Make code coverage report available

.coveragerc

@@ -0,0 +1,3 @@
+[run]
+relative_files = True
+source = metplus

.github/actions/run_tests/entrypoint.sh

@@ -12,7 +12,7 @@ source ${GITHUB_WORKSPACE}/${CI_JOBS_DIR}/bash_functions.sh
 
 # get branch name for push or pull request events
 # add -pull_request if pull request event to keep separated
-branch_name=`${GITHUB_WORKSPACE}/${CI_JOBS_DIR}/print_branch_name.py`
+branch_name=$(${GITHUB_WORKSPACE}/${CI_JOBS_DIR}/print_branch_name.py)
 if [ "$GITHUB_EVENT_NAME" == "pull_request" ]; then
   branch_name=${branch_name}-pull_request
 fi
@@ -23,57 +23,25 @@ time_command docker pull $DOCKERHUBTAG
 
 # if unsuccessful (i.e. pull request from a fork)
 # then build image locally
-docker inspect --type=image $DOCKERHUBTAG > /dev/null
-if [ $? != 0 ]; then
+if ! docker inspect --type=image $DOCKERHUBTAG > /dev/null; then
    # if docker pull fails, build locally
    echo docker pull failed. Building Docker image locally...
    ${GITHUB_WORKSPACE}/${CI_JOBS_DIR}/docker_setup.sh
 fi
 
-# running unit tests (pytests)
-if [[ "$INPUT_CATEGORIES" == pytests* ]]; then
-  export METPLUS_ENV_TAG="test.v5.1"
-  export METPLUS_IMG_TAG=${branch_name}
-  echo METPLUS_ENV_TAG=${METPLUS_ENV_TAG}
-  echo METPLUS_IMG_TAG=${METPLUS_IMG_TAG}
-
-  export RUN_TAG=metplus-run-env
-
-  # use BuildKit to build image
-  export DOCKER_BUILDKIT=1
-
-  start_seconds=$SECONDS
-
-  # build an image with the pytest conda env and the METplus branch image
-  # Note: adding --build-arg <arg-name> without any value tells docker to
-  #  use value from local environment (export METPLUS_IMG_TAG)
-  time_command docker build -t $RUN_TAG \
-	 --build-arg METPLUS_IMG_TAG \
-	 --build-arg METPLUS_ENV_TAG \
-	 -f .github/actions/run_tests/Dockerfile.run \
-	 .
-
-  echo Running Pytests
-  command="export METPLUS_TEST_OUTPUT_BASE=/data/output;"
-  command+="/usr/local/conda/envs/${METPLUS_ENV_TAG}/bin/pytest internal/tests/pytests -vv --cov=metplus --cov-append --cov-report=term-missing;"
-  command+="if [ \$? != 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}'`
-SUBSETLIST=`echo $INPUT_CATEGORIES | awk -F: '{print $2}'`
+CATEGORIES=$(echo $INPUT_CATEGORIES | awk -F: '{print $1}')
+SUBSETLIST=$(echo $INPUT_CATEGORIES | awk -F: '{print $2}')
 
 # run all cases if no subset list specified
 if [ -z "${SUBSETLIST}" ]; then
     SUBSETLIST="all"
 fi
 
 # get METviewer if used in any use cases
-all_requirements=`./${CI_JOBS_DIR}/get_requirements.py ${CATEGORIES} ${SUBSETLIST}`
+all_requirements=$(./${CI_JOBS_DIR}/get_requirements.py ${CATEGORIES} ${SUBSETLIST})
 echo All requirements: $all_requirements
 NETWORK_ARG=""
 if [[ "$all_requirements" =~ .*"metviewer".* ]]; then

.github/jobs/get_use_cases_to_run.sh

@@ -7,11 +7,9 @@ matrix="[]"
 
 run_use_cases=$1
 run_all_use_cases=$2
-run_unit_tests=$3
 
 echo Run use cases: $run_use_cases
 echo Run all use cases: $run_all_use_cases
-echo Run unit tests: $run_unit_tests
 
 # if running use cases, generate JQ filter to use
 if [ "$run_use_cases" == "true" ]; then
@@ -28,21 +26,6 @@ if [ "$run_use_cases" == "true" ]; then
 
 fi
 
-# if unit tests will be run, add "pytests" to beginning of matrix list
-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="[${pytests:0: -1}]"
-  # otherwise prepend item to list
-  else
-    matrix="[${pytests}${matrix:1}"
-  fi
-fi
-
 echo Array of groups to run is: $matrix
 # if matrix is still empty, exit 1 to fail step and skip rest of workflow
 if [ "$matrix" == "[]" ]; then

