AnyVLM/.github/workflows/python-package.yaml at main · GenomicMedLab/AnyVLM · 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
name: Python package

on:
  push:
  pull_request:

permissions:
  contents: read

jobs:
  test:
    name: test
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ["3.11", "3.12", "3.13"]
    services:
      postgres:
        image: postgres:17
        env:
          POSTGRES_PASSWORD: postgres
        options: >-
          --health-cmd pg_isready
          --health-interval 10s
          --health-timeout 5s
          --health-retries 5
        ports:
          - 5432:5432
    steps:
      - uses: actions/checkout@v4
        with:
          submodules: 'true'
      - name: Wait for Postgres
        run: |
          for i in {1..30}; do
            pg_isready -h localhost -p 5432 -U postgres && exit 0
            sleep 1
          done
          exit 1
      - name: Initialize GiST extension
        env:
          PGPASSWORD: postgres
        run: |
          psql -h localhost -p 5432 -U postgres -d postgres \
            -c "CREATE EXTENSION IF NOT EXISTS btree_gist;"
      - name: Set up Python
        uses: actions/setup-python@v5
        with:
          python-version: "${{ matrix.python-version }}"

      - name: Install uv
        uses: astral-sh/setup-uv@v6
        with:
          enable-cache: true

      - name: Install dependencies
        run: uv sync --extra test

      - name: Run tests
        run: uv run pytest
        env:
          ANYVLM_TEST_STORAGE_URI: postgresql://postgres:postgres@localhost:5432/postgres
          ANYVLM_ANYVAR_TEST_STORAGE_URI: postgresql://postgres:postgres@localhost:5432/postgres
          HANDOVER_TYPE_ID: "CUSTOM:GREGoR-NCH"
          HANDOVER_TYPE_LABEL: "GREGoR AnyVLM Reference"
          BEACON_HANDOVER_URL: https://variants.gregorconsortium.org/
          BEACON_NODE_ID: org.anyvlm.gregor
  lint:
    name: lint
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4

      - name: Setup Python
        uses: actions/setup-python@v5
        with:
          python-version: "3.11"

      - name: Install uv
        uses: astral-sh/setup-uv@v6
        with:
          enable-cache: true

      - name: Install dependencies
        run: uv sync --extra dev

      - name: Check style
        run: uv run ruff check && uv run ruff format --check
  precommit_hooks:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        cmd:
          - "end-of-file-fixer"
          - "trailing-whitespace"
          - "mixed-line-ending"
    steps:
      - uses: actions/checkout@v4

      - name: Set up Python 3.12
        uses: actions/setup-python@v5
        with:
          python-version: 3.12

      - uses: pre-commit/action@v3.0.1
        with:
          extra_args: ${{ matrix.cmd }} --all-files
  docs:
    runs-on: ubuntu-latest
    env:
      SPHINX_GITHUB_CHANGELOG_TOKEN: ${{ secrets.GITHUB_TOKEN }}
    steps:
      - uses: actions/checkout@v6

      - name: Set up Python
        uses: actions/setup-python@v6
        with:
          python-version: 3.11

      - name: Install uv
        uses: astral-sh/setup-uv@v7
        with:
          enable-cache: true

      - name: Install dependencies
        run: uv sync --extra docs

      - name: Attempt docs build
        working-directory: ./docs
        run: source ../.venv/bin/activate && make html