dMod2/.gitignore at master · dModverse/dMod2 · GitHub

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# RStudio / R session
.Rproj.user/
.Rhistory
.RData

# Editor and OS
*.swp
.DS_Store
Thumbs.db

# Build and check artefacts
*.tar.gz
*.Rcheck/
.Rcheck/
check/
inst/doc/
/doc/
/Meta/

# knitr and R Markdown
README.html
README_files/
*.knit.md
*.utf8.md
*_cache/
*_files/
.cache/
/notes/

# knitr output in vignettes/. The exception is a pre-rendered .asis vignette:
# there the PDF is the shipped content, not a build artefact.
vignettes/*.R
vignettes/*.html
vignettes/*.pdf
!vignettes/PEtab.pdf
!vignettes/Optimisation.pdf

# Compiled objects and scratch
*.o
*.so
*.dll
.f*
*.log
*.tmp
deriv2Tests/wd/

# Codegen and solver outputs written by tests under tests/testthat
tests/testthat/*.c
tests/testthat/*.cpp
tests/testthat/*.o
tests/testthat/*.so
tests/testthat/*.dll
tests/testthat/reactions_for_Alyssa*
tests/testthat/_snaps/

# bench baselines are transient, except the tracked pre-rewrite baseline
bench/baselines/*
!bench/baselines/focei_theoph_pre_rewrite.rds

# Python caches from the reticulate helpers under inst/code
__pycache__/
*.pyc

# Local tooling
.positai
.claude/
CLAUDE.md

# compile() object-reuse index
.dMod_objects

# Third-party fixture tree. Resolved at test time via DMOD_PETABTESTS or by
# walking up from the package root; test-petab.R skips cleanly when absent.
# It is tracked so the conformance runs are reproducible from a clone.

# Test-run artefact from a headless plot() call.
tests/testthat/Rplots.pdf

# HTML previews of the rendered demos
examples/*.html