Read the Docs build information Build id: 2593681 Project: institute-for-disease-modeling-laser-cholera Version: latest Commit: 2a4c1339301afe5d3b0d1eb6e05aef6af9d043a2 Date: 2024-11-05T20:58:17.243623Z State: finished Success: True [rtd-command-info] start-time: 2024-11-05T20:58:19.566808Z, end-time: 2024-11-05T20:58:20.869622Z, duration: 1, exit-code: 0 git clone --depth 1 git@github.com:InstituteforDiseaseModeling/laser-cholera.git . Cloning into '.'... Warning: Permanently added 'github.com' (ED25519) to the list of known hosts. [rtd-command-info] start-time: 2024-11-05T20:58:20.960250Z, end-time: 2024-11-05T20:58:22.019043Z, duration: 1, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 refs/heads/main:refs/remotes/origin/main Warning: Permanently added 'github.com' (ED25519) to the list of known hosts. [rtd-command-info] start-time: 2024-11-05T20:58:22.183513Z, end-time: 2024-11-05T20:58:22.236375Z, duration: 0, exit-code: 0 git checkout --force origin/main Note: switching to '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 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 2a4c133 Update from Cookiecutter Template [rtd-command-info] start-time: 2024-11-05T20:58:22.336916Z, end-time: 2024-11-05T20:58:22.397712Z, duration: 0, exit-code: 0 cat .readthedocs.yml # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details version: 2 sphinx: configuration: docs/conf.py formats: all build: os: ubuntu-22.04 tools: python: "3" python: install: - requirements: docs/requirements.txt - method: pip path: . # Optionally build your docs in additional formats such as PDF and ePub # formats: # - pdf # - epub [rtd-command-info] start-time: 2024-11-05T20:58:29.507834Z, end-time: 2024-11-05T20:58:29.584807Z, duration: 0, exit-code: 0 asdf global python 3.12.3 [rtd-command-info] start-time: 2024-11-05T20:58:30.021953Z, end-time: 2024-11-05T20:58:31.152204Z, duration: 1, exit-code: 0 python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH created virtual environment CPython3.12.3.final.0-64 in 783ms creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-cholera/envs/latest, clear=False, no_vcs_ignore=False, global=False) seeder FromAppData(download=False, pip=bundle, setuptools=bundle, wheel=bundle, via=copy, app_data_dir=/home/docs/.local/share/virtualenv) added seed packages: pip==23.1, setuptools==67.6.1, wheel==0.40.0 activators BashActivator,CShellActivator,FishActivator,NushellActivator,PowerShellActivator,PythonActivator [rtd-command-info] start-time: 2024-11-05T20:58:31.247269Z, end-time: 2024-11-05T20:58:45.494615Z, duration: 14, 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-laser-cholera/envs/latest/lib/python3.12/site-packages (23.1) Collecting pip Downloading pip-24.3.1-py3-none-any.whl (1.8 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.8/1.8 MB 11.3 MB/s eta 0:00:00 Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-cholera/envs/latest/lib/python3.12/site-packages (67.6.1) Collecting setuptools Downloading setuptools-75.3.0-py3-none-any.whl (1.3 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.3/1.3 MB 25.5 MB/s eta 0:00:00 Installing collected packages: setuptools, pip Attempting uninstall: setuptools Found existing installation: setuptools 67.6.1 Uninstalling setuptools-67.6.1: Successfully uninstalled setuptools-67.6.1 Attempting uninstall: pip Found existing installation: pip 23.1 Uninstalling pip-23.1: Successfully uninstalled pip-23.1 Successfully installed pip-24.3.1 setuptools-75.3.0 [rtd-command-info] start-time: 2024-11-05T20:58:45.589966Z, end-time: 2024-11-05T20:58:55.697091Z, duration: 10, exit-code: 0 python -m pip install --upgrade --no-cache-dir 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Collecting charset-normalizer<4,>=2 (from requests>=2.30.0->sphinx) Downloading charset_normalizer-3.4.