add new github action to execute Stefan's tests #57
Workflow file for this run
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name: Integration Tests & Code Style | |
on: | |
push: | |
branches: [ master, dev ] | |
pull_request: | |
branches: [ master, dev ] | |
jobs: | |
build-linux: | |
runs-on: ubuntu-latest | |
steps: | |
- name: Checkout Repo | |
uses: actions/checkout@v2 | |
with: | |
lfs: true | |
- name: Checkout LFS objects | |
run: git lfs checkout | |
- name: Set up Python | |
uses: actions/setup-python@v2 | |
- name: Install dependencies | |
run: | | |
$CONDA/bin/conda env update --file environment.yml --name base | |
- name: Lint with flake8 | |
run: | | |
$CONDA/bin/flake8 src/marbel/ | |
- name: Run tests with pytest | |
run: | | |
$CONDA/bin/pytest tests --doctest-modules --cov=src/marbel --cov-report=xml | |
- name: Convert coverage to lcov format | |
run: | | |
$CONDA/bin/coverage lcov | |
# - name: Send coverage report to Coveralls | |
# uses: coverallsapp/github-action@master | |
# with: | |
# github-token: ${{ secrets.GITHUB_TOKEN }} | |
# path-to-lcov: "coverage.lcov" | |
tests-functional: | |
runs-on: ubuntu-latest | |
defaults: | |
run: | |
shell: bash -l {0} | |
steps: | |
- name: Checkout Repo | |
uses: actions/checkout@v2 | |
with: | |
lfs: true | |
- name: Checkout LFS objects | |
run: git lfs checkout | |
- name: Set up Python | |
uses: actions/setup-python@v2 | |
- name: Create conda env | |
run: | | |
conda create -n marbel python=3.10 r-base | |
- name: Install the package | |
run: | | |
pip install -e . | |
- name: Simulate reads | |
run: | | |
marbel --n-species 3 --n-orthogroups 10 --n-samples 2 4 --library-size 5000 --outdir run_spec10_orth200_samp5-10/ | |
# - name: Create conda env for testing, i.e. install skbio and pandas | |
# uses: conda-incubator/setup-miniconda@v3 | |
# with: | |
# activate-environment: anaconda-client-env | |
# environment-file: tests/env_functional.yaml | |
# auto-activate-base: true | |
# - name: debug | |
# run: | | |
# pwd | |
- name: Create conda test-env | |
run: | | |
conda create -n marbel-tests scikit-bio | |
- name: Execute functional tests | |
run: | | |
conda info | |
conda env list | |
conda init | |
eval "$(conda shell.bash hook)" | |
conda activate marbel-tests | |
echo $CONDA_PREFIX | |
python tests/run_functional.py run_spec10_orth200_samp5-10/ |