Read the Docs build information Build id: 1317292 Project: beliveau-lab-tigerfish Version: latest Commit: 1415f150bc90b149ec8b5cd6b9daa0ce0cf4294f Date: 2023-02-24T22:09:42.159676Z State: finished Success: True [rtd-command-info] start-time: 2023-02-24T22:09:43.959057Z, end-time: 2023-02-24T22:09:51.600644Z, duration: 7, exit-code: 0 git clone --no-single-branch --depth 50 git@github.com:beliveau-lab/TigerFISH.git . Cloning into '.'... Warning: Permanently added 'github.com,192.30.255.112' (ECDSA) to the list of known hosts. [rtd-command-info] start-time: 2023-02-24T22:09:51.829631Z, end-time: 2023-02-24T22:09:52.480315Z, duration: 0, exit-code: 0 git checkout --force origin/master Note: switching to '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 switching back to a branch. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -c with the switch command. Example: git switch -c Or undo this operation with: git switch - Turn off this advice by setting config variable advice.detachedHead to false HEAD is now at 1415f15 Update README.md [rtd-command-info] start-time: 2023-02-24T22:09:52.667632Z, end-time: 2023-02-24T22:09:52.755757Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2023-02-24T22:09:54.000372Z, end-time: 2023-02-24T22:09:58.591828Z, duration: 4, exit-code: 0 python3.7 -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH Using base prefix '/home/docs/.pyenv/versions/3.7.9' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/bin/python3.7 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2023-02-24T22:09:58.796804Z, end-time: 2023-02-24T22:10:00.571439Z, duration: 1, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip setuptools<58.3.0 Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (23.0.1) Collecting setuptools<58.3.0 Downloading setuptools-58.2.0-py3-none-any.whl (946 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 946.1/946.1 kB 28.2 MB/s eta 0:00:00 Installing collected packages: setuptools Attempting uninstall: setuptools Found existing installation: setuptools 67.4.0 Uninstalling setuptools-67.4.0: Successfully uninstalled setuptools-67.4.0 Successfully installed setuptools-58.2.0 [rtd-command-info] start-time: 2023-02-24T22:10:00.759859Z, end-time: 2023-02-24T22:10:08.149234Z, duration: 7, exit-code: 0 python -m pip install --upgrade --no-cache-dir pillow mock==1.0.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.9.1 recommonmark==0.5.0 sphinx sphinx-rtd-theme readthedocs-sphinx-ext<2.3 Collecting pillow Downloading Pillow-9.4.0-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.3 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.3/3.3 MB 54.7 MB/s eta 0:00:00 Collecting mock==1.0.1 Downloading mock-1.0.1.zip (861 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 861.9/861.9 kB 230.5 MB/s eta 0:00:00 Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting alabaster!=0.7.5,<0.8,>=0.7 Downloading alabaster-0.7.13-py3-none-any.whl (13 kB) Collecting commonmark==0.9.1 Downloading commonmark-0.9.1-py2.py3-none-any.whl (51 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 51.1/51.1 kB 171.4 MB/s eta 0:00:00 Collecting recommonmark==0.5.0 Downloading recommonmark-0.5.0-py2.py3-none-any.whl (9.8 kB) Collecting sphinx Downloading sphinx-5.3.0-py3-none-any.whl (3.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.2/3.2 MB 141.0 MB/s eta 0:00:00 Collecting 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sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB) Collecting imagesize>=1.3 Downloading imagesize-1.4.1-py2.py3-none-any.whl (8.8 kB) Collecting snowballstemmer>=2.0 Downloading snowballstemmer-2.2.0-py2.py3-none-any.whl (93 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 93.0/93.0 kB 197.2 MB/s eta 0:00:00 Collecting importlib-metadata>=4.8 Downloading importlib_metadata-6.0.0-py3-none-any.whl (21 kB) Collecting sphinxcontrib-qthelp Downloading sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl (90 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 90.6/90.6 kB 213.0 MB/s eta 0:00:00 Collecting sphinxcontrib-jquery!=3.0.0,>=2.0.0 Downloading sphinxcontrib_jquery-2.0.0-py3-none-any.whl (3.2 kB) Collecting docutils>=0.11 Downloading docutils-0.18.1-py2.py3-none-any.whl (570 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 570.0/570.0 kB 245.7 MB/s eta 0:00:00 Collecting pytz>=2015.7 Downloading pytz-2022.7.1-py2.py3-none-any.whl (499 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 499.4/499.4 kB 241.1 MB/s eta 0:00:00 Collecting zipp>=0.5 Downloading zipp-3.14.0-py3-none-any.whl (6.7 kB) Collecting typing-extensions>=3.6.4 Downloading typing_extensions-4.5.0-py3-none-any.whl (27 kB) Collecting MarkupSafe>=2.0 Downloading MarkupSafe-2.1.2-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (25 kB) Collecting urllib3<1.27,>=1.21.1 Downloading urllib3-1.26.14-py2.py3-none-any.whl (140 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 140.6/140.6 kB 224.6 MB/s eta 0:00:00 Collecting idna<4,>=2.5 Downloading idna-3.4-py3-none-any.whl (61 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 61.5/61.5 kB 179.7 MB/s eta 0:00:00 Collecting charset-normalizer<4,>=2 Downloading charset_normalizer-3.0.1-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (170 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 170.5/170.5 kB 229.2 MB/s eta 0:00:00 Collecting certifi>=2017.4.17 Downloading certifi-2022.12.7-py3-none-any.whl (155 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 155.3/155.3 kB 223.2 MB/s eta 0:00:00 Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (from sphinxcontrib-jquery!