merged develop and resolved conflicts

.github/actions/run_tests/entrypoint.sh

@@ -8,6 +8,8 @@ WS_PATH=$RUNNER_WORKSPACE/$REPO_NAME
 # set CI jobs directory variable to easily move it
 CI_JOBS_DIR=.github/jobs
 
+PYTESTS_GROUPS_FILEPATH=.github/parm/pytest_groups.txt
+
 source ${GITHUB_WORKSPACE}/${CI_JOBS_DIR}/bash_functions.sh
 
 # get branch name for push or pull request events
@@ -30,10 +32,8 @@ if [ $? != 0 ]; then
    ${GITHUB_WORKSPACE}/${CI_JOBS_DIR}/docker_setup.sh
 fi
 
-#
 # running unit tests (pytests)
-#
-if [ "$INPUT_CATEGORIES" == "pytests" ]; then
+if [[ "$INPUT_CATEGORIES" == pytests* ]]; then
   export METPLUS_ENV_TAG="pytest"
   export METPLUS_IMG_TAG=${branch_name}
   echo METPLUS_ENV_TAG=${METPLUS_ENV_TAG}
@@ -56,14 +56,20 @@ if [ "$INPUT_CATEGORIES" == "pytests" ]; then
 	 .
 
   echo Running Pytests
-  command="export METPLUS_PYTEST_HOST=docker; cd internal_tests/pytests; /usr/local/envs/pytest/bin/pytest -vv --cov=../../metplus"
+  command="export METPLUS_PYTEST_HOST=docker; cd internal_tests/pytests;"
+  command+="status=0;"
+  for x in `cat $PYTESTS_GROUPS_FILEPATH`; do
+    marker="${x//_or_/ or }"
+    marker="${marker//not_/not }"
+    command+="/usr/local/envs/pytest/bin/pytest -vv --cov=../../metplus -m \"$marker\""
+    command+=";if [ \$? != 0 ]; then status=1; fi;"
+  done
+  command+="if [ \$status != 0 ]; then echo ERROR: Some pytests failed. Search for FAILED to review; false; fi"
   time_command docker run -v $WS_PATH:$GITHUB_WORKSPACE --workdir $GITHUB_WORKSPACE $RUN_TAG bash -c "$command"
   exit $?
 fi
 
-#
 # running use case tests
-#
 
 # split apart use case category and subset list from input
 CATEGORIES=`echo $INPUT_CATEGORIES | awk -F: '{print $1}'`

.github/jobs/free_disk_space.sh

@@ -3,12 +3,13 @@
 echo Checking disk usage before cleanup
 df -h
 
-echo Removing files as suggested by https://github.com/actions/virtual-environments/issues/2840
+printf "\nRemoving files as suggested by https://github.com/actions/virtual-environments/issues/2840"
 
 sudo rm -rf /usr/share/dotnet
 sudo rm -rf /opt/ghc
 sudo rm -rf "/usr/local/share/boost"
 sudo rm -rf "$AGENT_TOOLSDIRECTORY"
 
-echo Checking disk usage after cleanup
+printf "\nChecking disk usage after cleanup"
+
 df -h

.github/jobs/get_metviewer.sh

@@ -24,7 +24,7 @@ docker ps -a
 # TODO: when METviewer Dockerfile changes METdatadb to METdataio, update path to sql file accordingly
 # commands to run inside METviewer container
 cmd="mysql -hmysql_mv -uroot -pmvuser -e\"create database mv_metplus_test;\";"
-cmd+="mysql -hmysql_mv -uroot -pmvuser mv_metplus_test < /METviewer-python/METdatadb/METdbLoad/sql/mv_mysql.sql"
+cmd+="mysql -hmysql_mv -uroot -pmvuser mv_metplus_test < /METviewer-python/METdataio/METdbLoad/sql/mv_mysql.sql"
 cmd+=";mysql -hmysql_mv -uroot -pmvuser -e\"show databases;\""
 
 # execute commands inside metviewer container to create database

.github/jobs/get_use_cases_to_run.sh

@@ -1,6 +1,7 @@
 #! /bin/bash
 
 use_case_groups_filepath=.github/parm/use_case_groups.json
+
 # set matrix to string of an empty array in case no use cases will be run
 matrix="[]"
 
@@ -31,12 +32,14 @@ fi
 if [ "$run_unit_tests" == "true" ]; then
   echo Adding unit tests to list to run
 
+  pytests="\"pytests\","
+
   # if matrix is empty, set to an array that only includes pytests
   if [ "$matrix" == "[]" ]; then
-    matrix="[\"pytests\"]"
+    matrix="[${pytests:0: -1}]"
   # otherwise prepend item to list
   else
-    matrix="[\"pytests\", ${matrix:1}"
+    matrix="[${pytests}${matrix:1}"
   fi
 fi
 

.github/parm/pytest_groups.txt

@@ -0,0 +1,6 @@
+util
+wrapper
+wrapper_a
+wrapper_b
+wrapper_c
+plotting_or_long

.github/workflows/testing.yml

@@ -142,24 +142,24 @@ jobs:
       # copy logs with errors to error_logs directory to save as artifact
       - name: Save error logs
         id: save-errors
-        if: ${{ always() && steps.run_tests.conclusion == 'failure' && matrix.categories != 'pytests' }}
+        if: ${{ always() && steps.run_tests.conclusion == 'failure' && !startsWith(matrix.categories,'pytests') }}
         run: .github/jobs/save_error_logs.sh
 
       # run difference testing
       - name: Run difference tests
         id: run-diff
-        if: ${{ needs.job_control.outputs.run_diff == 'true' && steps.run_tests.conclusion == 'success'  && matrix.categories != 'pytests' }}
+        if: ${{ needs.job_control.outputs.run_diff == 'true' && steps.run_tests.conclusion == 'success'  && !startsWith(matrix.categories,'pytests') }}
         run: .github/jobs/run_difference_tests.sh ${{ matrix.categories }} ${{ steps.get-artifact-name.outputs.artifact_name }}
 
       # copy output data to save as artifact
       - name: Save output data
         id: save-output
-        if: ${{ always() && steps.run_tests.conclusion != 'skipped'  && matrix.categories != 'pytests' }}
+        if: ${{ always() && steps.run_tests.conclusion != 'skipped'  && !startsWith(matrix.categories,'pytests') }}
         run: .github/jobs/copy_output_to_artifact.sh ${{ steps.get-artifact-name.outputs.artifact_name }}
 
       - name: Upload output data artifact
         uses: actions/upload-artifact@v2
-        if: ${{ always() && steps.run_tests.conclusion != 'skipped'  && matrix.categories != 'pytests' }}
+        if: ${{ always() && steps.run_tests.conclusion != 'skipped'  && !startsWith(matrix.categories,'pytests') }}
         with:
           name: ${{ steps.get-artifact-name.outputs.artifact_name }}
           path: artifact/${{ steps.get-artifact-name.outputs.artifact_name }}