lighthouse/.github/workflows/ci.yml at develop · sanger/lighthouse · 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
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
name: CI

on:
  push:
    branches:
      - develop
      - master
  pull_request:
    branches:
      - develop
      - master

jobs:
  setup:
    runs-on: ubuntu-latest
    outputs:
      python_version: ${{ steps.read_python_version.outputs.python_version }}
    steps:
      - uses: actions/checkout@v4
      - name: Read Python version
        id: read_python_version
        run: echo "::set-output name=python_version::$(cat .python-version)"
  black:
    runs-on: ubuntu-latest
    needs: setup
    steps:
      - uses: actions/checkout@v4
      - name: Set up Python
        uses: actions/setup-python@v2
        with:
          python-version: ${{ needs.setup.outputs.python_version }}
      - uses: actions/cache@v4
        with:
          path: ~/.cache/pip
          key: ${{ runner.os }}-pip-${{ hashFiles('**/Pipfile') }}
          restore-keys: |
            ${{ runner.os }}-pip-
      - name: Install pipenv
        run: |
          pip install pipenv
      - name: Install dependencies
        run: |
          pipenv sync --dev --system
      - name: Check format with black
        run: |
          # stop the build if there are black formatting errors
          python -m black --check .
  flake8:
    runs-on: ubuntu-latest
    needs: setup
    steps:
      - uses: actions/checkout@v4
      - name: Set up Python
        uses: actions/setup-python@v2
        with:
          python-version: ${{ needs.setup.outputs.python_version }}
      - uses: actions/cache@v4
        with:
          path: ~/.cache/pip
          key: ${{ runner.os }}-pip-${{ hashFiles('**/Pipfile') }}
          restore-keys: |
            ${{ runner.os }}-pip-
      - name: Install pipenv
        run: |
          pip install pipenv
      - name: Install dependencies
        run: |
          pipenv sync --dev --system
      - name: Lint with flake8
        run: |
          # stop the build if there are Python syntax errors or undefined names
          flake8
  mypy:
    runs-on: ubuntu-latest
    needs: setup
    steps:
      - uses: actions/checkout@v4
      - name: Set up Python
        uses: actions/setup-python@v2
        with:
          python-version: ${{ needs.setup.outputs.python_version }}
      - uses: actions/cache@v4
        with:
          path: ~/.cache/pip
          key: ${{ runner.os }}-pip-${{ hashFiles('**/Pipfile') }}
          restore-keys: |
            ${{ runner.os }}-pip-
      - name: Install pipenv
        run: |
          pip install pipenv
      - name: Install dependencies
        run: |
          pipenv sync --dev --system
      - name: Run mypy
        run: |
          python -m mypy .
  test:
    runs-on: ubuntu-latest
    needs: setup
    services:
      mysql:
        image: mysql:8.0
        ports:
          - 3306:3306
        env:
          MYSQL_ALLOW_EMPTY_PASSWORD: yes
          MYSQL_DATABASE: unified_warehouse_test
      sqlserver:
        image: mcr.microsoft.com/mssql/server:2019-latest
        ports:
          - 1433:1433
        env:
          ACCEPT_EULA: Y
          SA_PASSWORD: MyS3cr3tPassw0rd
    steps:
      - uses: actions/checkout@v4
      - name: Set up Python
        uses: actions/setup-python@v2
        with:
          python-version: ${{ needs.setup.outputs.python_version }}
      - uses: actions/cache@v4
        with:
          path: ~/.cache/pip
          key: ${{ runner.os }}-pip-${{ hashFiles('**/Pipfile') }}
          restore-keys: |
            ${{ runner.os }}-pip-
      - name: Install dependencies for building Python wheels (Ubuntu)
        run: |
          sudo apt-get update
          sudo apt-get install -y build-essential python3-dev libffi-dev libssl-dev libpq-dev unixodbc-dev
      - name: Install pipenv
        run: |
          pip install pipenv
      - name: Install dependencies
        run: |
          pipenv sync --dev --system
      - name: Start MongoDB
        uses: supercharge/mongodb-github-action@1.12.0
        with:
          mongodb-version: 8.0
          mongodb-replica-set: heron_rs
      - name: Setup the test MLWH and Events databases
        run: |
          python setup_test_db.py
      - name: Create SQL Server testing database
        run: |
          curl https://packages.microsoft.com/keys/microsoft.asc | sudo apt-key add -
          curl https://packages.microsoft.com/config/ubuntu/$(lsb_release -rs)/prod.list | sudo tee /etc/apt/sources.list.d/mssql-release.list
          sudo apt-get update
          sudo ACCEPT_EULA=Y apt-get install -y msodbcsql18
          python setup_sqlserver_test_db.py
      - name: Test with pytest
        run: |
          python -m pytest -x
      - name: Upload coverage to Codecov
        uses: codecov/codecov-action@v3
        env:
          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}