diff --git a/.github/jobs/bash_functions.sh b/.github/jobs/bash_functions.sh
new file mode 100755
index 00000000..05cffc94
--- /dev/null
+++ b/.github/jobs/bash_functions.sh
@@ -0,0 +1,34 @@
+#! /bin/bash
+
+# utility function to run command get log the time it took to run
+# if CMD_LOGFILE is set, send output to that file and unset var
+function time_command {
+  local start_seconds=$SECONDS
+  echo "RUNNING: $*"
+
+  local error
+  # pipe output to log file if set
+  if [ "x$CMD_LOGFILE" == "x" ]; then
+      "$@"
+      error=$?
+  else
+      echo "Logging to ${CMD_LOGFILE}"
+      "$@" &>> $CMD_LOGFILE
+      error=$?
+      unset CMD_LOGFILE
+  fi
+
+  local duration=$(( SECONDS - start_seconds ))
+  echo "TIMING: Command took `printf '%02d' $(($duration / 60))`:`printf '%02d' $(($duration % 60))` (MM:SS): '$*'"
+  if [ ${error} -ne 0 ]; then
+    echo "ERROR: '$*' exited with status = ${error}"
+  fi
+  return $error
+}
+
+# utility function to construct the DockerHub tag name to be used,
+# replacing slashes with underscores in the branch name
+
+function get_dockerhub_tag {
+  echo ${DOCKERHUB_REPO}:$(echo ${SOURCE_BRANCH} | sed 's%/%_%g')
+}
diff --git a/.github/jobs/build_docker_image.sh b/.github/jobs/build_docker_image.sh
new file mode 100755
index 00000000..d8e0e963
--- /dev/null
+++ b/.github/jobs/build_docker_image.sh
@@ -0,0 +1,24 @@
+#!/bin/bash
+
+source ${GITHUB_WORKSPACE}/.github/jobs/bash_functions.sh
+
+DOCKERHUB_TAG=$(get_dockerhub_tag)
+
+DOCKERFILE_PATH=${GITHUB_WORKSPACE}/internal/scripts/docker/Dockerfile.copy
+
+CMD_LOGFILE=${GITHUB_WORKSPACE}/docker_build.log
+
+time_command docker build -t ${DOCKERHUB_TAG} \
+    --build-arg SOURCE_BRANCH \
+    --build-arg MET_BASE_REPO \
+    --build-arg MET_BASE_TAG \
+    -f $DOCKERFILE_PATH ${GITHUB_WORKSPACE}
+if [ $? != 0 ]; then
+  cat ${CMD_LOGFILE}
+  exit 1
+fi
+
+# Copy the dist directory from the image
+id=$(docker create ${DOCKERHUB_TAG})
+time_command docker cp $id:/METviewer/dist dist
+docker rm -v $id
diff --git a/.github/jobs/configure_sonarqube.sh b/.github/jobs/configure_sonarqube.sh
new file mode 100755
index 00000000..8e3d4fa0
--- /dev/null
+++ b/.github/jobs/configure_sonarqube.sh
@@ -0,0 +1,62 @@
+#!/bin/bash
+
+# Constants
+SONAR_PROPERTIES_DIR=internal/scripts/sonarqube
+SONAR_PROPERTIES=sonar-project.properties
+
+# Check that this is being run from the top-level METviewer directory
+if [ ! -e $SONAR_PROPERTIES_DIR/$SONAR_PROPERTIES ]; then
+  echo "ERROR: ${0} -> must be run from the top-level METviewer 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: ${0} -> \$SONAR_TOKEN not defined!"
+  exit 1
+fi
+
+# Define the version string
+export SONAR_PROJECT_VERSION=$(cat docs/version)
+
+#
+# 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 $SONAR_PROPERTIES
+sed -e "s|SONAR_PROJECT_VERSION|$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 86b368fd..dec23969 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..3e85000e
--- /dev/null
+++ b/.github/workflows/sonarqube.yml
@@ -0,0 +1,99 @@
+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
+
+env:
+  DOCKERHUB_REPO: dtcenter/metviewer-dev
+
+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: Create output directories
+      run: mkdir -p ${RUNNER_WORKSPACE}/logs
+
+    - name: Get branch name
+      id: get_branch_name
+      run: echo branch_name=${GITHUB_REF#refs/heads/} >> $GITHUB_OUTPUT
+
+    - name: Build METviewer in Docker
+      run: .github/jobs/build_docker_image.sh
+      env:
+        SOURCE_BRANCH: ${{ steps.get_branch_name.outputs.branch_name }}
+
+    - 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 }}
+
+    - name: Copy log files into logs directory
+      if: always()
+      run: cp ${GITHUB_WORKSPACE}/*.log ${RUNNER_WORKSPACE}/logs/
+
+    - name: Upload logs as artifact
+      if: always()
+      uses: actions/upload-artifact@v4
+      with:
+        name: logs_sonarqube
+        path: ${{ runner.workspace }}/logs
+        if-no-files-found: ignore
diff --git a/docker/hooks/build b/docker/hooks/build
deleted file mode 100644
index 631634c8..00000000
--- a/docker/hooks/build
+++ /dev/null
@@ -1,8 +0,0 @@
-#!/bin/bash
-
-docker build -t $IMAGE_NAME \
---build-arg METVIEWER_GIT_NAME=v6.0.0-beta1 \
---build-arg METCALCPY_GIT_NAME=v3.0.0-beta1 \
---build-arg METDATAIO_GIT_NAME=v3.0.0-beta1 \
---build-arg METPLOTPY_GIT_NAME=v3.0.0-beta1 .
-
diff --git a/docker/Dockerfile b/internal/scripts/docker/Dockerfile
similarity index 80%
rename from docker/Dockerfile
rename to internal/scripts/docker/Dockerfile
index a3f02588..0b57e51b 100644
--- a/docker/Dockerfile
+++ b/internal/scripts/docker/Dockerfile
@@ -3,24 +3,14 @@ FROM centos:7
 MAINTAINER Tatiana Burek <tatiana@ucar.edu>
 