=3.0.0,>=2.0.0->sphinx-rtd-theme) (58.2.0) Building wheels for collected packages: mock 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=eb4c2e1c577a42409b419a499ca62b4b06f259493d0c4fd8c9d0e42afad2794c Stored in directory: /tmp/pip-ephem-wheel-cache-yoh7ng7o/wheels/7a/94/b1/0fdc5339a5bd487a5cc15421ec200d9ba3e2aa7190e4a727f1 Successfully built mock Installing collected packages: snowballstemmer, pytz, mock, commonmark, charset-normalizer, zipp, urllib3, typing-extensions, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-jquery, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, Pygments, pillow, packaging, MarkupSafe, imagesize, idna, docutils, certifi, babel, alabaster, requests, Jinja2, importlib-metadata, sphinx, readthedocs-sphinx-ext, sphinx-rtd-theme, recommonmark Successfully installed Jinja2-3.1.2 MarkupSafe-2.1.2 Pygments-2.14.0 alabaster-0.7.13 babel-2.11.0 certifi-2022.12.7 charset-normalizer-3.0.1 commonmark-0.9.1 docutils-0.18.1 idna-3.4 imagesize-1.4.1 importlib-metadata-6.0.0 mock-1.0.1 packaging-23.0 pillow-9.4.0 pytz-2022.7.1 readthedocs-sphinx-ext-2.2.0 recommonmark-0.5.0 requests-2.28.2 snowballstemmer-2.2.0 sphinx-5.3.0 sphinx-rtd-theme-1.2.0 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.0 sphinxcontrib-jquery-2.0.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 sphinxcontrib-serializinghtml-1.1.5 typing-extensions-4.5.0 urllib3-1.26.14 zipp-3.14.0 [rtd-command-info] start-time: 2023-02-24T22:10:08.391614Z, end-time: 2023-02-24T22:10:15.666359Z, duration: 7, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt Collecting Sphinx==4.4.0 Downloading Sphinx-4.4.0-py3-none-any.whl (3.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.1/3.1 MB 58.9 MB/s eta 0:00:00 Collecting Pygments==2.11.2 Downloading Pygments-2.11.2-py3-none-any.whl (1.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 251.3 MB/s eta 0:00:00 Collecting sphinx_rtd_theme==1.0.0 Downloading sphinx_rtd_theme-1.0.0-py2.py3-none-any.whl (2.8 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.8/2.8 MB 228.1 MB/s eta 0:00:00 Collecting sphinx-tabs==3.2.0 Downloading sphinx_tabs-3.2.0-py3-none-any.whl (9.8 kB) Collecting sphinx-intl==2.0.1 Downloading sphinx-intl-2.0.1.tar.gz (17 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting readthedocs-sphinx-search==0.1.1 Downloading readthedocs_sphinx_search-0.1.1-py3-none-any.whl (18 kB) Collecting sphinxemoji==0.2.0 Downloading sphinxemoji-0.2.0.tar.gz (44 kB) 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/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (from Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (1.0.3) Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (from Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (3.1.2) Requirement already satisfied: requests>=2.5.0 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (from Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (2.28.2) Requirement already satisfied: sphinxcontrib-applehelp in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (from Sphinx==4.4.0->-r docs/requirements.txt (line 3)) (1.0.2) Requirement already satisfied: sphinxcontrib-serializinghtml>=1.1.5 in 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started Building wheel for rstcheck (setup.py): finished with status 'done' Created wheel for rstcheck: filename=rstcheck-3.3.1-py3-none-any.whl size=13738 sha256=5d4d7eba8080ad6d45718c2c8d1dfc0c56645bde2f62cca281986db35c6c5227 Stored in directory: /tmp/pip-ephem-wheel-cache-f6h4rnbo/wheels/54/66/a1/0e58261ec13ca13b14d11834d840917318f6f96457a47b3145 Successfully built sphinx-intl sphinxemoji rstcheck Installing collected packages: sphinx-notfound-page, tornado, six, readthedocs-sphinx-search, pyyaml, Pygments, mdurl, docutils, colorama, Sphinx, rstcheck, markdown-it-py, livereload, click, sphinxemoji, sphinxcontrib-httpdomain, sphinx-tabs, sphinx_rtd_theme, sphinx-prompt, sphinx-intl, sphinx-autobuild, mdit-py-plugins, myst_parser Attempting uninstall: Pygments Found existing installation: Pygments 2.14.0 Uninstalling Pygments-2.14.0: Successfully uninstalled Pygments-2.14.0 Attempting uninstall: docutils Found existing installation: docutils 0.18.1 Uninstalling docutils-0.18.1: Successfully uninstalled docutils-0.18.1 Attempting uninstall: Sphinx Found existing installation: Sphinx 5.3.0 Uninstalling Sphinx-5.3.0: Successfully uninstalled Sphinx-5.3.0 