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author fubar2
date Mon, 26 Apr 2021 04:18:54 +0000
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1 name: Galaxy Tool Linting and Tests for PR
2 # run planemo on a git repository containing a single tool
3 # as a github action.
4 # ross lazarus august 2020
5 on: [pull_request,push]
6 env:
7 GALAXY_REPO: https://github.com/galaxyproject/galaxy
8 GALAXY_RELEASE: release_20.05
9 jobs:
10 setup:
11 name: setup environment and python
12 runs-on: ubuntu-latest
13 strategy:
14 matrix:
15 python-version: [3.7]
16 steps:
17 - name: Print github context properties
18 run: |
19 echo 'event: ${{ github.event_name }}'
20 echo 'sha: ${{ github.sha }}'
21 echo 'ref: ${{ github.ref }}'
22 echo 'head_ref: ${{ github.head_ref }}'
23 echo 'base_ref: ${{ github.base_ref }}'
24 echo 'event.before: ${{ github.event.before }}'
25 echo 'event.after: ${{ github.event.after }}'
26 - uses: actions/setup-python@v1
27 with:
28 python-version: ${{ matrix.python-version }}
29 - uses: actions/checkout@v2
30 with:
31 # planemo does not seem to want to install the requirement galaxyxml
32 # into the venv it manages at tool testing so do it the old skool way
33 repository: 'galaxyproject/galaxy'
34 path: 'galaxy'
35 - name: make venv ready for this galaxy and planemo
36 run: |
37 python3 -m venv $GITHUB_WORKSPACE/galaxy/.venv
38 . $GITHUB_WORKSPACE/galaxy/.venv/bin/activate
39 pip install --upgrade pip
40 pip install wheel
41 pip install -r $GITHUB_WORKSPACE/galaxy/requirements.txt
42 - name: Upgrade pip
43 run: pip install --upgrade pip
44 # Install the `wheel` package so that when installing other packages which
45 # are not available as wheels, pip will build a wheel for them, which can be cached.
46 - name: Install wheel
47 run: pip install wheel
48 - name: Install Planemo and flake8
49 run: pip install planemo flake8 flake8-import-order
50 # galaxyxml temporarily removed until PR accepted
51 - uses: actions/checkout@v2
52 with:
53 fetch-depth: 1
54 - name: flake8 *.py
55 run: flake8 --ignore=E501,E203,W503,C901
56 - name: Planemo lint
57 run: planemo lint .
58 - name: Planemo test tool
59 run: planemo test --galaxy_root $GITHUB_WORKSPACE/galaxy --test_output tool_test_output.html --skip_venv --test_output_json tool_test_output.json --galaxy_python_version ${{ matrix.python-version }} .
60 - name: Copy artifacts into place
61 run: |
62 mkdir upload
63 mv tool_test_output.json tool_test_output.html upload/
64 - uses: actions/upload-artifact@v2.0.1
65 with:
66 name: 'All tool test results'
67 path: upload