diff --git a/.github/workflows/ci-cd.yml b/.github/workflows/ci-cd.yml
new file mode 100644
index 0000000..0409842
--- /dev/null
+++ b/.github/workflows/ci-cd.yml
@@ -0,0 +1,218 @@
+name: CI/CD Pipeline
+
+on:
+  pull_request:
+    branches: [main, nwm-main, development, release-candidate]
+  push:
+    branches: [main, nwm-main, development, release-candidate]
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+  packages: write
+  security-events: write
+
+env:
+  REGISTRY: ghcr.io
+  PYTHON_VERSION: '3.11'
+
+jobs:
+  setup:
+    runs-on: ubuntu-latest
+    outputs:
+      image_base: ${{ steps.vars.outputs.image_base }}
+      pr_tag: ${{ steps.vars.outputs.pr_tag }}
+      commit_sha: ${{ steps.vars.outputs.commit_sha }}
+      commit_sha_short: ${{ steps.vars.outputs.commit_sha_short }}
+      test_image_tag: ${{ steps.vars.outputs.test_image_tag }}
+    steps:
+      - name: Compute image vars
+        id: vars
+        shell: bash
+        run: |
+          set -euo pipefail
+          ORG="$(echo "${GITHUB_REPOSITORY_OWNER}" | tr '[:upper:]' '[:lower:]')"
+          REPO="$(basename "${GITHUB_REPOSITORY}")"
+          IMAGE_BASE="${REGISTRY}/${ORG}/${REPO}"
+          echo "image_base=${IMAGE_BASE}" >> "$GITHUB_OUTPUT"
+
+          if [ "${GITHUB_EVENT_NAME}" = "pull_request" ]; then
+            PR_NUM="${{ github.event.pull_request.number }}"
+            PR_TAG="pr-${PR_NUM}-build"
+            echo "pr_tag=${PR_TAG}" >> "$GITHUB_OUTPUT"
+            echo "test_image_tag=${PR_TAG}" >> "$GITHUB_OUTPUT"
+          fi
+
+          if [ "${GITHUB_EVENT_NAME}" = "push" ]; then
+            COMMIT_SHA="${GITHUB_SHA}"
+            SHORT_SHA="${COMMIT_SHA:0:12}"
+            echo "commit_sha=${COMMIT_SHA}" >> "$GITHUB_OUTPUT"
+            echo "commit_sha_short=${SHORT_SHA}" >> "$GITHUB_OUTPUT"
+            echo "test_image_tag=${SHORT_SHA}" >> "$GITHUB_OUTPUT"
+          fi
+
+  build:
+    name: build
+    if: github.event_name == 'pull_request' || github.event_name == 'push'
+    runs-on: ubuntu-latest
+    needs: setup
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Log in to registry
+        uses: docker/login-action@v3
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Build & push image
+        uses: docker/build-push-action@v6
+        with:
+          context: .
+          push: true
+          tags: ${{ needs.setup.outputs.image_base }}:${{ needs.setup.outputs.test_image_tag }}
+          build-args: |
+            NGEN_IMAGE_TAG=${{ env.NGEN_IMAGE_TAG || 'latest' }}
+            CI_COMMIT_REF_NAME=${{ github.ref_name }}
+
+  unit-test:
+    name: unit-test
+    if: github.event_name == 'pull_request' || github.event_name == 'push'
+    runs-on: ubuntu-latest
+    needs: [setup, build]
+    container:
+      image: ${{ needs.setup.outputs.image_base }}:${{ needs.setup.outputs.test_image_tag }}
+    steps:
+      - name: Run unit tests
+        run: |
+          echo "TODO: add unit tests here"
+
+  codeql-scan:
+    if: github.event_name == 'pull_request' || github.event_name == 'push'
+    runs-on: ubuntu-latest
+    needs: [setup, build]
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ env.PYTHON_VERSION }}
+      - name: Initialize CodeQL
+        uses: github/codeql-action/init@v3
+        with:
+          languages: python
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+      - name: Perform CodeQL Analysis
+        uses: github/codeql-action/analyze@v3
+
+  container-scanning:
+    if: github.event_name == 'pull_request' || github.event_name == 'push'
+    runs-on: ubuntu-latest
+    needs: [setup, build]
+    steps:
+      - name: Scan container with Trivy
+        uses: aquasecurity/trivy-action@0.20.0
+        with:
+          image-ref: ${{ needs.setup.outputs.image_base }}:${{ needs.setup.outputs.test_image_tag }}
+          format: 'template'
+          template: '@/contrib/sarif.tpl'
+          output: 'trivy-results.sarif'
+          severity: 'CRITICAL,HIGH'
+      - name: Upload Trivy SARIF
+        uses: github/codeql-action/upload-sarif@v3
+        with:
+          sarif_file: 'trivy-results.sarif'
+
+  deploy-latest-on-development:
+    name: deploy-latest-on-development
+    if: github.event_name == 'push' && github.ref_name == 'development'
+    runs-on: ubuntu-latest
+    needs: [setup, build, unit-test, codeql-scan, container-scanning]
+    steps:
+      - name: Tag image with 'latest'
+        shell: bash
+        run: |
+          set -euo pipefail
+          IMAGE_BASE="${{ needs.setup.outputs.image_base }}"
+          SHORT_SHA="${{ needs.setup.outputs.commit_sha_short }}"
+
+          # ensure skopeo is available
+          if ! command -v skopeo >/dev/null 2>&1; then
+            sudo apt-get update -y
+            sudo apt-get install -y --no-install-recommends skopeo
+          fi
+
+          skopeo copy \
+            --src-creds "${{ github.actor }}:${{ secrets.GITHUB_TOKEN }}" \
+            --dest-creds "${{ github.actor }}:${{ secrets.GITHUB_TOKEN }}" \
+            docker://"${IMAGE_BASE}:${SHORT_SHA}" docker://"${IMAGE_BASE}:latest"
+
+  release:
+    name: release
+    if: github.event_name == 'release' && github.event.action == 'published'
+    runs-on: ubuntu-latest
+    needs: setup
+    steps:
+      - name: Get commit sha for the tag
+        id: rev
+        shell: bash
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          set -euo pipefail
+          TAG="${{ github.event.release.tag_name }}"
+          REPO="${{ github.repository }}"
+
+          # ensure jq is available
+          if ! command -v jq >/dev/null 2>&1; then
+            sudo apt-get update -y
+            sudo apt-get install -y --no-install-recommends jq
+          fi
+
+          # ensure gh cli is available
+          if ! command -v gh >/dev/null 2>&1; then
+            sudo apt-get update -y
+            sudo apt-get install -y --no-install-recommends gh
+          fi
+
+          REF_JSON="$(gh api "repos/${REPO}/git/refs/tags/${TAG}")"
+          OBJ_SHA="$(jq -r '.object.sha' <<<"$REF_JSON")"
+          OBJ_TYPE="$(jq -r '.object.type' <<<"$REF_JSON")"
+
+          if [ "$OBJ_TYPE" = "tag" ]; then
+            TAG_OBJ="$(gh api "repos/${REPO}/git/tags/${OBJ_SHA}")"
+            COMMIT_SHA="$(jq -r '.object.sha' <<<"$TAG_OBJ")"
+          else
+            COMMIT_SHA="$OBJ_SHA"
+          fi
+
+          SHORT_SHA="${COMMIT_SHA:0:12}"
+          echo "short_sha=${SHORT_SHA}" >> "$GITHUB_OUTPUT"
+
+      - name: Tag image with release tag
+        shell: bash
+        run: |
+          set -euo pipefail
+          IMAGE_BASE="${{ needs.setup.outputs.image_base }}"
+          SHORT_SHA="${{ steps.rev.outputs.short_sha }}"
+          RELEASE_TAG="${{ github.event.release.tag_name }}"
+
+          # ensure skopeo is available
+          if ! command -v skopeo >/dev/null 2>&1; then
+            sudo apt-get update -y
+            sudo apt-get install -y --no-install-recommends skopeo
+          fi
+
+          skopeo copy \
+            --src-creds "${{ github.actor }}:${{ secrets.GITHUB_TOKEN }}" \
+            --dest-creds "${{ github.actor }}:${{ secrets.GITHUB_TOKEN }}" \
+            docker://"${IMAGE_BASE}:${SHORT_SHA}" docker://"${IMAGE_BASE}:${RELEASE_TAG}"
diff --git a/.gitignore b/.gitignore
index 2d5316f..4ebe459 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,2 +1,94 @@
+# Compiled source #
+###################
+*.com
+*.class
+*.dll
+*.exe
+*.o
+*.so
+_site/
+
+# Packages #
+############
+# it's better to unpack these files and commit the raw source
+# git has its own built in compression methods
+*.7z
+*.dmg
+*.gz
+*.iso
+*.jar
+*.rar
+*.tar
+*.zip
+
+# Logs and databases #
+######################
+*.log
+*.sql
+*.sqlite
+
+# OS generated files #
+######################
+.DS_Store
+.DS_Store?
+.Spotlight-V100
+.Trashes
+Icon?
+ehthumbs.db
+Thumbs.db
+
+# Vim swap files #
+##################
+*.swp
+
+# Python #
+#################
+*.pyc
+*.egg-info/
+__pycache__/
+*.py[cod]
+.env
+.python-version
+venv
+*.pytest_cache
+build
+
+# pyenv #
+#########
+.python-version
+
+# Django #
+#################
+*.egg-info
+.installed.cfg
+
+# Unit test / coverage reports
+#################
+htmlcov/
+.tox/
+.coverage
+.cache
+nosetests.xml
+coverage.xml
+
+# Front-End #
+#############
+node_modules/
+bower_components/
+.grunt/
+src/vendor/
+dist/
+
+# Temporary Directories #
+*tmp/
+*temp/
+
+# Other
 .idea
 /git_info.json
+
+# Ngen FIles #
+#############
+cat*
+nex*
+troute*
diff --git a/Dockerfile b/Dockerfile
index 21296c8..b224149 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,27 +1,39 @@
-ARG  NGEN_VERSION=latest
-FROM registry.sh.nextgenwaterprediction.com/ngwpc/nwm-ngen/ngen:${NGEN_VERSION}
+# syntax=docker/dockerfile:1.4
+ARG  NGEN_IMAGE_TAG=latest
+FROM ghcr.io/ngwpc/ngen:${NGEN_IMAGE_TAG}
 
