reproducible-mortality-prediction/.gitignore at main · lehdermann/reproducible-mortality-prediction · GitHub

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# Python
venv/
env/
__pycache__/
*.py[cod]
*$py.class
*.so
.Python

# Jupyter
.ipynb_checkpoints/
*.ipynb_checkpoints

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

# Data - Real MIMIC-III (cannot be shared publicly)
data/root/
data/in-hospital-mortality*/

# Data - Large synthetic datasets (keep only small example)
data/mimic3_synthetic/train/
data/mimic3_synthetic/test/
data/mimic3_synthetic_v2_1/
# Keep: data/mimic3_synthetic_v3/ (small example for reproducibility)

# Models - Large files (optional: use Git LFS or releases)
models/*.h5
models/*.pb
models/scaler.pkl
# Consider keeping for reproducibility:
# !models/best_model_calibrated.keras
# !models/calibrator.pkl
# !models/optimal_threshold.txt

# Logs (generated during execution)
logs/
*.log

# Results - Ignore generated files, keep reference outputs
results/plots/*.png
!results/plots/roc_curve.png
!results/plots/summary_metrics.png
!results/plots/comparison_table.png
!results/plots/calibration_curve.png
!results/plots/confusion_matrix.png
!results/plots/fbeta_vs_threshold.png
!results/plots/improvement_chart.png
!results/plots/learning_curves_dl.png
!results/plots/metrics_comparison.png
!results/plots/pr_comparison.png
!results/plots/precision_recall_curve.png
!results/plots/probability_distribution.png
!results/plots/roc_comparison.png
!results/plots/threshold_vs_metrics.png
results/*.npy
results/*.pdf
!results/*.json
!results/*.md

# Documentation - Keep compiled paper
!docs/*.pdf

# OS
.DS_Store
Thumbs.db

# Temporary
*.tmp
*.bak

# Archived - Not versioned (local reference only)
# Includes: LaTeX source, Portuguese docs, planning/analysis documents
archived/

# External dependencies (cloned repositories)
mimic3-benchmarks/

# Old project directories (not part of current structure)
systematic_review/