Attempting uninstall: sphinx_rtd_theme Found existing installation: sphinx-rtd-theme 1.2.0 Uninstalling sphinx-rtd-theme-1.2.0: Successfully uninstalled sphinx-rtd-theme-1.2.0 Successfully installed Pygments-2.11.2 Sphinx-4.4.0 click-8.1.3 colorama-0.4.6 docutils-0.16 livereload-2.6.3 markdown-it-py-2.2.0 mdit-py-plugins-0.3.4 mdurl-0.1.2 myst_parser-0.16.1 pyyaml-6.0 readthedocs-sphinx-search-0.1.1 rstcheck-3.3.1 six-1.16.0 sphinx-autobuild-2021.3.14 sphinx-intl-2.0.1 sphinx-notfound-page-0.8 sphinx-prompt-1.4.0 sphinx-tabs-3.2.0 sphinx_rtd_theme-1.0.0 sphinxcontrib-httpdomain-1.8.0 sphinxemoji-0.2.0 tornado-6.2 [rtd-command-info] start-time: 2023-02-24T22:10:17.032720Z, end-time: 2023-02-24T22:10:17.094657Z, duration: 0, exit-code: 0 cat docs/source/conf.py # Configuration file for the Sphinx documentation builder. # # This file only contains a selection of the most common options. For a full # list see the documentation: # https://www.sphinx-doc.org/en/master/usage/configuration.html # -- Path setup -------------------------------------------------------------- # If extensions (or modules to document with autodoc) are in another directory, # add these directories to sys.path here. If the directory is relative to the # documentation root, use os.path.abspath to make it absolute, like shown here. # import os import sys import subprocess from configparser import RawConfigParser import sphinx_rtd_theme sys.path.insert(0, os.path.abspath(os.path.join("..", ".."))) #sys.path.insert(0, os.path.abspath('..')) #sys.path.append(os.path.dirname(__file__)) #try: # import numpydoc #except ModuleNotFoundError: # subprocess.run(["pip", "install", "numpydoc"], check=True) # -- Project information ----------------------------------------------------- project = 'Tigerfish' copyright = '2022, Robin Aguilar' author = 'Robin Aguilar' # The full version, including alpha/beta/rc tags release = '2022' # -- General configuration --------------------------------------------------- #def get_version(): # """Return package version from setup.cfg.""" # config = RawConfigParser() # config.read(os.path.join('.', 'setup.cfg')) # return config.get('metadata', 'version') # Add any Sphinx extension module names here, as strings. They can be # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. extensions = [ 'sphinx.ext.duration', 'sphinx.ext.doctest', 'sphinx.ext.autodoc', 'sphinx_tabs.tabs', 'sphinx-prompt', 'sphinx_search.extension', 'sphinx.ext.autosummary', 'sphinx.ext.intersphinx', 'sphinxemoji.sphinxemoji' ] nbsphinx_execute = "never" #autosummary_generate = True #autodoc_default_options = { # "members": True, # "inherited-members": True, # "member-order": "bysource", #} #numpydoc_show_class_members = True #numpydoc_show_inherited_class_members = True #numpydoc_attributes_as_param_list = True #intersphinx_mapping = { # "pandas": ("https://pandas.pydata.org/docs", None), # "sklearn": ("https://scikit-learn.org/stable", None), # "numpy": ("https://numpy.org/doc/stable", None), # "matplotlib": ("https://matplotlib.org", None), #} # Add any paths that contain templates here, relative to this directory. templates_path = ['_templates'] # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. # This pattern also affects html_static_path and html_extra_path. exclude_patterns = ["build", "Thumbs.db", ".DS_Store", "**.ipynb_checkpoints"] # -- Options for HTML output ------------------------------------------------- # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. # html_theme = 'sphinx_rtd_theme' html_static_path = ["_static"] master_doc = "index" source_suffix = [".rst", ".md"] html_theme_options = { "style_nav_header_background": "#343131", "logo_only": True, } html_css_files = [ "custom.css", ] # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". html_logo = "_static/tigerfish.png" ########################################################################### # 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/main/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: html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} # This following legacy behavior will gradually be sliced out until its deprecated and removed. # Skipped for Sphinx 6+ # Skipped by internal Feature flag SKIP_SPHINX_HTML_THEME_PATH # Skipped by all new projects since SKIP_SPHINX_HTML_THEME_PATH's introduction (jan 2023) if ( using_rtd_theme and version_info < (6,0) and not False ): theme = importlib.import_module('sphinx_rtd_theme') if 'html_theme_path' in globals(): html_theme_path.append(theme.get_html_theme_path()) else: html_theme_path = [theme.get_html_theme_path()] # Define websupport2_base_url and websupport2_static_url 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", 'proxied_static_path': "/_/static/", 'versions': [ ], 'downloads': [ ], 'subprojects': [ ], 'slug': 'beliveau-lab-tigerfish', 'name': u'TigerFISH', 'rtd_language': u'en', 'programming_language': u'py', 'canonical_url': 