smoke-test.yml

# Create a smoketest that just installs the biobear python package and reads an example file

name: Smoke Test

on:
  workflow_dispatch:
  schedule:
    - cron: '0 0 */5 * *'

jobs:
  test-package-conda:
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        os: [ubuntu-latest, macos-latest, windows-latest]
        python-version: ['3.10']

    steps:
      - name: Checkout
        uses: actions/checkout@v4

      - name: Set up Python
        uses: conda-incubator/setup-miniconda@v3
        with:
          python-version: ${{ matrix.python-version }}
          channels: conda-forge
          miniconda-version: 'latest'
          activate-environment: biobear

      - name: Read example fasta file
        shell: bash -l {0}
        run: |
          conda info
          conda install -c conda-forge -n biobear biobear polars
          conda run -n biobear python ./.github/workflows/smoketest.py

  test-package-pip:
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        os: [ubuntu-latest, macos-latest, windows-latest]
        python-version: ['3.10']

    steps:
      - name: Checkout
        uses: actions/checkout@v4

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

      - name: Install biobear
        run: |
          python -m pip install --upgrade pip
          pip install biobear polars

      - name: Read example fasta file
        shell: bash
        run: |
          python ./.github/workflows/smoketest.py