From 239cde95e313030662ff164274a6c2b336001a8a Mon Sep 17 00:00:00 2001
From: Andrew Collard <andrew.collard@noaa.gov>
Date: Thu, 31 Jul 2025 18:54:47 +0000
Subject: [PATCH 1/6] Update paths for run_ufo_hofx_test.sh

---
 ush/ufoeval/run_ufo_hofx_test.sh | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/ush/ufoeval/run_ufo_hofx_test.sh b/ush/ufoeval/run_ufo_hofx_test.sh
index 2bd4799b2..768ac58d5 100755
--- a/ush/ufoeval/run_ufo_hofx_test.sh
+++ b/ush/ufoeval/run_ufo_hofx_test.sh
@@ -79,11 +79,11 @@ if [ $machine = orion ]; then
    GDASApp=${GDASApp:-/work2/noaa/da/$LOGNAME/git/GDASApp/} # Change this to your own branch
    JCBinstall=${JCBinstall:-/work2/noaa/da/cmartin/CI/GDASApp/opt}
    JCBpylib=$JCBinstall/lib/python3.7/site-packages
-elif [ $machine = hera ]; then
+elif [ $machine = ursa ]; then
    if [ $run_filtering == NO ]; then
-      workdir=/scratch1/NCEPDEV/stmp2/$LOGNAME/ufoeval/$cycle/${obtype}_noqc
+      workdir=/scratch3/NCEPDEV/stmp/$LOGNAME/ufoeval/$cycle/${obtype}_noqc
    else
-      workdir=/scratch1/NCEPDEV/stmp2/$LOGNAME/ufoeval/$cycle/${obtype}
+      workdir=/scratch3/NCEPDEV/stmp/$LOGNAME/ufoeval/$cycle/${obtype}
    fi
    GDASApp=${GDASApp:-/scratch1/NCEPDEV/da/$LOGNAME/git/GDASApp/} # Change this to your own branch
    JCBinstall=${JCBinstall:-/scratch1/NCEPDEV/da/Cory.R.Martin/CI/GDASApp/opt}
@@ -117,9 +117,9 @@ fi
 if [ $machine = orion ]; then
     export Datapath='/work2/noaa/da/acollard/UFO_eval/data/gsi_geovals_l127/nofgat_feb2024/'$dataprocdate 
     FixDir=/work2/noaa/da/cmartin/GDASApp/fix
-elif [ $machine = hera ]; then
-    export Datapath='/scratch1/NCEPDEV/da/Emily.Liu/UFO_eval/data/gsi_geovals_l127/nofgat_aug2021/'$dataprocdate
-    FixDir=/scratch1/NCEPDEV/da/Cory.R.Martin/GDASApp/fix
+elif [ $machine = ursa ]; then
+    export Datapath='/scratch3/NCEPDEV/da/Andrew.Collard/UFO_eval/data/gsi_geovals_l127/nofgat_Feb2024/'$dataprocdate
+    FixDir=/scratch3/NCEPDEV/da/Andrew.Collard/GDASApp/fix
 else
    echo "Machine " $machine "not found"
    exit

From 4c7cd51fe49e31e649d34c9f3e15043ca77ea08a Mon Sep 17 00:00:00 2001
From: Andrew Collard <andrew.collard@noaa.gov>
Date: Thu, 31 Jul 2025 20:06:22 +0000
Subject: [PATCH 2/6] reinstate hera and add hercules

---
 ush/ufoeval/run_ufo_hofx_test.sh | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/ush/ufoeval/run_ufo_hofx_test.sh b/ush/ufoeval/run_ufo_hofx_test.sh
index 768ac58d5..6f0497c4e 100755
--- a/ush/ufoeval/run_ufo_hofx_test.sh
+++ b/ush/ufoeval/run_ufo_hofx_test.sh
@@ -69,7 +69,7 @@ obtype=$1
 
 machine=${machine:-orion} 
 
-if [ $machine = orion ]; then
+if [ $machine = orion || $machine = hercules ]; then
    if [ $run_filtering == NO ]; then
       workdir=/work2/noaa/da/$LOGNAME/ufoeval/$cycle/${obtype}_noqc
       echo "Run without data filtering"
@@ -79,7 +79,7 @@ if [ $machine = orion ]; then
    GDASApp=${GDASApp:-/work2/noaa/da/$LOGNAME/git/GDASApp/} # Change this to your own branch
    JCBinstall=${JCBinstall:-/work2/noaa/da/cmartin/CI/GDASApp/opt}
    JCBpylib=$JCBinstall/lib/python3.7/site-packages
-elif [ $machine = ursa ]; then
+elif [ $machine = ursa || $machine = hera ]; then
    if [ $run_filtering == NO ]; then
       workdir=/scratch3/NCEPDEV/stmp/$LOGNAME/ufoeval/$cycle/${obtype}_noqc
    else
@@ -114,10 +114,10 @@ else
    radiance="NO"
 fi
 