-RUN set -eux; \
-    dnf install -y \
-        jq; \
-    dnf clean all
+# Uncomment when building ngen locally or if ngen-int image is available locally
+# modify to use image tag for local ngen image if needed
+#FROM ngen
 
-COPY requirements.txt .
-RUN set -eux; \
-	\
-    pip3 install -r requirements.txt ; \
-    pip3 cache purge ; \
-    rm --force requirements.txt ;
+# Activate the existing virtual environment
+ENV PATH="/ngen-app/ngen-python/bin:${PATH}"
 
+RUN set -eux; \
+    dnf install -y jq; \
+    dnf clean all
 
 COPY . /ngen-app/ngen-fcst/
 COPY ./docker/run-ngen-fcst.sh /ngen-app/bin/
+
 RUN set -eux; \
-	\
     chmod +x /ngen-app/bin/run-ngen-fcst.sh
 
 WORKDIR /ngen-app/ngen-fcst
 
+# Install missing dependencies that aren't in base image
+RUN --mount=type=cache,target=/root/.cache/pip,id=pip-cache \
+    set -eux; \
+    pip3 install \
+        "matplotlib~=3.10.6"; \
+        #"geopandas~=1.1.1"; \
+    pip3 cache purge
+
+# Install into the existing virtual environment without upgrading base packages
+RUN set -eux; \
+    pip3 install --no-deps . || pip3 install .; \
+    pip3 cache purge;
+
 ARG CI_COMMIT_REF_NAME
 
 RUN set -eux; \
@@ -47,4 +59,4 @@ RUN set -eux; \
 
 WORKDIR /
 
-ENTRYPOINT [ "/ngen-app/bin/run-ngen-fcst.sh" ] 
+ENTRYPOINT [ "/ngen-app/bin/run-ngen-fcst.sh" ]
diff --git a/README.md b/README.md
index e2957f1..8e5f37b 100644
--- a/README.md
+++ b/README.md
@@ -1,18 +1,13 @@
-# ngen-fcst
-
-
-
-## Name
-ngen Forecast
+# nwm-fcst-mgr
 
 ## Description
-A program to run ngen given the forecast forcing provided via a .nc file and a configuration file from validation with ngen-cal
+A program to execute ngen cold start and forecast runs provided a configuration file from validation with nwm-cal-mgr and realization files for the cold start and forecast periods
 
 ## Installation
 
-### Clone ngen-fcst
+### Clone nwm-fcst-mgr
 
-git clone -b development --recurse-submodules https://gitlab.sh.nextgenwaterprediction.com/NGWPC/nwm-ngen/ngen-fcst.git
+git clone -b development --recurse-submodules https://github.com/NGWPC/nwm-fcst-mgr.git
 
 ### Build the environment
 
@@ -38,62 +33,48 @@ where [VENV_ROOT] and [NGEN_ROOT] refer to the directory to install the python v
 Follow the following steps to test the program:
 
 1. source [VENV_ROOT]/env.ngen/bin/activate
-2. cd [NGEN-FCST_ROOT]/ngen-fcst
-3. python python/run_ngen_fcst.py test_data/forcing.nc test_data/valid_config.yaml fcst_run1
+2. cd [NWM-FCST-MGR_ROOT]/nwm-fcst-mgr
+3. pip install .
+
+where [NWM-FCST-MGR_ROOT] is where nwm-fcst-mgr is installed.
+
+The program takes three arguments:
+1) Path to the config yaml file for a validation run (from nwm-cal-mgr)
+2) Path to a realization file for the forecast run (generated by nwm-msw-mgr)
+3) Optional Path to a realization file for the cold start run in provided by user (generated by nwm-msw-mgr)
 
-where [NGEN-FCST_ROOT] is where ngen-fcst is installed
+Nwm-fcst-mgr can be run from the CLI or from Python code directly. 
 
-The program takes three command line arguments:
-1) Path to the NetCDF forcing file
-2) Path to the config yaml file for a validation run (from ngen-cal)
-3) Path to the folder to be created for storing inputs/outputs from running ngen, relative to the Output directory of the calibration run as indicated in the config yaml file. For example, if "fcst_run1" is the 3rd argument, and "yaml_file" in the "general" section of the config file is '/home/yuqiong.liu/work/Gitlab/run/kge_DDS/noah_cfes/01123000/Output/Validation_Run/01123000_config_valid_best.yaml', then the new output directory to be created for the ngen-fcst run would be:
+### Python
+1. from nwm_fcst_mgr.forecast import run_fcst
+2. valid_yaml = '~/ngwpc/run_ngen/kge_dds/noah_cfes/01123000/Output/Validation_Run/01123000_config_valid_best.yaml'
+3. real_path = '~/ngwpc/run_ngen/kge_dds/noah_cfes/01123000/Output/Forecast_Run/fcst_run1/01123000_realization_config_bmi_fcst.json'
+4. run_fcst(valid_yaml=valid_yaml, real_path=real_path)
+
+If the user wishes to run a cold_start_period, then real_path would be replaced by the path to the cold start realization file.
+
+### CLI
+python -m nwm_fcst_mgr.forecast valid_yaml real_path
+
+where the arguments are replaced by the paths above.
 
-/home/yuqiong.liu/work/Gitlab/run/kge_DDS/noah_cfes/01123000/Output/Forecast_Run/fcst_run1
 
 ## Docker container
 
 ### Requirements
 
-To build and run ngen-fcst, you will need the following software installed and running on your system:
+To build and run nwm-fcst-mgr, you will need the following software installed and running on your system:
 - Docker Engine
 
-You will also need the following data:
-- a forcing file in NetCDF format
-- a YAML-formatted configuration file
-
 ### Build
 
-To build the ngen-fcst container, execute the following command:
+To build the nwm-fcst-mgr container, execute the following command:
 ```
-docker build --tag=ngen-fcst .
+docker build --tag=nwm-fcst-mgr .
 ```
 
 ### Running
 
-To run the ngen-fcst applicaton, execute the following command:
-```
-docker run ngen-fcst
-```
-
-This will print a usage statement for the container:
-```
-Usage: run-ngen-fcst.sh <forcing_file> <config_file> <output_path> [log_file] [venv_path]
-
-FORCING_FILE: Path to the NetCDF forcing file.
-CONFIG_FILE: Path to the config yaml file for a validation run (from ngen-cal).
-OUTPUT_PATH: Path to the folder to be created for storing inputs/outputs from running ngen.
-LOG_FILE (optional): Path to the output file where the script's output will be saved.  Used when running in LOCAL or DOCKER environment
-VENV_PATH (optional): Path to the Python virtual environment.  Used when running in the LOCAL environment.
-
-Examples:
-  run-ngen-fcst.sh test_data/forcing.nc test_data/valid_config.yaml fcst_run1
-  run-ngen-fcst.sh test_data/forcing.nc test_data/valid_config.yaml fcst_run1 /path/to/output /path/to/venv
-```
-
-The path provided for any files should match the path within the container, as well as the paths insider your configuration file. So if `forcing.nc` is located at `~/ngencerf/data/ngen-cal-data/forcing/forcing.nc` and `valid_config.yaml` is located at `~/ngencerf/data/ngen-cal-data/configs/valid_config.yaml`, you should run the command:
-```
-docker run -v ~/ngencerf/data/ngen-cal-data/forcing/:/ngencerf/data/forcing/ -v  ~/ngencerf/data/ngen-cal-data/configs/:/ngencerf/data/configs/ ngen-fcst /ngencerf/data/forcing/forcing.nc /ngencerf/data/configs/valid_config.yaml fcst_run1
-```
 
