stages:
  - test
  - lint
  - snakemake

test_project:
  stage: test
  image: python:3.12-slim
  tags: 
    - public
  before_script:
    - python3 -m venv venv
    - source venv/bin/activate
    - pip install --upgrade pip
    - pip install -r requirements.txt
  script:
    - pytest


lint_project:
  stage: lint
  image: python:3.12-slim
  tags:
    - public
  before_script:
    - python3 -m venv venv
    - source venv/bin/activate
    - pip install --upgrade pip
    - pip install pylint
    - pip install -r requirements.txt
  script:
    - pylint workflow/scripts tests

snakemake_project:
  stage: snakemake
  image: python:3.12-slim
  tags:
    - public
  before_script:
    - pip install --upgrade pip
    - pip install -r requirements.txt
  script:
    - snakemake --cores 1 --forceall
  after_script:
    - rm -r results