From e48325e02f7d1bd3b9430696517a423cbdc7f725 Mon Sep 17 00:00:00 2001
From: John Halley Gotway <johnhg@ucar.edu>
Date: Thu, 4 Apr 2024 12:01:21 -0600
Subject: [PATCH 1/6] Per #366, add SonarQube workflow for METcalcpy

---
 .github/jobs/configure_sonarqube.sh           | 65 ++++++++++++++++
 .github/pull_request_template.md              |  3 +
 .github/workflows/sonarqube.yml               | 76 +++++++++++++++++++
 .../installation/modulefiles/2.1.0_hera       | 13 ----
 internal/scripts/sonarqube/run_sonarqube.sh   | 42 ++++++----
 .../sonarqube/sonar-project.properties        | 22 ++----
 6 files changed, 181 insertions(+), 40 deletions(-)
 create mode 100755 .github/jobs/configure_sonarqube.sh
 create mode 100644 .github/workflows/sonarqube.yml
 delete mode 100644 internal/scripts/scripts/installation/modulefiles/2.1.0_hera

diff --git a/.github/jobs/configure_sonarqube.sh b/.github/jobs/configure_sonarqube.sh
new file mode 100755
index 00000000..929b03fa
--- /dev/null
+++ b/.github/jobs/configure_sonarqube.sh
@@ -0,0 +1,65 @@
+#!/bin/bash
+
+# Constants
+SONAR_PROPERTIES_DIR=internal/scripts/sonarqube
+SONAR_PROPERTIES=sonar-project.properties
+
+# Check that this is being run from the top-level METdataio directory
+if [ ! -e $SONAR_PROPERTIES_DIR/$SONAR_PROPERTIES ]; then
+  echo "ERROR: ${0} -> must be run from the top-level METdataio directory"
+  exit 1
+fi
+
+# Check required environment variables
+if [ -z ${SOURCE_BRANCH+x} ]; then
+  echo "ERROR: ${0} -> \$SOURCE_BRANCH not defined!"
+  exit 1
+fi
+if [ -z ${WD_REFERENCE_BRANCH+x} ]; then
+  echo "ERROR: ${0} -> \$WD_REFERENCE_BRANCH not defined!"
+  exit 1
+fi
+if [ -z ${SONAR_HOST_URL+x} ]; then
+  echo "ERROR: ${0} -> \$SONAR_HOST_URL not defined!"
+  exit 1
+fi
+if [ -z ${SONAR_TOKEN+x} ]; then
+  echo "ERROR: ${0} -> \$SONAR_TOKEN not defined!"
+  exit 1
+fi
+
+# Define the version string
+SONAR_PROJECT_VERSION=$(cat docs/version | cut -d'=' -f2 | tr -d '" ')
+
+#
+# Define the $SONAR_REFERENCE_BRANCH as the
+#   - Target of any requests
+#   - Manual setting for workflow dispatch
+#   - Source branch for any pushes (e.g. develop)
+#
+if [ "$GITHUB_EVENT_NAME" == "pull_request" ]; then
+  export SONAR_REFERENCE_BRANCH=$GITHUB_BASE_REF
+elif [ "$GITHUB_EVENT_NAME" == "workflow_dispatch" ]; then
+  export SONAR_REFERENCE_BRANCH=$WD_REFERENCE_BRANCH
+else
+  export SONAR_REFERENCE_BRANCH=$SOURCE_BRANCH
+fi
+
+# Configure the sonar-project.properties
+[ -e $SONAR_PROPERTIES ] && rm $SONAR_PROPERTIES
+sed -e "s|SONAR_PROJECT_KEY|METdataio-GHA|" \
+    -e "s|SONAR_PROJECT_NAME|METdataio GHA|" \
+    -e "s|SONAR_PROJECT_VERSION|$SONAR_PROJECT_VERSION|" \
+    -e "s|SONAR_HOST_URL|$SONAR_HOST_URL|" \
+    -e "s|SONAR_TOKEN|$SONAR_TOKEN|" \
+    -e "s|SONAR_BRANCH_NAME|$SOURCE_BRANCH|" \
+    $SONAR_PROPERTIES_DIR/$SONAR_PROPERTIES > $SONAR_PROPERTIES
+
+# Define new code when the source and reference branches differ
+if [ "$SOURCE_BRANCH" != "$SONAR_REFERENCE_BRANCH" ]; then
+  echo "sonar.newCode.referenceBranch=${SONAR_REFERENCE_BRANCH}" >> $SONAR_PROPERTIES
+fi
+
+echo "Contents of the $SONAR_PROPERTIES file:"
+cat $SONAR_PROPERTIES
+
diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
index dda54835..342abeb9 100644
--- a/.github/pull_request_template.md
+++ b/.github/pull_request_template.md
@@ -11,6 +11,9 @@
 - [ ] Will this PR result in changes to the test suite? **[Yes or No]**</br>
 If **yes**, describe the new output and/or changes to the existing output:</br>
 
