.history/

__pycache__/
.pytest_cache/
.ruff_cache/
.mypy_cache/
*.pyc
*.pyo
*.pyd

venv/
env/
env.bak/
env1/
env2/
.env

.vscode/
*.code-workspace

build/
dist/
*.egg-info/
*.egg

# setuptools-scm generated version file
pdb2reaction/_version.py

test-reports/
.coverage

# Sphinx documentation
docs/_build/
docs/_static/*.css.map
docs/_static/*.js.map
docs/_autosummary/
docs/.myst_cache/
docs/.ipynb_checkpoints/

*.bak
*.swp
*.tmp
*.tmp.*
*~
optimizer.log
pysisyphus.log
dimer.log

# Smoke test outputs (generated by tests/smoke/run.sh from the bundled
# fixtures; safe to ignore if someone runs smoke from a clone).
tests/smoke/test*/
tests/smoke/test*.out
tests/smoke/result_*/
tests/smoke/internal_coords.log
tests/smoke/p_complex_model.pdb
tests/smoke/model_r.pdb
tests/smoke/r_complex_elem.pdb
tests/smoke/r_complex_fixalt.pdb
cos.log

# release-process scratch — not distributed in the repo
RELEASE_NOTES*