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (34 kB) Collecting idna<4,>=2.5 (from requests>=2.30.0->sphinx) Downloading idna-3.10-py3-none-any.whl.metadata (10 kB) Collecting urllib3<3,>=1.21.1 (from requests>=2.30.0->sphinx) Downloading urllib3-2.2.3-py3-none-any.whl.metadata (6.5 kB) Collecting certifi>=2017.4.17 (from requests>=2.30.0->sphinx) Downloading certifi-2024.8.30-py3-none-any.whl.metadata (2.2 kB) Downloading sphinx-8.1.3-py3-none-any.whl (3.5 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.5/3.5 MB 92.0 MB/s eta 0:00:00 Downloading alabaster-1.0.0-py3-none-any.whl (13 kB) Downloading babel-2.16.0-py3-none-any.whl (9.6 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 9.6/9.6 MB 169.4 MB/s eta 0:00:00 Downloading docutils-0.21.2-py3-none-any.whl (587 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 587.4/587.4 kB 309.7 MB/s eta 0:00:00 Downloading imagesize-1.4.1-py2.py3-none-any.whl (8.8 kB) Downloading jinja2-3.1.4-py3-none-any.whl (133 kB) Downloading packaging-24.1-py3-none-any.whl (53 kB) Downloading pygments-2.18.0-py3-none-any.whl (1.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 334.8 MB/s eta 0:00:00 Downloading requests-2.32.3-py3-none-any.whl (64 kB) Downloading snowballstemmer-2.2.0-py2.py3-none-any.whl (93 kB) Downloading sphinxcontrib_applehelp-2.0.0-py3-none-any.whl (119 kB) Downloading sphinxcontrib_devhelp-2.0.0-py3-none-any.whl (82 kB) Downloading sphinxcontrib_htmlhelp-2.1.0-py3-none-any.whl (98 kB) Downloading sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB) Downloading sphinxcontrib_qthelp-2.0.0-py3-none-any.whl (88 kB) Downloading sphinxcontrib_serializinghtml-2.0.0-py3-none-any.whl (92 kB) Downloading certifi-2024.8.30-py3-none-any.whl (167 kB) Downloading charset_normalizer-3.4.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (143 kB) Downloading idna-3.10-py3-none-any.whl (70 kB) Downloading MarkupSafe-3.0.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (23 kB) Downloading urllib3-2.2.3-py3-none-any.whl (126 kB) Installing collected packages: snowballstemmer, urllib3, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, Pygments, packaging, MarkupSafe, imagesize, idna, docutils, charset-normalizer, certifi, babel, alabaster, requests, Jinja2, sphinx Successfully installed Jinja2-3.1.4 MarkupSafe-3.0.2 Pygments-2.18.0 alabaster-1.0.0 babel-2.16.0 certifi-2024.8.30 charset-normalizer-3.4.0 docutils-0.21.2 idna-3.10 imagesize-1.4.1 packaging-24.1 requests-2.32.3 snowballstemmer-2.2.0 sphinx-8.1.3 sphinxcontrib-applehelp-2.0.0 sphinxcontrib-devhelp-2.0.0 sphinxcontrib-htmlhelp-2.1.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-2.0.0 sphinxcontrib-serializinghtml-2.0.0 urllib3-2.2.3 [rtd-command-info] start-time: 2024-11-05T20:58:55.801272Z, end-time: 2024-11-05T20:58:57.221902Z, duration: 1, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt Requirement already satisfied: sphinx>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-cholera/envs/latest/lib/python3.12/site-packages (from -r docs/requirements.txt (line 1)) (8.1.3) Collecting furo (from -r docs/requirements.txt (line 2)) Downloading furo-2024.8.6-py3-none-any.whl.metadata (5.9 kB) Requirement already satisfied: sphinxcontrib-applehelp>=1.0.7 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-cholera/envs/latest/lib/python3.12/site-packages (from sphinx>=1.3->-r docs/requirements.txt (line 1)) (2.0.0) Requirement already satisfied: sphinxcontrib-devhelp>=1.0.6 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-cholera/envs/latest/lib/python3.12/site-packages (from sphinx>=1.3->-r docs/requirements.txt (line 1)) (2.0.0) Requirement already satisfied: sphinxcontrib-htmlhelp>=2.0.6 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-cholera/envs/latest/lib/python3.12/site-packages (from sphinx>=1.3->-r docs/requirements.txt (line 1)) (2.1.0) Requirement already satisfied: sphinxcontrib-jsmath>=1.