-if [ $machine = orion ]; then
+if [ $machine = orion || $machine = hercules ]; then
     export Datapath='/work2/noaa/da/acollard/UFO_eval/data/gsi_geovals_l127/nofgat_feb2024/'$dataprocdate 
     FixDir=/work2/noaa/da/cmartin/GDASApp/fix
-elif [ $machine = ursa ]; then
+elif [ $machine = ursa || $machine" = hera ]; then
     export Datapath='/scratch3/NCEPDEV/da/Andrew.Collard/UFO_eval/data/gsi_geovals_l127/nofgat_Feb2024/'$dataprocdate
     FixDir=/scratch3/NCEPDEV/da/Andrew.Collard/GDASApp/fix
 else

From e333a9e56026a1bd59cdcb5ab9d8cbd71e42cf8b Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Thu, 31 Jul 2025 20:39:04 +0000
Subject: [PATCH 3/6] Initial plan


From c647bf380979afe4472c34befd5189fb97f9b1da Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Thu, 31 Jul 2025 20:49:09 +0000
Subject: [PATCH 4/6] Add jcb installation to CMake build system

Co-authored-by: CoryMartin-NOAA <6354668+CoryMartin-NOAA@users.noreply.github.com>
---
 bundle/CMakeLists.txt | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/bundle/CMakeLists.txt b/bundle/CMakeLists.txt
index f00ba70cb..463ae4c5c 100644
--- a/bundle/CMakeLists.txt
+++ b/bundle/CMakeLists.txt
@@ -125,6 +125,17 @@ if(BUILD_GDASBUNDLE)
 # GDASApp
   ecbuild_bundle( PROJECT gdas SOURCE "../")
 
+# Install jcb (JEDI Configuration Builder) Python package
+  message(STATUS "Installing jcb (JEDI Configuration Builder)")
+  execute_process(
+    COMMAND ${Python3_EXECUTABLE} -m pip install --prefix ${CMAKE_INSTALL_PREFIX} .
+    WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/../sorc/jcb
+    RESULT_VARIABLE jcb_install_result
+  )
+  if(NOT jcb_install_result EQUAL 0)
+    message(FATAL_ERROR "Failed to install jcb Python package")
+  endif()
+
 # ioda, ufo, fv3-jedi, and saber test data
 #---------------------------------
   if(CLONE_JCSDADATA)

From 4a16ca94bca5a76d5617891d5841b18ea60803e2 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Thu, 31 Jul 2025 20:54:02 +0000
Subject: [PATCH 5/6] Add integration test for jcb installation verification

Co-authored-by: CoryMartin-NOAA <6354668+CoryMartin-NOAA@users.noreply.github.com>
---
 test/test_jcb_installation.sh | 63 +++++++++++++++++++++++++++++++++++
 1 file changed, 63 insertions(+)
 create mode 100755 test/test_jcb_installation.sh