 ## Contributing
 State if you are open to contributions and what your requirements are for accepting them.
diff --git a/docker/run-ngen-fcst.sh b/docker/run-ngen-fcst.sh
index 73ff0d4..755a2ad 100755
--- a/docker/run-ngen-fcst.sh
+++ b/docker/run-ngen-fcst.sh
@@ -1,34 +1,37 @@
 #!/bin/bash
+
 # Define valid commands
-VALID_COMMANDS=("forecast")
+VALID_COMMANDS=("cold_start" "forecast")
 
-# This shell script lives in the ngen-fcst repo.  It is used by CerfServer when calling ngen-fcst
+# This shell script lives in the nwm-fcst-mgr repo.  It is used by CerfServer when calling nwm-fcst-mgr
 #
 # It is used by CerfServer directly when running in LOCAL mode.
-# It is used by the ngen-fcst docker container when the server is running in DOCKER or PARALLEL_WORKS mode
+# It is used by the nwm-fcst-mgr docker container when the server is running in DOCKER or PARALLEL_WORKS mode
 
-FORECAST_SCRIPT=/ngen-app/ngen-fcst/python/run_ngen_fcst.py
+FORECAST_SCRIPT=nwm_fcst_mgr.forecast
+COLD_START_SCRIPT=nwm_fcst_mgr.forecast
 
 # Set the umask so files and directories are created with 777 permissions
 umask 000
 
 # Function to display help message
 show_help() {
-  echo "Usage: $(basename "$0") <command> <forcing_file> <config_file> <output_dir> [stdout_file] [venv_path]"
-  echo ""
+  echo "Usage: $(basename "$0") <command> <validation_yaml> <realization_file> [stdout_file] [venv_path]"
   echo ""
   echo "COMMAND:"
-  echo "  forecast          Run forecast script."
+  echo "  forecast    Run forecast script (requires validation_yaml + forecast_realization)."
+  echo "  cold_start  Run cold start script (requires validation_yaml + cold_start_realization)."
   echo ""
-  echo "FORCING_FILE: Path to the NetCDF forcing file."
-  echo "CONFIG_FILE: Path to the config yaml file for a validation run (from ngen-cal)."
-  echo "FORECAST_DIR: Name of the folder to to store the forecast output."
+  echo "VALIDATION_YAML: Path to the config yaml file for a validation run (from MSWM)."
+  echo "FORECAST_REALIZATION: (Required for forecast) Path to the forecast realization file."
+  echo "COLD_START_REALIZATION: (Required for cold_start) Path to the cold start realization file."
   echo "STDOUT_FILE (optional): Path to the stdout file where the script's console output will be saved.  Used when running in LOCAL or DOCKER environment"
   echo "VENV_PATH (optional): Path to the Python virtual environment.  Used when running in the LOCAL environment."
   echo ""
   echo "Examples:"
-  echo "  $(basename "$0") forecast test_data/forcing.nc test_data/valid_config.yaml fcst_run1"
-  echo "  $(basename "$0") forecast test_data/forcing.nc test_data/valid_config.yaml fcst_run1 /path/to/output/ngen-fcst.log /path/to/venv"
+  echo "  $(basename "$0") forecast validation.yaml realization.yaml"
+  echo "  $(basename "$0") cold_start validation.yaml cold_start_realization.yaml"
+  echo "  $(basename "$0") forecast validation.yaml realization.yaml cold_start_realization.yaml"
   echo ""
   exit 1
 }
@@ -40,7 +43,7 @@ fi
 
 # Check if the command for the script is provided as the first argument
 if [ -z "$1" ]; then
-  echo "Error: No script command provided. Allowable commands are: ${VALID_COMMANDS[*]}."
+  echo "[run-ngen-fcst.sh] Error: No script command provided. Allowable commands are: ${VALID_COMMANDS[*]}."
   show_help
 fi
 
@@ -51,48 +54,51 @@ shift 1
 case "$SCRIPT_COMMAND" in
   "forecast")
     SCRIPT_PATH=$FORECAST_SCRIPT
-    REQUIRED_ARGS=3
+    REQUIRED_ARGS=2
+    ;;
+  "cold_start")
+    SCRIPT_PATH=$COLD_START_SCRIPT
+    REQUIRED_ARGS=2
     ;;
   *)
-    echo "Error: Invalid script command: '$SCRIPT_COMMAND'. Allowable commands are: ${VALID_COMMANDS[*]}."
+    echo "[run-ngen-fcst.sh] Error: Invalid script command: '$SCRIPT_COMMAND'. Allowable commands are: ${VALID_COMMANDS[*]}."
     show_help
     ;;
 esac
 
-# Check if the selected script exists
-if [ ! -f "$SCRIPT_PATH" ]; then
-  echo "Error: Script not found at $SCRIPT_PATH"
-  exit 1
-fi
-
 # Check if the correct number of arguments are provided for the selected command
 if [ $# -lt $REQUIRED_ARGS ]; then
-  echo "Error: Insufficient arguments. $SCRIPT_COMMAND requires $REQUIRED_ARGS arguments."
+  echo "[run-ngen-fcst.sh] Error: Insufficient arguments. $SCRIPT_COMMAND requires $REQUIRED_ARGS arguments."
   show_help
 fi
 
-FORCING_FILE=$1
-CONFIG_FILE=$2
-FORECAST_DIR=$3
-shift $REQUIRED_ARGS
+VALIDATION_YAML=$1
+REALIZATION_FILE=$2
+shift 2
 
-echo "FORCING_FILE: ${FORCING_FILE}"
-echo "CONFIG_FILE: ${CONFIG_FILE}"
-echo "FORECAST_DIR: ${FORECAST_DIR}"
+echo "[run-ngen-fcst.sh]  VALIDATION_YAML: ${VALIDATION_YAML}"
+echo "[run-ngen-fcst.sh] REALIZATION_FILE: ${REALIZATION_FILE}"
 
-# Check if the forcing data exists
-if [ ! -f "${FORCING_FILE}" ]; then
-  echo "Forcing data not found at ${FORCING_FILE}"
+# File existence checks (fatal if missing)
+if [[ ! -f "${VALIDATION_YAML}" && ! -d "${VALIDATION_YAML}" ]]; then
+  echo "[run-ngen-fcst.sh] Fatal: Config file not found at ${VALIDATION_YAML}"
+  exit 1
 fi
 
-# Check if the configuration file exists
-if [ ! -f "${CONFIG_FILE}" ]; then
-  echo "Configuration file not found at ${CONFIG_FILE}"
+if [ ! -f "${REALIZATION_FILE}" ]; then
+  if [ "$SCRIPT_COMMAND" == "forecast" ]; then
+    echo "[run-ngen-fcst.sh] Fatal: Forecast realization file not found at ${REALIZATION_FILE}"
+  else
+    echo "[run-ngen-fcst.sh] Fatal: Cold start realization file not found at ${REALIZATION_FILE}"
+  fi
+  exit 1
 fi
 
+# Handle optional stdout file
+STDOUT_FILE=""
 if [ $# -ge 1 ]; then
   STDOUT_FILE=$1
-  echo "Output file: $STDOUT_FILE"
+  echo "[run-ngen-fcst.sh] Output file: $STDOUT_FILE"
 
   # Create output directory if it doesn't exist
   STDOUT_DIR=$(dirname "$STDOUT_FILE")
@@ -103,9 +109,11 @@ if [ $# -ge 1 ]; then
   shift 1
 fi
 
+# Handle optional virtual environment
+VENV_PATH=""
 if [ $# -ge 1 ]; then
   VENV_PATH=$1
-  echo "Virtual environment: $VENV_PATH"
+  echo "[run-ngen-fcst.sh] Virtual environment: $VENV_PATH"
   shift 1
 fi
 
@@ -114,34 +122,35 @@ if [ -n "$VENV_PATH" ]; then
   if [ -d "$VENV_PATH/bin" ]; then
     source "$VENV_PATH/bin/activate"
   else
-    echo "Error: Virtual environment path '$VENV_PATH' is invalid."
+    echo "[run-ngen-fcst.sh] Fatal: Virtual environment path '$VENV_PATH' is invalid."
     exit 1
   fi
 else
-  echo "No virtual environment provided, running with default Python environment."
+  echo "[run-ngen-fcst.sh] No virtual environment provided, running with default Python environment."
 fi
 
 # Run the Python script, redirecting its output if an output file is provided
-echo "   Running $(basename "$SCRIPT_PATH") with input file: $CONFIG_FILE"
+echo "[run-ngen-fcst.sh] Running $SCRIPT_PATH ($SCRIPT_COMMAND) with inputs: ${VALIDATION_YAML} ${REALIZATION_FILE}"
+
 if [ -z "$STDOUT_FILE" ]; then
-  python "${SCRIPT_PATH}" "${FORCING_FILE}" "${CONFIG_FILE}" "${FORECAST_DIR}"
+  python -m $SCRIPT_PATH "$VALIDATION_YAML" "$REALIZATION_FILE"
 else
-  python "${SCRIPT_PATH}" "${FORCING_FILE}" "${CONFIG_FILE}" "${FORECAST_DIR}" &> "${STDOUT_FILE}" 2>&1
+  python -m $SCRIPT_PATH "$VALIDATION_YAML" "$REALIZATION_FILE" &> "$STDOUT_FILE" 2>&1
 fi
 
 python_exit_code=$?
 if [ $python_exit_code -ne 0 ]; then
-  echo "$(basename "$SCRIPT_PATH") exited with code $python_exit_code"
+  echo "[run-ngen-fcst.sh] $SCRIPT_PATH exited with code $python_exit_code"
 fi
 
