From 13c5e90a021048dd88fa23679d49111edeb350fa Mon Sep 17 00:00:00 2001 From: Christopher Tomkins-Tinch Date: Thu, 25 Apr 2024 18:54:28 -0400 Subject: [PATCH] attempt to fix coverage reporting due to breaking changes in coveralls reporter see: https://github.com/coverallsapp/coverage-reporter/issues/124 https://github.com/coverallsapp/github-action/issues/205 additional refs: https://github.com/coverallsapp/github-action?tab=readme-ov-file https://github.com/coverallsapp/coverage-reporter#supported-coverage-report-formats --- .github/workflows/build.yml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index c624d0da..16f7fdaf 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -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