diff --git a/test/test_jcb_installation.sh b/test/test_jcb_installation.sh
new file mode 100755
index 000000000..e8be58e58
--- /dev/null
+++ b/test/test_jcb_installation.sh
@@ -0,0 +1,63 @@
+#!/bin/bash
+
+# Test script to verify that jcb is properly installed during build
+# This script should be run after a successful CMake build
+
+set -e
+
+echo "Testing jcb installation in build directory..."
+
+# Get the build directory - assuming it's passed as first argument or use default
+BUILD_DIR="${1:-${CMAKE_INSTALL_PREFIX:-./install}}"
+
+if [ ! -d "$BUILD_DIR" ]; then
+    echo "Error: Build directory '$BUILD_DIR' does not exist"
+    exit 1
+fi
+
+echo "Using build directory: $BUILD_DIR"
+
+# Find the Python site-packages directory
+PYTHON_SITE_PACKAGES=$(find "$BUILD_DIR" -path "*/lib/python*/dist-packages" -o -path "*/lib/python*/site-packages" | head -1)
+if [ -z "$PYTHON_SITE_PACKAGES" ]; then
+    echo "Error: Could not find Python site-packages directory in $BUILD_DIR"
+    exit 1
+fi
+
+# Find the bin directory
+BIN_DIR=$(find "$BUILD_DIR" -name "bin" -type d | head -1)
+if [ -z "$BIN_DIR" ]; then
+    echo "Error: Could not find bin directory in $BUILD_DIR"
+    exit 1
+fi
+
+echo "Python packages directory: $PYTHON_SITE_PACKAGES"
+echo "Binary directory: $BIN_DIR"
+
+# Check if jcb package is installed
+if [ ! -d "$PYTHON_SITE_PACKAGES/jcb" ]; then
+    echo "Error: jcb Python package not found in $PYTHON_SITE_PACKAGES"
+    exit 1
+fi
+
+# Check if jcb command is available
+if [ ! -f "$BIN_DIR/jcb" ]; then
+    echo "Error: jcb command not found in $BIN_DIR"
+    exit 1
+fi
+
+# Test if jcb command works
+export PYTHONPATH="$PYTHON_SITE_PACKAGES:$PYTHONPATH"  
+export PATH="$BIN_DIR:$PATH"
+
+echo "Testing jcb command..."
+if ! jcb --version; then
+    echo "Error: jcb command failed to run"
+    exit 1
+fi
+
+echo "✓ jcb is properly installed and functional"
+echo "✓ jcb command is available at: $BIN_DIR/jcb"
+echo "✓ jcb package is installed at: $PYTHON_SITE_PACKAGES/jcb"
+
+exit 0
\ No newline at end of file

From 9917dfa92d2c642657cae499d3a9074531c16fbc Mon Sep 17 00:00:00 2001
From: Andrew Collard <andrew.collard@noaa.gov>
Date: Fri, 1 Aug 2025 14:27:22 +0000
Subject: [PATCH 6/6] Module updates

---
 modulefiles/EVA/hercules.lua     | 18 ++++++++++++
 modulefiles/EVA/ursa.lua         | 48 ++++++++++++++++++++++++++++++++
 ush/ufoeval/run_ufo_hofx_test.sh | 20 ++++++-------
 3 files changed, 76 insertions(+), 10 deletions(-)
 create mode 100644 modulefiles/EVA/hercules.lua
 create mode 100644 modulefiles/EVA/ursa.lua

