From 67ed723dd9bf3972af05a1954b917769b1bae6cf Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 2 Aug 2023 09:57:40 -0600
Subject: [PATCH 01/26] run pytest from GHA environment instead of through Use
 Case Test action and try to run coveralls to generate coverage report

---
 .github/actions/run_tests/entrypoint.sh | 31 -----------------------
 .github/jobs/get_use_cases_to_run.sh    | 17 -------------
 .github/jobs/set_job_controls.sh        |  3 ++-
 .github/workflows/testing.yml           | 33 ++++++++++++++++++++-----
 internal/tests/pytests/.coveragerc      |  2 ++
 internal/tests/pytests/requirements.txt | 19 ++++++++++++++
 6 files changed, 50 insertions(+), 55 deletions(-)
 create mode 100644 internal/tests/pytests/.coveragerc
 create mode 100644 internal/tests/pytests/requirements.txt

diff --git a/.github/actions/run_tests/entrypoint.sh b/.github/actions/run_tests/entrypoint.sh
index 78ce25e08..732be6499 100644
--- a/.github/actions/run_tests/entrypoint.sh
+++ b/.github/actions/run_tests/entrypoint.sh
@@ -30,37 +30,6 @@ if [ $? != 0 ]; then
    ${GITHUB_WORKSPACE}/${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
diff --git a/.github/jobs/get_use_cases_to_run.sh b/.github/jobs/get_use_cases_to_run.sh
index 0d06a85df..d937f1f7a 100755
--- a/.github/jobs/get_use_cases_to_run.sh
+++ b/.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
diff --git a/.github/jobs/set_job_controls.sh b/.github/jobs/set_job_controls.sh
index f03c4809a..032197ff4 100755
--- a/.github/jobs/set_job_controls.sh
+++ b/.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
diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index aff2d9a49..0f2cc13e9 100644
--- a/.github/workflows/testing.yml
+++ b/.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
@@ -121,6 +122,26 @@ 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: pytest internal/tests/pytests --cov=metplus --cov-report=term-missing
+      - name: Run Coveralls
+        uses: AndreMiras/coveralls-python-action@v20201129
+
   use_case_tests:
     name: Use Case Tests
     runs-on: ubuntu-latest
@@ -158,24 +179,24 @@ 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 }}
diff --git a/internal/tests/pytests/.coveragerc b/internal/tests/pytests/.coveragerc
new file mode 100644
index 000000000..4edd7b1a2
--- /dev/null
+++ b/internal/tests/pytests/.coveragerc
@@ -0,0 +1,2 @@
+[run]
+relative_files = True
diff --git a/internal/tests/pytests/requirements.txt b/internal/tests/pytests/requirements.txt
new file mode 100644
index 000000000..0a4449537
--- /dev/null
+++ b/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

From 51588cb9ee941fcae19d2bca604db3bb01cc71b1 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 2 Aug 2023 10:52:00 -0600
Subject: [PATCH 02/26] set env var needed to run pytests

---
 .github/workflows/testing.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 0f2cc13e9..97fe391cd 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -139,6 +139,8 @@ jobs:
           python3 -m pip install -r internal/tests/pytests/requirements.txt
       - name: Run Pytests
         run: pytest internal/tests/pytests --cov=metplus --cov-report=term-missing
+        env:
+          METPLUS_TEST_OUTPUT_BASE: ${{ runner.workspace }}/pytest_output
       - name: Run Coveralls
         uses: AndreMiras/coveralls-python-action@v20201129
 

From 952dc15b407cbe172c6f673f3c8a5de0e1beb1c2 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 2 Aug 2023 11:03:32 -0600
Subject: [PATCH 03/26] add lcov report