+- [ ] Do these changes introduce new SonarQube findings? **[Yes or No]**</br>
+If **yes**, please describe:
+
 - [ ] Please complete this pull request review by **[Fill in date]**.</br>
 
 ## Pull Request Checklist ##
diff --git a/.github/workflows/sonarqube.yml b/.github/workflows/sonarqube.yml
new file mode 100644
index 00000000..d48e1237
--- /dev/null
+++ b/.github/workflows/sonarqube.yml
@@ -0,0 +1,76 @@
+name: SonarQube Scan
+
+# Run SonarQube for Pull Requests and changes to the develop and main_vX.Y branches
+
+on:
+
+  # Trigger analysis for pushes to develop and main_vX.Y branches
+  push:
+    branches:
+      - develop
+      - 'main_v**'
+    paths-ignore:
+      - 'docs/**'
+      - '.github/pull_request_template.md'
+      - '.github/ISSUE_TEMPLATE/**'
+      - '**/README.md'
+      - '**/LICENSE.md'
+
+  # Trigger analysis for pull requests to develop and main_vX.Y branches
+  pull_request:
+    types: [opened, synchronize, reopened]
+    branches:
+      - develop
+      - 'main_v**'
+    paths-ignore:
+      - 'docs/**'
+      - '.github/pull_request_template.md'
+      - '.github/ISSUE_TEMPLATE/**'
+      - '**/README.md'
+      - '**/LICENSE.md'
+
+  workflow_dispatch:
+    inputs:
+      reference_branch:
+        description: 'Reference Branch'
+        default: develop
+        type: string
+
+jobs:
+  sonarqube:
+    name: SonarQube Scan
+    runs-on: ubuntu-latest
+
+    steps:
+
+    - uses: actions/checkout@v4
+      with:
+        # Disable shallow clones for better analysis
+        fetch-depth: 0
+
+    - name: Get branch name
+      id: get_branch_name
+      run: echo branch_name=${GITHUB_REF#refs/heads/} >> $GITHUB_OUTPUT
+
+    - name: Configure SonarQube
+      run: .github/jobs/configure_sonarqube.sh
+      env:
+        SOURCE_BRANCH: ${{ steps.get_branch_name.outputs.branch_name }}
+        WD_REFERENCE_BRANCH: ${{ github.event.inputs.reference_branch }}
+        SONAR_HOST_URL: ${{ secrets.SONAR_HOST_URL }}
+        SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
+
+    - name: SonarQube Scan
+      uses: sonarsource/sonarqube-scan-action@master
+      env:
+        SONAR_HOST_URL: ${{ secrets.SONAR_HOST_URL }}
+        SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
+
+    - name: SonarQube Quality Gate check
+      id: sonarqube-quality-gate-check
+      uses: sonarsource/sonarqube-quality-gate-action@master
+      # Force to fail step after specific time.
+      timeout-minutes: 5
+      env:
+       SONAR_HOST_URL: ${{ secrets.SONAR_HOST_URL }}
+       SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
diff --git a/internal/scripts/scripts/installation/modulefiles/2.1.0_hera b/internal/scripts/scripts/installation/modulefiles/2.1.0_hera
deleted file mode 100644
index f0863ba0..00000000
--- a/internal/scripts/scripts/installation/modulefiles/2.1.0_hera
+++ /dev/null
@@ -1,13 +0,0 @@
-#%Module######################################################################
-##
-##      METcalcpy
-##
-proc ModulesHelp { } {
-  puts stderr "Sets up the paths and environment variables to use the METcalcpy-2.1.0.
-     *** For help see the official MET webpage at http://www.dtcenter.org/met/users ***"
-}
-
-prereq intel
-
-prepend-path PATH /scratch1/BMC/dtc/miniconda/miniconda3/envs/metplus_v5.1_py3.10/bin
-prepend-path PYTHONPATH /contrib/METcalcpy/METcalcpy-2.1.0
diff --git a/internal/scripts/sonarqube/run_sonarqube.sh b/internal/scripts/sonarqube/run_sonarqube.sh
index b3d57817..d43df3ec 100755
--- a/internal/scripts/sonarqube/run_sonarqube.sh
+++ b/internal/scripts/sonarqube/run_sonarqube.sh
@@ -1,10 +1,10 @@
 #!/bin/bash
 #
-# Run SonarQube Source Code Analyzer on a specified revision of MET
+# Run SonarQube Source Code Analyzer for METcalcpy
 #=======================================================================
 #
 # This run_sonarqube.sh script will check out the specified version
-# of MET and run the SonarQube Source Code Analyzer on it.  First,
+# of METcalcpy and run the SonarQube Source Code Analyzer on it.  First,
 # go to the directory where you would like the SCA output written and
 # then run:
 #
@@ -12,9 +12,9 @@
 #    METcalcpy/sonarqube/run_sonarqube.sh name
 #
 # Usage: run_sonarqube.sh name
-#    Test the specified branched version of MET:
+#    Test the specified branched version of METcalcpy:
 #       run_sonarqube.sh {branch name}
-#    Test the specified tagged version of MET:
+#    Test the specified tagged version of METcalcpy:
 #       run_sonarqube.sh {tag name}
 #
 #=======================================================================
@@ -24,15 +24,25 @@ GIT_REPO_NAME=METcalcpy
 GIT_REPO="https://github.com/dtcenter/${GIT_REPO_NAME}"
 