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-cholera/envs/latest/lib/python3.12/site-packages (from sphinx>=1.3->-r docs/requirements.txt (line 1)) (1.0.1) Requirement already satisfied: sphinxcontrib-qthelp>=1.0.6 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-cholera/envs/latest/lib/python3.12/site-packages (from sphinx>=1.3->-r docs/requirements.txt (line 1)) (2.0.0) Requirement already satisfied: sphinxcontrib-serializinghtml>=1.1.9 in 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/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-cholera/envs/latest/lib/python3.12/site-packages (from sphinx>=1.3->-r docs/requirements.txt (line 1)) (2.2.0) Requirement already satisfied: babel>=2.13 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-cholera/envs/latest/lib/python3.12/site-packages (from sphinx>=1.3->-r docs/requirements.txt (line 1)) (2.16.0) Requirement already satisfied: alabaster>=0.7.14 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-cholera/envs/latest/lib/python3.12/site-packages (from sphinx>=1.3->-r docs/requirements.txt (line 1)) (1.0.0) Requirement already satisfied: imagesize>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-cholera/envs/latest/lib/python3.12/site-packages (from sphinx>=1.3->-r docs/requirements.txt (line 1)) (1.4.1) Requirement already satisfied: requests>=2.30.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-cholera/envs/latest/lib/python3.12/site-packages (from sphinx>=1.3->-r docs/requirements.txt (line 1)) (2.32.3) Requirement already satisfied: packaging>=23.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-cholera/envs/latest/lib/python3.12/site-packages (from sphinx>=1.3->-r docs/requirements.txt (line 1)) (24.1) Collecting beautifulsoup4 (from furo->-r docs/requirements.txt (line 2)) Downloading beautifulsoup4-4.12.3-py3-none-any.whl.metadata (3.8 kB) Collecting sphinx-basic-ng>=1.0.0.beta2 (from furo->-r docs/requirements.txt (line 2)) Downloading sphinx_basic_ng-1.0.0b2-py3-none-any.whl.metadata (1.5 kB) Requirement already satisfied: MarkupSafe>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-cholera/envs/latest/lib/python3.12/site-packages (from Jinja2>=3.1->sphinx>=1.3->-r docs/requirements.txt (line 1)) (3.0.2) Requirement already satisfied: charset-normalizer<4,>=2 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-cholera/envs/latest/lib/python3.12/site-packages (from requests>=2.30.0->sphinx>=1.3->-r docs/requirements.txt (line 1)) (3.4.0) Requirement already satisfied: idna<4,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-cholera/envs/latest/lib/python3.12/site-packages (from requests>=2.30.0->sphinx>=1.3->-r docs/requirements.txt (line 1)) (3.10) Requirement already satisfied: urllib3<3,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-cholera/envs/latest/lib/python3.12/site-packages (from requests>=2.30.0->sphinx>=1.3->-r docs/requirements.txt (line 1)) (2.2.3) Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-cholera/envs/latest/lib/python3.12/site-packages (from requests>=2.30.0->sphinx>=1.3->-r docs/requirements.txt (line 1)) (2024.8.30) Collecting soupsieve>1.2 (from beautifulsoup4->furo->-r docs/requirements.txt (line 2)) Downloading soupsieve-2.6-py3-none-any.whl.metadata (4.6 kB) Downloading furo-2024.8.6-py3-none-any.whl (341 kB) Downloading sphinx_basic_ng-1.0.0b2-py3-none-any.whl (22 kB) Downloading beautifulsoup4-4.12.3-py3-none-any.whl (147 kB) Downloading soupsieve-2.6-py3-none-any.whl (36 kB) Installing collected packages: soupsieve, beautifulsoup4, sphinx-basic-ng, furo Successfully installed beautifulsoup4-4.12.3 furo-2024.8.6 soupsieve-2.6 sphinx-basic-ng-1.0.0b2 [rtd-command-info] start-time: 2024-11-05T20:58:57.319069Z, end-time: 2024-11-05T20:59:06.741386Z, duration: 9, exit-code: 0 python -m pip install --upgrade --upgrade-strategy only-if-needed --no-cache-dir . Processing /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-cholera/checkouts/latest Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'done' Preparing metadata (pyproject.toml): started Preparing metadata (pyproject.toml): finished with status 'done' Collecting click (from laser-cholera==0.0.1) Downloading click-8.1.7-py3-none-any.whl.metadata (3.0 kB) Downloading click-8.1.7-py3-none-any.whl (97 kB) Building wheels for collected packages: laser-cholera Building wheel for laser-cholera (pyproject.toml): started Building wheel for laser-cholera (pyproject.toml): finished with status 'done' Created wheel for laser-cholera: filename=laser_cholera-0.0.1-cp312-cp312-linux_x86_64.whl size=14306 sha256=271f849a0518b0681a9a5f57cd7fd746de72f62e231d349d667aaade516853f2 Stored in directory: /tmp/pip-ephem-wheel-cache-9f2r7m7y/wheels/e4/41/c4/e967a23ddfd8af9e99deb8dc754220f53ccbffc4fec8d1d152 Successfully built laser-cholera