Read the Docs build information Build id: 1131272 Project: beliveau-lab-tigerfish Version: latest Commit: 0e537e26e61585eb01b14314dff794003e1b2a15 Date: 2022-10-07T21:32:46.596537Z State: finished Success: True [rtd-command-info] start-time: 2022-10-07T21:33:34.350835Z, end-time: 2022-10-07T21:33:37.041363Z, duration: 2, exit-code: 0 git clone --no-single-branch --depth 50 git@github.com:beliveau-lab/TigerFISH.git . Cloning into '.'... Warning: Permanently added 'github.com,192.30.255.113' (ECDSA) to the list of known hosts. [rtd-command-info] start-time: 2022-10-07T21:33:37.305543Z, end-time: 2022-10-07T21:33:37.461425Z, 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 0e537e2 condensed envs to shared_conda_envs [rtd-command-info] start-time: 2022-10-07T21:33:37.671576Z, end-time: 2022-10-07T21:33:37.766366Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2022-10-07T21:33:38.887263Z, end-time: 2022-10-07T21:33:43.563976Z, duration: 4, exit-code: 0 python3.7 -mvirtualenv 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: 2022-10-07T21:33:43.784963Z, end-time: 2022-10-07T21:33:45.569232Z, 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 (22.2.2) Collecting setuptools<58.3.0 Downloading setuptools-58.2.0-py3-none-any.whl (946 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 946.1/946.1 kB 36.5 MB/s eta 0:00:00 Installing collected packages: setuptools Attempting uninstall: setuptools Found existing installation: setuptools 65.4.1 Uninstalling setuptools-65.4.1: Successfully uninstalled setuptools-65.4.1 Successfully installed setuptools-58.2.0 [rtd-command-info] start-time: 2022-10-07T21:33:45.755145Z, end-time: 2022-10-07T21:33:53.339491Z, 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<2.2 Collecting pillow Downloading Pillow-9.2.0-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.1/3.1 MB 53.0 MB/s eta 0:00:00 Collecting mock==1.0.1 Downloading mock-1.0.1.zip (861 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 861.9/861.9 kB 238.4 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-0.7.12-py2.py3-none-any.whl (14 kB) Collecting commonmark==0.9.1 Downloading commonmark-0.9.1-py2.py3-none-any.whl (51 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 51.1/51.1 kB 169.4 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-5.2.3-py3-none-any.whl (3.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.2/3.2 MB 172.7 MB/s eta 0:00:00 Collecting sphinx-rtd-theme Downloading sphinx_rtd_theme-1.0.0-py2.py3-none-any.whl (2.8 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.8/2.8 MB 190.5 MB/s eta 0:00:00 Collecting readthedocs-sphinx-ext<2.2 Downloading readthedocs_sphinx_ext-2.1.9-py2.py3-none-any.whl (11 kB) Collecting docutils>=0.11 Downloading docutils-0.19-py3-none-any.whl (570 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 570.5/570.5 kB 240.2 MB/s eta 0:00:00 Collecting imagesize>=1.3 Downloading imagesize-1.4.1-py2.py3-none-any.whl (8.8 kB) Collecting packaging>=21.0 Downloading packaging-21.3-py3-none-any.whl (40 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 40.8/40.8 kB 146.0 MB/s eta 0:00:00 Collecting sphinxcontrib-serializinghtml>=1.1.5 Downloading sphinxcontrib_serializinghtml-1.1.5-py2.py3-none-any.whl (94 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 94.0/94.0 kB 197.4 MB/s eta 0:00:00 Collecting importlib-metadata>=4.8 Downloading importlib_metadata-5.0.0-py3-none-any.whl (21 kB) Collecting sphinxcontrib-devhelp Downloading sphinxcontrib_devhelp-1.0.2-py2.py3-none-any.whl (84 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 84.7/84.7 kB 193.4 MB/s eta 0:00:00 Collecting babel>=2.9 Downloading Babel-2.10.3-py3-none-any.whl (9.5 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 9.5/9.5 MB 174.2 MB/s eta 0:00:00 Collecting sphinxcontrib-jsmath Downloading sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB) Collecting Pygments>=2.12 Downloading Pygments-2.13.0-py3-none-any.whl (1.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 242.4 MB/s eta 0:00:00 Collecting sphinxcontrib-applehelp Downloading sphinxcontrib_applehelp-1.0.2-py2.py3-none-any.whl (121 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 121.2/121.2 kB 210.5 MB/s eta 0:00:00 Collecting Jinja2>=3.0 Downloading Jinja2-3.1.2-py3-none-any.whl (133 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 133.1/133.1 kB 217.2 MB/s eta 0:00:00 Collecting sphinxcontrib-qthelp Downloading sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl (90 kB) 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typing-extensions>=3.6.4 Downloading typing_extensions-4.4.0-py3-none-any.whl (26 kB) Collecting MarkupSafe>=2.0 Downloading MarkupSafe-2.1.1-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (25 kB) Collecting pyparsing!