 function usage {
-        echo
-        echo "USAGE: $(basename $0) name"
-        echo "   where \"name\" specifies a branch, tag, or hash."
-        echo
+  echo
+  echo "USAGE: $(basename $0) name"
+  echo "   where \"name\" specifies a branch, tag, or hash."
+  echo
 }
 
 # Check for arguments
 if [[ $# -lt 1 ]]; then usage; exit; fi
 
+# Check that SONAR_TOKEN and SONAR_HOST_URL are defined
+if [ -z ${SONAR_TOKEN} ]; then
+  echo "ERROR: SONAR_TOKEN must be set"
+  exit 1
+fi
+if [ -z ${SONAR_HOST_URL} ]; then
+  echo "ERROR: SONAR_HOST_URL must be set"
+  exit 1
+fi
+
 # Check that SONARQUBE_WRAPPER_BIN is defined
 if [ -z ${SONARQUBE_WRAPPER_BIN} ]; then
   which build-wrapper-linux-x86-64 2> /dev/null
@@ -87,7 +97,6 @@ function run_command() {
   return ${STATUS}
 }
 
-
 # Store the full path to the scripts directory
 SCRIPT_DIR=`dirname $0`
 if [[ ${0:0:1} != "/" ]]; then SCRIPT_DIR=$(pwd)/${SCRIPT_DIR}; fi 
@@ -102,14 +111,21 @@ run_command "git clone ${GIT_REPO} ${REPO_DIR}"
 run_command "cd ${REPO_DIR}"
 run_command "git checkout ${1}"
 
+# Define the version string
+SONAR_PROJECT_VERSION=$(cat docs/version | cut -d'=' -f2 | tr -d '" ')
+
 SONAR_PROPERTIES=sonar-project.properties
 
-# Copy sonar-project.properties for Python code
+# Configure the sonar-project.properties
 [ -e $SONAR_PROPERTIES ] && rm $SONAR_PROPERTIES
-cp -p $SCRIPT_DIR/sonar-project.properties $SONAR_PROPERTIES
+sed -e "s|SONAR_PROJECT_KEY|METcalcpy_NB|" \
+    -e "s|SONAR_PROJECT_NAME|METcalcpy Nightly Build|" \
+    -e "s|SONAR_PROJECT_VERSION|$SONAR_PROJECT_VERSION|" \
+    -e "s|SONAR_HOST_URL|$SONAR_HOST_URL|" \
+    -e "s|SONAR_TOKEN|$SONAR_TOKEN|" \
+    -e "s|SONAR_BRANCH_NAME|${1}|" \
+    $SCRIPT_DIR/$SONAR_PROPERTIES > $SONAR_PROPERTIES
 
 # Run SonarQube scan for Python code
 run_command "${SONARQUBE_SCANNER_BIN}/sonar-scanner"
 
-# Run SonarQube report generator to make a PDF file
-#TODAY=`date +%Y%m%d`
diff --git a/internal/scripts/sonarqube/sonar-project.properties b/internal/scripts/sonarqube/sonar-project.properties
index 35335020..37755f03 100644
--- a/internal/scripts/sonarqube/sonar-project.properties
+++ b/internal/scripts/sonarqube/sonar-project.properties
@@ -1,17 +1,11 @@
-sonar.projectKey=org.sonarqube:METcalcpy_NB
-sonar.projectName=METcalcpy Nightly Build
-sonar.projectVersion=1.0
-
+# Project and source code settings
+sonar.projectKey=SONAR_PROJECT_KEY
+sonar.projectName=SONAR_PROJECT_NAME
+sonar.projectVersion=SONAR_PROJECT_VERSION
+sonar.branch.name=SONAR_BRANCH_NAME
 sonar.sources=metcalcpy,scratch,test
-
-# The build-wrapper output dir
-
-# Encoding of the source files
 sonar.sourceEncoding=UTF-8
 