 #
-# This Dockerfile checks out METviewer from GitHub and builds the specified branch or tag.
+# This Dockerfile checks out METviewer and its dependencies from GitHub and builds the specified branch or tag.
+# Use the develop branches for dependencies by default but override with "--build-arg".
 #
-ENV METVIEWER_GIT_NAME v6.0.0-beta2
-ENV METCALCPY_GIT_NAME v3.0.0-beta2
-ENV METPLOTPY_GIT_NAME v3.0.0-beta2
-ENV METDATAIO_GIT_NAME v3.0.0-beta2
 
-#
-# Constants
-#
-ENV TOMCAT_MINOR_VERSION 5.61
-ENV TOMCAT_MAJOR_VERSION 8
-ENV TOMCAT_VERSION ${TOMCAT_MAJOR_VERSION}.${TOMCAT_MINOR_VERSION}
-
-ENV METVIEWER_GIT_URL  https://github.com/dtcenter/METviewer
-ENV METCALCPY_GIT_URL  https://github.com/dtcenter/METcalcpy
-ENV METPLOTPY_GIT_URL  https://github.com/dtcenter/METplotpy
-ENV METDATAIO_GIT_URL  https://github.com/dtcenter/METdataio
+ARG METVIEWER_GIT_NAME
+ARG METPLOTPY_GIT_NAME=develop
+ARG METCALCPY_GIT_NAME=develop
+ARG METDATAIO_GIT_NAME=develop
 
 #
 # METVIEWER_GIT_NAME is required.
@@ -28,39 +18,27 @@ ENV METDATAIO_GIT_URL  https://github.com/dtcenter/METdataio
 RUN if [ "x${METVIEWER_GIT_NAME}" = "x" ]; then \
       echo "ERROR: METVIEWER_GIT_NAME undefined! Rebuild with \"--build-arg METVIEWER_GIT_NAME={branch, tag, or hash}\""; \
       exit 1; \
-    else \
-      echo "Build Argument METVIEWER_GIT_NAME=${METVIEWER_GIT_NAME}"; \
-    fi
+    fi 
 
-#
-# METCALCPY_GIT_NAME is required.
-#
-RUN if [ "x${METCALCPY_GIT_NAME}" = "x" ]; then \
-      echo "ERROR: METCALCPY_GIT_NAME undefined! Rebuild with \"--build-arg METCALCPY_GIT_NAME={branch, tag, or hash}\""; \
-      exit 1; \
-    else \
-      echo "Build Argument METCALCPY_GIT_NAME=${METCALCPY_GIT_NAME}"; \
-    fi
+RUN echo "Build Argument METVIEWER_GIT_NAME=${METVIEWER_GIT_NAME}" \
+ && echo "Build Argument METPLOTPY_GIT_NAME=${METPLOTPY_GIT_NAME}" \
+ && echo "Build Argument METCALCPY_GIT_NAME=${METCALCPY_GIT_NAME}" \
+ && echo "Build Argument METDATAIO_GIT_NAME=${METDATAIO_GIT_NAME}"
 
 #
-# METPLOTPY_GIT_NAME is required.
+# Repository URLs
 #
-RUN if [ "x${METPLOTPY_GIT_NAME}" = "x" ]; then \
-      echo "ERROR: METPLOTPY_GIT_NAME undefined! Rebuild with \"--build-arg METPLOTPY_GIT_NAME={branch, tag, or hash}\""; \
-      exit 1; \
-    else \
-      echo "Build Argument METPLOTPY_GIT_NAME=${METPLOTPY_GIT_NAME}"; \
-    fi
+ENV METVIEWER_GIT_URL https://github.com/dtcenter/METviewer
+ENV METPLOTPY_GIT_URL https://github.com/dtcenter/METplotpy
+ENV METCALCPY_GIT_URL https://github.com/dtcenter/METcalcpy
+ENV METDATAIO_GIT_URL https://github.com/dtcenter/METdataio
 
 #
-# METDATAIO_GIT_NAME is required.
+# Constants
 #
-RUN if [ "x${METDATAIO_GIT_NAME}" = "x" ]; then \
-      echo "ERROR: METDATAIO_GIT_NAME undefined! Rebuild with \"--build-arg METDATAIO_GIT_NAME={branch, tag, or hash}\""; \
-      exit 1; \
-    else \
-      echo "Build Argument METDATAIO_GIT_NAME=${METDATAIO_GIT_NAME}"; \
-    fi
+ENV TOMCAT_MINOR_VERSION 5.61
+ENV TOMCAT_MAJOR_VERSION 8
+ENV TOMCAT_VERSION ${TOMCAT_MAJOR_VERSION}.${TOMCAT_MINOR_VERSION}
 
