# Build artifacts
build/
CMakeFiles/
CMakeCache.txt
cmake-build-*/
compile_commands.json
Makefile
*.o
*.a
*.so
*.dylib

# Binaries (in-source / installed). The shell wrapper at bin/fastCDS
# and the Python package at python/fastCDS/ are checked-in source and
# must NOT be ignored.
fastCDS
!bin/fastCDS
!python/fastCDS/
!python/fastCDS/**

# Python caches
__pycache__/
*.pyc

# Editor/system
*.log
*.swp
.DS_Store
benchmarks/work/
benchmarks/proteins_list.txt

# Python build outputs
python/dist/
*.egg-info/
.pytest_cache/
.venv/

# Packaging / release tooling — kept local, not published.
# The bioconda recipe lives upstream in bioconda/bioconda-recipes; pypi
# artifacts are re-buildable via `python -m build`.
/packaging/

# Python build artifacts
dist/
*.egg-info/
*.egg

# Editor
.vscode/
.idea/


tutorial/generate_notebooks.py