-#----- Default SonarQube server
-#sonar.host.url=http://localhost:9000
-sonar.host.url=http://mandan:9000
-
-sonar.login=met
-sonar.password=met@sonar.ucar
+# SonarQube server
+sonar.host.url=SONAR_HOST_URL
+sonar.token=SONAR_TOKEN

From 5d9b1923db785faeb0313728c65625b1ea644f7e Mon Sep 17 00:00:00 2001
From: John Halley Gotway <johnhg@ucar.edu>
Date: Thu, 4 Apr 2024 12:24:49 -0600
Subject: [PATCH 2/6] Per #366, update nightly build email list.

---
 internal/scripts/sonarqube/run_nightly.sh | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/internal/scripts/sonarqube/run_nightly.sh b/internal/scripts/sonarqube/run_nightly.sh
index ad1935ea..fe257b6c 100755
--- a/internal/scripts/sonarqube/run_nightly.sh
+++ b/internal/scripts/sonarqube/run_nightly.sh
@@ -12,7 +12,7 @@
 #    METcalcpy/sonarqube/run_nightly.sh name
 #
 # Usage: run_nightly.sh name
-#    where "name" speci1fies a branch, tag, or hash
+#    where "name" specifies a branch, tag, or hash
 #
 # For example, scan the develop branch:
 #    run_nightly.sh develop
@@ -20,8 +20,7 @@
 #=======================================================================
 
 # Constants
-EMAIL_LIST="johnhg@ucar.edu hsoh@ucar.edu mccabe@ucar.edu minnawin@ucar.edu"
-TEST_EMAIL_LIST="hsoh@ucar.edu"
+EMAIL_LIST="johnhg@ucar.edu hsoh@ucar.edu jpresto@ucar.edu minnawin@ucar.edu"
 KEEP_DAYS=5
 GIT_REPO_NAME=METcalcpy
 
@@ -68,12 +67,9 @@ LOGFILE=${RUN_DIR}/run_sonarqube_${TODAY}.log
 # Run scan and check for bad return status
 ${SCRIPT_DIR}/run_sonarqube.sh ${1} >& ${LOGFILE}
 if [[ $? -ne 0 ]]; then
-  [ ! -z $2 ] && EMAIL_LIST=$TEST_EMAIL_LIST
   echo "$0: The nightly SonarQube scanning for $GIT_REPO_NAME FAILED in `basename ${RUN_DIR}`." >> ${LOGFILE}
   cat ${LOGFILE} | mail -s "$GIT_REPO_NAME SonarQube scanning failed for ${1} in `basename ${RUN_DIR}` (autogen msg)" ${EMAIL_LIST}
   exit 1
 fi
 
-# Convert SonarQube report from pdf to html
-
 exit 0

From 46ba354b83b7d055a846094b5fb8384901ba653a Mon Sep 17 00:00:00 2001
From: John Halley Gotway <johnhg@ucar.edu>
Date: Thu, 4 Apr 2024 21:07:07 +0000
Subject: [PATCH 3/6] Per #366, fix cut/paste error in the
 configure_sonarqube.sh script.

---
 .github/jobs/configure_sonarqube.sh | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/jobs/configure_sonarqube.sh b/.github/jobs/configure_sonarqube.sh
index 929b03fa..aedcb9ae 100755
--- a/.github/jobs/configure_sonarqube.sh
+++ b/.github/jobs/configure_sonarqube.sh
@@ -4,9 +4,9 @@
 SONAR_PROPERTIES_DIR=internal/scripts/sonarqube
 SONAR_PROPERTIES=sonar-project.properties
 
-# Check that this is being run from the top-level METdataio directory
+# Check that this is being run from the top-level METcalcpy directory
 if [ ! -e $SONAR_PROPERTIES_DIR/$SONAR_PROPERTIES ]; then
-  echo "ERROR: ${0} -> must be run from the top-level METdataio directory"
+  echo "ERROR: ${0} -> must be run from the top-level METcalcpy directory"
   exit 1
 fi
 