'https://beliveau-lab-tigerfish.readthedocs-hosted.com/en/latest/', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/docs/source/', 'api_host': 'https://readthedocs.com', 'github_user': 'beliveau-lab', 'proxied_api_host': '/_', 'github_repo': 'TigerFISH', '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, 'docsearch_disabled': False, 'user_analytics_code': '', 'global_analytics_code': 'UA-17997319-2', 'commit': '1415f150', } # 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/beliveau-lab-tigerfish/builds/1317292/' 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: 2023-02-24T22:10:17.281847Z, end-time: 2023-02-24T22:10:18.898284Z, duration: 1, exit-code: 0 python -m sphinx -T -E -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html Running Sphinx v4.4.0 loading translations [en]... done making output directory... done [autosummary] generating autosummary for: cli.rst, faq.rst, index.rst, parameters.rst, snakemake_view.rst, tutorials.rst building [mo]: targets for 0 po files that are out of date building [html]: targets for 6 source files that are out of date updating environment: [new config] 6 added, 0 changed, 0 removed reading sources... [ 16%] cli reading sources... [ 33%] faq reading sources... [ 50%] index reading sources... [ 66%] parameters reading sources... [ 83%] snakemake_view reading sources... [100%] tutorials /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/cli.rst:17: WARNING: Title underline too short. Named Arguments in `config.yml `_ for main workflow ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/faq.rst:40: WARNING: Title underline too short. How do I do with Tigerfish? --------------------------------------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/faq.rst:40: WARNING: Title underline too short. How do I do with Tigerfish? --------------------------------------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/index.rst:68: WARNING: toctree contains reference to nonexisting document 'vignettes/index' /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:5: WARNING: Title underline too short. `Main workflow `_ ^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:35: WARNING: Title underline too short. generate_bt2_indices ------------------ /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:35: WARNING: Title underline too short. generate_bt2_indices ------------------ /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:58: WARNING: Title underline too short. `generate_jf_idx `_ ----------------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:58: WARNING: Title underline too short. `generate_jf_idx `_ ----------------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:88: WARNING: Title underline too short. `split_bed `_ --------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:88: WARNING: Title underline too short. `split_bed `_ --------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:112: WARNING: Title underline too short. `repeat_ID `_ --------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:112: WARNING: Title underline too short. `repeat_ID `_ --------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:143: WARNING: Title underline too short. `design_probes `_ ------------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:143: WARNING: Title underline too short. `design_probes `_ ------------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:175: WARNING: Title underline too short. `kmer_filter `_ ----------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:175: WARNING: Title underline too short. `kmer_filter `_ ----------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:203: WARNING: Title underline too short. `probe_mer_filter `_ ---------------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:203: WARNING: Title underline too short. `probe_mer_filter `_ ---------------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:259: WARNING: Title underline too short. `make_chrom_dir (checkpoint) `_ --------------------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:259: WARNING: Title underline too short. `make_chrom_dir (checkpoint) `_ --------------------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:283: WARNING: Title underline too short. `alignment_filter `_ ---------------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:283: WARNING: Title underline too short. `alignment_filter `_ ---------------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:344: WARNING: Title underline too short. `split_rm_alignments `_ ------------------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:344: WARNING: Title underline too short. `split_rm_alignments `_ ------------------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:367: WARNING: Title underline too short. `align_probes `_ ------------ /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:367: WARNING: Title underline too short. `align_probes `_ ------------ /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:395: WARNING: Title underline too