Installing collected packages: click, laser-cholera Successfully installed click-8.1.7 laser-cholera-0.0.1 [rtd-command-info] start-time: 2024-11-05T20:59:06.970152Z, end-time: 2024-11-05T20:59:07.035563Z, duration: 0, exit-code: 0 cat docs/conf.py extensions = [ "sphinx.ext.autodoc", "sphinx.ext.autosummary", "sphinx.ext.coverage", "sphinx.ext.doctest", "sphinx.ext.extlinks", "sphinx.ext.ifconfig", "sphinx.ext.napoleon", "sphinx.ext.todo", "sphinx.ext.viewcode", ] source_suffix = ".rst" master_doc = "index" project = "LASER Cholera" year = "2024" author = "Christopher Lorton" copyright = f"{year}, {author}" version = release = "0.0.1" pygments_style = "trac" templates_path = ["."] extlinks = { "issue": ("https://github.com/InstituteforDiseaseModeling/laser-cholera/issues/%s", "#%s"), "pr": ("https://github.com/InstituteforDiseaseModeling/laser-cholera/pull/%s", "PR #%s"), } html_theme = "furo" html_theme_options = { # "githuburl": "https://github.com/InstituteforDiseaseModeling/laser-cholera/", } html_use_smartypants = True html_last_updated_fmt = "%b %d, %Y" html_split_index = False html_short_title = f"{project}-{version}" napoleon_use_ivar = True napoleon_use_rtype = False napoleon_use_param = False [rtd-command-info] start-time: 2024-11-05T20:59:07.129160Z, end-time: 2024-11-05T20:59:08.387195Z, duration: 1, exit-code: 0 python -m sphinx -T -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html Running Sphinx v8.1.3 loading translations [en]... done making output directory... done Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`. [autosummary] generating autosummary for: authors.rst, changelog.rst, contributing.rst, index.rst, installation.rst, readme.rst, reference/index.rst, reference/laser_cholera.rst, usage.rst building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 9 source files that are out of date updating environment: [new config] 9 added, 0 changed, 0 removed reading sources... [ 11%] authors reading sources... [ 22%] changelog reading sources... [ 33%] contributing reading sources... [ 44%] index reading sources... [ 56%] installation reading sources... [ 67%] readme reading sources... [ 78%] reference/index reading sources... [ 89%] reference/laser_cholera reading sources... [100%] usage looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done copying assets... copying static files... 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[100%] usage generating indices... genindex py-modindex done highlighting module code... [100%] laser_cholera._core writing additional pages... search done dumping search index in English (code: en)... done dumping object inventory... done build succeeded. The HTML pages are in ../_readthedocs/html. [rtd-command-info] start-time: 2024-11-05T20:59:08.476652Z, end-time: 2024-11-05T20:59:09.511947Z, duration: 1, exit-code: 0 python -m sphinx -T -b singlehtml -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/htmlzip Running Sphinx v8.1.3 loading translations [en]... done making output directory... done Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`. loading pickled environment... The configuration has changed (1 option: 'pygments_dark_style') done [autosummary] generating autosummary for: authors.rst, changelog.rst, contributing.rst, index.rst, installation.rst, readme.rst, reference/index.rst, reference/laser_cholera.rst, usage.rst building [mo]: targets for 0 po files that are out of date writing output... building [singlehtml]: all documents updating environment: 0 added, 0 changed, 0 removed reading sources... looking for now-outdated files... none found preparing documents... done copying assets... copying static files... Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-cholera/checkouts/latest/_readthedocs/htmlzip/_static/basic.css Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-cholera/checkouts/latest/_readthedocs/htmlzip/_static/language_data.js Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-cholera/checkouts/latest/_readthedocs/htmlzip/_static/documentation_options.js copying static files: done copying extra files... copying extra files: done copying assets: done assembling single document... index readme installation usage reference/index reference/laser_cholera contributing authors changelog assembling single document: done writing... done writing additional files... done copying static files... Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-cholera/checkouts/latest/_readthedocs/htmlzip/_static/basic.css Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-cholera/checkouts/latest/_readthedocs/htmlzip/_static/language_data.js Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-cholera/checkouts/latest/_readthedocs/htmlzip/_static/documentation_options.js copying static files: done copying extra files... copying extra files: done dumping object inventory... done build succeeded. The HTML page is in ../_readthedocs/htmlzip. [rtd-command-info] start-time: 2024-11-05T20:59:09.882351Z, end-time: 2024-11-05T20:59:13.729697Z, duration: 3, exit-code: 0 python -m sphinx -T -b latex -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/pdf Running Sphinx v8.1.3 loading translations [en]... done making output directory... done Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`. loading pickled environment... The configuration has changed (1 option: 'pygments_dark_style') done [autosummary] generating autosummary for: authors.rst, changelog.rst, contributing.rst, index.rst, installation.rst, readme.rst, reference/index.rst, reference/laser_cholera.rst, usage.rst building [mo]: targets for 0 po files that are out of date writing output... building [latex]: all documents updating environment: 0 added, 0 changed, 0 removed reading sources... looking for now-outdated files... none found preparing documents... done copying assets... copying TeX support files... Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-cholera/checkouts/latest/_readthedocs/pdf/make.bat Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-cholera/checkouts/latest/_readthedocs/pdf/latexmkrc Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-cholera/checkouts/latest/_readthedocs/pdf/latexmkjarc Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-cholera/checkouts/latest/_readthedocs/pdf/Makefile done copying assets: done processing lasercholera.tex... index readme installation usage reference/index reference/laser_cholera contributing authors changelog resolving references... WARNING: Could not fetch remote image: https://github.com/InstituteforDiseaseModeling/laser-cholera/actions/workflows/github-actions.yml/badge.svg [404] WARNING: Could not fetch remote image: https://github.com/InstituteforDiseaseModeling/laser-cholera/actions/workflows/github-actions.yml/badge.svg [404] /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-cholera/checkouts/latest/README.rst:16: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] (https://readthedocs.org/projects/laser-cholera/badge/?style=flat) /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-cholera/checkouts/latest/README.rst:24: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] (https://codecov.io/gh/InstituteforDiseaseModeling/laser-cholera/branch/main/graphs/badge.svg?branch=main) /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-cholera/checkouts/latest/README.rst:28: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] (https://img.shields.io/pypi/v/laser-cholera.svg) /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-cholera/checkouts/latest/README.rst:32: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] (https://img.shields.io/pypi/wheel/laser-cholera.svg) /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-cholera/checkouts/latest/README.rst:36: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] (https://img.shields.io/pypi/pyversions/laser-cholera.svg) /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-cholera/checkouts/latest/README.rst:40: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] (https://img.shields.io/pypi/implementation/laser-cholera.svg) /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-cholera/checkouts/latest/README.rst:44: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] (https://img.shields.io/github/commits-since/InstituteforDiseaseModeling/laser-cholera/v0.0.1.svg) processing lasercholera.tex: done writing... done