From 886658658c33655a3b6139c6fa94ac3ad6ab9f02 Mon Sep 17 00:00:00 2001 From: Christopher Tomkins-Tinch Date: Thu, 21 Mar 2024 21:20:51 -0400 Subject: [PATCH] mount .coveragerc within /viral-ngs/source rather than /viral-ngs/viral-phylo --- .github/workflows/build.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index fc886faf..85d3cec2 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -190,7 +190,7 @@ jobs: mkdir coverage - name: test with docker run: | - docker run -e _JAVA_OPTIONS -e PYTEST_ADDOPTS -v `pwd`/.coveragerc:/opt/viral-ngs/viral-phylo/.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; env; echo "LD_LIBRARY_PATH: $LD_LIBRARY_PATH"; export LD_LIBRARY_PATH="/opt/miniconda/envs/viral-ngs-env/lib:/usr/local/lib:${LD_LIBRARY_PATH}"; echo "nproc: $(nproc)"; python -c "import locale; print(locale.getpreferredencoding(False))"; cat .coveragerc; 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; env; echo "LD_LIBRARY_PATH: $LD_LIBRARY_PATH"; export LD_LIBRARY_PATH="/opt/miniconda/envs/viral-ngs-env/lib:/usr/local/lib:${LD_LIBRARY_PATH}"; echo "nproc: $(nproc)"; python -c "import locale; print(locale.getpreferredencoding(False))"; cat .coveragerc; pytest -n $(nproc) test/unit; cp .coverage /coverage' - name: Run coveralls uses: coverallsapp/github-action@v2 with: