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attempt to fix coverage reporting due to breaking changes in coverall…
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tomkinsc committed Apr 25, 2024
1 parent d54f646 commit 13c5e90
Showing 1 changed file with 4 additions and 1 deletion.
5 changes: 4 additions & 1 deletion .github/workflows/build.yml
Original file line number Diff line number Diff line change
Expand Up @@ -187,9 +187,12 @@ jobs:
mkdir coverage
- name: test with docker
run: |
docker run -e _JAVA_OPTIONS -e PYTEST_ADDOPTS -v `pwd`/coverage:/coverage -v `pwd`/test:/opt/viral-ngs/source/test --entrypoint /bin/bash $DOCKER_TAG -c 'set -e; cd /opt/viral-ngs/source; pytest -n $(nproc) test/unit; cp .coverage /coverage'
docker run -e _JAVA_OPTIONS -e PYTEST_ADDOPTS -v `pwd`/.coveragerc:/opt/viral-ngs/source/.coveragerc -v `pwd`/coverage:/coverage -v `pwd`/test:/opt/viral-ngs/source/test:rw --entrypoint /bin/bash $DOCKER_TAG -c 'set -e; cd /opt/viral-ngs/source; pytest -n $(nproc) test/unit; ls -lah; cp coverage.xml /coverage/coverage.xml;'
- name: Run coveralls
uses: coverallsapp/github-action@v2
with:
file: coverage/coverage.xml
format: lcov

## note: this test_docs job does not actually produce the output on readthedocs
## readthedocs does its own build trigger. this job exists simply to alert us
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