---
 .github/workflows/testing.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 97fe391cd..05029c4fe 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -138,7 +138,7 @@ jobs:
           python3 -m pip install --upgrade pip
           python3 -m pip install -r internal/tests/pytests/requirements.txt
       - name: Run Pytests
-        run: pytest internal/tests/pytests --cov=metplus --cov-report=term-missing
+        run: pytest internal/tests/pytests --cov=metplus --cov-report=term-missing --cov-report lcov
         env:
           METPLUS_TEST_OUTPUT_BASE: ${{ runner.workspace }}/pytest_output
       - name: Run Coveralls

From 57c45f9e96a1c7a126964e2e38f5af6d4c53965d Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 2 Aug 2023 11:09:54 -0600
Subject: [PATCH 04/26] pass coverage config file to pytest command

---
 .github/workflows/testing.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 05029c4fe..b7d457430 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -138,7 +138,7 @@ jobs:
           python3 -m pip install --upgrade pip
           python3 -m pip install -r internal/tests/pytests/requirements.txt
       - name: Run Pytests
-        run: pytest internal/tests/pytests --cov=metplus --cov-report=term-missing --cov-report lcov
+        run: pytest internal/tests/pytests --cov=metplus --cov-report=term-missing --cov-config=.coveragerc
         env:
           METPLUS_TEST_OUTPUT_BASE: ${{ runner.workspace }}/pytest_output
       - name: Run Coveralls

From 4bda6d908c3bebcb1f0a76b53f1dc5503f6b6525 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 2 Aug 2023 11:46:14 -0600
Subject: [PATCH 05/26] pass github token

---
 .github/workflows/testing.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index b7d457430..84f5f8ba9 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -143,6 +143,8 @@ jobs:
           METPLUS_TEST_OUTPUT_BASE: ${{ runner.workspace }}/pytest_output
       - name: Run Coveralls
         uses: AndreMiras/coveralls-python-action@v20201129
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
 
   use_case_tests:
     name: Use Case Tests

From 18d0fe267594971733ee2ac16e3bfdd36efd7a1b Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 2 Aug 2023 12:20:07 -0600
Subject: [PATCH 06/26] call coverage to run pytests

---
 .github/workflows/testing.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 84f5f8ba9..9cca5adc3 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -138,7 +138,7 @@ jobs:
           python3 -m pip install --upgrade pip
           python3 -m pip install -r internal/tests/pytests/requirements.txt
       - name: Run Pytests
-        run: pytest internal/tests/pytests --cov=metplus --cov-report=term-missing --cov-config=.coveragerc
+        run: coverage run -m pytest internal/tests/pytests --cov=metplus --cov-report=term-missing --cov-config=.coveragerc
         env:
           METPLUS_TEST_OUTPUT_BASE: ${{ runner.workspace }}/pytest_output
       - name: Run Coveralls

From 3a4211ff7d81f050e8dfe93434b2efaf23741e90 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 2 Aug 2023 12:25:41 -0600
Subject: [PATCH 07/26] try running with lcov output

---
 .github/workflows/testing.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 9cca5adc3..228a8e0c1 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -138,7 +138,7 @@ jobs:
           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 --cov=metplus --cov-report=term-missing --cov-config=.coveragerc
+        run: coverage run -m pytest internal/tests/pytests --cov=metplus --cov-report=term-missing --cov-config=.coveragerc --cov-report lcov
         env:
           METPLUS_TEST_OUTPUT_BASE: ${{ runner.workspace }}/pytest_output
       - name: Run Coveralls

From d4a2c560868ea6f0d219c96263d067c1f5838467 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 2 Aug 2023 12:25:54 -0600
Subject: [PATCH 08/26] moved file back to top level

---
 internal/tests/pytests/.coveragerc => .coveragerc | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename internal/tests/pytests/.coveragerc => .coveragerc (100%)

diff --git a/internal/tests/pytests/.coveragerc b/.coveragerc
similarity index 100%
rename from internal/tests/pytests/.coveragerc
rename to .coveragerc

From cc1e6402737ce4d9bea6d058b7a69ae01ff731be Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 2 Aug 2023 12:40:27 -0600
Subject: [PATCH 09/26] use better shell syntax