 #
 # Install system updates
@@ -123,17 +101,14 @@ RUN mkdir /METviewer-python \
 WORKDIR /METviewer-python/
 RUN git clone --branch ${METCALCPY_GIT_NAME} ${METCALCPY_GIT_URL}
 
-
 RUN echo "Checking out METplotpy ${METPLOTPY_GIT_NAME} from ${METPLOTPY_GIT_URL}"
 WORKDIR /METviewer-python/
 RUN git clone --branch ${METPLOTPY_GIT_NAME} ${METPLOTPY_GIT_URL}
 
-
-RUN echo "Checking out METdataio ${METDATAIO_GIT_NAME} from ${METDATAIO_GIT_URL}" \
+RUN echo "Checking out METdataio ${METDATAIO_GIT_NAME} from ${METDATAIO_GIT_URL}"
 WORKDIR /METviewer-python/
 RUN git clone --branch ${METDATAIO_GIT_NAME} ${METDATAIO_GIT_URL}
 
-
 #
 # Install METviewer
 #
@@ -221,7 +196,7 @@ RUN ln -sf /usr/local/bin/pip3.10  /usr/bin/pip3
 RUN ln -sf /usr/bin/pip3  /usr/bin/pip
 
 #
-# install GEOS - needed for cartopy
+# Install GEOS - needed for cartopy
 #
 WORKDIR /tmp
 RUN wget http://download.osgeo.org/geos/geos-3.7.2.tar.bz2
@@ -268,31 +243,30 @@ RUN pip install cartopy \
  && pip install python-dateutil==2.8.2 \
  && pip install opencv-python \
  && pip install pandas==1.5.2
-#
-#
-
-
 
 #
-# set env vars
+# Set env vars
 #
 ENV PYTHONPATH "${PYTHONPATH}:/METviewer-python/METcalcpy/:/METviewer-python/METplotpy/"
 ENV METPLOTPY_BASE "/METviewer-python/METplotpy/"
 
-# remove unneeded scripts
+#
+# Remove unneeded scripts
+#
 RUN rm /METviewer/bin/auto_test.sh \
-    && rm /METviewer/bin/mv_test.sh \
-    && rm /METviewer/bin/nightly_test.sh \
-    && rm /METviewer/bin/prep_dist.sh \
-    && rm /METviewer/bin/mv_compare.sh \
-    && rm -r  /METviewer/test
+ && rm /METviewer/bin/mv_test.sh \
+ && rm /METviewer/bin/nightly_test.sh \
+ && rm /METviewer/bin/prep_dist.sh \
+ && rm /METviewer/bin/mv_compare.sh \
+ && rm -r /METviewer/test
 
-# change permissions of the scripts
+#
+# Change permissions of the scripts
+#
 RUN chmod 755 /METviewer/bin/mv_batch.sh \
-  && chmod 755 /METviewer/bin/mv_load.sh \
-  && chmod 755 /METviewer/bin/mv_prune.sh \
-  && chmod 755 /METviewer/bin/mv_scorecard.sh
-
+ && chmod 755 /METviewer/bin/mv_load.sh \
+ && chmod 755 /METviewer/bin/mv_prune.sh \
+ && chmod 755 /METviewer/bin/mv_scorecard.sh
 
 ENTRYPOINT ${CATALINA_HOME}/bin/startup.sh  && /bin/bash
 CMD ["true"]
diff --git a/docker/Dockerfile_for_Singularity b/internal/scripts/docker/Dockerfile.apptainer
similarity index 80%
rename from docker/Dockerfile_for_Singularity
rename to internal/scripts/docker/Dockerfile.apptainer
index 007ce009..4f18ba12 100644
--- a/docker/Dockerfile_for_Singularity
+++ b/internal/scripts/docker/Dockerfile.apptainer
@@ -3,27 +3,14 @@ FROM centos:7
 MAINTAINER Tatiana Burek <tatiana@ucar.edu>
 
 #
-# This Dockerfile checks out METviewer from GitHub and builds the specified branch or tag.
+# This Dockerfile checks out METviewer and its dependencies from GitHub and builds the specified branch or tag.
+# Use the develop branches for dependencies by default but override with "--build-arg".
 #
-ARG METVIEWER_GIT_NAME
-ARG METCALCPY_GIT_NAME
-ARG METPLOTPY_GIT_NAME
-ARG METDATAIO_GIT_NAME
-
-#
-# Constants
-#
-ENV TOMCAT_MINOR_VERSION 5.61
-ENV TOMCAT_MAJOR_VERSION 8
-ENV TOMCAT_VERSION ${TOMCAT_MAJOR_VERSION}.${TOMCAT_MINOR_VERSION}
-
-ENV METVIEWER_GIT_URL  https://github.com/dtcenter/METviewer
-ENV METCALCPY_GIT_URL  https://github.com/dtcenter/METcalcpy
-ENV METPLOTPY_GIT_URL  https://github.com/dtcenter/METplotpy
-ENV METDATAIO_GIT_URL  https://github.com/dtcenter/METdataio
 
-# this umask is needed for Tomcat
-ENV UMASK 002
+ARG METVIEWER_GIT_NAME
+ARG METPLOTPY_GIT_NAME=develop
+ARG METCALCPY_GIT_NAME=develop
+ARG METDATAIO_GIT_NAME=develop
 
 #
 # METVIEWER_GIT_NAME is required.
@@ -31,39 +18,27 @@ ENV UMASK 002
 RUN if [ "x${METVIEWER_GIT_NAME}" = "x" ]; then \
       echo "ERROR: METVIEWER_GIT_NAME undefined! Rebuild with \"--build-arg METVIEWER_GIT_NAME={branch, tag, or hash}\""; \
       exit 1; \
-    else \
-      echo "Build Argument METVIEWER_GIT_NAME=${METVIEWER_GIT_NAME}"; \
     fi
 
-#
-# METCALCPY_GIT_NAME is required.
-#
-RUN if [ "x${METCALCPY_GIT_NAME}" = "x" ]; then \
-      echo "ERROR: METCALCPY_GIT_NAME undefined! Rebuild with \"--build-arg METCALCPY_GIT_NAME={branch, tag, or hash}\""; \
-      exit 1; \
-    else \
-      echo "Build Argument METCALCPY_GIT_NAME=${METCALCPY_GIT_NAME}"; \
-    fi
+RUN echo "Build Argument METVIEWER_GIT_NAME=${METVIEWER_GIT_NAME}" \
+ && echo "Build Argument METPLOTPY_GIT_NAME=${METPLOTPY_GIT_NAME}" \
+ && echo "Build Argument METCALCPY_GIT_NAME=${METCALCPY_GIT_NAME}" \
+ && echo "Build Argument METDATAIO_GIT_NAME=${METDATAIO_GIT_NAME}"
 
 #
-# METPLOTPY_GIT_NAME is required.
+# Repository URLs
 #
-RUN if [ "x${METPLOTPY_GIT_NAME}" = "x" ]; then \
-      echo "ERROR: METPLOTPY_GIT_NAME undefined! Rebuild with \"--build-arg METPLOTPY_GIT_NAME={branch, tag, or hash}\""; \
-      exit 1; \
-    else \
-      echo "Build Argument METPLOTPY_GIT_NAME=${METPLOTPY_GIT_NAME}"; \
-    fi
+ENV METVIEWER_GIT_URL https://github.com/dtcenter/METviewer
+ENV METPLOTPY_GIT_URL https://github.com/dtcenter/METplotpy
+ENV METCALCPY_GIT_URL https://github.com/dtcenter/METcalcpy
+ENV METDATAIO_GIT_URL https://github.com/dtcenter/METdataio
 
 #
-# METDATAIO_GIT_NAME is required.
+# Constants
 #
-RUN if [ "x${METDATAIO_GIT_NAME}" = "x" ]; then \
-      echo "ERROR: METDATAIO_GIT_NAME undefined! Rebuild with \"--build-arg METDATAIO_GIT_NAME={branch, tag, or hash}\""; \
-      exit 1; \
-    else \
-      echo "Build Argument METDATAIO_GIT_NAME=${METDATAIO_GIT_NAME}"; \
-    fi
+ENV TOMCAT_MINOR_VERSION 5.61
+ENV TOMCAT_MAJOR_VERSION 8
+ENV TOMCAT_VERSION ${TOMCAT_MAJOR_VERSION}.${TOMCAT_MINOR_VERSION}
 
 #
 # Install system updates
@@ -89,8 +64,7 @@ RUN yum -y install wget tar git ant  R mysql ksh \
  && rm -rf /var/cache/yum/* \
  && yum clean all
 
-RUN  yum  install java-1.8.0-openjdk-devel
-
+RUN yum install java-1.8.0-openjdk-devel
 
 #
 # Install gsl-2.5 on which the R gsl package depends.
@@ -138,13 +112,11 @@ RUN mkdir /METviewer-python \
 WORKDIR /METviewer-python/
 RUN git clone --branch ${METCALCPY_GIT_NAME} ${METCALCPY_GIT_URL}
 
-
 RUN echo "Checking out METplotpy ${METPLOTPY_GIT_NAME} from ${METPLOTPY_GIT_URL}"
 WORKDIR /METviewer-python/
 RUN git clone --branch ${METPLOTPY_GIT_NAME} ${METPLOTPY_GIT_URL}
 
-
-RUN echo "Checking out METdataio ${METDATAIO_GIT_NAME} from ${METDATAIO_GIT_URL}" \
+RUN echo "Checking out METdataio ${METDATAIO_GIT_NAME} from ${METDATAIO_GIT_URL}"
 WORKDIR /METviewer-python/
 RUN git clone --branch ${METDATAIO_GIT_NAME} ${METDATAIO_GIT_URL}
 
@@ -202,7 +174,6 @@ RUN git clone --branch ${METVIEWER_GIT_NAME} ${METVIEWER_GIT_URL} /METviewer \
     >  mv_prune.sh-DOCKER \
  && mv mv_prune.sh-DOCKER mv_prune.sh
 
