# --- xpr2bind ----------------------------------------------------------------
# Pipeline artifacts
runs/
results/
.snakemake/
*.parquet
*.tar.gz
*.zip
!tests/fixtures/**/*.parquet
!tests/fixtures/**/*.tar.gz

# Vendored data dependencies and local caches (not committed)
data/surface_bind/
!data/surface_bind/README.md
data/gdc_cache/
data/target_structures/

# Generated reports
report.html
*_report.html
report_files/
# ...but the committed validation deliverable is kept
!benchmarks/validation/report.html

# RO-Crate exports
*.crate.zip

# --- Python ------------------------------------------------------------------
__pycache__/
*.py[cod]
*$py.class
*.so
.Python
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
wheels/
share/python-wheels/
*.egg-info/
.installed.cfg
*.egg
MANIFEST

# Testing & coverage
.pytest_cache/
.coverage
.coverage.*
htmlcov/
.tox/
.nox/
coverage.xml
*.cover
*.py,cover
.hypothesis/

# Type checking
.mypy_cache/
.pyre/
.pytype/
.ruff_cache/

# Virtual environments
.venv/
venv/
env/
ENV/
.conda/

# Jupyter
.ipynb_checkpoints/
*.ipynb_checkpoints

# IDE
.vscode/
.idea/
*.swp
*.swo
*~
.DS_Store
Thumbs.db

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

# OS
desktop.ini



# mkdocs build output
site/

# LaTeX build intermediates. No compiled PDF is committed either: CI typesets
# paper/biorxiv/manuscript.tex and attaches the PDF to every release.
paper/**/*.aux
paper/**/*.bbl
paper/**/*.bcf
paper/**/*.blg
paper/**/*.log
paper/**/*.out
paper/**/*.run.xml
paper/**/*.toc
paper/**/*.fls
paper/**/*.fdb_latexmk
paper/**/*.synctex.gz

# Designer-benchmark scratch (the --out run dir + transient submit spec dirs)
benchmarks/designer_benchmark/run/
_bindsight_spec_*/

# Compiled manuscripts are built at submission time, never committed
paper/biorxiv/*.pdf

# Designer-benchmark staging. A run writes here first so a failure cannot
# overwrite the committed result; only the promoted artifacts are tracked.
# The wheel built for the remote job lives here too and is a build product.
benchmarks/designer_benchmark/run/
benchmarks/designer_benchmark/run_t4/

# Editor and agent tooling, not part of the project.
.claude/