---
 .github/actions/run_tests/entrypoint.sh | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/.github/actions/run_tests/entrypoint.sh b/.github/actions/run_tests/entrypoint.sh
index 732be6499..eecb719a2 100644
--- a/.github/actions/run_tests/entrypoint.sh
+++ b/.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
@@ -23,8 +23,7 @@ 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
@@ -33,8 +32,8 @@ 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 "${SUBSETLIST}" ]; then
@@ -42,7 +41,7 @@ if [ -z "${SUBSETLIST}" ]; then
 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

From 4e505bead101748611a454c437d4d0c9e59e4e27 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 2 Aug 2023 12:40:38 -0600
Subject: [PATCH 10/26] try again

---
 .github/workflows/testing.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 228a8e0c1..8973c4305 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -138,7 +138,7 @@ jobs:
           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 --cov=metplus --cov-report=term-missing --cov-config=.coveragerc --cov-report lcov
+        run: coverage run -m pytest internal/tests/pytests --cov=metplus --cov-report=term-missing
         env:
           METPLUS_TEST_OUTPUT_BASE: ${{ runner.workspace }}/pytest_output
       - name: Run Coveralls

From af996997ac0eb585c4f9241a0916eb1b4d909a9c Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 2 Aug 2023 12:45:33 -0600
Subject: [PATCH 11/26] run debug

---
 .github/workflows/testing.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 8973c4305..59c19827d 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -145,6 +145,7 @@ jobs:
         uses: AndreMiras/coveralls-python-action@v20201129
         with:
           github-token: ${{ secrets.GITHUB_TOKEN }}
+          debug: true
 
   use_case_tests:
     name: Use Case Tests

From a2ba6b74560b224dd23c3231d9228fd5b9797d57 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 2 Aug 2023 12:49:20 -0600
Subject: [PATCH 12/26] remove token and test if git is available

---
 .github/workflows/testing.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 59c19827d..a95228a3e 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -141,10 +141,10 @@ jobs:
         run: coverage run -m pytest internal/tests/pytests --cov=metplus --cov-report=term-missing
         env:
           METPLUS_TEST_OUTPUT_BASE: ${{ runner.workspace }}/pytest_output
+      - run: git config
       - name: Run Coveralls
         uses: AndreMiras/coveralls-python-action@v20201129
         with:
-          github-token: ${{ secrets.GITHUB_TOKEN }}
           debug: true
 
   use_case_tests:

From bdd14557b787eab9a621cf1c61f66c72b4c4e4b6 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 2 Aug 2023 12:52:50 -0600
Subject: [PATCH 13/26] remove git test

---
 .github/workflows/testing.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index a95228a3e..ef1bc59fc 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -141,7 +141,6 @@ jobs:
         run: coverage run -m pytest internal/tests/pytests --cov=metplus --cov-report=term-missing
         env:
           METPLUS_TEST_OUTPUT_BASE: ${{ runner.workspace }}/pytest_output
-      - run: git config
       - name: Run Coveralls
         uses: AndreMiras/coveralls-python-action@v20201129
         with:

From 060e08cd607c24517073a6e160b41c0a2ba06990 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 2 Aug 2023 12:55:32 -0600
Subject: [PATCH 14/26] try develop versiong

---
 .github/workflows/testing.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index ef1bc59fc..eaf71fad6 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -142,7 +142,7 @@ jobs:
         env:
           METPLUS_TEST_OUTPUT_BASE: ${{ runner.workspace }}/pytest_output
       - name: Run Coveralls
-        uses: AndreMiras/coveralls-python-action@v20201129
+        uses: AndreMiras/coveralls-python-action@develop
         with:
           debug: true
 

From e258e271b454f670a8db086e482459c2bcc763b3 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 2 Aug 2023 13:01:04 -0600
Subject: [PATCH 15/26] add token using dev

