Read the Docs build information Build id: 2634728 Project: institute-for-disease-modeling-laser-cholera Version: latest Commit: fbb96cf6735831744f36c1f6ca420a4b76013f4c Date: 2024-11-22T01:17:22.050008Z State: finished Success: True [rtd-command-info] start-time: 2024-11-22T01:17:23.338295Z, end-time: 2024-11-22T01:17:24.380275Z, 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: 2024-11-22T01:17:24.473145Z, end-time: 2024-11-22T01:17:26.772146Z, duration: 2, 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. Warning: Permanently added 'github.com' (ED25519) to the list of known hosts. From github.com:InstituteforDiseaseModeling/laser-cholera * [new tag] v0.0.0 -> v0.0.0 [rtd-command-info] start-time: 2024-11-22T01:17:26.911247Z, end-time: 2024-11-22T01:17:26.965283Z, 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 fbb96cf custom devcontainer Avoid default with NumPy 2.x [rtd-command-info] start-time: 2024-11-22T01:17:27.046182Z, end-time: 2024-11-22T01:17:27.101948Z, 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: "3.9" 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: 2024-11-22T01:17:33.018344Z, end-time: 2024-11-22T01:17:33.105098Z, duration: 0, exit-code: 0 asdf global python 3.9.20 [rtd-command-info] start-time: 2024-11-22T01:17:33.529139Z, end-time: 2024-11-22T01:17:34.768698Z, duration: 1, exit-code: 0 python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH created virtual environment CPython3.9.20.final.0-64 in 884ms 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: 2024-11-22T01:17:34.838887Z, end-time: 2024-11-22T01:17:50.741612Z, duration: 15, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip setuptools Looking in indexes: https://pypi.org/simple, https://packages.idmod.org/api/pypi/pypi-production/simple Requirement already satisfied: pip in 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sphinxcontrib-serializinghtml-2.0.0 tomli-2.1.0 urllib3-2.2.3 zipp-3.21.0 [rtd-command-info] start-time: 2024-11-22T01:18:04.055950Z, end-time: 2024-11-22T01:18:06.093928Z, duration: 2, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt Looking in indexes: https://pypi.org/simple, https://packages.idmod.org/api/pypi/pypi-production/simple Requirement already satisfied: sphinx>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-cholera/envs/latest/lib/python3.9/site-packages (from -r docs/requirements.txt (line 1)) (7.4.7) Collecting furo (from -r docs/requirements.txt (line 2)) Downloading https://packages.idmod.org/api/pypi/pypi-production/packages/packages/27/48/e791a7ed487dbb9729ef32bb5d1af16693d8925f4366befef54119b2e576/furo-2024.8.6-py3-none-any.whl (341 kB) Requirement already satisfied: sphinxcontrib-applehelp in 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/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-laser-cholera/envs/latest/lib/python3.9/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/python3.9/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 https://packages.idmod.org/api/pypi/pypi-production/packages/packages/d1/c2/fe97d779f3ef3b15f05c94a2f1e3d21732574ed441687474db9d342a7315/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: 2024-11-22T01:18:06.169263Z, end-time: 2024-11-22T01:18:10.464212Z, duration: 4, exit-code: 0 python -m pip install --upgrade --upgrade-strategy only-if-needed --no-cache-dir . Looking in indexes: https://pypi.org/simple, https://packages.idmod.org/api/pypi/pypi-production/simple 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 https://packages.idmod.org/api/pypi/pypi-production/packages/packages/00/2e/d53fa4befbf2cfa713304affc7ca780ce4fc1fd8710527771b58311a3229/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-cp39-cp39-linux_x86_64.whl size=13638 sha256=c1683420510028aa5840ceea987787972cdc8c01f89f0c15d7177faedd5f1af8 Stored in directory: /tmp/pip-ephem-wheel-cache-n7f5xek4/wheels/1b/0f/7b/74575a95d73415b690356a84d8e4acd186a7ab4685a6a42455 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: 2024-11-22T01:18:10.662798Z, end-time: 2024-11-22T01:18:10.726448Z, 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: 2024-11-22T01:18:10.816538Z, end-time: 2024-11-22T01:18:12.014762Z, duration: 1, exit-code: 0 python -m sphinx -T -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html Running Sphinx v7.4.7 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... done copying extra files... done copying assets: done writing output... [ 11%] authors writing output... [ 22%] changelog writing output... [ 33%] contributing writing output... [ 44%] index writing output... [ 56%] installation writing output... [ 67%] readme writing output... [ 78%] reference/index writing output... [ 89%] reference/laser_cholera writing output... [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: 2024-11-22T01:18:12.085570Z, end-time: 2024-11-22T01:18:13.031458Z, duration: 0, exit-code: 0 python -m sphinx -T -b singlehtml -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/htmlzip Running Sphinx v7.4.7 loading translations [en]... done making output directory... done Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`. loading pickled environment... 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 assembling single document... readme installation usage reference/index reference/laser_cholera contributing authors changelog done writing... done writing additional files... done copying static files... done copying extra files... done dumping object inventory... done build succeeded. The HTML page is in ../_readthedocs/htmlzip. [rtd-command-info] start-time: 2024-11-22T01:18:13.358846Z, end-time: 2024-11-22T01:18:16.162039Z, duration: 2, exit-code: 0 python -m sphinx -T -b latex -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/pdf Running Sphinx v7.4.7 loading translations [en]... done making output directory... done Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`. loading pickled environment... 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 copying TeX support files... copying TeX support files... done processing lasercholera.tex... index readme installation usage reference/index reference/laser_cholera contributing authors changelog resolving references... /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:20: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] (https://github.com/InstituteforDiseaseModeling/laser-cholera/actions/workflows/github-actions.yml/badge.svg) /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) done writing... done build succeeded, 8 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: 2024-11-22T01:18:16.236562Z, end-time: 2024-11-22T01:18:16.295801Z, 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: 2024-11-22T01:18:16.362294Z, end-time: 2024-11-22T01:18:20.842829Z, 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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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 448. [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 56962 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 448 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. 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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' Latexmk: Examining 'institute-for-disease-modeling-laser-cholera.log' === TeX engine is 'pdfTeX' Latexmk: Errors, in force_mode: so I tried finishing targets 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 [rtd-command-info] start-time: 2024-11-22T01:18:21.199850Z, end-time: 2024-11-22T01:18:23.504058Z, duration: 2, exit-code: 0 python -m sphinx -T -b epub -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/epub Running Sphinx v7.4.7 loading translations [en]... done making output directory... done Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`. loading pickled environment... 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 [epub]: targets for 9 source files that are out of date 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... done copying extra files... done copying assets: done writing output... 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