=3.0.5,>=2.0.2 Downloading pyparsing-3.0.9-py3-none-any.whl (98 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 98.3/98.3 kB 184.7 MB/s eta 0:00:00 Collecting charset-normalizer<3,>=2 Downloading charset_normalizer-2.1.1-py3-none-any.whl (39 kB) Collecting certifi>=2017.4.17 Downloading certifi-2022.9.24-py3-none-any.whl (161 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 161.1/161.1 kB 218.8 MB/s eta 0:00:00 Collecting urllib3<1.27,>=1.21.1 Downloading urllib3-1.26.12-py2.py3-none-any.whl (140 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 140.4/140.4 kB 204.3 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 167.5 MB/s eta 0:00:00 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=23773 sha256=862f5829e24aa0adf4c59e3c533a796c18f01f67d0376c906ba136e577d60b90 Stored in directory: /tmp/pip-ephem-wheel-cache-n20hpjaw/wheels/7a/94/b1/0fdc5339a5bd487a5cc15421ec200d9ba3e2aa7190e4a727f1 Successfully built mock Installing collected packages: snowballstemmer, pytz, mock, commonmark, alabaster, zipp, urllib3, typing-extensions, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, pyparsing, Pygments, pillow, MarkupSafe, imagesize, idna, docutils, charset-normalizer, certifi, babel, requests, packaging, Jinja2, importlib-metadata, sphinx, readthedocs-sphinx-ext, sphinx-rtd-theme, recommonmark Successfully installed Jinja2-3.1.2 MarkupSafe-2.1.1 Pygments-2.13.0 alabaster-0.7.12 babel-2.10.3 certifi-2022.9.24 charset-normalizer-2.1.1 commonmark-0.9.1 docutils-0.17.1 idna-3.4 imagesize-1.4.1 importlib-metadata-5.0.0 mock-1.0.1 packaging-21.3 pillow-9.2.0 pyparsing-3.0.9 pytz-2022.4 readthedocs-sphinx-ext-2.1.9 recommonmark-0.5.0 requests-2.28.1 snowballstemmer-2.2.0 sphinx-5.2.3 sphinx-rtd-theme-1.0.0 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 sphinxcontrib-serializinghtml-1.1.5 typing-extensions-4.4.0 urllib3-1.26.12 zipp-3.8.1 [rtd-command-info] start-time: 2022-10-07T21:33:53.561267Z, end-time: 2022-10-07T21:34:01.371761Z, 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 74.5 MB/s eta 0:00:00 Collecting Pygments==2.11.2 Downloading Pygments-2.11.2-py3-none-any.whl (1.1 MB) 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sphinxcontrib_httpdomain-1.8.0-py2.py3-none-any.whl (19 kB) Collecting sphinx-prompt==1.4.0 Downloading sphinx_prompt-1.4.0-py3-none-any.whl (4.1 kB) Collecting sphinx-notfound-page==0.8 Downloading sphinx_notfound_page-0.8-py3-none-any.whl (15 kB) Collecting sphinx-autobuild==2021.3.14 Downloading sphinx_autobuild-2021.3.14-py3-none-any.whl (9.9 kB) Collecting rstcheck==3.3.1 Downloading rstcheck-3.3.1.tar.gz (13 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting myst_parser==0.16.1 Downloading myst_parser-0.16.1-py3-none-any.whl (48 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 48.8/48.8 kB 175.1 MB/s eta 0:00:00 Requirement already satisfied: alabaster<0.8,>=0.7 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)) (0.7.12) Requirement already satisfied: sphinxcontrib-serializinghtml>=1.1.5 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)) (1.1.5) Requirement already satisfied: importlib-metadata>=4.4 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)) (5.0.0) Requirement already satisfied: docutils<0.18,>=0.14 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)) (0.17.1) Requirement already satisfied: sphinxcontrib-qthelp 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)) (1.0.3) Requirement already satisfied: babel>=1.3 in 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sphinxemoji (setup.py): finished with status 'done' Created wheel for sphinxemoji: filename=sphinxemoji-0.2.0-py3-none-any.whl size=44427 sha256=978866d09100d976f5b5f62db0cbf49d49ce31591ae2a59df9b6b3241de3feaa Stored in directory: /tmp/pip-ephem-wheel-cache-0g9wardr/wheels/09/10/81/0438103576aeaea47d55fe341a8e89d7561afc4e414741bf87 Building wheel for rstcheck (setup.py): 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=13737 sha256=b065e4a0ade6e313f519107b4c8eefad7c9ea034f95f3afa2dcffec3eb09d4b4 Stored in directory: /tmp/pip-ephem-wheel-cache-0g9wardr/wheels/54/66/a1/0e58261ec13ca13b14d11834d840917318f6f96457a47b3145 Building wheel for livereload (setup.py): started Building wheel for livereload (setup.py): finished with status 'done' Created wheel for livereload: filename=livereload-2.6.3-py2.py3-none-any.whl size=24724 sha256=ebf2ec1bee72a7619cb94b87b0cc0deaae70071a5fa7f3c33ac56f196066567f Stored in directory: /tmp/pip-ephem-wheel-cache-0g9wardr/wheels/d4/f2/03/55f37093eb8cb0c89d7efb206f792dba55cd5bd67b1c5b1ce1 Successfully built sphinx-intl sphinxemoji rstcheck livereload 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-prompt, sphinx-intl, sphinx-autobuild, mdit-py-plugins, myst_parser Attempting uninstall: Pygments Found existing installation: Pygments 2.13.0 Uninstalling Pygments-2.13.0: Successfully uninstalled Pygments-2.13.0 Attempting uninstall: docutils Found existing installation: docutils 0.17.1 Uninstalling docutils-0.17.1: