spras/.github/workflows/test-spras.yml at c271322e51a076aba18213d282b23940b876ea75 · Reed-CompBio/spras · 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
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
name: Test SPRAS

on: [push, pull_request]

jobs:
  # Installs the conda environment but does not run tests because the tests require Linux Docker images
  conda-only:
    name: Test conda environment
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        os: [macos-latest, windows-latest]
    steps:
      - name: Checkout repository
        uses: actions/checkout@v2
      - name: Install conda environment
        uses: conda-incubator/setup-miniconda@v2
        with:
          activate-environment: spras
          environment-file: environment.yml
          auto-activate-base: false
          miniconda-version: 'latest'
      - name: Log conda environment
        # Log conda environment contents
        shell: bash --login {0}
        run: conda list

  test_windows:
    name: Run weakened windows tests
    runs-on: windows-latest
    steps:
      - name: Checkout repository
        uses: actions/checkout@v4
      - name: Install conda environment
        uses: conda-incubator/setup-miniconda@v2
        with:
          activate-environment: spras
          environment-file: environment.yml
          auto-activate-base: false
          miniconda-version: 'latest'
      - name: Run tests
        shell: bash --login {0}
        # Verbose output and disable stdout and stderr capturing
        run: pytest -vs --ignore=test/AllPairs --ignore=test/BowTieBuilder --ignore=test/DOMINO --ignore=test/analysis/test_cytoscape.py --ignore=test/MEO --ignore=test/MinCostFlow --ignore=test/OmicsIntegrator1 --ignore=test/OmicsIntegrator2 --ignore=test/PathLinker --ignore=test/ResponseNet --ignore=test/RWR --ignore=test/ST_RWR

  # Runs the test code and Snakemake workflow in the conda environment
  test:
    name: Run tests
    # The Docker images will be pulled in both the docker job and this test job
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        # We later use this with `pytest-split` to split our test CI into two
        # (with the max specified by `--splits 2`), to save CI time by parallelization
        test_group: [1, 2]
        os: [ubuntu-latest]
    steps:
      - name: Checkout repository
        uses: actions/checkout@v4
      - name: Install conda environment
        uses: conda-incubator/setup-miniconda@v2
        with:
          activate-environment: spras
          environment-file: environment.yml
          auto-activate-base: false
          miniconda-version: 'latest'
      - name: Install spras in conda env
        # Install spras in the environment using pip
        shell: bash --login {0}
        run: pip install .
      - name: Log conda environment
        # Log conda environment contents
        shell: bash --login {0}
        run: conda list
      - name: Install Apptainer
        # Formerly used Singularity instead of Apptainer (see https://github.com/eWaterCycle/setup-singularity/issues/6)
        uses: eWaterCycle/setup-apptainer@v2
        with:
          # Choose version from https://github.com/apptainer/apptainer/releases
          apptainer-version: 1.3.6
      - name: Run tests
        shell: bash --login {0}
        # Verbose output and disable stdout and stderr capturing
        # [this pytest-split workflow was borrowed from Snakemake CI]
        run: pytest -vs --splits 2 --group ${{ matrix.test_group }}
  workflow:
    name: Run workflow
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        os: [ubuntu-latest]
    steps:
      # TODO: is it worth it to make this setup into a composite action?
      - name: Checkout repository
        uses: actions/checkout@v4
      - name: Install conda environment
        uses: conda-incubator/setup-miniconda@v2
        with:
          activate-environment: spras
          environment-file: environment.yml
          auto-activate-base: false
          miniconda-version: 'latest'
      # Install spras in the environment using pip
      - name: Install spras in conda env
        shell: bash --login {0}
        run: pip install .
      - name: Run Snakemake workflow
        shell: bash --login {0}
        # We enable high parallelization (cores 4) to test our way out of the experienced
        # race conditions from #268 and #279
        # We also enforce strict DAG evaluation to catch DAG problems before they appear as user errors. (#359)
        run: snakemake --cores 4 --configfile config/config.yaml --show-failed-logs --strict-dag-evaluation cyclic-graph --strict-dag-evaluation functions --strict-dag-evaluation periodic-wildcards

  # Run pre-commit checks on source files
  pre-commit:
    name: Run pre-commit checks
    runs-on: ubuntu-latest
    steps:
      - name: Checkout repository
        uses: actions/checkout@v3
      - name: Install conda environment
        uses: conda-incubator/setup-miniconda@v2
        with:
          activate-environment: spras
          environment-file: environment.yml
          auto-activate-base: false
          miniconda-version: 'latest'
      - name: Run pre-commit
        shell: bash --login {0}
        # https://github.com/pre-commit/action/blob/576ff52938d158a24ac7e009dfa94b1455e7df99/action.yml#L19
        run: pre-commit run --show-diff-on-failure --color=always