 # Display output if redirected to a file
 if [ -n "$STDOUT_FILE" ]; then
-  echo "Output from running $(basename "$SCRIPT_PATH")"
+  echo "Output from running $SCRIPT_PATH"
   echo "-------------- start of $STDOUT_FILE -----------------------------"
   cat "$STDOUT_FILE"
   echo "---------------- end of $STDOUT_FILE -----------------------------"
 fi
 
-echo "Done running $(basename "$SCRIPT_PATH")"
+echo "[run-ngen-fcst.sh] Done running $SCRIPT_PATH"
 
 exit $python_exit_code
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..672e0cf
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,21 @@
+[build-system]
+requires = ["setuptools>=65", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "nwm_fcst_mgr"
+version = "0.1.1"           # or mark as dynamic if you use setuptools-scm
+requires-python = ">=3.10"
+dependencies = [
+  "geopandas~=1.1.1",
+  "pandas~=2.3.1",
+  "netCDF4==1.6.3",
+  "matplotlib~=3.10.6",
+  "PyYAML~=6.0.2",
+]
+
+[tool.setuptools]
+package-dir = {"" = "python"}
+
+[tool.setuptools.packages.find]
+where = ["python"]
diff --git a/python/nwm_fcst_mgr/__init__.py b/python/nwm_fcst_mgr/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/python/nwm_fcst_mgr/forecast.py b/python/nwm_fcst_mgr/forecast.py
new file mode 100644
index 0000000..30fdd32
--- /dev/null
+++ b/python/nwm_fcst_mgr/forecast.py
@@ -0,0 +1,228 @@
+import glob
+import json
+import logging
+import os
+import shutil
+import subprocess
+from pathlib import Path
+import geopandas as gpd
+import pandas as pd
+import netCDF4
+
+import matplotlib.pyplot as plt
+import yaml
+import argparse
+
+from nwm_fcst_mgr.log_level import log_level_set
+from nwm_fcst_mgr.git_util import print_git_info_all
+
+# setup the logger
+log_level_set()
+logger = logging.getLogger(__name__)
+
+
+def run_fcst(valid_yaml: str, real_path: str):
+    """
+    Execute ngen run for forecast period and cold start period (if provided)
+    valid_yaml: path to validation yaml file from past calibration run
+    real_path: path to realization file for a cold start or forecast period
+    """
+
+    # set environment variable for ngencerf backend
+    os.environ["NGEN_RESULTS_DIR"] = str(Path(real_path).parent)
+    logging.info(
+        f"Set environment variable NGEN_RESULTS_DIR to: {os.environ['NGEN_RESULTS_DIR']}"
+    )
+
+    # Read validation yaml file
+    valid_config = load_yaml(valid_yaml)
+
+    logger.info(f'Validation file loaded from: {valid_yaml}')
+
+    # Retrieve output_dir
+    real_file = Path(real_path)
+    out_dir = real_file.parent
+
+    # Retrieve hydrofabric gpkg
+    gpkg_cats = valid_config['model']['catchments']
+    gpkg_nexus = valid_config['model']['nexus']
+
+    # Retrieve ngen executable
+    ngen_exe = valid_config['model']['binary']
+
+    # get gage ID and make sure it is not empty
+    try:
+        gage0 = valid_config['model']['eval_params']['basinID']
+    except ValueError as e:
+        logger.critical(f'Key model/eval_params/basinID not found in {valid_yaml}\n{e}')
+        raise
+    if gage0 == "":
+        try:
+            raise ValueError(f'basinID in {valid_yaml} cannot be empty')
+        except ValueError as e:
+            logger.critical(e)
+            raise
+
+    # Execute ngen run for either cold-start or forecast period
+    cmd = f'{ngen_exe} {gpkg_cats} "all" {gpkg_nexus} "all" {real_path}'
+
+    logger.info(f'Initializing NGEN run from:  {real_path}')
+
+    # kick off ngen run and save stdout & stderr to ngen_stdout_stderr.log
+    log_file = out_dir / "ngen_stdout_stderr.log"
+    try:
+        with open(log_file, 'a+') as log:
+            subprocess.check_call(cmd, stdout=log, stderr=log, shell=True, cwd=str(out_dir))
+    except subprocess.CalledProcessError as e:
+        logger.critical(f'Ngen run failed with return code {e.returncode}. Command: {e.cmd}')
+        raise
+    except Exception as e:
+        logger.critical(f'Ngen run failed while running command: {e}')
+        raise
+
+    logger.info('NGEN run completed successfully')
+
+    # move output files to output directory
+    run_output_dir = out_dir / "output/"
+    run_output_dir.mkdir(parents=True, exist_ok=True)
+    for pat1 in ['cat*.csv', 'nex*.csv', 'troute*.nc']:
+        for f1 in glob.glob(f'{out_dir}/{pat1}'):
+            shutil.move(f1, Path(run_output_dir, os.path.basename(f1)))
+
+    logger.info(f'NGEN outputs moved to: {run_output_dir}')
+
+    # read troute output file
+    outfile = glob.glob(f'{run_output_dir}/troute*.nc')[0]
+    output = read_troute_output(gage0, valid_config['model']['crosswalk'], gpkg_cats, outfile)
+
+    logger.info(f'Reading T-route output file: {outfile}')
+
+    # plot the hydrograph
+    plot_path = Path(run_output_dir, gage0 + '_hydrograph.png')
+    output.plot(y='sim_flow', kind='line')
+    plt.xlabel('Time')
+    plt.ylabel('Streamflow (m^3/s)')
+    plt.savefig(plot_path, bbox_inches="tight")
+
+    logger.info(f'Hydrograph plot saved to: {plot_path}')
+
+    # save streamflow simulation to csv
+    output.to_csv(Path(run_output_dir, gage0 + '_output.csv'))
+
+    logger.info(f'Fcst-mgr NGEN run outputs saved at: {run_output_dir}')
+
+
+def load_yaml(file_path: str) -> dict:
+    """
+    Read yaml-based configuration file from previous ngen calibration run
+    """
+    # Confirm input file exists
+    file_path = Path(file_path).absolute()
+    if not file_path.exists():
+        try:
+            raise FileNotFoundError(f'Input file not found: {file_path}')
+        except FileNotFoundError as e:
+            logger.critical(e)
+            raise
+
+    # Read the yaml-based configuration file
+    try:
+        with open(file_path) as file:
+            yaml_dict = yaml.safe_load(file)
+    except FileNotFoundError as e:
+        logger.critical(f'Config valid yaml file does not exist: {file_path}\n{e}')
+        raise
+    except yaml.YAMLError as e:
+        logger.critical(f"YAML parsing error in valid config yaml file: {file_path}\n{e}")
+        raise
+    except Exception as e:
+        logger.critical(f"Unexpected error loading valid config yaml file at: {file_path}\n{e}")
+        raise
+
+    return yaml_dict
+
+
+def read_troute_output(
+        gage0: str,
+        cwt_file: Path,
+        gpkg_file: Path,
+        out_file: Path,
+) -> pd.DataFrame:
+
+    """
+    Arguments:
+    ---------
+    gage0: gage ID to retrieve streamflow simulations
+    cwt_file: path to crosswalk file mapping gage to catchments
+    gpkg_file: path to geopackage file
+    out_file: path to t-route output file (in NetCDF format)
+
+    Returns:
+    ---------
+    dataframe containing time and streamflow simulations
+
+    """
+    # Handle crosswalk file (in order to get the correct feature_id when reading t-route data)
+    x_walk = pd.Series(dtype=object)
+    try:
+        with open(cwt_file) as fp:
+            data = json.load(fp)
+            for id, values in data.items():
+                gage = values.get('Gage_no')
+                if gage:
+                    if not isinstance(gage, str):
+                        gage = gage[0]
+                    if gage == gage0:
+                        x_walk[id] = gage
+                        break
+    except FileNotFoundError as e:
+        logger.critical(f'Crosswalk file not found: {cwt_file}\n{e}')
+        raise
+    except json.JSONDecodeError as e:
+        logger.critical(f'Failed to parse JSON from crosswalk file: {cwt_file}\n{e}')
+        raise
+
+    if x_walk.empty:
+        try:
+            raise Exception(f'{gage0} is not found in crosswalk file {cwt_file}')
+        except Exception as e:
+            logger.critical(e)
+            raise
+
+    # get catchment at basin outlet for reading from t-route output
+    catchment_hydro_fabric = gpd.read_file(gpkg_file, layer='divides')
+    catchment_hydro_fabric.set_index('id', inplace=True)
+    nexus_id = catchment_hydro_fabric.loc[x_walk.index[0].replace('cat', 'wb')]['toid']
+    wb_lst = [x.split('-')[1] for x in catchment_hydro_fabric.index[catchment_hydro_fabric['toid'] == nexus_id]]
+
+    # read troute output
+    ncvar = netCDF4.Dataset(out_file, "r")
+    fid_index = [list(ncvar['feature_id'][0:]).index(int(fid)) for fid in wb_lst]
+    output = pd.DataFrame(data={'sim_flow': pd.DataFrame(ncvar['flow'][fid_index], index=fid_index).T.sum(axis=1)})
+    t0 = pd.to_datetime(ncvar.file_reference_time, format="%Y-%m-%d_%H:%M:%S")
+    output.index = [t0 + pd.Timedelta(seconds=int(t1)) for t1 in ncvar['time']]
+    output.index.name = 'Time'
+
+    return output
+
+
+def parse_args():
+    # Create command line parser
+    parser = argparse.ArgumentParser()
+
+    # Add arguments
+    parser.add_argument('valid_yaml', type=str, help=('Path to validation yaml file from previous run of nwm-cal-mgr'))
+    parser.add_argument('real_path', type=str, help=('Path to cold start or forecast period realization file'))
+
+    return parser.parse_args()
+
+
+def main():
+    args = parse_args()
+
+    run_fcst(args.valid_yaml, args.real_path)
+
+
+if __name__ == "__main__":
+    print_git_info_all()
+    main()
diff --git a/python/git_util.py b/python/nwm_fcst_mgr/git_util.py
similarity index 80%
rename from python/git_util.py
rename to python/nwm_fcst_mgr/git_util.py
index 5e0a65d..f41d6d0 100644
--- a/python/git_util.py
+++ b/python/nwm_fcst_mgr/git_util.py
@@ -1,4 +1,7 @@
 import json
+import logging
+
+logger = logging.getLogger(__name__)
 
