peppro/.github/workflows/tests.yml at 6bf1f806a2e865ed7a1f355c8509debaa5905341 · databio/peppro · 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
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
name: Tests

on:
  push:
    branches: [master, dev, looper-update]
  pull_request:
    branches: [master, dev]
  workflow_dispatch:
    inputs:
      run_integration:
        description: "Run integration tests (requires self-hosted runner)"
        required: false
        default: "false"

jobs:
  # --------------------------------------------------------------------------
  # Tier 1: Unit tests — no genome data or bioinformatics tools required.
  # Runs on every push and pull request.
  # --------------------------------------------------------------------------
  unit-tests:
    name: Unit tests (Python ${{ matrix.python-version }})
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        python-version: ["3.9", "3.11", "3.12"]

    steps:
      - uses: actions/checkout@v4

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

      - name: Install Python dependencies
        run: pip install -r requirements.txt pytest

      - name: Run unit tests
        run: pytest tests/test_unit.py -v --tb=short

  # --------------------------------------------------------------------------
  # Tier 2: Integration tests — full pipeline runs.
  # Requires a self-hosted runner with genome indices and tools installed.
  # Triggered manually via workflow_dispatch or by setting
  # RUN_INTEGRATION_TESTS=true in the environment.
  # --------------------------------------------------------------------------
  integration-tests:
    name: Integration tests (${{ matrix.scenario }})
    if: >
      github.event_name == 'workflow_dispatch' &&
      github.event.inputs.run_integration == 'true'
    runs-on: self-hosted
    strategy:
      fail-fast: false
      matrix:
        scenario:
          - se_basic
          - pe_basic
          - se_groseq
          - se_umi
          - pe_umi
          - se_fastp
          - se_fastx
          - se_fqdedup
          - se_scale
          - se_no_complexity
          - se_nofifo
          - se_coverage

    steps:
      - uses: actions/checkout@v4

      - name: Install Python dependencies
        run: pip install -r requirements.txt pytest

      - name: Run integration test for ${{ matrix.scenario }}
        env:
          RUN_INTEGRATION_TESTS: "true"
        run: >
          pytest tests/test_integration.py -v --tb=short
          -k "${{ matrix.scenario }}"