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build.yml
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name: CI
on:
push:
pull_request:
branches: [main]
jobs:
build-and-test:
name: ${{ matrix.toolchain }}
runs-on: ${{ matrix.os }}
strategy:
matrix:
toolchain:
- linux-gcc
- macos-clang
#- windows-msvc
configuration:
- debug
include:
- toolchain: linux-gcc
os: ubuntu-latest
compiler: gcc
- toolchain: macos-clang
os: macos-latest
compiler: clang
#- toolchain: windows-msvc
# os: windows-latest
# compiler: msvc
steps:
- name: Checkout Code
uses: actions/checkout@v2
with:
submodules: true
- name: Setup ARTIC environment
uses: conda-incubator/setup-miniconda@v2
with:
python-version: 3.6
activate-environment: artic
environment-file: environment.yml
- name: Print ARTIC environment
shell: bash -l {0}
run: |
conda info
conda list
- name: Install ARTIC pipeline
shell: bash -l {0}
run: |
pip install .
artic --help
artic --version
- name: Run ARTIC pipeline unit tests
shell: bash -l {0}
run: pytest -s artic/*_unit_test.py
#- name: Run ARTIC pipeline pipeline tests
# shell: bash -l {0}
# run: |
# ./test-runner.sh medaka
# ./test-runner.sh nanopolish
- name: Run ARTIC pipeline validation tests
shell: bash -l {0}
run: |
pytest -s artic/minion_validator.py --workFlow nanopolish --numValidations 1
pytest -s artic/minion_validator.py --workFlow medaka --numValidations 2