 
 def transform_component(component_git_info):
@@ -50,17 +53,17 @@ def recursive_print(d: dict, indent: int = 0) -> None:
     """
     for key, value in d.items():
         if isinstance(value, dict):
-            print(" " * indent + f"{key}:")
+            logger.info(" " * indent + f"{key}:")
             recursive_print(value, indent + 2)
         elif isinstance(value, list):
-            print(" " * indent + f"{key}:")
+            logger.info(" " * indent + f"{key}:")
             for item in value:
                 if isinstance(item, dict):
                     recursive_print(item, indent + 2)
                 else:
-                    print(" " * (indent + 2) + str(item))
+                    logger.info(" " * (indent + 2) + str(item))
         else:
-            print(" " * indent + f"{key}: {value}")
+            logger.info(" " * indent + f"{key}: {value}")
 
 
 def print_git_info(git_info_file: str):
@@ -72,21 +75,23 @@ def print_git_info(git_info_file: str):
     :param git_info_file: Path to the JSON file containing Git information.
     """
     try:
-        with open(git_info_file, 'r') as f:
+        with open(git_info_file, "r") as f:
             git_info = json.load(f)
     except FileNotFoundError:
-        print(f'{git_info_file} not found')
+        logger.warning(f"{git_info_file} not found")
         return
     except json.decoder.JSONDecodeError as e:
-        print(f"Error reading {git_info_file}: {e}")
+        logger.warning(f"Error reading {git_info_file}: {e}")
         return
 
     if not git_info:
-        print(f"Failed to retrieve git information from {git_info_file}.")
+        logger.error(f"Failed to retrieve git information from {git_info_file}.")
         return
 
     # Transform each top-level component without removing the keys.
-    transformed_git_info = {key: transform_component(value) for key, value in git_info.items()}
+    transformed_git_info = {
+        key: transform_component(value) for key, value in git_info.items()
+    }
 
     recursive_print(transformed_git_info)
 