.github/jobs/set_job_controls.sh

@@ -87,6 +87,7 @@ fi
 echo "run_get_image=$run_get_image" >> $GITHUB_OUTPUT
 echo "run_get_input_data=$run_get_input_data" >> $GITHUB_OUTPUT
 echo "run_diff=$run_diff" >> $GITHUB_OUTPUT
+echo "run_unit_tests=$run_unit_tests" >> $GITHUB_OUTPUT
 echo "run_save_truth_data=$run_save_truth_data" >> $GITHUB_OUTPUT
 echo "external_trigger=$external_trigger" >> $GITHUB_OUTPUT
 
@@ -96,7 +97,7 @@ branch_name=`${GITHUB_WORKSPACE}/.github/jobs/print_branch_name.py`
 echo "branch_name=$branch_name" >> $GITHUB_OUTPUT
 
 # get use cases to run
-.github/jobs/get_use_cases_to_run.sh $run_use_cases $run_all_use_cases $run_unit_tests
+.github/jobs/get_use_cases_to_run.sh $run_use_cases $run_all_use_cases
 
 # echo output variables to review in logs
 echo branch_name: $branch_name

.github/workflows/testing.yml

@@ -79,6 +79,7 @@ jobs:
       run_get_image: ${{ steps.job_status.outputs.run_get_image }}
       run_get_input_data: ${{ steps.job_status.outputs.run_get_input_data }}
       run_diff: ${{ steps.job_status.outputs.run_diff }}
+      run_unit_tests: ${{ steps.job_status.outputs.run_unit_tests }}
       run_save_truth_data: ${{ steps.job_status.outputs.run_save_truth_data }}
       external_trigger: ${{ steps.job_status.outputs.external_trigger }}
       branch_name: ${{ steps.job_status.outputs.branch_name }}
@@ -87,7 +88,7 @@ jobs:
     name: Docker Setup - Get METplus Image
     runs-on: ubuntu-latest
     needs: job_control
-    if: ${{ needs.job_control.outputs.run_get_image == 'true' }}
+    if: ${{ needs.job_control.outputs.run_get_image == 'true' && needs.job_control.outputs.run_some_tests == 'true' }}
     steps:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
@@ -105,7 +106,7 @@ jobs:
     name: Docker Setup - Update Data Volumes
     runs-on: ubuntu-latest
     needs: job_control
-    if: ${{ needs.job_control.outputs.run_get_input_data == 'true' }}
+    if: ${{ needs.job_control.outputs.run_get_input_data == 'true' && needs.job_control.outputs.run_some_tests == 'true' }}
     continue-on-error: true
     steps:
       - uses: dtcenter/metplus-action-data-update@v2
@@ -121,10 +122,38 @@ jobs:
           use_feature_data: true
           tag_max_pages: 15
 
+  unit_tests:
+    name: Unit Tests
+    runs-on: ubuntu-latest
+    needs: [job_control]
+    if: ${{ needs.job_control.outputs.run_unit_tests == 'true' }}
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+          cache: 'pip'
+      - name: Install Python Test Dependencies
+        run: |
+          python3 -m pip install --upgrade pip
+          python3 -m pip install -r internal/tests/pytests/requirements.txt
+      - name: Run Pytests
+        run: coverage run -m pytest internal/tests/pytests
+        env:
+          METPLUS_TEST_OUTPUT_BASE: ${{ runner.workspace }}/pytest_output
+      - name: Generate coverage report
+        run: coverage report -m
+        if: always()
+      - name: Run Coveralls
+        uses: AndreMiras/coveralls-python-action@develop
+        if: always()
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+
   use_case_tests:
     name: Use Case Tests
     runs-on: ubuntu-latest
-    needs: [get_image, update_data_volumes, job_control]
+    needs: [get_image, update_data_volumes, job_control, unit_tests]
     if: ${{ needs.job_control.outputs.run_some_tests == 'true' }}
     strategy:
       fail-fast: false
@@ -158,24 +187,24 @@ 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' && !startsWith(matrix.categories,'pytests') }}
+        if: ${{ always() && steps.run_tests.conclusion == 'failure' }}
         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'  && !startsWith(matrix.categories,'pytests') }}
+        if: ${{ needs.job_control.outputs.run_diff == 'true' && steps.run_tests.conclusion == 'success' }}
         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'  && !startsWith(matrix.categories,'pytests') }}
+        if: ${{ always() && steps.run_tests.conclusion != 'skipped' }}
         run: .github/jobs/copy_output_to_artifact.sh ${{ steps.get-artifact-name.outputs.artifact_name }}
 
