neoswga/.gitignore at main · FOI-Bioinformatics/neoswga · GitHub

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# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
*$py.class

# C extensions
*.so

# Distribution / packaging
.Python
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
wheels/
*.egg-info/
.installed.cfg
*.egg

# PyInstaller
*.manifest
*.spec

# Installer logs
pip-log.txt
pip-delete-this-directory.txt

# Unit test / coverage reports
htmlcov/
.tox/
.nox/
.coverage
.coverage.*
.cache
nosetests.xml
coverage.xml
*.cover
*.py,cover
.hypothesis/
.pytest_cache/

# Translations
*.mo
*.pot

# Jupyter Notebook
.ipynb_checkpoints

# IPython
profile_default/
ipython_config.py

# pyenv
.python-version

# Environments
.env
.venv
env/
venv/
ENV/
env.bak/
venv.bak/

# Spyder project settings
.spyderproject
.spyproject

# Rope project settings
.ropeproject

# mkdocs documentation
/site

# mypy
.mypy_cache/
.dmypy.json
dmypy.json

# IDE
.idea/
.vscode/
*.swp
*.swo
*~

# macOS
.DS_Store
.AppleDouble
.LSOverride

# Project-specific
# Large test output directories (regenerated as needed)
francisella_equiphi29/
francisella_test/
neoswga_results/

# Benchmark outputs (regenerated)
benchmarks/benchmark_results.csv
benchmarks/checkpoint.json

# H5 position files (large, regenerated)
*.h5

# Jellyfish k-mer database files (large, regenerated)
*.jf

# Coverage reports (regenerated)
htmlcov/
.coverage

# Jellyfish k-mer files (large, regenerated)
*_*mer_all.txt

# Pipeline output files (keep in results directories only)
step*_output.txt
step*_debug*.txt

# Temporary conda error logs
h5py

# Validation test results (regenerated)
validation_tests/results/

# ML model files (large, can be retrained with scripts/retrain_rf_model.py)
# neoswga/core/models/*.p  # Tracked: required for score step

# Large genome files in test data (download separately)
tests/integration/**/human_*.fna
tests/integration/**/human_*.fasta

# Integration test output data (regenerated)
tests/integration/**/data/

# Integration test working directories (local experiments)
tests/integration/francisella_clinical/
tests/integration/francisella_e2e/
tests/integration/equiphi29_long/
tests/integration/equiphi29_validation/
tests/integration/equiphi29_full_factorial/

# Test data H5 files (large, regenerated)
test_data/*.h5

# Example generated files (run examples locally)
examples/**/kmer_files/
examples/**/step*.csv
examples/**/step*.json
examples/**/*.h5
examples/**/report.html
examples/**/*.bedgraph
examples/**/*_all.txt
examples/**/export/
examples/**/params_backup.json
examples/**/run_manifest.json
examples/**/filter_stats.json
examples/**/*technical_report.html
examples/ecoli_environmental/ecoli_K12_MG1655.fasta

# Root-level pipeline run artifacts
/step4_improved_df_validation.json
/step*_df.csv

# Local planning/spec scratch (not part of the package)
docs/superpowers/

# Git worktrees
.worktrees/