divbase/.github/workflows/release.yaml at d3a23ed7a71bbf78508adfcfd0a0ef6b991b4f86 · ScilifelabDataCentre/divbase · 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
132
133
134
135
136
137
138
139
140
141
142
143
name: Release a new version of DivBase
# Triggered when a GitHub release is published
# Order: Build Docker images -> run pytest -> push images.
# If that works, 2 separate jobs run: (1) build and publish the PyPI packages and (2) make a new release of the docs.
# docker images are tagged with commit hash, the commit tag (semver) and "latest".
# pypi packages have version numbering set by their __init__.py, which should be updated in the release commit.

on:
  release:
    types: [published]

jobs:

  build-test-publish-images:
    name: Run pytest, if successful publish docker images
    if: github.repository == 'ScilifelabDataCentre/divbase'
    runs-on: ubuntu-latest
    permissions:
      contents: read
      packages: write # ghcr publishing needs write

    steps:
      - name: Check out the repo
        uses: actions/checkout@v6

      - name: Build fastapi image, no push
        uses: docker/build-push-action@v7
        with:
          push: false
          load: true
          context: .
          file: ./docker/fastapi.dockerfile
          tags: divbase-fastapi:test

      - name: Build worker image, no push
        uses: docker/build-push-action@v7
        with:
          push: false
          load: true
          context: .
          file: ./docker/worker.dockerfile
          tags: divbase-worker:test

      - name: Install uv
        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
        with:
          version: "0.11.19"
          enable-cache: true

      - name: Install project and test dependencies
        run: |
          uv sync --locked --dev
          uv run playwright install chromium

      - name: Allow container to write to test fixtures # actions runner uid=1001, but container runs as 1000
        # So container does not have permissions to write to the mounted test fixtures, required by test_bcftools_pipe_cli_integration_with_eager_mode
        # volume mount made in docker/divbase_compose.tests.yaml
        run: chmod -R a+w tests/fixtures

      - name: Run pytest including slow tests
        env:
          GITHUB_ACTIONS_RUNNER: "true"
          DIVBASE_FASTAPI_IMAGE: divbase-fastapi:test
          DIVBASE_WORKER_IMAGE: divbase-worker:test
        run: FORCE_TERMINAL=1 COLUMNS=1000 uv run pytest --run-slow

      # publish images to GHCR
      - name: Login to GitHub Container Registry
        uses: docker/login-action@v4
        with:
          registry: ghcr.io
          username: ${{ github.actor }}
          password: ${{ secrets.GITHUB_TOKEN }}
      - name: Push fastapi image
        uses: docker/build-push-action@v7
        with:
          push: true
          context: .
          file: ./docker/fastapi.dockerfile
          tags: |
            ghcr.io/scilifelabdatacentre/divbase-fastapi:${{ github.event.release.tag_name }}
            ghcr.io/scilifelabdatacentre/divbase-fastapi:${{ github.sha }}
            ghcr.io/scilifelabdatacentre/divbase-fastapi:latest
      - name: Push worker image
        uses: docker/build-push-action@v7
        with:
          push: true
          context: .
          file: ./docker/worker.dockerfile
          tags: |
            ghcr.io/scilifelabdatacentre/divbase-worker:${{ github.event.release.tag_name }}
            ghcr.io/scilifelabdatacentre/divbase-worker:${{ github.sha }}
            ghcr.io/scilifelabdatacentre/divbase-worker:latest

  build-pypi-packages:
    if: github.repository == 'ScilifelabDataCentre/divbase'
    uses: ./.github/workflows/build-pypi-packages.yaml

  # NOTE: artifacts are scoped to the current workflow run, so you don't need to worry that this
  # action will publish older packages built from other runs/release attempts that e.g. failed pytest.
  publish-to-pypi:
    name: Publish divbase-lib and divbase-cli to PyPI
    if: github.repository == 'ScilifelabDataCentre/divbase'
    needs: [build-test-publish-images, build-pypi-packages]
    runs-on: ubuntu-latest
    permissions:
      id-token: write # For trusted publishing
    environment:
      name: pypi

    steps:
      - name: Download built packages
        uses: actions/download-artifact@v7
        with:
          name: Packages
          path: dist/

      - name: Publish to PyPI
        uses: pypa/gh-action-pypi-publish@release/v1


  # Publish docs to GitHub pages
  deploy-docs:
    name: Publish DivBase documentation to GitHub Pages
    if: github.repository == 'ScilifelabDataCentre/divbase'
    needs: build-test-publish-images
    runs-on: ubuntu-latest
    permissions:
      contents: write # for pushing to gh-pages branch
    steps:
      - uses: actions/checkout@v6

      - name: Install uv
        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
        with:
          version: "0.11.19"
          enable-cache: true

      - name: Install the project
        run: uv sync --locked --dev

      - name: Deploy documentation
        run: uv run mkdocs gh-deploy --force