-
 #
 # Install Python 3.10.4
 #
@@ -235,9 +206,8 @@ RUN ln -sf /usr/bin/python3  /usr/bin/python
 RUN ln -sf /usr/local/bin/pip3.10  /usr/bin/pip3
 RUN ln -sf /usr/bin/pip3  /usr/bin/pip
 
-
 #
-# install GEOS - needed for cartopy
+# Install GEOS - needed for cartopy
 #
 WORKDIR /tmp
 RUN wget http://download.osgeo.org/geos/geos-3.7.2.tar.bz2
@@ -249,7 +219,6 @@ RUN ldconfig
 WORKDIR /tmp
 RUN rm -r geos-3.7.2.tar.bz2
 
-
 #
 # Install Python packages
 #
@@ -286,34 +255,32 @@ RUN pip install cartopy \
  && pip install opencv-python \
  && pip install pandas==1.5.2
 
-
-
 #
-# set env vars
+# Set env vars
 #
 ENV PYTHONPATH "${PYTHONPATH}:/METviewer-python/METcalcpy/:/METviewer-python/METplotpy/"
 ENV METPLOTPY_BASE "/METviewer-python/METplotpy/"
 
-
-# remove unneeded scripts
+#
+# Remove unneeded scripts
+#
 RUN rm /METviewer/bin/auto_test.sh \
-    && rm /METviewer/bin/mv_test.sh \
-    && rm /METviewer/bin/nightly_test.sh \
-    && rm /METviewer/bin/prep_dist.sh \
-    && rm /METviewer/bin/mv_compare.sh \
-    && rm -r  /METviewer/test
+ && rm /METviewer/bin/mv_test.sh \
+ && rm /METviewer/bin/nightly_test.sh \
+ && rm /METviewer/bin/prep_dist.sh \
+ && rm /METviewer/bin/mv_compare.sh \
+ && rm -r /METviewer/test
 
 #
-# Change permission on exe's
+# Change permissions of the scripts
 #
 RUN chmod 755 /METviewer/bin/mv_batch.sh \
-  && chmod 755 /METviewer/bin/mv_load.sh \
-  && chmod 755 /METviewer/bin/mv_prune.sh \
-  && chmod 755 /METviewer/bin/mv_scorecard.sh
-
+ && chmod 755 /METviewer/bin/mv_load.sh \
+ && chmod 755 /METviewer/bin/mv_prune.sh \
+ && chmod 755 /METviewer/bin/mv_scorecard.sh
 
 #
-# database install
+# Database install
 #
 
 #
@@ -321,9 +288,9 @@ RUN chmod 755 /METviewer/bin/mv_batch.sh \
 #
 COPY fix-permissions.sh ./
 RUN chmod 777 ./fix-permissions.sh
-RUN ./fix-permissions.sh /var/lib/mysql/   && \
-    ./fix-permissions.sh /var/log/mariadb/ && \
-    ./fix-permissions.sh /var/run/
+RUN ./fix-permissions.sh /var/lib/mysql/ \
+ && ./fix-permissions.sh /var/log/mariadb/ \
+ && ./fix-permissions.sh /var/run/
 
