adjust pytest calls in workflows to use coverage to call pytest as mo…

…dule, for appropriate data collection. adjust paths to globs in coveragerc

.github/workflows/create_test_conda_env.yml

@@ -33,7 +33,7 @@ jobs:
           export PATH="/opt/views/view/bin:$PATH"
 
           # run pytest
-          pytest --junit-xml=pytest_results.xml --config-file=fre/pytest.ini --cov-config=fre/coveragerc --cov-report=xml --cov=fre fre/
+          coverage run -m pytest --junit-xml=pytest_results.xml --config-file=fre/pytest.ini --cov-config=fre/coveragerc --cov-report=xml --cov=fre fre/
 
           # restore original path and install genbadge to generate coverage badge based on xml
           export PATH="$path_save"

fre/coveragerc

@@ -4,3 +4,12 @@ omit =
     fre/list/*
     fre/run/*
     fre/test/*
+    fre/tests/*
+    fre/analysis/tests/*
+    fre/app/generate_time_averages/tests/*
+    fre/app/regrid_xy/tests/*
+    fre/catalog/tests/*
+    fre/cmor/tests/*
+    fre/make/tests/*
+    fre/pp/tests/*
+    fre/yamltools/tests/*

fre/pytest.ini

@@ -1,11 +1,11 @@
 [pytest]
 testpaths =
     fre/tests
+    fre/analysis/tests
+    fre/app/generate_time_averages/tests
+    fre/app/regrid_xy/tests
     fre/catalog/tests
     fre/cmor/tests
     fre/make/tests
     fre/pp/tests
     fre/yamltools/tests
-    fre/analysis/tests
-    fre/app/generate_time_averages/tests
-    fre/app/regrid_xy/tests

meta.yaml

@@ -67,7 +67,7 @@ test:
   commands:
     - pylint --max-line-length 120 --max-args 6 -ry --ignored-modules netCDF4,cmor fre/ || echo "pylint returned non-zero exit code and will kill the workflow. guarding against this now."
     # run pytest but ignore any tests that require compilation
-    - pytest --ignore=fre/make/tests/compilation --config-file=fre/pytest.ini --cov-report term-missing --cov-config=fre/coveragerc --cov=fre fre/ 
+    - coverage run -m pytest --ignore=fre/make/tests/compilation --config-file=fre/pytest.ini --cov-report term-missing --cov-config=fre/coveragerc --cov=fre fre/ 
     - fre --help
     - fre app --help
     - fre catalog --help