@@ -47,8 +47,8 @@ fi
 
 # Configure the sonar-project.properties
 [ -e $SONAR_PROPERTIES ] && rm $SONAR_PROPERTIES
-sed -e "s|SONAR_PROJECT_KEY|METdataio-GHA|" \
-    -e "s|SONAR_PROJECT_NAME|METdataio GHA|" \
+sed -e "s|SONAR_PROJECT_KEY|METcalcpy-GHA|" \
+    -e "s|SONAR_PROJECT_NAME|METcalcpy GHA|" \
     -e "s|SONAR_PROJECT_VERSION|$SONAR_PROJECT_VERSION|" \
     -e "s|SONAR_HOST_URL|$SONAR_HOST_URL|" \
     -e "s|SONAR_TOKEN|$SONAR_TOKEN|" \

From 8ce98e87c90e85bf8fefcf03d0b3b83deb749511 Mon Sep 17 00:00:00 2001
From: John Halley Gotway <johnhg@ucar.edu>
Date: Thu, 4 Apr 2024 18:35:23 -0600
Subject: [PATCH 4/6] Per #366, just whitespace change to trigger another GHA
 run for the PR

---
 internal/scripts/sonarqube/sonar-project.properties | 1 +
 1 file changed, 1 insertion(+)

diff --git a/internal/scripts/sonarqube/sonar-project.properties b/internal/scripts/sonarqube/sonar-project.properties
index 37755f03..8b24cea0 100644
--- a/internal/scripts/sonarqube/sonar-project.properties
+++ b/internal/scripts/sonarqube/sonar-project.properties
@@ -9,3 +9,4 @@ sonar.sourceEncoding=UTF-8
 # SonarQube server
 sonar.host.url=SONAR_HOST_URL
 sonar.token=SONAR_TOKEN
+

From ceac1820d09ce281b4a5f67b6301a1da727aa26b Mon Sep 17 00:00:00 2001
From: John Halley Gotway <johnhg@ucar.edu>
Date: Thu, 4 Apr 2024 18:47:33 -0600
Subject: [PATCH 5/6] Per #366, whitespace

---
 internal/scripts/sonarqube/run_nightly.sh           | 1 -
 internal/scripts/sonarqube/sonar-project.properties | 1 -
 2 files changed, 2 deletions(-)

diff --git a/internal/scripts/sonarqube/run_nightly.sh b/internal/scripts/sonarqube/run_nightly.sh
index fe257b6c..50645f11 100755
--- a/internal/scripts/sonarqube/run_nightly.sh
+++ b/internal/scripts/sonarqube/run_nightly.sh
@@ -34,7 +34,6 @@ function usage {
 # Check for arguments
 if [ $# -lt 1 ]; then usage; exit 1; fi
 
-
 # Store the full path to the scripts directory
 SCRIPT_DIR=`dirname $0`
 if [[ ${0:0:1} != "/" ]]; then SCRIPT_DIR=$(pwd)/${SCRIPT_DIR}; fi 
diff --git a/internal/scripts/sonarqube/sonar-project.properties b/internal/scripts/sonarqube/sonar-project.properties
index 8b24cea0..37755f03 100644
--- a/internal/scripts/sonarqube/sonar-project.properties
+++ b/internal/scripts/sonarqube/sonar-project.properties
@@ -9,4 +9,3 @@ sonar.sourceEncoding=UTF-8
 # SonarQube server
 sonar.host.url=SONAR_HOST_URL
 sonar.token=SONAR_TOKEN
-

From 2084dd5e3b1e2b31de4edd587feaaf37848e0d84 Mon Sep 17 00:00:00 2001
From: John Halley Gotway <johnhg@ucar.edu>
Date: Thu, 4 Apr 2024 18:47:33 -0600
Subject: [PATCH 6/6] Per #366, exclude test code from code coverage
 statistics.

---
 internal/scripts/sonarqube/sonar-project.properties | 1 +
 1 file changed, 1 insertion(+)

diff --git a/internal/scripts/sonarqube/sonar-project.properties b/internal/scripts/sonarqube/sonar-project.properties
index 37755f03..c3534080 100644
--- a/internal/scripts/sonarqube/sonar-project.properties
+++ b/internal/scripts/sonarqube/sonar-project.properties
@@ -4,6 +4,7 @@ sonar.projectName=SONAR_PROJECT_NAME
 sonar.projectVersion=SONAR_PROJECT_VERSION
 sonar.branch.name=SONAR_BRANCH_NAME
 sonar.sources=metcalcpy,scratch,test
+sonar.coverage.exclusions=test/**
 sonar.sourceEncoding=UTF-8
 
 # SonarQube server