@@ -95,6 +100,7 @@ def print_git_info_all():
     """
     Convenience function to print Git information from multiple JSON files.
     """
-    print_git_info('/ngen-app/ngen-fcst_git_info.json')
-    print_git_info('/ngen-app/ngen_git_info.json')
-    print()
+    print_git_info("/ngen-app/nwm-fcst-mgr_git_info.json")
+    print_git_info("/ngen-app/ngen-bmi-forcing_git_info.json")
+    print_git_info("/ngen-app/ngen_git_info.json")
+    logger.info(" ")
diff --git a/python/nwm_fcst_mgr/log_level.py b/python/nwm_fcst_mgr/log_level.py
new file mode 100644
index 0000000..e1196e7
--- /dev/null
+++ b/python/nwm_fcst_mgr/log_level.py
@@ -0,0 +1,97 @@
+import logging
+import os
+import sys
+import time
+from datetime import datetime, timezone
+from pathlib import Path
+
+log_level = logging.INFO
+MODULE_NAME = "FCST-MGR"
+LOG_MODULE_NAME_LEN = 8
+
+
+class CustomFormatter(logging.Formatter):
+    LEVEL_NAME_MAP = {
+        logging.DEBUG: "DEBUG",
+        logging.INFO: "INFO",
+        logging.WARNING: "WARNING",
+        logging.ERROR: "SEVERE",
+        logging.CRITICAL: "FATAL"
+    }
+
+    def format(self, record):
+        original_levelname = record.levelname
+        record.levelname = self.LEVEL_NAME_MAP.get(record.levelno, original_levelname)
+        record.levelname_padded = record.levelname.ljust(7)[:7]  # Exactly 7 chars
+        formatted = super().format(record)
+        record.levelname = original_levelname  # Restore original in case it's reused
+        return formatted
+
+
+def create_timestamp(date_only: bool = False, iso: bool = False, append_ms: bool = False) -> str:
+    now = datetime.now(timezone.utc)
+
+    if date_only:
+        ts_base = now.strftime("%Y%m%d")
+    elif iso:
+        ts_base = now.strftime("%Y-%m-%dT%H:%M:%S")
+    else:
+        ts_base = now.strftime("%Y%m%dT%H%M%S")
+
+    if append_ms:
+        ms_str = f".{now.microsecond // 1000:03d}"
+        return ts_base + ms_str
+    else:
+        return ts_base
+
+
+def log_level_set():
+    '''
+    Set logging level and specify logger configuration.
+
+    Arguments
+    ---------
+    None
+
+    Returns
+    -------
+    None
+
+    Notes
+    -----
+    In the absense of user-specified logging level, level defaults to DEBUG
+    See also https://docs.python.org/3/library/logging.html
+
+    '''
+
+    BASE_DIR = Path(__file__).resolve().parent.parent
+
+    if Path("/ngencerf/data").exists():
+        log_file_dir = Path('/ngencerf/data/run-logs/nwm-fcst-mgr/')
+    else:
+        log_file_dir = Path(BASE_DIR) / 'run-logs/nwm-fcst-mgr/'
+
+    log_file_name = f"nwm-fcst-mgr_{create_timestamp()}.log"
+    os.makedirs(log_file_dir, exist_ok=True)
+    logFilePath = os.path.join(log_file_dir, log_file_name)
+
+    formatted_module = MODULE_NAME.upper().ljust(LOG_MODULE_NAME_LEN)[:LOG_MODULE_NAME_LEN]
+
+    try:
+        handler = logging.FileHandler(logFilePath, mode='a')
+        formatter = CustomFormatter(
+            fmt=f"%(asctime)s.%(msecs)03d {formatted_module} %(levelname_padded)s %(message)s",
+            datefmt="%Y-%m-%dT%H:%M:%S"
+        )
+        handler.setFormatter(formatter)
+
+        logging.Formatter.converter = time.gmtime
+
+        logger = logging.getLogger()
+        logger.setLevel(log_level)
+        logger.handlers.clear()
+        logger.addHandler(handler)
+
+        print(f"Logging into: {logFilePath}")
+    except OSError:
+        print(f"Can't Open local directory Log File: {logFilePath}", file=sys.stderr)
diff --git a/python/run_ngen_fcst.py b/python/run_ngen_fcst.py
deleted file mode 100644
index adb70fc..0000000
--- a/python/run_ngen_fcst.py
+++ /dev/null
@@ -1,302 +0,0 @@
-# python program to run ngen for realtime forecasting given the forcing data in .nc and 
-# validation configuration file in .yaml 
-
-import glob
-import json
-import logging
-import os
-import shutil
-import subprocess
-import sys
-import time
-from datetime import datetime, timezone
-from pathlib import Path
-
-import geopandas as gpd
-import matplotlib.pyplot as plt
-import netCDF4
-import pandas as pd
-import yaml
-
-from git_util import print_git_info_all
-
-logger = logging.getLogger(__name__)
-
-
-#logging.basicConfig(level=logging.INFO)
-
-#LOG = logging.getLogger(__name__)
-
-def create_timestamp() -> str:
-    now = datetime.now(timezone.utc)
-    return now.strftime("%Y-%m-%d")
-
-
-def log_level_set():
-    '''
-    Set logging level and specify logger configuration.
-    
-    Arguments
-    ---------
-    input_parameters (dict): User input logging parameters
-    
-    Returns
-    -------
-    None
-    
-    Notes
-    -----
-    In the absense of user-specified logging level, level defaults to DEBUG
-    See also https://docs.python.org/3/library/logging.html
-    
-    '''
-
-    log_level = 'INFO'
-    if True:
-        BASE_DIR = Path(__file__).resolve().parent.parent
-
-        if Path("/ngencerf/data").exists():
-            log_file_dir = Path(f'/ngencerf/data/run-logs/ngen_fcst_{create_timestamp()}/')
-        else:
-            log_file_dir = Path(BASE_DIR) / f'run-logs/ngen_fcst_{create_timestamp()}/'
-
-        log_file_name = "ngen_fcst.log"
-        os.makedirs(log_file_dir, exist_ok=True)
-        logFilePath = os.path.join(log_file_dir, log_file_name)
-        try:
-            logFile = open(logFilePath, "a")
-            print(f"Logging into: {logFilePath}")
-        except IOError:
-            print(f"Can't Open local directory Log File: {logFilePath}", file=sys.stderr)
-
-        logging.Formatter.converter = time.gmtime
-        logging.basicConfig(
-            force=True,
-            level=log_level,
-            format='%(asctime)s.%(msecs)03d NGEN_FCST %(levelname)s    %(message)s',
-            datefmt='%Y-%m-%dT%H:%M:%S',
-            handlers=[
-                logging.FileHandler(logFilePath, mode='a'),  # Log to a file
-                #logging.StreamHandler(sys.stdout)
-            ])
-    else:
-        logging.basicConfig(
-            level=log_level,
-            format='%(asctime)s - %(name)s - %(levelname)s - [%(filename)s:%(lineno)s - %(funcName)s]: %(message)s',
-            stream=sys.stderr,
-        )
-
-
-import argparse
-
-
-# setup the logger
-log_level_set()
-
-print_git_info_all()
-
-# set environment variable for ngencerf backend - @TODO
-#os.environ['NGEN_RESULTS_DIR'] = str(Path(agent.workdir).parent.parent)
-#logging.info(f'Set environment variable NGEN_RESULTS_DIR to: {os.environ["NGEN_RESULTS_DIR"]}')
-
-# Create the parser
-parser = argparse.ArgumentParser()
-
-# Add arguments
-parser.add_argument('forcing_file', type=str, help='Path to the NetCDF forcing file')
-parser.add_argument('config_file', type=str, help='Path to the config yaml file for a validation run (e.g., 01123000_config_valid_best.yaml from ngen-cal)')
-parser.add_argument('output_folder', type=str, help='Path to the folder to be created for storing inputs/outputs from running ngen')
-
-# Parse the arguments
-args = parser.parse_args()
-logger.info(f"Forcing file to use: {args.forcing_file}")
-logger.info(f"Validation config file to use: {args.config_file}")
-logger.info(f"Relative folder path to outputs: {args.output_folder}")
-
-# define forcing file and valid_best config file
-forcing_file = Path(args.forcing_file).resolve(strict=True)
-config_file = Path(args.config_file).resolve(strict=True)
-
-# make sure forcing file exists as netcdf
-if os.path.splitext(forcing_file)[1] != '.nc':
-    logger.warning(f'{forcing_file} does not have .nc extension. Assuming it is a netcdf file')
-
-# read forcing to get start and end times
-ncvar = netCDF4.Dataset(forcing_file, "r")
-
-t0 = pd.to_datetime(ncvar.model_initialization_time, format="%Y-%m-%d_%H:%M:%S")
-times = [t1 for t1 in ncvar['Time']]
-start_time = t0 + pd.Timedelta(seconds=3600)
-end_time = t0 + pd.Timedelta(seconds=(times[-1] - times[0] + 60) * 60)
-logger.info(f'Start time: {start_time}')
-logger.info(f'End time: {end_time}')
-
-# read yaml configuration file for best validation
-with open(config_file) as file:
-    conf = yaml.safe_load(file)
-
-# read the realization file
-real_file = Path(conf['model']['realization'])
-real_file.resolve(strict=True)
-with open(real_file) as fp:
-    real_config = json.load(fp)
-
-# update forcing in realization file
-real_config['global']['forcing'] = dict([('path', str(forcing_file)), ('provider', 'NetCDF')])
-
-# update time period in realization file
-real_config['time']['start_time'] = str(start_time)
-real_config['time']['end_time'] = str(end_time)
-
-# create output directory in Calibration Output directory
