Capture code coverage from intgration tests #42
Workflow file for this run
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name: CI | |
on: | |
pull_request: | |
push: | |
workflow_dispatch: | |
jobs: | |
tests: | |
runs-on: ubuntu-latest | |
steps: | |
- name: Checkout Repository | |
uses: actions/checkout@v2 | |
- name: Set up MicroMamba | |
uses: mamba-org/setup-micromamba@v1 | |
with: | |
environment-file: environment.yml | |
condarc: | | |
channels: | |
- conda-forge | |
- default | |
cache-environment: true | |
- name: Unit test with code coverage | |
shell: bash -l {0} | |
run: python -m pytest -vv --cov=postprocessing --cov=scripts --cov-report=xml --cov-report=term | |
- name: Upload coverage reports to Codecov | |
uses: codecov/codecov-action@v3 | |
env: | |
CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} | |
integration-tests: | |
runs-on: ubuntu-latest | |
needs: tests | |
steps: | |
- name: Checkout Repository | |
uses: actions/checkout@v2 | |
- name: Set up MicroMamba | |
uses: mamba-org/setup-micromamba@v1 | |
with: | |
environment-file: environment.yml | |
condarc: | | |
channels: | |
- conda-forge | |
- default | |
cache-environment: true | |
- name: start docker containers | |
run: docker-compose -f tests/integration/docker-compose.yml up --build -d | |
- name: sleep to wait for containers to start up | |
run: sleep 2 | |
- name: Run integration tests | |
shell: bash -l {0} | |
run: python -m pytest tests/integration | |
- name: stop docker containers | |
run: docker-compose -f tests/integration/docker-compose.yml stop | |
- name: copy code coverage out | |
run: docker cp integration_post_processing_agent_1:/opt/postprocessing/ /tmp/ | |
- name: combine and show coverage | |
run: | | |
cd /tmp/postprocessing | |
python -m coverage combine | |
python -m coverage report | |
- name: down docker containers | |
run: docker-compose -f tests/integration/docker-compose.yml down | |
rpm: | |
runs-on: ubuntu-latest | |
steps: | |
- name: Checkout Repository | |
uses: actions/checkout@v2 | |
- name: Build RPM inside Docker | |
run: | | |
docker build --tag postprocess --target=package -f Dockerfile . | |
fname=`docker run -v $(pwd):/store postprocess ls /root/rpmbuild/RPMS/noarch` | |
docker run -v `pwd`:/store postprocess mv /root/rpmbuild/RPMS/noarch/$fname /store | |
one=${fname#*postprocessing-} | |
two=${one%.noarch*} | |
echo "::set-output name=version::$two" | |
echo "::set-output name=fname::$fname" | |
continue-on-error: false | |
# TODO: uncomment this once we have switched to python3 and can conda install the module build | |
# wheel: | |
# runs-on: ubuntu-latest | |
# steps: | |
# - name: Checkout Repository | |
# uses: actions/checkout@v2 | |
# | |
# - name: Set up MicroMamba | |
# uses: mamba-org/setup-micromamba@v1 | |
# with: | |
# environment-file: environment.yml | |
# condarc: | | |
# channels: | |
# - conda-forge | |
# - default | |
# cache-environment: true | |
# | |
# - name: Build wheel | |
# shell: bash -l {0} | |
# run: python -m build --wheel |