DEBUGGING: mount .coveragerc within testing docker container

.coveragerc

@@ -8,10 +8,10 @@ disable_warnings =
 relative_files = True
 #data_file = '.coverage'
 
-[paths]
-source =
-    viral-phylo/
-    /opt/viral-ngs/viral-phylo
+# [paths]
+# source =
+#     viral-phylo/
+#     /opt/viral-ngs/viral-phylo
 
 [report]
 exclude_lines =

.github/workflows/build.yml

@@ -190,14 +190,9 @@ 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: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))"; pytest -n $(nproc) test/unit; cp .coverage /coverage'
+          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))"; pytest -n $(nproc) test/unit; cp .coverage /coverage'
       - name: Run coveralls
         uses: coverallsapp/github-action@v2
-      #- name: run coveralls
-      #  run: |
-      #    mv coverage/.coverage .
-      #    pip install coveralls>=1.3.0
-      #    coveralls --service=github
 
   ## 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

.gitignore

@@ -53,7 +53,8 @@ htmlcov/
 nosetests.xml
 pytest.xml
 coverage.xml
-.coverage*
+.coverage
+coverage/
 
 test/input/TestVPhaser2/in.bam.bti
 

conftest.py

@@ -46,8 +46,6 @@ def pytest_configure(config):
         "markers", "slow: marks tests as slow (deselect with '-m \"not slow\"')"
     )
 
-
-
 def pytest_collection_modifyitems(config, items):
     if config.getoption("--runslow"):
         # --runslow given in cli: do not skip slow tests