Writing evaluated template result to /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-cholera/checkouts/latest/_readthedocs/pdf/sphinxmessages.sty build succeeded, 9 warnings. The LaTeX files are in ../_readthedocs/pdf. Run 'make' in that directory to run these through (pdf)latex (use `make latexpdf' here to do that automatically). [rtd-command-info] start-time: 2024-11-05T20:59:13.826314Z, end-time: 2024-11-05T20:59:13.881805Z, duration: 0, exit-code: 0 cat latexmkrc $latex = 'latex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $pdflatex = 'pdflatex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $lualatex = 'lualatex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $xelatex = 'xelatex --no-pdf ' . $ENV{'LATEXOPTS'} . ' %O %S'; $makeindex = 'makeindex -s python.ist %O -o %D %S'; add_cus_dep( "glo", "gls", 0, "makeglo" ); sub makeglo { return system( "makeindex -s gglo.ist -o '$_[0].gls' '$_[0].glo'" ); } [rtd-command-info] start-time: 2024-11-05T20:59:13.974940Z, end-time: 2024-11-05T20:59:18.372895Z, duration: 4, exit-code: 0 latexmk -r latexmkrc -pdf -f -dvi- -ps- -jobname=institute-for-disease-modeling-laser-cholera -interaction=nonstopmode Use of uninitialized value in concatenation (.) or string at (eval 10) line 1. Use of uninitialized value in concatenation (.) or string at (eval 10) line 2. Use of uninitialized value in concatenation (.) or string at (eval 10) line 3. Use of uninitialized value in concatenation (.) or string at (eval 10) line 4. Subroutine makeglo redefined at (eval 11) line 7. Use of uninitialized value in concatenation (.) or string at (eval 11) line 1. Use of uninitialized value in concatenation (.) or string at (eval 11) line 2. 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LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.120 \end{tabulary} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.120 \end{tabulary} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.120 \end{tabulary} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.120 \end{tabulary} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.120 \end{tabulary} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.120 \end{tabulary} ! LaTeX Error: Unknown graphics extension: .svg. 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See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.120 \end{tabulary} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.120 \end{tabulary} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.120 \end{tabulary} ! LaTeX Error: Unknown graphics extension: .svg. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.120 \end{tabulary} (/usr/share/texmf/tex/latex/tex-gyre/ts1qtm.fd) (/usr/share/texlive/texmf-dist/tex/latex/txfonts/t1txtt.fd) Underfull \hbox (badness 10000) in paragraph at lines 173--175 []|\T1/qhv/m/n/10 Win- [1] [2] Chapter 2. [3] [4] Chapter 3. [5] [6] Chapter 4. [7] [8] Chapter 5. [9] [10] Chapter 6. [11] [12] Chapter 7. [13] [14] Chapter 8. [15] [16] LaTeX Warning: Reference `reference/laser_cholera:module-laser_cholera' on page 17 undefined on input line 451. [17] No file institute-for-disease-modeling-laser-cholera.ind. (./institute-for-disease-modeling-laser-cholera.aux) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. Package rerunfilecheck Warning: File `institute-for-disease-modeling-laser-chol era.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information){/usr/share/texmf/fonts/enc /dvips/tex-gyre/q-ec.enc}{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ts1.enc}< /usr/share/texmf/fonts/type1/public/tex-gyre/qhvb.pfb> Output written on institute-for-disease-modeling-laser-cholera.pdf (21 pages, 1 57229 bytes). Transcript written on institute-for-disease-modeling-laser-cholera.log. Latexmk: Index file 'institute-for-disease-modeling-laser-cholera.idx' was written Latexmk: Missing input file 'institute-for-disease-modeling-laser-cholera.ind' (or dependence on it) from following: 'No file institute-for-disease-modeling-laser-cholera.ind.' Latexmk: References changed. Latexmk: References changed. Latexmk: Log file says output to 'institute-for-disease-modeling-laser-cholera.pdf' Latexmk: Log file says output to 