CopraRNA/.github/workflows/python.yml at master · BackofenLab/CopraRNA · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
name: CopraRNA 3
on:
  push:
  pull_request:
  workflow_dispatch:

env:
  OPENBLAS_CORETYPE: Haswell

jobs:
  python:
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        include:
          - python: '3.11'
            biopython: '1.84'
          - python: '3.12'
            biopython: '1.88'
          - python: '3.13'
            biopython: '1.88'
    steps:
      - uses: actions/checkout@v4
      - uses: actions/setup-python@v5
        with:
          python-version: ${{ matrix.python }}
      - run: python -m pip install '.[test,build]' 'biopython==${{ matrix.biopython }}'
      - run: python -m pytest -q
      - run: python -m build
      - name: Check installed wheel outside the source directory
        shell: bash
        run: |
          python -m venv --system-site-packages /tmp/coprarna-wheel
          /tmp/coprarna-wheel/bin/python -m pip install --force-reinstall --no-deps dist/*.whl
          cd /tmp
          /tmp/coprarna-wheel/bin/coprarna --version
          /tmp/coprarna-wheel/bin/coprarna helpers
          /tmp/coprarna-wheel/bin/coprarna helper archive-readme

  scientific:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - uses: mamba-org/setup-micromamba@v2
        with:
          environment-file: environment.yml
          cache-environment: true
      - name: Install Python package and browser
        shell: bash -el {0}
        run: |
          python -m pip install --no-deps .
          python -m pip install ".[web]"
          python -m playwright install chromium --only-shell
      - name: Native scientific workflow and browser integration
        shell: bash -el {0}
        env:
          COPRARNA_PIPELINE_TESTS: '1'
          COPRARNA_BROWSER_TESTS: '1'
          COPRARNA_REFERENCE_TESTS: '1'
        run: python -m pytest -q