Development¶

Prerequisites¶

Python 3.10+
Docker, Docker Compose
NVIDIA GPU + CUDA driver (for Ollama)
Node.js 24+ (frontend development only)

CLI Entry Points¶

Defined in pyproject.toml under [project.scripts]:

Command	Entry Point	Description
`bsllmner2_extract`	`bsllmner2.cli_extract:run_cli_extract`	Extract mode CLI
`bsllmner2_select`	`bsllmner2.cli_select:run_cli_select`	Select mode CLI

Local Development Setup¶

Python Package¶

uv sync --all-extras

Docker Environment¶

docker compose up -d --build
docker compose exec app bash

Running Tests¶

# Tests
uv run pytest

# Type checking
uv run mypy

# Linter
uv run ruff check bsllmner2/ tests/ scripts/

# Formatter
uv run ruff format bsllmner2/ tests/ scripts/

# Format check (for CI)
uv run ruff format --check bsllmner2/ tests/ scripts/

For details on test structure, mutation testing, and model evaluation, see Testing.

Release Process¶

Version is managed via git tags using hatch-vcs. No manual version editing in pyproject.toml is required.

Merge PR to main
Create and push a version tag:
```
git tag X.Y.Z
git push origin X.Y.Z
```
The tag push triggers .github/workflows/release.yml:
Build and push Docker image to ghcr.io/dbcls/bsllmner-mk2
Create GitHub Release with auto-generated notes

scripts/ Utility Scripts¶

Script	Description
`download_ontology_files.py`	Download ontology files
`ncbi_gene_to_owl.py`	Convert NCBI Gene data to OWL
`prepare_bs_entries.py`	Prepare BioSample entries for ChIP-Atlas
`print_select_result.py`	Display and analyze select results
`list_unmapped.py`	List unmapped entries
`select-config.json`	General select config (7 fields)
`select-config-hg38.json`	Human (hg38) select config
`select-config-mm10.json`	Mouse (mm10) select config