galaxy_codex/.github/workflows/run_tests.yaml at main · galaxyproject/galaxy_codex · 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
name: Run tests

# This GitHub Actions workflow is designed to automate testing for the project.
# It triggers under two conditions:
# 1. Pull requests targeting the main branch, ensuring that internal changes
#    are validated before merging.
# 2. Pushes to the dev branch, allowing for continuous integration
#    as changes are made directly to the development branch.
#
# The workflow consists of three main jobs:
# - **test-tools**: Runs tests for tools extracted from the repository.
# - **test-tutorials**: Runs tests for community tutorials.
# - **test-workflows**: Runs tests for workflow scripts.
#
# Each job includes the following steps:
# - Checkout the repository code.
# - Set up the Python environment using the specified version.
# - Install required dependencies.
# - Execute scripts for extraction and filtering of tools, tutorials, or workflows.
#
# This ensures that the code remains reliable and functional as new changes are introduced.

on:
  pull_request:
    branches:
      - main  # Trigger on pull requests targeting the main branch
  push:
    branches:
      - dev  # Trigger on pushes to the dev branch

jobs:
  test-tools:
    runs-on: ubuntu-latest
    # This job runs tests for tools.
    # It checks for internal pull requests targeting the main branch,
    # as well as pushes to the dev branch.
    # The workflow performs the following steps:
    # 1. Checkout the repository code.
    # 2. Set up Python environment using the specified version.
    # 3. Install required Python packages.
    # 4. Extract tools using a provided script.
    # 5. Filter community tools using a provided script.
    # 6. Format tools into an interactive table and generate a word cloud.
    if: github.event.pull_request.head.repo.full_name == github.repository || github.ref == 'refs/heads/dev'
    strategy:
      matrix:
        python-version: ['3.11']
    environment: fetch-tools
    steps:
      - name: Checkout
        uses: actions/checkout@v6
      - uses: actions/setup-python@v6
        with:
          python-version: ${{ matrix.python-version }}
      - name: Install requirements
        run: python -m pip install -r requirements.txt
      - name: Tool extraction
        run: |
          bash sources/bin/extract_all_tools.sh test
        env:
          GITHUB_API_KEY: ${{ secrets.GH_API_TOKEN }}
      - name: Tool filter
        run: |
          bash sources/bin/get_community_tools.sh test
      - name: Create interactive table and wordcloud
        run: |
          bash sources/bin/format_tools.sh test

  test-tutorials:
    runs-on: ubuntu-latest
    # This job runs tests for tutorials.
    # Similar to the tools job, it checks for internal pull requests
    # to the main branch and pushes to the dev branch.
    # The workflow performs the following steps:
    # 1. Checkout the repository code.
    # 2. Set up Python environment using the specified version.
    # 3. Install required Python packages.
    # 4. Extract tutorials using a provided script.
    # 5. Filter community tutorials using a provided script.
    if: github.event.pull_request.head.repo.full_name == github.repository || github.ref == 'refs/heads/dev'
    strategy:
      matrix:
        python-version: ['3.11']
    steps:
      - name: Checkout
        uses: actions/checkout@v6
      - uses: actions/setup-python@v6
        with:
          python-version: ${{ matrix.python-version }}
      - name: Install requirements
        run: python -m pip install -r requirements.txt
      - name: Tutorial extraction
        run: |
          bash sources/bin/extract_all_tutorials.sh test
        env:
          PLAUSIBLE_API_KEY: ${{ secrets.PLAUSIBLE_API_TOKEN }}
      - name: Tutorial filtering
        run: |
          bash sources/bin/get_community_tutorials.sh test

  test-workflows:
    runs-on: ubuntu-latest
    # This job runs tests for workflows.
    # It performs the same checks as the other jobs, ensuring
    # quality for workflow scripts.
    if: github.event.pull_request.head.repo.full_name == github.repository || github.ref == 'refs/heads/dev'
    strategy:
      matrix:
        python-version: ['3.11']
    steps:
      - name: Checkout
        uses: actions/checkout@v6
      - uses: actions/setup-python@v6
        with:
          python-version: ${{ matrix.python-version }}
      - name: Install requirements
        run: python -m pip install -r requirements.txt
      - name: Workflow extraction
        run: |
          bash sources/bin/extract_all_workflows.sh test
      - name: Workflow filtering
        run: |
          bash sources/bin/get_community_workflows.sh test


#  test-citations:
#    runs-on: ubuntu-latest
    # This job runs tests for citations.
    # Similar to the tools job, it checks for internal pull requests
    # to the main branch and pushes to the dev branch.
    # The workflow performs the following steps:
    # 1. Checkout the repository code.
    # 2. Set up Python environment using the specified version.
    # 3. Install required Python packages.
    # 4. Extract citations using a provided script.
    # 5. Filter community citations using a provided script.
#    if: github.event.pull_request.head.repo.full_name == github.repository || github.ref == 'refs/heads/dev'
#    strategy:
#      matrix:
#        python-version: ['3.11']
#    steps:
#      - name: Checkout
#        uses: actions/checkout@v6
#      - uses: actions/setup-python@v6
#        with:
#          python-version: ${{ matrix.python-version }}
#      - name: Install requirements
#        run: python -m pip install -r requirements.txt
#      - name: Citation extraction
#        run: |
#          bash sources/bin/extract_all_citations.sh test
#      - name: Citation filtering
#        run: |
#          bash sources/bin/get_community_citations.sh test