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planemo.yml
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name: Planemo
on: [push, pull_request]
env:
GALAXY_BRANCH: release_23.1
defaults:
run:
shell: bash -l {0}
# setup micromamba doesn't work as galaxy setup by planemo requires conda.
# installing conda over into micromamba built env screws up the PATH
# setup-miniconda + changing over to libmamba to solve is the easiest workaround
jobs:
planemo_test:
name: Planemo test
runs-on: ubuntu-latest
strategy:
matrix:
chunk: [1, 2, 3]
steps:
- uses: actions/checkout@v3
- uses: conda-incubator/setup-miniconda@v2
with:
miniconda-version: "latest"
auto-activate-base: true
- name: setup env
run: |
conda env list
conda install -n base conda-libmamba-solver
conda config --set solver libmamba
conda env create -f .github/test_and_build.yml -n test_and_build
- name: pip install
run: |
conda activate test_and_build
pip install .
- name: planemo
run: |
conda activate test_and_build
./.planemo.sh ${{ matrix.chunk }} ${{ env.GALAXY_BRANCH }}
- uses: actions/upload-artifact@v3
with:
name: 'Tool test output ${{ matrix.chunk }}'
path: upload
planemo_combine_outputs:
name: Combine chunked test results
needs: planemo_test
runs-on: ubuntu-latest
strategy:
matrix:
python-version: ['3.8', '3.11']
steps:
- uses: actions/download-artifact@v3
with:
path: artifacts
- uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}
- name: Cache .cache/pip
uses: actions/cache@v3
id: cache-pip
with:
path: ~/.cache/pip
key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ env.GALAXY_BRANCH }}
- name: Combine outputs
uses: galaxyproject/planemo-ci-action@v1
id: combine
with:
mode: combine
html-report: true
- uses: actions/upload-artifact@v3
with:
name: 'All tool test results'
path: upload
- name: Check outputs
uses: galaxyproject/planemo-ci-action@v1
id: check
with:
mode: check