short. `derived_beds `_ ------------ /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:395: WARNING: Title underline too short. `derived_beds `_ ------------ /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:419: WARNING: Title underline too short. `get_region_bed `_ -------------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:419: WARNING: Title underline too short. `get_region_bed `_ -------------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:451: ERROR: Error in "code-block" directive: maximum 1 argument(s) allowed, 22 supplied. .. code-block:: bash "bedtools intersect -wa -wb -a {input.derived_bed} -b {input.genome_bin} > {output.alignments_out} |" "bedtools intersect -wa -wb -a {input.repeat_bed} -b {input.genome_bin} > {output.repeat_out}" /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:470: WARNING: Title underline too short. `get_alignments `_ -------------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:470: WARNING: Title underline too short. `get_alignments `_ -------------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:501: WARNING: Title underline too short. `generate_chromomap `_ ------------------ /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:501: WARNING: Title underline too short. `generate_chromomap `_ ------------------ /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:518: WARNING: Title underline too short. `map_region_coords `_ -------------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:518: WARNING: Title underline too short. `map_region_coords `_ -------------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:569: WARNING: Title underline too short. `summary `_ ------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:569: WARNING: Title underline too short. `summary `_ ------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/tutorials.rst:3: WARNING: Duplicate explicit target name: "here". /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/tutorials.rst:3: WARNING: Duplicate explicit target name: "here". /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/tutorials.rst:3: WARNING: Duplicate explicit target name: "here". /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/tutorials.rst:3: WARNING: Duplicate explicit target name: "here". /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/tutorials.rst:3: WARNING: Duplicate explicit target name: "here". /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/tutorials.rst:3: WARNING: Duplicate explicit target name: "here". /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/tutorials.rst:3: WARNING: Duplicate explicit target name: "this directory". /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/tutorials.rst:3: WARNING: Duplicate explicit target name: "this directory". /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/tutorials.rst:3: WARNING: Duplicate explicit target name: "here". /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/tutorials.rst:502: WARNING: Title underline too short. Probe Analysis Mode on a Test Genome ---------------------------------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/tutorials.rst:502: WARNING: Title underline too short. Probe Analysis Mode on a Test Genome ---------------------------------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/tutorials.rst:3: WARNING: Duplicate explicit target name: "here". looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [ 16%] cli writing output... [ 33%] faq writing output... [ 50%] index writing output... [ 66%] parameters writing output... [ 83%] snakemake_view writing output... [100%] tutorials generating indices... genindex done writing additional pages... search done copying images... [ 5%] imgs/tigerfish_fish.jpg copying images... [ 11%] imgs/tiger.jpg copying images... [ 16%] imgs/DAG.pdf copying images... [ 22%] imgs/repeat_disc_fasta.png copying images... [ 27%] imgs/chrom_sizes_repeat_disc.png copying images... [ 33%] imgs/bt2_repeat_disc.png copying images... [ 38%] imgs/run_pipeline_repeat_disc.png copying images... [ 44%] imgs/check_repeat_disc.png copying images... [ 50%] imgs/step_2_repeat_disc.png copying images... [ 55%] imgs/step_4_repeat_disc.png copying images... [ 61%] imgs/step_5_repeat_disc.png copying images... [ 66%] imgs/step_6_repeat_disc.png copying images... [ 72%] imgs/step_7_repeat_disc.png copying images... [ 77%] imgs/step_1_probe_design.png copying images... [ 83%] imgs/step_2_probe_design.png copying images... [ 88%] imgs/step_3_probe_design.png copying images... [ 94%] imgs/step_4_probe_design.png copying images... [100%] imgs/chm13_probe_design_dir.png copying static files... done copying extra files... done dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 52 warnings. The HTML pages are in ../../_readthedocs/html. Updating searchtools for Read the Docs search... ====================== slowest reading durations ======================= 0.144 tutorials 0.112 snakemake_view 0.082 cli 0.053 index 0.039 parameters