AGENTS.md

AGENTS.md

Project summary

Krill is a Django application for managing biological sample storage, tracking, and reporting.

Key locations

• krill/: Django project and apps (person, sample, storage, reports, transaction)
• templates/: top-level template overrides (admin UI)
• tests/: anonymized test data, fixtures, scripts, run_tests.py
• scripts/: utility scripts (e.g., clean_whitespace.py)
• config/: configuration files
• Dockerfile, docker-compose.yml, build.sh, Makefile: build and runtime tooling

Local setup

1. Python 3.10+, pip, and (recommended) a virtual environment.
2. Install dependencies:
   • pip install -r requirements.txt
3. Database defaults to SQLite; for PostgreSQL set env vars from env.example or env.production.
4. manage.py lives under krill/:
   • From repo root: python krill/manage.py <command>
   • Or cd krill then python manage.py <command>

Common commands (Makefile helpers)

• Run server: make server
• Migrations: make migrate
• Create superuser: make createsuperuser
• Django tests: make test-local
• Test data scripts: make test-data
• Lint/whitespace cleanup: make lint
• Docker tests: make test-docker or ./build.sh test

Test data notes

• Anonymized fixtures live in tests/fixtures/sample_fixtures.json.
• Regenerating anonymized data requires the original ln2_cane4_export.csv in the repo root (not committed).
• make setup-test loads fixtures and creates a test superuser (admin / admin).

Change guidance

• Add or update tests for custom business logic.
• Keep docs in sync when changing setup, env vars, or tooling.
• Never commit secrets; use env files or platform secret stores.