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ci.yml
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name: Continous integration
on:
pull_request:
push:
branches:
- develop
- master
jobs:
lint:
runs-on: ubuntu-latest
strategy:
matrix:
python-version:
- "3.8"
steps:
- uses: actions/[email protected]
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v2
with:
python-version: ${{ matrix.python-version }}
- name: Install tox
run: pip install tox
- name: Lint
run: tox -e lint
docs:
runs-on: ubuntu-latest
steps:
- uses: actions/[email protected]
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v2
with:
python-version: ${{ matrix.python-version }}
- name: Install tox
run: pip install tox
- name: Build docs
run: tox -e docs
test:
runs-on: ubuntu-latest
strategy:
matrix:
python-version:
- "3.8"
- "3.9"
- "3.10"
- "3.11"
- "3.12"
steps:
- uses: actions/[email protected]
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v2
with:
python-version: ${{ matrix.python-version }}
- name: Install tox
run: pip install tox
- name: Run tests
run: tox -e py3
- name: Upload coverage report
uses: codecov/codecov-action@v1
test-functional-python-tools:
runs-on: ubuntu-latest
strategy:
matrix:
python-version: ["3.8"]
test-program: [snakemake, miniwdl]
steps:
- uses: actions/[email protected]
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v2
with:
python-version: ${{ matrix.python-version }}
- name: Install tox
run: pip install tox
- name: Test
shell: bash -l {0} # Needed for conda
run: tox -e ${{ matrix.test-program }}
test-functional-other:
runs-on: ubuntu-latest
strategy:
matrix:
test-program: [ cromwell, nextflow ]
steps:
- uses: actions/[email protected]
- name: Install conda
uses: conda-incubator/[email protected] # https://github.com/conda-incubator/setup-miniconda.
with:
channels: conda-forge,bioconda,defaults
installer-url: https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh
channel-priority: true
- name: Install test program and tox
shell: bash -l {0} # Needed for conda
run: mamba install ${{ matrix.test-program }} tox
- name: Test
shell: bash -l {0} # Needed for conda
run: tox -e ${{ matrix.test-program }}