---
 .github/workflows/testing.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index eaf71fad6..4c6d32e20 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -144,6 +144,7 @@ jobs:
       - name: Run Coveralls
         uses: AndreMiras/coveralls-python-action@develop
         with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
           debug: true
 
   use_case_tests:

From feb6b88313bf8f5ccd4df0c01c419c39cfae0c5b Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 2 Aug 2023 13:06:11 -0600
Subject: [PATCH 16/26] try with lcov

---
 .github/workflows/testing.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 4c6d32e20..2b6a17900 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -138,7 +138,7 @@ jobs:
           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 --cov=metplus --cov-report=term-missing
+        run: coverage run -m pytest internal/tests/pytests --cov=metplus --cov-report=term-missing --cov-report lcov
         env:
           METPLUS_TEST_OUTPUT_BASE: ${{ runner.workspace }}/pytest_output
       - name: Run Coveralls

From c4f3caff749e7e48cd4e30b272269b180f1d10f7 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 2 Aug 2023 13:14:03 -0600
Subject: [PATCH 17/26] set source in coverage config

---
 .coveragerc | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.coveragerc b/.coveragerc
index 4edd7b1a2..d561722b1 100644
--- a/.coveragerc
+++ b/.coveragerc
@@ -1,2 +1,3 @@
 [run]
 relative_files = True
+source = metplus

From 4597024accb8f1e326008f65c3418bd640b86456 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 2 Aug 2023 13:23:54 -0600
Subject: [PATCH 18/26] run coverage then generate report

---
 .github/workflows/testing.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 2b6a17900..f2f116cfd 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -138,7 +138,9 @@ jobs:
           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 --cov=metplus --cov-report=term-missing --cov-report lcov
+        run: |
+          coverage run -m pytest internal/tests/pytests
+          coverage report -m
         env:
           METPLUS_TEST_OUTPUT_BASE: ${{ runner.workspace }}/pytest_output
       - name: Run Coveralls

From 2977a3b2ed039354b8d905bc27a013f822c11315 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 2 Aug 2023 13:29:14 -0600
Subject: [PATCH 19/26] split pytest run and coverage report into separate
 steps to catch failure if any tests fail

---
 .github/workflows/testing.yml | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index f2f116cfd..df6d4f59f 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -138,16 +138,15 @@ jobs:
           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
-          coverage report -m
+        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
       - name: Run Coveralls
         uses: AndreMiras/coveralls-python-action@develop
         with:
           github-token: ${{ secrets.GITHUB_TOKEN }}
-          debug: true
 
   use_case_tests:
     name: Use Case Tests

From c83575f5264653980530966200f52402defd3540 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 2 Aug 2023 13:30:10 -0600
Subject: [PATCH 20/26] force tests to fall to ensure that failure is properly
 captured

---
 .../tests/pytests/wrappers/grid_stat/test_grid_stat_wrapper.py  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/internal/tests/pytests/wrappers/grid_stat/test_grid_stat_wrapper.py b/internal/tests/pytests/wrappers/grid_stat/test_grid_stat_wrapper.py
index 80dfe6117..db29500a0 100644
--- a/internal/tests/pytests/wrappers/grid_stat/test_grid_stat_wrapper.py
+++ b/internal/tests/pytests/wrappers/grid_stat/test_grid_stat_wrapper.py
@@ -89,7 +89,7 @@ def set_minimum_config_settings(config):
 )
 @pytest.mark.wrapper_b
 def test_grid_stat_is_prob(metplus_config, config_overrides, expected_values):
-
+    assert False
     config = metplus_config
 
     set_minimum_config_settings(config)

From 0d354c06de4474351797ace02808c73f3226d080 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 2 Aug 2023 13:38:58 -0600
Subject: [PATCH 21/26] generate coverage report even if a test fails

---
 .github/workflows/testing.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index df6d4f59f..ba6fd4b45 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -143,8 +143,10 @@ jobs:
           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 }}
 

From 09a1317d9dc89a91e997264f8f9ef3ebc03de654 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 2 Aug 2023 13:49:48 -0600
Subject: [PATCH 22/26] require unit tests to pass to run use case tests

