# Python
__pycache__/
*.py[cod]
*.egg-info/
.eggs/
build/
dist/
*.so

# Rust extension build artifacts (source is committed; builds are not)
rust/target/
*.whl

# Testing / envs
.pytest_cache/
.venv/
venv/
.ipynb_checkpoints/

# Simulation outputs
out/
/tmp/

# Built docs site
site/
_site/

# Private didactic material (kept locally, not published)
docs/non_independence.pdf
docs/non_independence.tex

# Local publication-prep working files (not part of the public repo)
PUBLICATION_READINESS_REPORT.md
PUBLICATION_READINESS_REPORT.pdf
coleman_biorxiv.pdf

# --- Generated artifacts: regenerable outputs; the sources that produce them ARE tracked ---

# Offline single-file docs mirror (rebuild with tools/build_docs_html.py)
/zombi2-docs.html

# figures/svg/ and figures/png/ are the tracked home of every figure the manual and the site use;
# docs/img/ holds symlinks into them. Renders are committed so neither build needs the toolchain.

# Compiled analysis reports and regenerated figures
# (run scripts, *.json results and *.tex sources stay tracked)
analyses/**/*.pdf
analyses/**/figures/*.png
analyses/**/figures/*.svg
analyses/**/figs/*.png
analyses/**/figs/*.svg

# LaTeX build artifacts
*.aux
*.log
*.out
*.toc
.texmf-var/
.tmptex/

# OS
.DS_Store

# Multi-agent coordination log (shared via the working tree, not committed)
HANDOFF.md

# Phylustrator is a separate editable git checkout (figure tool), not vendored here
tools/Phylustrator/