       - name: Upload output data artifact
         uses: actions/upload-artifact@v3
-        if: ${{ always() && steps.run_tests.conclusion != 'skipped'  && !startsWith(matrix.categories,'pytests') }}
+        if: ${{ always() && steps.run_tests.conclusion != 'skipped' }}
         with:
           name: ${{ steps.get-artifact-name.outputs.artifact_name }}
           path: artifact/${{ steps.get-artifact-name.outputs.artifact_name }}

docs/Contributors_Guide/basic_components.rst

@@ -252,21 +252,21 @@ used to easily add support for overriding MET configuration variables that
 were not previously supported in METplus configuration files.
 
 There is a utility that can be used to easily see what changes are needed to
-add support for a new variable. The doc_util.py script can be run from the
+add support for a new variable. The add_met_config_helper.py script can be run from the
 command line to output a list of instructions to add new support. It can
 be run from the top level of the METplus repository. The script can be called
 to add a single MET configuration variable by supplying the MET tool name and
 the variable name::
 
-    ./metplus/util/doc_util.py point_stat sid_exc
+    ./internal/scripts/dev_tools/add_met_config_helper.py point_stat sid_exc
 
 This command will provide guidance for adding support for the sid_exc variable
 found in the PointStatConfig file.
 
 The script can also be called with the name of a dictionary and the names of
 each dictionary variable::
 
-    ./metplus/util/doc_util.py grid_stat distance_map baddeley_p baddeley_max_dist fom_alpha zhu_weight beta_value_n
+    ./internal/scripts/dev_tools/add_met_config_helper.py grid_stat distance_map baddeley_p baddeley_max_dist fom_alpha zhu_weight beta_value_n
 
 This command will provide guidance for adding support for the distance_map
 dictionary found in the GridStatConfig file. The list of variables found inside

metplus/util/doc_util.py → internal/scripts/dev_tools/add_met_config_helper.py

@@ -11,10 +11,13 @@
 import os
 
 try:
-    from .string_manip import get_wrapper_name
+    from metplus.util.string_manip import get_wrapper_name
 except ImportError:
-    sys.path.insert(0, os.path.abspath(os.path.dirname(__file__)))
-    from string_manip import get_wrapper_name
+    # if metplus package is not installed, find util relative to this script
+    metplus_home = os.path.join(os.path.dirname(__file__),
+                                os.pardir, os.pardir, os.pardir)
+    sys.path.insert(0, os.path.abspath(metplus_home))
+    from metplus.util.string_manip import get_wrapper_name
 
 SCRIPT_INFO_TEXT = (
     'This script is intended to help developers add support for setting '

internal/tests/pytests/requirements.txt

@@ -0,0 +1,19 @@
+certifi==2023.7.22
+cftime==1.6.2
+coverage==7.2.7
+exceptiongroup==1.1.2
+iniconfig==2.0.0
+netCDF4==1.6.4
+numpy==1.25.2
+packaging==23.1
+pandas==2.0.3
+pdf2image==1.16.3
+Pillow==10.0.0
+pluggy==1.2.0
+pytest==7.4.0
+pytest-cov==4.1.0
+python-dateutil==2.8.2
+pytz==2023.3
+six==1.16.0
+tomli==2.0.1
+tzdata==2023.3

internal/tests/pytests/wrappers/grid_stat/test_grid_stat_wrapper.py

@@ -89,7 +89,6 @@ def set_minimum_config_settings(config):
 )
 @pytest.mark.wrapper_b
 def test_grid_stat_is_prob(metplus_config, config_overrides, expected_values):
-
     config = metplus_config
 
     set_minimum_config_settings(config)

metplus/util/__init__.py

@@ -7,7 +7,6 @@
 from .config_util import *
 from .config_metplus import *
 from .config_validate import *
-from .doc_util import *
 from .run_util import *
 from .met_config import *
 from .time_looping import *