Successfully uninstalled docutils-0.17.1 Attempting uninstall: Sphinx Found existing installation: Sphinx 5.2.3 Uninstalling Sphinx-5.2.3: Successfully uninstalled Sphinx-5.2.3 Successfully installed Pygments-2.11.2 Sphinx-4.4.0 click-8.1.3 colorama-0.4.5 docutils-0.16 livereload-2.6.3 markdown-it-py-2.1.0 mdit-py-plugins-0.3.1 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 sphinxcontrib-httpdomain-1.8.0 sphinxemoji-0.2.0 tornado-6.2 [rtd-command-info] start-time: 2022-10-07T21:34:02.896868Z, end-time: 2022-10-07T21:34:02.976119Z, 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: 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", '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': '0e537e26', } # 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/1131272/' 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: 2022-10-07T21:34:03.168013Z, end-time: 2022-10-07T21:34:04.622357Z, duration: 1, exit-code: 0 python -m sphinx -T -E -b html -d _build/doctrees -D language=en . _build/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:13: 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/cli.rst:95: WARNING: Title underline too short. Named Arguments in `config.yml `_ for the Post-process workflow ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/cli.rst:95: WARNING: Title underline too short. Named Arguments in `config.yml `_ for the Post-process workflow ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/cli.rst:2: WARNING: Duplicate explicit target name: "config.yml". /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:57: WARNING: Duplicate explicit target name: "here". /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/index.rst:90: 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:256: WARNING: Title underline too short. `alignment_filter `_ ---------------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:256: WARNING: Title underline too short. `alignment_filter `_ ---------------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:291: WARNING: Title underline too short. `gather_repeat_regions (checkpoint) `_ --------------------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:291: WARNING: Title underline too short. `gather_repeat_regions (checkpoint) `_ --------------------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:315: WARNING: Title underline too short. `summary `_ ------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:315: WARNING: Title underline too short. `summary `_ ------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:339: WARNING: Title underline too short. `Post-process Workflow `_ ^^^^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:339: WARNING: Title underline too short. `Post-process Workflow `_ ^^^^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:369: WARNING: Title underline too short. `gather_repeat_regions `_ --------------------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:369: WARNING: Title underline too short. `gather_repeat_regions `_ --------------------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:395: 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. `align_probes `_ ------------ /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:422: WARNING: Title underline too short. `derived_beds `_ ------------ /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:422: WARNING: Title underline too short. `derived_beds `_ ------------ /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:446: 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:446: 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:478: 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:497: WARNING: Title underline too short. `get_alignments `_ -------------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:497: WARNING: Title underline too short. `get_alignments `_ -------------- /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:526: WARNING: Title underline too short. `generate_chromomap `_ ------------------ /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/snakemake_view.rst:526: WARNING: Title underline too short. `generate_chromomap `_ ------------------ /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: "config.yml". /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... [ 20%] imgs/tigerfish_main_overview.png copying images... [ 40%] imgs/tigerfish_postprocess_overview.png copying images... [ 60%] imgs/tigerfish_fish.jpg copying images... [ 80%] imgs/tiger.jpg copying images... [100%] imgs/tutorials_summary.png copying static files... done copying extra files... done dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 47 warnings. The HTML pages are in _build/html. Updating searchtools for Read the Docs search... ====================== slowest reading durations ======================= 0.104 snakemake_view 0.068 cli 0.058 parameters 0.028 index 0.024 tutorials