pr_push_validation.yml

name: Python dev

on:
  pull_request:
  push:
    branches:
      - main

jobs:
  testing:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python: ["3.10", "3.11", "3.12"]
    name: Testing Python ${{ matrix.python }}
    steps:
      - name: Checkout fedpydeseq2
        uses: actions/checkout@v4

      - name: Set up Python
        uses: actions/setup-python@v5
        with:
          python-version: ${{ matrix.python }}

      - name: Install Poetry
        run: |
          python --version
          pip install poetry==1.8.2

      - name: Install dependencies
        run: |
          which python
          python --version
          poetry install --with testing

      - name: Download data
        run: |
          mkdir -p /opt/conda
          wget https://repo.anaconda.com/miniconda/Miniconda3-py39_24.5.0-0-Linux-x86_64.sh -O /opt/conda/miniconda.sh
          bash /opt/conda/miniconda.sh -b -p /opt/miniconda
          poetry run fedpydeseq2-download-data --only_luad --raw_data_output_path /home/runner/work/fedpydeseq2/fedpydeseq2/data/raw --conda_activate_path /opt/miniconda/bin/activate
          ls /home/runner/work/fedpydeseq2/fedpydeseq2/data/raw
          ls /home/runner/work/fedpydeseq2/fedpydeseq2/data/raw/tcga
      - name: Testing
        run: |
          poetry run pytest -v tests -m "not self_hosted_slow and not self_hosted_fast and not local and not docker"

  linting:
    runs-on: ubuntu-latest
    name: Test Linting
    steps:
      - uses: actions/checkout@v4
      - name: Set up Python
        uses: actions/setup-python@v5
        with:
          python-version: "3.11"
      - name: Install Poetry
        run: pip install poetry==1.8.2

      - name: Install dependencies
        run: |
          which python
          python --version
          poetry install --with linting

      - name: Pre-commit checks
        run: |
          poetry run pre-commit run --all-files --show-diff-on-failure