 COPY docker-entrypoint.sh /
 RUN chmod 777 /docker-entrypoint.sh
diff --git a/internal/scripts/docker/Dockerfile.copy b/internal/scripts/docker/Dockerfile.copy
new file mode 100644
index 00000000..8b73beea
--- /dev/null
+++ b/internal/scripts/docker/Dockerfile.copy
@@ -0,0 +1,284 @@
+FROM centos:7
+
+MAINTAINER Tatiana Burek <tatiana@ucar.edu>
+
+#
+# This Dockerfile checks out the METviewer dependencies from GitHub and builds the local METviewer repository.
+# Use the develop branches for dependencies by default but override with "--build-arg".
+#
+
+ARG SOURCE_BRANCH
+ARG METPLOTPY_GIT_NAME=develop
+ARG METCALCPY_GIT_NAME=develop
+ARG METDATAIO_GIT_NAME=develop
+
+#
+# SOURCE_BRANCH is required to define the branch of the local METviewer repository.
+#
+RUN if [ "x${SOURCE_BRANCH}" = "x" ]; then \
+      echo "ERROR: SOURCE_BRANCH undefined! Rebuild with \"--build-arg SOURCE_BRANCH={branch name}\""; \
+      exit 1; \
+    else \
+      echo "Build Argument SOURCE_BRANCH=${SOURCE_BRANCH}"; \
+    fi
+ENV METVIEWER_GIT_NAME ${SOURCE_BRANCH}
+
+RUN echo "Build Argument METVIEWER_GIT_NAME=${METVIEWER_GIT_NAME}" \
+ && echo "Build Argument METPLOTPY_GIT_NAME=${METPLOTPY_GIT_NAME}" \
+ && echo "Build Argument METCALCPY_GIT_NAME=${METCALCPY_GIT_NAME}" \
+ && echo "Build Argument METDATAIO_GIT_NAME=${METDATAIO_GIT_NAME}"
+
+#
+# Repository URLs
+#
+ENV METVIEWER_GIT_URL https://github.com/dtcenter/METviewer
+ENV METPLOTPY_GIT_URL https://github.com/dtcenter/METplotpy
+ENV METCALCPY_GIT_URL https://github.com/dtcenter/METcalcpy
+ENV METDATAIO_GIT_URL https://github.com/dtcenter/METdataio
+
+#
+# Constants
+#
+ENV TOMCAT_MINOR_VERSION 5.61
+ENV TOMCAT_MAJOR_VERSION 8
+ENV TOMCAT_VERSION ${TOMCAT_MAJOR_VERSION}.${TOMCAT_MINOR_VERSION}
+
+#
+# Install system updates
+#
+RUN yum -y update \
+ && yum -y install epel-release \
+ && yum -y install 'dnf-command(config-manager)' \
+ && yum-config-manager --enable PowerTools
+
+#
+# Install required packages
+#
+RUN yum -y install wget tar git ant java R mysql ksh \
+ && rm -rf /var/cache/yum/* \
+ && yum clean all
+
+#
+# Install gsl-2.5 on which the R gsl package depends.
+# The centos7 gal package is too old (version 1.5).
+#
+RUN echo "Compiling gsl-2.5" \
+ && curl -SL http://gnu.askapache.com/gsl/gsl-2.5.tar.gz | tar zxC /lib \
+ && cd /lib/gsl-2.5 \
+ && ./configure --prefix=/usr --libdir=/usr/lib64 >& configure.log \
+ && make >& make.log \
+ && make install >& make_install.log
+
+#
+# Setup default cran repo
+#
+RUN echo "r <- getOption('repos'); r['CRAN'] <- 'http://cran.us.r-project.org'; options(repos = r);" > ~/.Rprofile
+
+#
+# Install required R packages
+#
+RUN Rscript -e "install.packages('boot')" \
+ && Rscript -e "install.packages('plotrix')" \
+ && Rscript -e "install.packages('gsl')" \
+ && Rscript -e "install.packages('data.table')" \
+ && Rscript -e "install.packages('verification')"
+
+#
+# Install Tomcat
+#
+ENV CATALINA_HOME /opt/tomcat
+
+RUN wget https://archive.apache.org/dist/tomcat/tomcat-${TOMCAT_MAJOR_VERSION}/v${TOMCAT_VERSION}/bin/apache-tomcat-${TOMCAT_VERSION}.tar.gz \
+ && tar -xvf apache-tomcat-${TOMCAT_VERSION}.tar.gz \
+ && rm apache-tomcat*.tar.gz \
+ && mv apache-tomcat* ${CATALINA_HOME} \
+ && chmod +x ${CATALINA_HOME}/bin/*sh
+
+EXPOSE 8080
+
+#
+# Install METplus python components
+#
+RUN mkdir /METviewer-python \
+ && echo "Checking out METcalcpy ${METCALCPY_GIT_NAME} from ${METCALCPY_GIT_URL}"
+WORKDIR /METviewer-python/
+RUN git clone --branch ${METCALCPY_GIT_NAME} ${METCALCPY_GIT_URL}
+
+RUN echo "Checking out METplotpy ${METPLOTPY_GIT_NAME} from ${METPLOTPY_GIT_URL}"
+WORKDIR /METviewer-python/
+RUN git clone --branch ${METPLOTPY_GIT_NAME} ${METPLOTPY_GIT_URL}
+
+RUN echo "Checking out METdataio ${METDATAIO_GIT_NAME} from ${METDATAIO_GIT_URL}"
+WORKDIR /METviewer-python/
+RUN git clone --branch ${METDATAIO_GIT_NAME} ${METDATAIO_GIT_URL}
+
+#
+# Copy in the local METviewer repository
+#
+RUN echo "Copying METviewer into /METviewer" \
+ && mkdir -p /METviewer
+
+COPY . /METviewer
+
+RUN if [ ! -e "/METviewer/build.xml" ]; then \
+    echo "ERROR: docker build must be run from the top-level METviewer directory"; \
+    exit 1; \
+  fi
+
+RUN echo "Configuring and building METviewer" \
+ && cd /METviewer \
