py3plex/.gitignore at master · SkBlaz/py3plex · GitHub

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./py3plex/visualization/fa2/fa2util.c
./py3plex.egg-info
./dist

# Python cache files
__pycache__/
*.py[cod]
*$py.class

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

# Test artifacts and temporary files
datasets/animation*.png
datasets/animation/
datasets/stored_network.gpickle
datasets/mirna_*.list
datasets/test.edgelist
datasets/test_embedding.emb
datasets/embedding_coordinates.json
tests/out/
tests/custom_dir/
tests/*.txt
tests/*.png

# Virtual environment
.venv/
venv/

# Test and coverage reports
htmlcov/
.coverage
.pytest_cache/
.mypy_cache/
.ruff_cache/
.hypothesis/

# Benchmark results
benchmark-*.json

# Documentation builds
docfiles/_build/
docfiles/build/

# Ignore build artifacts in docs/ but track the deployed HTML
# The docs/ folder is served by GitHub Pages and contains:
# - index.html and other HTML files (tracked)
# - _static/, _images/, _sources/ directories (tracked)
# - py3plex_documentation.pdf (tracked)
# - README.md (tracked)
# - .nojekyll file (tracked)
docs/.buildinfo
docs/.doctrees/

# Auto-generated API documentation (not needed in git, regenerated on build)
docfiles/AUTOGEN_results/
docfiles/sources/
docfiles/source/
docfiles/_sources/

# Binaries (users should install separately)
bin/Infomap
bin/node2vec
bin/*.exe
bin/*.dll
_build_test/

# Fuzzing artifacts
fuzzing/crashes/
fuzzing/*.log
crash-*
leak-*
timeout-*
slow-unit-*
doc-coverage.json
loc-stats.json
test-stats.json
coverage.json
coverage_*.json
property_coverage_*.json
property_test_coverage_*.json

# Generated report/summary txt files (agent-produced, not project assets)
PROJECT_SUMMARY.txt
*_REPORT.txt
auto/
LLM_ORIGINAL_BACKUP.md
mutants/
.mutmut-cache

# GUI data directories (runtime data, not source)
gui/data/uploads/*
gui/data/artifacts/*
gui/data/workspaces/*
!gui/data/**/.gitkeep

# Example output files (generated by examples)
output/
outputs/
examples/output/
examples/*/outputs/
examples/workflows/*.png
*_results/
workflow_results/
comparison_results/
network.gpickle
network.txt
book/_build/
*.csv
results/
/tmp/
tmp/