'institute-for-disease-modeling-laser-cholera.pdf' Latexmk: List of undefined refs and citations: Reference `reference/laser_cholera:module-laser_cholera' on page 17 undefined on input line 451 Rule 'makeindex institute-for-disease-modeling-laser-cholera.idx': File changes, etc: Changed files, or newly in use since previous run(s): 'institute-for-disease-modeling-laser-cholera.idx' ------------ Run number 1 of rule 'makeindex institute-for-disease-modeling-laser-cholera.idx' ------------ ------------ Running 'makeindex -s python.ist -o "institute-for-disease-modeling-laser-cholera.ind" "institute-for-disease-modeling-laser-cholera.idx"' ------------ Latexmk: Examining 'institute-for-disease-modeling-laser-cholera.log' === TeX engine is 'pdfTeX' Latexmk: applying rule 'makeindex institute-for-disease-modeling-laser-cholera.idx'... This is makeindex, version 2.15 [TeX Live 2022/dev] (kpathsea + Thai support). Scanning style file ./python.ist.......done (7 attributes redefined, 0 ignored). Scanning input file institute-for-disease-modeling-laser-cholera.idx....done (3 entries accepted, 0 rejected). Sorting entries....done (4 comparisons). Generating output file institute-for-disease-modeling-laser-cholera.ind....done (20 lines written, 0 warnings). Output written in institute-for-disease-modeling-laser-cholera.ind. Transcript written in institute-for-disease-modeling-laser-cholera.ilg. Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'institute-for-disease-modeling-laser-cholera.aux' 'institute-for-disease-modeling-laser-cholera.ind' 'institute-for-disease-modeling-laser-cholera.out' ------------ Run number 2 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="institute-for-disease-modeling-laser-cholera" "lasercholera.tex"' ------------ Latexmk: applying rule 'pdflatex'... 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[15] [16] [17] (./institute-for-disease-modeling-laser-cholera.ind [18] [19]) (./institute-for-disease-modeling-laser-cholera.aux) Package rerunfilecheck Warning: File `institute-for-disease-modeling-laser-chol era.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information){/usr/share/texmf/fonts/enc /dvips/tex-gyre/q-ec.enc}{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ts1.enc}< /usr/share/texmf/fonts/type1/public/tex-gyre/qhvb.pfb> Output written on institute-for-disease-modeling-laser-cholera.pdf (23 pages, 1 71080 bytes). Transcript written on institute-for-disease-modeling-laser-cholera.log. Latexmk: Index file 'institute-for-disease-modeling-laser-cholera.idx' was written Latexmk: References changed. 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[15] [16] [17] (./institute-for-disease-modeling-laser-cholera.ind [18] [19]) (./institute-for-disease-modeling-laser-cholera.aux) ) (see the transcript file for additional information){/usr/share/texmf/fonts/enc /dvips/tex-gyre/q-ec.enc}{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ts1.enc}< /usr/share/texmf/fonts/type1/public/tex-gyre/qhvb.pfb> Output written on institute-for-disease-modeling-laser-cholera.pdf (23 pages, 1 71114 bytes). Transcript written on institute-for-disease-modeling-laser-cholera.log. Latexmk: Index file 'institute-for-disease-modeling-laser-cholera.idx' was written Latexmk: Log file says output to 'institute-for-disease-modeling-laser-cholera.pdf' Latexmk: Log file says output to 'institute-for-disease-modeling-laser-cholera.pdf' Collected error summary (may duplicate other messages): pdflatex: Command for 'pdflatex' gave return code 1 Refer to 'institute-for-disease-modeling-laser-cholera.log' for details Latexmk: Examining 'institute-for-disease-modeling-laser-cholera.log' === TeX engine is 'pdfTeX' Latexmk: Errors, in force_mode: so I tried finishing targets [rtd-command-info] start-time: 2024-11-05T20:59:18.807937Z, end-time: 2024-11-05T20:59:22.175755Z, duration: 3, exit-code: 0 python -m sphinx -T -b epub -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/epub Running Sphinx v8.1.3 loading translations [en]... done making output directory... done Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`. loading pickled environment... 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