-out_dir0 = Path(conf['general']['yaml_file']).parent.parent.resolve(strict=True)
-out_dir = Path(out_dir0, 'Forecast_Run', args.output_folder)
-out_dir.mkdir(parents=True, exist_ok=True)
-out_dir = out_dir.resolve()
-logger.info(f'New run directory created at: {out_dir}')
-
-# for noah-owp-modular & UEB, update path to BMI config files in realization file
-# as well as start/end times in BMI config files 
-modules = real_config['global']['formulations'][0]['params']['modules']
-mod_dict = {'NoahOWP': 'noah-owp-modular', 'UEB': 'ueb'}
-
-startdate = start_time.strftime("%Y%m%d%H%M")
-enddate = end_time.strftime("%Y%m%d%H%M")
-
-for i1, m1 in enumerate(modules):
-    if m1['params']['model_type_name'] in ['NoahOWP', 'UEB']:
-
-        # read the BMI config files from the source directory in the realization file
-        src0 = real_config['global']['formulations'][0]['params']['modules'][i1]['params']['init_config']
-        src = Path(src0.replace('{{id}}', '*'))
-        dst = Path(out_dir, mod_dict[m1['params']['model_type_name']] + '_input')
-        dst.mkdir(parents=True, exist_ok=True)
-        for f1 in glob.glob(f'{src}'):
-            with open(f1) as f:
-                lines = f.readlines()
-
-            # update start/end times
-            for i2, l1 in enumerate(lines):
-                if m1['params']['model_type_name'] == 'NoahOWP':
-                    if 'startdate' in l1:
-                        lines[i2] = "  " + "startdate".ljust(19) + "= " + "'" + startdate + "'" + "               ! UTC time start of simulation (YYYYMMDDhhmm)\n"
-                    elif 'enddate' in l1:
-                        lines[i2] = "  " + "enddate".ljust(19) + "= " + "'" + enddate + "'" + "               ! UTC time end of simulation (YYYYMMDDhhmm)\n"
-                elif m1['params']['model_type_name'] == 'UEB':
-                    lines[8] = f'{startdate[:4]} {startdate[4:6]} {startdate[6:8]} {startdate[8:10]}.0\n'
-                    lines[9] = f'{enddate[:4]} {enddate[4:6]} {enddate[6:8]} {enddate[8:10]}.0\n'
-
-                    # write to new BMI config files
-            with open(Path(dst, os.path.basename(f1)), 'w') as outfile:
-                outfile.writelines(lines)
-
-        # replace path to BMI config file in realization file
-        real_config['global']['formulations'][0]['params']['modules'][i1]['params']['init_config'] = str(Path(dst, os.path.basename(src0)))
-
-# For t-route, update path to config file as well as time-related info in the config file
-src = Path(real_config['routing']['t_route_config_file_with_path'])
-src.resolve(strict=True)
-with open(src) as fp1:
-    rt_config = yaml.safe_load(fp1)
-
-# compute number of time steps and max_loop_size
-nts = len(pd.date_range(start=start_time, end=end_time, freq='5min')) - 1
-max_loop_size = divmod(nts * 300, 3600)[0] + 1
-stream_output_time = divmod(nts * 300, 3600)[0] + 1
-
-# update t-route config
-rt_config['compute_parameters']['restart_parameters']['start_datetime'] = str(start_time)
-rt_config['compute_parameters']['forcing_parameters']['nts'] = nts
-rt_config['compute_parameters']['forcing_parameters']['max_loop_size'] = max_loop_size
-rt_config['output_parameters']['stream_output']['stream_output_time'] = stream_output_time
-
-# write to new t-route config file
-new_file = Path(out_dir, os.path.basename(src))
-with open(new_file, 'w') as file:
-    yaml.dump(rt_config, file, sort_keys=False, default_flow_style=False, indent=4)
-
-# update path to new t-route config in realization
-real_config['routing']['t_route_config_file_with_path'] = str(new_file)
-
-# save the new realization file
-new_real_file = Path(out_dir, os.path.basename(real_file))
-with open(new_real_file, 'w') as outfile:
-    json.dump(real_config, outfile, indent=4, separators=(", ", ": "), sort_keys=False)
-
-# hydrofabric gpkg
-gpkg_cats = conf['model']['catchments']
-gpkg_nexus = conf['model']['nexus']
-
-# ngen executable
-ngen_exe = conf['model']['binary']
-
-# run command
-cmd = f'{ngen_exe} {gpkg_cats} "all" {gpkg_nexus} "all" {new_real_file}'
-
-# kick off ngen run and save stdout & stderr to ngen_stdout_stderr.log
-log_file = Path(out_dir, 'ngen_stdout_stderr.log')
-with open(log_file, 'a+') as log:
-    subprocess.check_call(cmd, stdout=log, stderr=log, shell=True, cwd=str(out_dir))
-
-# move output files to output directory
-output_dir = Path(out_dir, "output/")
-output_dir.mkdir(parents=True, exist_ok=True)
-for pat1 in ['cat*.csv', 'nex*.csv', 'troute*.nc']:
-    for f1 in glob.glob(f'{out_dir}/{pat1}'):
-        shutil.move(f1, Path(output_dir, os.path.basename(f1)))
-logger.info(f'Outputs are saved at: {output_dir}')
-
-# get gage ID and make sure it is not empty
-try:
-    gage0 = conf['model']['eval_params']['basinID']
-except:
-    raise ValueError(f'Key model/eval_params/basinID not found in {config_file}')
-if gage0=="":
-    raise ValueError(f'basinID in {config_file} cannot be empty')
-
-# Handle crosswalk file (in order to get the correct feature_id when reading t-route data)
-x_walk = pd.Series(dtype=object)
-cwt_file = conf['model']['crosswalk']
-try:
-    with open(cwt_file) as fp:
-        data = json.load(fp)
-        for id, values in data.items():
-            gage = values.get('Gage_no')
-            if gage:
-                if not isinstance(gage, str):
-                    gage = gage[0]
-                if gage==gage0:
-                    x_walk[id] = gage
-                    break
-except FileNotFoundError:
-    raise FileNotFoundError(f"Crosswalk file '{cwt_file}' not found.")
-except json.JSONDecodeError:
-    raise ValueError(f"Failed to parse JSON from crosswalk file '{cwt_file}'.")
-
-if x_walk.empty:
-    raise Exception(f'{gage0} is not found in crosswalk file {cwt_file}')
-
-# get catchment at basin outlet for reading from t-route output
-catchment_hydro_fabric = gpd.read_file(gpkg_cats, layer='divides')
-catchment_hydro_fabric.set_index('id', inplace=True)
-nexus_id = catchment_hydro_fabric.loc[x_walk.index[0].replace('cat', 'wb')]['toid']
-wb_lst = [x.split('-')[1] for x in list(catchment_hydro_fabric.query('toid==@nexus_id').index)]
-
-# read troute output
-file1 = glob.glob(f'{output_dir}/troute*.nc')[0]
-ncvar = netCDF4.Dataset(file1, "r")
-fid_index = [list(ncvar['feature_id'][0:]).index(int(fid)) for fid in wb_lst]
-output = pd.DataFrame(data={'sim_flow': pd.DataFrame(ncvar['flow'][fid_index], index=fid_index).T.sum(axis=1)})
-t0 = pd.to_datetime(ncvar.file_reference_time, format="%Y-%m-%d_%H:%M:%S")
-output.index = [t0 + pd.Timedelta(seconds=int(t1)) for t1 in ncvar['time']]
-output.index.name = 'Time'
-
-# plot the hydrograph
-output.plot(y='sim_flow', kind='line')
-plt.xlabel('Time')
-plt.ylabel('Streamflow (m^3/s)')
-plt.savefig(Path(output_dir, gage0 + '_hydrograph.png'), bbox_inches ="tight")
-
-# save streamflow simulation to csv
-output.to_csv(Path(output_dir, gage0 + '_output.csv'))
-logger.info('Run completed!')
\ No newline at end of file
diff --git a/test_data/01123000_config_valid_best.yaml b/test_data/01123000_config_valid_best.yaml
new file mode 100644
index 0000000..a519f08
--- /dev/null
+++ b/test_data/01123000_config_valid_best.yaml
@@ -0,0 +1,117 @@
+general:
+  strategy:
+    type: estimation
+    algorithm: dds
+  name: valid_best
+  log: true
+  workdir: /home/jeff.wade/ngwpc/run_ngen/kge_DDS/noah_cfes/01123000
+  yaml_file: /home/jeff.wade/ngwpc/run_ngen/kge_DDS/noah_cfes/01123000/Output/Validation_Run/01123000_config_valid_best.yaml
+  start_iteration: 0
+  iterations: 2
+  restart: 0
+  calibration_run_id: 1
+  ngen_cerf: false
+  auth_token: ''
+CFE: &id001
+- name: b
+  min: 2.0
+  max: 15.0
+  init: 4.05
+- name: satpsi
+  min: 0.03
+  max: 0.955
+  init: 0.355
+- name: satdk
+  min: 1.0e-07
+  max: 0.000726
+  init: 3.38e-06
+- name: maxsmc
+  min: 0.16
+  max: 0.59
+  init: 0.439
+- name: refkdt
+  min: 0.1
+  max: 4.0
+  init: 1.0
+- name: slope
+  min: 0.0
+  max: 1.0
+  init: 0.1
+- name: max_gw_storage
+  min: 0.01
+  max: 0.25
+  init: 0.05
+- name: expon
+  min: 1.0
+  max: 8.0
+  init: 3.0
+- name: Cgw
+  min: 1.8e-06
+  max: 0.0018
+  init: 1.8e-05
+- name: Klf
+  min: 0.0
+  max: 1.0
+  init: 0.01
+- name: Kn
+  min: 0.0
+  max: 1.0
+  init: 0.03
+NoahOWP: &id002
+- name: RSURF_EXP
+  min: 1.0
+  max: 6.0
+  init: 5.0
+- name: CWP
+  min: 0.09
+  max: 0.36
+  init: 0.18
+- name: MP
+  min: 3.6
+  max: 12.6
+  init: 9.0
+- name: VCMX25
+  min: 24.0
+  max: 112.0
+  init: 52.2
+- name: MFSNO
+  min: 0.5
+  max: 4.0
+  init: 2.0
+- name: RSURF_SNOW
+  min: 0.136
+  max: 100.0
+  init: 50.0
+- name: SCAMAX
+  min: 0.7
+  max: 1.0
+  init: 0.9
+model:
+  type: ngen
