docs/contributing.md

Contributing

Running Tests

# Full test suite
pytest tests/

# Single test
pytest tests/test_run.py::test_run_pirads_training

Tests run in --dry_run mode (2 epochs, batch_size=2, no W&B logging).

Linting

This project uses Ruff for linting and formatting:

# Check for lint errors
ruff check .

# Auto-format code
ruff format .

Ruff configuration (from pyproject.toml):

Setting	Value
Line length	100
Quote style	Double quotes
Rules	E (errors), W (warnings)
Ignored	E501 (line too long)

SLURM Job Scripts

Job scripts are in job_scripts/ and are configured for GPU partitions:

sbatch job_scripts/train_pirads.sh
sbatch job_scripts/train_cspca.sh

Key SLURM settings used:

Setting	Value
Partition	gpu
Memory	128 GB
GPUs	1
Time limit	48 hours

!!! tip The SLURM job name (--job-name) automatically becomes the run_name, which determines the log directory at logs/<run_name>/.

Project Conventions

• Configs are stored in config/ as YAML files
• Logs are written to logs/<run_name>/ including TensorBoard events and training logs
• Models are saved to logs/<run_name>/ during training; best models are saved to models/ for deployment
• Cache is stored at logs/<run_name>/cache/ and cleaned up automatically after training