+ && cat webapp/metviewer/WEB-INF/classes/build.properties | \
+    sed -r 's%db.host=.*%db.host=mysql_mv%g' | \
+    sed -r 's%db.user=.*%db.user=root%g' | \
+    sed -r 's%db.password=.*%db.password=mvuser%g' | \
+    sed -r 's%db.management.system=.*%db.management.system=mysql%g' | \
+    sed -r 's%output.dir=.*%output.dir=/opt/tomcat/webapps/metviewer_output/%g' | \
+    sed -r 's%webapps.dir=.*%webapps.dir=/opt/tomcat/webapps/metviewer/%g' | \
+    sed -r 's%url.output=.*%url.output=http://localhost:8080/metviewer_output/%g' | \
+    sed -r 's%python.env=.*%python.env=/usr/%g' | \
+    sed -r 's%metcalcpy.home=.*%metcalcpy.home=/METviewer-python/METcalcpy/%g' | \
+    sed -r 's%metplotpy.home=.*%metplotpy.home=/METviewer-python/METplotpy/%g' \
+    > build.properties \
+ && ant -Dbuild.properties.file=./build.properties \
+        -Ddb.management.system=mysql \
+        -Dmetcalcpy.path=/METviewer-python/METcalcpy/ \
+        -Dmetplotpy.path=/METviewer-python/METplotpy/ \
+        -Dpython.env.path=/usr/ war \
+ && mv /METviewer/dist/*.war ${CATALINA_HOME}/webapps \
+ && echo "Configuring METviewer scripts" \
+ && cd /METviewer/bin \
+ && cat mv_batch.sh | \
+    sed -r 's%JAVA=.*%JAVA=java\nMV_HOME=/METviewer%g' | \
+    sed -r 's%PYTHON_ENV=.*%PYTHON_ENV=/usr%g' | \
+    sed -r 's%METCALCPY_HOME=.*%METCALCPY_HOME=/METviewer-python/METcalcpy/%g' | \
+    sed -r 's%METPLOTPY_HOME=.*%METPLOTPY_HOME=/METviewer-python/METplotpy/%g' \
+    >  mv_batch.sh-DOCKER \
+ && mv mv_batch.sh-DOCKER mv_batch.sh \
+ && cat mv_load.sh | \
+    sed -r 's%PYTHON_ENV=.*%PYTHON_ENV=/usr%g'  | \
+    sed -r 's%METDATAIO_HOME=.*%METDATAIO_HOME=/METviewer-python/METdataio/%g' \
+    >  mv_load.sh-DOCKER \
+ && mv mv_load.sh-DOCKER mv_load.sh \
+ && cat mv_scorecard.sh | \
+    sed -r 's%JAVA=.*%JAVA=java\nMV_HOME=/METviewer%g' | \
+    sed -r 's%PYTHON_ENV=.*%PYTHON_ENV=/usr%g' | \
+    sed -r 's%METCALCPY_HOME=.*%METCALCPY_HOME=/METviewer-python/METcalcpy/%g' | \
+    sed -r 's%METPLOTPY_HOME=.*%METPLOTPY_HOME=/METviewer-python/METplotpy/%g' \
+    >  mv_scorecard.sh-DOCKER \
+ && mv mv_scorecard.sh-DOCKER mv_scorecard.sh \
+ && cat mv_prune.sh | \
+    sed -r 's%JAVA=.*%JAVA=java\nMV_HOME=/METviewer%g' | \
+    sed -r 's%PYTHON_ENV=.*%PYTHON_ENV=/usr%g' | \
+    sed -r 's%METCALCPY_HOME=.*%METCALCPY_HOME=/METviewer-python/METcalcpy/%g' | \
+    sed -r 's%METPLOTPY_HOME=.*%METPLOTPY_HOME=/METviewer-python/METplotpy/%g' \
+    >  mv_prune.sh-DOCKER \
+ && mv mv_prune.sh-DOCKER mv_prune.sh
+
+#
+# Install Python 3.10.4
+#
+RUN yum install gcc openssl11 openssl11-devel libreadline-gplv2-dev libncursesw5-dev libsqlite3-dev tk-dev libgdbm-dev libc6-dev libbz2-dev openssl-devel libssl-dev bzip2-devel libffi-devel zlib-devel libproj-dev proj-data proj-bin libgeos-dev bzip2 -y
+RUN mkdir /usr/local/openssl11
+WORKDIR /usr/local/openssl11
+RUN ln -s /usr/lib64/openssl11 lib
+RUN ln -s /usr/include/openssl11 include
+
+RUN curl https://www.python.org/ftp/python/3.10.4/Python-3.10.4.tgz --output /tmp/Python-3.10.4.tgz
+WORKDIR /tmp
+RUN tar xzf Python-3.10.4.tgz
+WORKDIR /tmp/Python-3.10.4
+RUN ./configure --enable-optimizations --with-openssl=/usr/local/openssl11
+RUN yum install make -y
+RUN make altinstall
+RUN yum install which -y
+WORKDIR /tmp
+RUN rm -r Python-3.10.4.tgz
+RUN yum -y install epel-release
+RUN curl -sS https://bootstrap.pypa.io/get-pip.py -o get-pip.py | python3.10
+RUN python3.10 -m pip install --trusted-host pypi.python.org --trusted-host files.pythonhosted.org --trusted-host pypi.org --upgrade pip
+
+#
+# Create a link for python3
+#
+RUN ln -sf /usr/local/bin/python3.10  /usr/bin/python3
+RUN ln -sf /usr/bin/python3  /usr/bin/python
+
+RUN ln -sf /usr/local/bin/pip3.10  /usr/bin/pip3
+RUN ln -sf /usr/bin/pip3  /usr/bin/pip
+
+#
+# Install GEOS - needed for cartopy
+#
+WORKDIR /tmp
+RUN wget http://download.osgeo.org/geos/geos-3.7.2.tar.bz2
+RUN tar xjf geos-3.7.2.tar.bz2
+WORKDIR /tmp/geos-3.7.2
+RUN ./configure --enable-php; make clean ; make
+RUN make install
+RUN ldconfig
+WORKDIR /tmp
+RUN rm -r geos-3.7.2.tar.bz2
+
+#
+# Install Python packages
+#
+RUN pip install cartopy \
+ && pip install eofs \
+ && pip install imutils==0.5.4 \
+ && pip install imageio==2.19.2 \
+ && pip install lxml==4.9.1 \
