site-packages (from sphinx->-r requirements.txt (line 1)) (2.26.0) Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm/envs/latest/lib/python3.8/site-packages (from sphinx->-r requirements.txt (line 1)) (1.2.0) Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm/envs/latest/lib/python3.8/site-packages (from sphinx->-r requirements.txt (line 1)) (2.1.0) Requirement already satisfied: sphinxcontrib-websupport in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm/envs/latest/lib/python3.8/site-packages (from sphinx->-r requirements.txt (line 1)) (1.2.4) Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm/envs/latest/lib/python3.8/site-packages (from sphinx->-r requirements.txt (line 1)) (21.0) Requirement already satisfied: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm/envs/latest/lib/python3.8/site-packages (from sphinx->-r requirements.txt (line 1)) (2.10.0) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm/envs/latest/lib/python3.8/site-packages (from sphinx->-r requirements.txt (line 1)) (58.2.0) Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm/envs/latest/lib/python3.8/site-packages (from sphinx->-r requirements.txt (line 1)) (0.7.12) Requirement already satisfied: pytz>=2015.7 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm/envs/latest/lib/python3.8/site-packages (from babel!=2.0,>=1.3->sphinx->-r requirements.txt (line 1)) (2021.3) Requirement already satisfied: MarkupSafe>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm/envs/latest/lib/python3.8/site-packages (from Jinja2>=2.3->sphinx->-r requirements.txt (line 1)) (2.0.1) Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm/envs/latest/lib/python3.8/site-packages (from requests>=2.0.0->sphinx->-r requirements.txt (line 1)) (2021.5.30) Requirement already satisfied: idna<4,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm/envs/latest/lib/python3.8/site-packages (from requests>=2.0.0->sphinx->-r requirements.txt (line 1)) (3.2) Requirement already satisfied: urllib3<1.27,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm/envs/latest/lib/python3.8/site-packages (from requests>=2.0.0->sphinx->-r requirements.txt (line 1)) (1.26.7) Requirement already satisfied: charset-normalizer~=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm/envs/latest/lib/python3.8/site-packages (from requests>=2.0.0->sphinx->-r requirements.txt (line 1)) (2.0.6) Requirement already satisfied: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm/envs/latest/lib/python3.8/site-packages (from packaging->sphinx->-r requirements.txt (line 1)) (2.4.7) Requirement already satisfied: sphinxcontrib-serializinghtml in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-idm/envs/latest/lib/python3.8/site-packages (from sphinxcontrib-websupport->sphinx->-r requirements.txt (line 1)) (1.1.5) [rtd-command-info] start-time: 2021-10-07T23:16:29.688020Z, end-time: 2021-10-07T23:16:29.755525Z, duration: 0, exit-code: 0 cat conf.py # Configuration file for the Sphinx documentation builder. # # Documentation: https://www.sphinx-doc.org/en/master/usage/configuration.html import sphinx_rtd_theme from datetime import date # -- Project information ----------------------------------------------------- project = 'idm' copyright = f'{date.today().year}, Bill & Melinda Gates Foundation. All rights reserved.' author = 'Institute for Disease Modeling' # -- General configuration --------------------------------------------------- extensions = [ 'sphinx_rtd_theme' ] exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', '.venv'] master_doc = 'index' primary_domain = None source_suffix = { '.rst': 'restructuredtext' } templates_path = ['_templates'] # -- Options for HTML output ------------------------------------------------- # Variables used in the html Jinja templates html_context = dict( docs_title = "Documentation | IDMOD", docs_home_url = "https://idmod.org/documentation" ) html_favicon = "_static/favicon.ico" html_show_sourcelink = False html_show_sphinx = False html_static_path = ['_static'] html_use_index = False html_theme = 'sphinx_rtd_theme' ########################################################################### # 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 # # Note: this file shouldn't rely on extra dependencies. import importlib import sys import os.path # Borrowed from six. PY3 = sys.version_info[0] == 3 string_types = str if PY3 else basestring 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/"), ], 'downloads': [ ], 'subprojects': [ ("institute-for-disease-modeling-synthpops-test", "https://docs.idmod.org/projects/synthpops/en/latest/"), ("institute-for-disease-modeling-idmtools", "https://docs.idmod.org/projects/idmtools/en/latest/"), ("institute-for-disease-modeling-covasim", "https://docs.idmod.org/projects/covasim/en/latest/"), ("institute-for-disease-modeling-vis-tools", "https://docs.idmod.org/projects/vis-tools/en/latest/"), ("institute-for-disease-modeling-emodpy", "https://docs.idmod.org/projects/emodpy/en/latest/"), ("institute-for-disease-modeling-emod-api", "https://docs.idmod.org/projects/emod-api/en/latest/"), ("institute-for-disease-modeling-idm-cms", "https://docs.idmod.org/projects/cms/en/latest/"), 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("institute-for-disease-modeling-dymodetron", "https://docs.idmod.org/projects/dymodetron/en/latest/"), ("institute-for-disease-modeling-doc-guidance", "https://docs.idmod.org/projects/doc-guidance/en/latest/"), ("institute-for-disease-modeling-poliosim", "https://docs.idmod.org/projects/poliosim/en/latest/"), ("institute-for-disease-modeling-jupyter-notebooks-emodpy", "https://docs.idmod.org/projects/jupyter-notebooks-emodpy/en/latest/"), ], 'slug': 'institute-for-disease-modeling-idm', 'name': u'idm', 'rtd_language': u'en', 'programming_language': u'words', 'canonical_url': 'https://docs.idmod.org/', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/', 'api_host': 'https://readthedocs.com', 'github_user': 'InstituteforDiseaseModeling', 'proxied_api_host': '/_', 'github_repo': 'docs.idmod.org', 'github_version': 'main', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'main', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'main', 'display_gitlab': False, 'READTHEDOCS': True, 'using_theme': (html_theme == "default"), 'new_theme': (html_theme == "sphinx_rtd_theme"), 'source_suffix': SUFFIX, 'ad_free': False, 'docsearch_disabled': False, 'user_analytics_code': '', 'global_analytics_code': 'UA-17997319-2', 'commit': '64c6f8c6', } # For sphinx >=1.8 we can use html_baseurl to set the canonical URL. # https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_baseurl if version_info >= (1, 8): if not globals().get('html_baseurl'): html_baseurl = context['canonical_url'] context['canonical_url'] = None 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") readthedocs_vcs_url = 'None' readthedocs_build_url = 'https://readthedocs.com/projects/institute-for-disease-modeling-idm/builds/740952/' 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' # Make sure our build directory is always excluded exclude_patterns = globals().get('exclude_patterns', []) exclude_patterns.extend(['_build']) [rtd-command-info] start-time: 2021-10-07T23:16:29.869945Z, end-time: 2021-10-07T23:16:30.585949Z, duration: 0, exit-code: 0 python -m sphinx -T -W --keep-going -b html -d _build/doctrees -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 [html]: targets for 1 source files that are out of date updating environment: 1 added, 0 changed, 0 removed reading sources... [100%] index looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [100%] index generating indices... writing additional pages... search copying static files... done copying extra files... done dumping search index in English (code: en) ... done dumping object inventory... done build succeeded. The HTML pages are in _build/html. Updating searchtools for Read the Docs search...