# Python
__pycache__/
*.py[cod]
*$py.class
*.so
*.egg-info/
build/
dist/
.eggs/
.venv*/
.pytest_cache/
.ruff_cache/
.coverage
htmlcov/
.mypy_cache/

# R
.Rhistory
.RData
.Rproj.user/
*.Rcheck/
*.tar.gz

# OS
.DS_Store
Thumbs.db

# Editor / local tooling
.idea/
.vscode/
.serena/
*.swp

# Docs build
docs/build/
.sphinx-doctrees/

# Local data caches (downloaded on demand, not committed)
data/cache/
data/manifest/outputs/

# Secrets / local config
.env
.env.local
*.pem
*.key

# OS metadata
.DS_Store
Thumbs.db
*.swp
*~

# Large datasets (downloaded via moirais download-bootstrap)
src/moirais/data/*.db

# ad-hoc smoke harnesses (use tests/parity/ for the canonical ones)
_smoke_*
_smoke_stdout.txt
scripts/_smoke*
scripts/_ksr_smoke*

# Vignette build artifacts (LaTeX intermediate files)
r-package/morie/vignettes/*.log
r-package/morie/vignettes/*.aux
r-package/morie/vignettes/*.toc
r-package/morie/vignettes/*.out
r-package/morie/vignettes/*.synctex.gz
r-package/morie/vignettes/*.tex
backups/

# papers/ is the authoring tree (emails, drafts, working PDFs, etc.).
# It must NEVER be tracked wholesale — a previous public publish
# leaked papers/emails/ and cost ~40,000 deleted changes to recover.
#
# We allow ONLY the public JSS .tex sources + their bibs +
# the JSS class files + an explanatory README.  Any new addition to
# this allowlist requires a security review of the file.
papers/*
!papers/README.md
!papers/jss.cls
!papers/jss.bst
!papers/hawkes-paper/
!papers/morie-empirical-paper/
!papers/morie-py-paper/
!papers/morie-r-paper/
!papers/mrm-formulations-paper/
papers/hawkes-paper/*
papers/morie-empirical-paper/*
papers/morie-py-paper/*
papers/morie-r-paper/*
papers/mrm-formulations-paper/*
!papers/hawkes-paper/main.tex
!papers/hawkes-paper/refs.bib
!papers/morie-empirical-paper/main.tex
!papers/morie-empirical-paper/refs.bib
!papers/morie-py-paper/main.tex
!papers/morie-py-paper/refs.bib
!papers/morie-r-paper/main.tex
!papers/morie-r-paper/refs.bib
!papers/mrm-formulations-paper/main.tex
!papers/mrm-formulations-paper/refs.bib
# Explicit deny — never under any circumstances:
papers/emails/
papers/azm/
papers/dirty-frag-research/
papers/**/*.pdf
papers/**/arxiv-bundle/
papers/**/*-pre-jss-*.tex
papers/**/results/
papers/PAPERS_*.txt

# Email drafts — NEVER push (contains personal addresses)
RELEASE-EMAILS-*.md
*-EMAILS-*.md
morie-private/
data-snapshots/