+ && pip install matplotlib==3.5.2 \
+ && pip install netcdf4==1.6.2 \
+ && pip install numpy==1.22.0 \
+ && pip install pytest==7.1.2 \
+ && pip install metpy==1.3.1 \
+ && pip install pyyaml==6.0 \
+ && pip install scikit-image==0.19.3 \
+ && pip install scikit-learn \
+ && pip install scipy==1.11.1 \
+ && pip install xarray==2022.3.0 \
+ && pip install PyMySQL==1.0.2 \
+ && pip install pint==0.19.2 \
+ && pip install plotly==5.9.0 \
+ && pip install kaleido==0.2.1 \
+ && pip install attrs==22.1.0 \
+ && pip install exceptiongroup==1.0.4 \
+ && pip install iniconfig==1.1.1 \
+ && pip install packaging==22.0 \
+ && pip install pluggy==1.0.0 \
+ && pip install pytz==2022.6 \
+ && pip install setuptools==65.5.1 \
+ && pip install six==1.16.0 \
+ && pip install tomli==2.0.1 \
+ && pip install wheel==0.38.1 \
+ && pip install python-dateutil==2.8.2 \
+ && pip install opencv-python \
+ && pip install pandas==1.5.2
+
+#
+# Set env vars
+#
+ENV PYTHONPATH "${PYTHONPATH}:/METviewer-python/METcalcpy/:/METviewer-python/METplotpy/"
+ENV METPLOTPY_BASE "/METviewer-python/METplotpy/"
+
+#
+# Remove unneeded scripts
+#
+RUN rm /METviewer/bin/auto_test.sh \
+ && rm /METviewer/bin/mv_test.sh \
+ && rm /METviewer/bin/nightly_test.sh \
+ && rm /METviewer/bin/prep_dist.sh \
+ && rm /METviewer/bin/mv_compare.sh \
+ && rm -r  /METviewer/test
+
+#
+# Change permissions of the scripts
+#
+RUN chmod 755 /METviewer/bin/mv_batch.sh \
+ && chmod 755 /METviewer/bin/mv_load.sh \
+ && chmod 755 /METviewer/bin/mv_prune.sh \
+ && chmod 755 /METviewer/bin/mv_scorecard.sh
+
+ENTRYPOINT ${CATALINA_HOME}/bin/startup.sh  && /bin/bash
+CMD ["true"]
+
diff --git a/docker/README b/internal/scripts/docker/README
similarity index 100%
rename from docker/README
rename to internal/scripts/docker/README
diff --git a/docker/check_env.sh b/internal/scripts/docker/check_env.sh
similarity index 100%
rename from docker/check_env.sh
rename to internal/scripts/docker/check_env.sh
diff --git a/docker/docker-clean b/internal/scripts/docker/docker-clean
similarity index 100%
rename from docker/docker-clean
rename to internal/scripts/docker/docker-clean
diff --git a/docker/docker-compose.yml b/internal/scripts/docker/docker-compose.yml
similarity index 100%
rename from docker/docker-compose.yml
rename to internal/scripts/docker/docker-compose.yml
diff --git a/docker/docker-entrypoint.sh b/internal/scripts/docker/docker-entrypoint.sh
similarity index 100%
rename from docker/docker-entrypoint.sh
rename to internal/scripts/docker/docker-entrypoint.sh
diff --git a/docker/fix-permissions.sh b/internal/scripts/docker/fix-permissions.sh
similarity index 100%
rename from docker/fix-permissions.sh
rename to internal/scripts/docker/fix-permissions.sh
diff --git a/internal/scripts/docker/hooks/build b/internal/scripts/docker/hooks/build
new file mode 100644
index 00000000..53917e2b
--- /dev/null
+++ b/internal/scripts/docker/hooks/build
@@ -0,0 +1,13 @@
+#!/bin/bash
+
+# TODO: Add logic for handling dependencies
+#  - develop or branches from develop should build against develop
+#  - main_vX.Y or branches from main_vX.Y should build against main_v{X-3}.Y
+#  - vX.Y.Z tags should build against v{X-3}.Y.? tags
+
+docker build -t $IMAGE_NAME \
+--build-arg METVIEWER_GIT_NAME=$SOURCE_BRANCH \
+--build-arg METCALCPY_GIT_NAME=develop \
+--build-arg METDATAIO_GIT_NAME=develop \
+--build-arg METPLOTPY_GIT_NAME=develop .
+
diff --git a/docker/init_singularity.sh b/internal/scripts/docker/init_singularity.sh
similarity index 100%
rename from docker/init_singularity.sh
rename to internal/scripts/docker/init_singularity.sh
diff --git a/internal/scripts/sonarqube/sonar-project.properties b/internal/scripts/sonarqube/sonar-project.properties
new file mode 100644
index 00000000..3586fc31
--- /dev/null
+++ b/internal/scripts/sonarqube/sonar-project.properties
@@ -0,0 +1,13 @@
+# Project and source code settings
+sonar.projectKey=METviewer
+sonar.projectName=METviewer
+sonar.projectVersion=SONAR_PROJECT_VERSION
+sonar.branch.name=SONAR_BRANCH_NAME
+sonar.sources=java
+sonar.java.libraries=dist/lib
+sonar.java.binaries=dist/metviewer/WEB-INF/classes
+sonar.sourceEncoding=UTF-8
+
+# SonarQube server
+sonar.host.url=SONAR_HOST_URL
+sonar.token=SONAR_TOKEN