---
 .github/workflows/testing.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index ba6fd4b45..148d3de5b 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -153,7 +153,7 @@ jobs:
   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

From 6f6924947247eef9cd75b09b4367f74e4a88cb2e Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 2 Aug 2023 13:49:58 -0600
Subject: [PATCH 23/26] turn on use case group to test

---
 .github/parm/use_case_groups.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/parm/use_case_groups.json b/.github/parm/use_case_groups.json
index e8cc31f58..9ba895754 100644
--- a/.github/parm/use_case_groups.json
+++ b/.github/parm/use_case_groups.json
@@ -122,7 +122,7 @@
   {
     "category": "pbl",
     "index_list": "0",
-    "run": false
+    "run": true
   },
   {
     "category": "precipitation",

From 3aa3c6e1f851ee7fb304f9d1ed90e0564b7eb9ec Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 2 Aug 2023 13:53:11 -0600
Subject: [PATCH 24/26] remove force failure of unit test to test that use case
 will run

---
 .../tests/pytests/wrappers/grid_stat/test_grid_stat_wrapper.py   | 1 -
 1 file changed, 1 deletion(-)

diff --git a/internal/tests/pytests/wrappers/grid_stat/test_grid_stat_wrapper.py b/internal/tests/pytests/wrappers/grid_stat/test_grid_stat_wrapper.py
index db29500a0..c971c44ff 100644
--- a/internal/tests/pytests/wrappers/grid_stat/test_grid_stat_wrapper.py
+++ b/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):
-    assert False
     config = metplus_config
 
     set_minimum_config_settings(config)

From ca2eb5f688e4ea32441aad5910efe915d57944e3 Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 2 Aug 2023 14:06:01 -0600
Subject: [PATCH 25/26] turn off use case after test

---
 .github/parm/use_case_groups.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/parm/use_case_groups.json b/.github/parm/use_case_groups.json
index 9ba895754..e8cc31f58 100644
--- a/.github/parm/use_case_groups.json
+++ b/.github/parm/use_case_groups.json
@@ -122,7 +122,7 @@
   {
     "category": "pbl",
     "index_list": "0",
-    "run": true
+    "run": false
   },
   {
     "category": "precipitation",

From 109316a0326c0ea895ea8539e83402a17f0e073f Mon Sep 17 00:00:00 2001
From: George McCabe <23407799+georgemccabe@users.noreply.github.com>
Date: Wed, 2 Aug 2023 15:03:25 -0600
Subject: [PATCH 26/26] move helper script that is only used internally to
 internals directory

---
 docs/Contributors_Guide/basic_components.rst             | 6 +++---
 .../scripts/dev_tools/add_met_config_helper.py           | 9 ++++++---
 metplus/util/__init__.py                                 | 1 -
 3 files changed, 9 insertions(+), 7 deletions(-)
 rename metplus/util/doc_util.py => internal/scripts/dev_tools/add_met_config_helper.py (97%)

diff --git a/docs/Contributors_Guide/basic_components.rst b/docs/Contributors_Guide/basic_components.rst
index c386c03f7..441bb9320 100644
--- a/docs/Contributors_Guide/basic_components.rst
+++ b/docs/Contributors_Guide/basic_components.rst
@@ -252,13 +252,13 @@ 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.
@@ -266,7 +266,7 @@ 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
diff --git a/metplus/util/doc_util.py b/internal/scripts/dev_tools/add_met_config_helper.py
similarity index 97%
rename from metplus/util/doc_util.py
rename to internal/scripts/dev_tools/add_met_config_helper.py
index 05b826949..6cd8faaef 100755
--- a/metplus/util/doc_util.py
+++ b/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 '
diff --git a/metplus/util/__init__.py b/metplus/util/__init__.py
index 752469810..b5e7eeb8a 100644
--- a/metplus/util/__init__.py
+++ b/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 *