+  binary: /home/jeff.wade/ngwpc/run_ngen/kge_DDS/noah_cfes/01123000/Input/ngen
+  realization: /home/jeff.wade/ngwpc/run_ngen/kge_DDS/noah_cfes/01123000/Output/Validation_Run/01123000_realization_config_bmi_valid_best.json
+  catchments: /home/jeff.wade/ngwpc/run_ngen/kge_DDS/noah_cfes/01123000/Input/gauge_01123000.gpkg
+  nexus: /home/jeff.wade/ngwpc/run_ngen/kge_DDS/noah_cfes/01123000/Input/gauge_01123000.gpkg
+  crosswalk: /home/jeff.wade/ngwpc/run_ngen/kge_DDS/noah_cfes/01123000/Input/01123000_crosswalk.json
+  obsflow: null
+  strategy: uniform
+  params:
+    CFE: *id001
+    NoahOWP: *id002
+  eval_params:
+    objective: kge
+    evaluation_start: '2016-10-01 00:00:00'
+    evaluation_stop: '2017-09-30 23:00:00'
+    valid_start_time: '2014-10-01 00:00:00'
+    valid_end_time: '2017-09-30 23:00:00'
+    valid_eval_start_time: '2015-10-01 00:00:00'
+    valid_eval_end_time: '2016-09-30 23:00:00'
+    full_eval_start_time: '2015-10-01 00:00:00'
+    full_eval_end_time: '2017-09-30 23:00:00'
+    save_output_iteration: 0
+    save_plot_iteration: 0
+    save_plot_iter_freq: 1
+    basinID: '01123000'
+    threshold: 3.88
+    site_name: 'USGS 01123000: "Little River Near Hanover, CT"'
+    user: ''
diff --git a/test_data/Gage_01123000_csv/cat-11466.csv b/test_data/Gage_01123000_csv/cat-11466.csv
new file mode 100644
index 0000000..1e82171
--- /dev/null
+++ b/test_data/Gage_01123000_csv/cat-11466.csv
@@ -0,0 +1,19 @@
+Time,U2D,V2D,LWDOWN,RAINRATE,T2D,Q2D,PSFC,SWDOWN
+2025-02-20 15:00:00,0.792,-2.814,191.328,0,266.9,0.001349,99149.5,539.232
+2025-02-20 16:00:00,0.109,-2.05,198.545,0,268.02,0.001483,98998.1,611.038
+2025-02-20 17:00:00,1.044,-2.056,202.387,0,269.13,0.001609,99029.5,650.483
+2025-02-20 18:00:00,0.702,-1.589,214.491,0,269.73,0.001823,98934.7,582.878
+2025-02-20 19:00:00,0.712,-2.757,239.591,0,270.03,0.002107,98758.1,441.591
+2025-02-20 20:00:00,0.699,-2.393,285.533,0,269.85,0.002417,98698.1,146.196
+2025-02-20 21:00:00,0.871,-2.21,285.905,1.99466558825634e-08,269.55,0.002408,98708.1,65.686
+2025-02-20 22:00:00,1.16,-1.65,285.135,1.56998922307139e-07,269.27,0.002408,98798.1,8.292
+2025-02-20 23:00:00,1.35,-1.556,282.701,1.37052268200932e-07,268.92,0.002354,98882.9,0
+2025-02-21 00:00:00,1.126,-1.475,281.208,4.10320035371114e-06,268.61,0.002307,98907.4,0
+2025-02-21 01:00:00,2.177,-1.808,281.035,8.98366215551505e-06,268.28,0.002286,98864,0
+2025-02-21 02:00:00,3.328,-2.844,280.598,7.67198162066052e-06,267.86,0.002214,98860.1,0
+2025-02-21 03:00:00,3.551,-2.953,274.01,3.49171727975772e-06,267.19,0.002025,98857.4,0
+2025-02-21 04:00:00,4.323,-3.511,237.324,1.60811384830595e-06,266.06,0.001849,98765.3,0
+2025-02-21 05:00:00,4.294,-3.625,222.341,5.74366549699334e-06,265.51,0.001769,98745.3,0
+2025-02-21 06:00:00,4.374,-4.081,260.361,1.01648311101599e-06,265.86,0.001773,98785.3,0
+2025-02-21 07:00:00,4.366,-4.145,266.781,3.52459181840459e-07,266.1,0.001782,98947.4,0
+2025-02-21 08:00:00,4.428,-2.926,247.543,0,265.87,0.001763,99026.7,0
diff --git a/test_data/Gage_01123000_csv/cat-11467.csv b/test_data/Gage_01123000_csv/cat-11467.csv
new file mode 100644
index 0000000..29e8beb
--- /dev/null
+++ b/test_data/Gage_01123000_csv/cat-11467.csv
@@ -0,0 +1,19 @@
+Time,U2D,V2D,LWDOWN,RAINRATE,T2D,Q2D,PSFC,SWDOWN
+2025-02-20 15:00:00,0.758,-2.851,192.956,0,267.26,0.00141,99640.4,537.832
+2025-02-20 16:00:00,0.523,-2.426,197.546,0,268.37,0.00151,99484.1,627.121
+2025-02-20 17:00:00,0.855,-2.042,206.172,0,269.57,0.001621,99527.7,641.23
+2025-02-20 18:00:00,0.596,-1.747,208.462,0,270.1,0.001835,99427.7,616.255
+2025-02-20 19:00:00,0.784,-3.035,236.852,0,270.3,0.002082,99247.7,430.428
+2025-02-20 20:00:00,0.618,-2.488,284.795,0,270.25,0.0023,99197.7,172.695
+2025-02-20 21:00:00,0.26,-2.371,287.52,0,269.9,0.002393,99207.7,45.438
+2025-02-20 22:00:00,0.62,-2.113,287.299,1.17783451969444e-06,269.76,0.002391,99297.7,7.782
+2025-02-20 23:00:00,0.4,-1.709,285.371,3.56382588506676e-06,269.62,0.002412,99377.7,0
+2025-02-21 00:00:00,0.884,-1.32,282.467,1.2050659279339e-05,269.39,0.0024,99407.7,0
+2025-02-21 01:00:00,1.973,-1.658,282.189,9.8840391729027e-06,269.03,0.002232,99368.2,0
+2025-02-21 02:00:00,2.919,-2.037,282.106,9.38357879931573e-06,268.63,0.002231,99358.2,0
+2025-02-21 03:00:00,3.371,-2.767,278.065,4.51473715656903e-06,268.06,0.002022,99348.8,0
+2025-02-21 04:00:00,4.306,-3.252,239.9,8.95100868092413e-07,267.06,0.001841,99249.3,0
+2025-02-21 05:00:00,4.184,-3.59,240.403,3.11436951960786e-06,266.54,0.001761,99234.1,0
+2025-02-21 06:00:00,4.032,-4.083,264.086,1.25582755572395e-06,266.73,0.001722,99274.1,0
+2025-02-21 07:00:00,3.918,-4.279,266.154,1.76601261614451e-07,267.02,0.001732,99444.1,0
+2025-02-21 08:00:00,4.363,-2.819,233.758,0,266.63,0.001706,99528.2,0
diff --git a/test_data/Gage_01123000_csv/cat-11468.csv b/test_data/Gage_01123000_csv/cat-11468.csv
new file mode 100644
index 0000000..5f69190
--- /dev/null
+++ b/test_data/Gage_01123000_csv/cat-11468.csv
@@ -0,0 +1,19 @@
+Time,U2D,V2D,LWDOWN,RAINRATE,T2D,Q2D,PSFC,SWDOWN
+2025-02-20 15:00:00,1.049,-3.097,194.012,0,267.64,0.001388,99899.4,538.833
+2025-02-20 16:00:00,0.859,-2.472,197.599,0,268.77,0.00144,99761,629.704
+2025-02-20 17:00:00,1.042,-2.052,204.894,0,269.84,0.001545,99814.4,648.795
+2025-02-20 18:00:00,1.132,-1.756,206.135,0,270.41,0.001719,99699,620.776
+2025-02-20 19:00:00,1.363,-2.974,225.007,0,270.67,0.001942,99514.9,468.159
+2025-02-20 20:00:00,0.888,-2.582,274.586,0,270.66,0.002167,99474.4,228.357
+2025-02-20 21:00:00,0.415,-2.254,287.74,0,270.29,0.002314,99478.2,41.091
+2025-02-20 22:00:00,0.891,-2.019,287.287,9.33754620291438e-08,270.11,0.002297,99574.4,12.185
+2025-02-20 23:00:00,0.881,-1.731,285.052,1.20095103284257e-06,269.87,0.002256,99654.4,0
+2025-02-21 00:00:00,1.046,-1.468,282.259,4.83463645650772e-06,269.61,0.002251,99684.4,0
+2025-02-21 01:00:00,2.249,-1.431,282.579,7.62731997383526e-06,269.31,0.002213,99654.4,0
+2025-02-21 02:00:00,3.344,-1.753,282.767,1.77536730916472e-05,268.68,0.002173,99651.8,0
+2025-02-21 03:00:00,3.563,-3.079,278.598,4.73335740025504e-06,268.28,0.002007,99635.6,0
+2025-02-21 04:00:00,4.31,-3.274,252.871,1.34906053972372e-06,267.5,0.001835,99536.8,0
+2025-02-21 05:00:00,4.306,-3.639,243.142,2.44010925598559e-06,266.85,0.001743,99516.3,0
+2025-02-21 06:00:00,4.101,-4.076,255.891,1.66666666245874e-06,266.89,0.00169,99555.6,0
+2025-02-21 07:00:00,4.006,-4.283,250.621,1.26259971366949e-08,267.02,0.0017,99722.2,0
+2025-02-21 08:00:00,4.482,-3.241,242.697,0,266.98,0.00169,99816.3,0
diff --git a/test_data/Gage_01123000_csv/cat-11469.csv b/test_data/Gage_01123000_csv/cat-11469.csv
new file mode 100644
index 0000000..9ee4a93
--- /dev/null
+++ b/test_data/Gage_01123000_csv/cat-11469.csv
@@ -0,0 +1,19 @@
+Time,U2D,V2D,LWDOWN,RAINRATE,T2D,Q2D,PSFC,SWDOWN
+2025-02-20 15:00:00,0.924,-3.005,193.576,0,267.4,0.001388,99653.3,538.293
+2025-02-20 16:00:00,0.731,-2.498,196.844,0,268.52,0.001454,99502.8,628.996
+2025-02-20 17:00:00,0.987,-2.078,205.213,0,269.64,0.001556,99558.1,645.443
+2025-02-20 18:00:00,0.904,-1.78,205.45,0,270.21,0.001756,99451.3,619.84
+2025-02-20 19:00:00,1.132,-3.03,229.556,0,270.44,0.001994,99265.5,447.186
+2025-02-20 20:00:00,0.778,-2.555,282.015,0,270.41,0.002216,99221.3,198.286
+2025-02-20 21:00:00,0.24,-2.379,287.328,0,270.03,0.002355,99231.3,39.195
+2025-02-20 22:00:00,0.823,-2.131,286.732,3.82554389943834e-07,269.87,0.00233,99321.3,11.062
+2025-02-20 23:00:00,0.793,-1.794,284.898,2.17054912354797e-06,269.68,0.002299,99401.3,0
+2025-02-21 00:00:00,1.009,-1.535,282.171,7.37064465283765e-06,269.45,0.002301,99431.3,0
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diff --git a/test_data/Gage_01123000_csv/cat-11470.csv b/test_data/Gage_01123000_csv/cat-11470.csv
new file mode 100644
index 0000000..44f1e92
--- /dev/null
+++ b/test_data/Gage_01123000_csv/cat-11470.csv
@@ -0,0 +1,19 @@
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diff --git a/test_data/Gage_01123000_csv/cat-11475.csv b/test_data/Gage_01123000_csv/cat-11475.csv
new file mode 100644
index 0000000..101d16d
--- /dev/null
+++ b/test_data/Gage_01123000_csv/cat-11475.csv
@@ -0,0 +1,19 @@
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diff --git a/test_data/Gage_01123000_csv/cat-11476.csv b/test_data/Gage_01123000_csv/cat-11476.csv
new file mode 100644
index 0000000..6597f2b
--- /dev/null
+++ b/test_data/Gage_01123000_csv/cat-11476.csv
@@ -0,0 +1,19 @@
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diff --git a/version.txt b/version.txt
deleted file mode 100644
index 7b0d70e..0000000
--- a/version.txt
+++ /dev/null
@@ -1,3 +0,0 @@
-version=1.2.0
-date=2025-03-19
-commit=bc9d7fe866e87bacb0626ba7f699961f65261ecc