diff --git a/modulefiles/EVA/hercules.lua b/modulefiles/EVA/hercules.lua
new file mode 100644
index 000000000..398156f00
--- /dev/null
+++ b/modulefiles/EVA/hercules.lua
@@ -0,0 +1,18 @@
+-- NOAA HPC Orion Modulefile for EVA
+help([[
+]])
+
+local pkgName    = myModuleName()
+local pkgVersion = myModuleVersion()
+local pkgNameVer = myModuleFullName()
+
+prepend_path("MODULEPATH", '/work2/noaa/da/python/opt/modulefiles/stack')
+
+load("hpc/1.2.0")
+load("miniconda3/4.6.14")
+load("eva/1.0.0")
+
+whatis("Name: ".. pkgName)
+whatis("Version: " .. pkgVersion)
+whatis("Category: EVA")
+whatis("Description: Load all libraries needed for EVA")
diff --git a/modulefiles/EVA/ursa.lua b/modulefiles/EVA/ursa.lua
new file mode 100644
index 000000000..768fb2fae
--- /dev/null
+++ b/modulefiles/EVA/ursa.lua
@@ -0,0 +1,48 @@
+help([[
+Load python virtual environment for obs-monitor
+]])
+
+local pkgName    = myModuleName()
+local pkgVersion = myModuleVersion()
+
+conflict(pkgName)
+
+-- Load dependencies
+prepend_path("MODULEPATH", "/contrib/spack-stack/spack-stack-1.9.2/envs/ue-oneapi-2024.2.1/install/modulefiles/Core")
+
+load("stack-oneapi/2024.2.1")
+load("stack-intel-oneapi-mpi/2021.13")
+load("intel-oneapi-mkl/2024.2.1")
+load("stack-python/3.11.7")
+load("rocoto/1.3.7")
+
+-- Python packages
+load("py-jinja2/3.1.4")
+load("py-netcdf4/1.7.1.post2")
+load("py-pybind11/2.13.5")
+load("py-pycodestyle/2.11.0")
+load("py-pyyaml/6.0.2")
+load("py-scipy/1.14.1")
+load("py-xarray/2024.7.0")
+load("py-pip/23.1.2")
+load("py-matplotlib/3.7.4")
+load("py-cartopy/0.24.1")
+load("proj/9.4.1")
+load("py-wxflow/0.2.0")
+
+-- Set the venv path
+local venv_root = "/scratch3/NCEPDEV/da/Edward.Safford/noscrub/python/envs/obs-mon"
+local bin_path  = pathJoin(venv_root, "bin")
+local lib_path  = pathJoin(venv_root, "lib/python3.11/site-packages")  -- adjust Python version if needed
+
+-- Modify environment variables to emulate virtualenv activation
+prepend_path("PATH", bin_path)
+prepend_path("PYTHONPATH", lib_path)
+
+-- Optional: If you want to make this environment more self-contained
+setenv("VIRTUAL_ENV", venv_root)
+
+whatis("Name: " .. pkgName)
+whatis("Version: " .. tostring(pkgVersion))
+whatis("Category: Obs-monitor")
+whatis("Description: Load all libraries needed for obs-monitor")
\ No newline at end of file
diff --git a/ush/ufoeval/run_ufo_hofx_test.sh b/ush/ufoeval/run_ufo_hofx_test.sh
index 6f0497c4e..e2384aa2b 100755
--- a/ush/ufoeval/run_ufo_hofx_test.sh
+++ b/ush/ufoeval/run_ufo_hofx_test.sh
@@ -67,9 +67,9 @@ obtype=$1
 
 #--------------- User modified options below -----------------
 
-machine=${machine:-orion} 
+machine=${machine:-ursa} 
 
-if [ $machine = orion || $machine = hercules ]; then
+if [[ "$machine" = "orion" || "$machine" = "hercules" ]]; then
    if [ $run_filtering == NO ]; then
       workdir=/work2/noaa/da/$LOGNAME/ufoeval/$cycle/${obtype}_noqc
       echo "Run without data filtering"
@@ -79,15 +79,15 @@ if [ $machine = orion || $machine = hercules ]; then
    GDASApp=${GDASApp:-/work2/noaa/da/$LOGNAME/git/GDASApp/} # Change this to your own branch
    JCBinstall=${JCBinstall:-/work2/noaa/da/cmartin/CI/GDASApp/opt}
    JCBpylib=$JCBinstall/lib/python3.7/site-packages
-elif [ $machine = ursa || $machine = hera ]; then
+elif [[ "$machine" = "ursa" || "$machine" = "hera" ]]; then
    if [ $run_filtering == NO ]; then
       workdir=/scratch3/NCEPDEV/stmp/$LOGNAME/ufoeval/$cycle/${obtype}_noqc
    else
       workdir=/scratch3/NCEPDEV/stmp/$LOGNAME/ufoeval/$cycle/${obtype}
    fi
-   GDASApp=${GDASApp:-/scratch1/NCEPDEV/da/$LOGNAME/git/GDASApp/} # Change this to your own branch
-   JCBinstall=${JCBinstall:-/scratch1/NCEPDEV/da/Cory.R.Martin/CI/GDASApp/opt}
-   JCBpylib=$JCBinstall/lib/python3.10/site-packages
+   GDASApp=${GDASApp:-/scratch3/NCEPDEV/da/$LOGNAME/git/GDASApp/} # Change this to your own branch
+   JCBinstall=${JCBinstall:-/scratch3/NCEPDEV/da/Andrew.Collard/jcb}
+   JCBpylib=$JCBinstall/lib/python3.9/site-packages
 else
    echo "Machine " $machine "not found"
    exit 1
@@ -103,7 +103,7 @@ exename=test_ObsFilters.x
 #-------------- Do not modify below this line ----------------
 # paths that should only be changed by an expert user
 
-dataprocdate=20240815 # Production date of test data
+dataprocdate=20250731 # Production date of test data
 
 obtype_short=${obtype:0:4}
 if [ $obtype_short = "cris" ] || [ $obtype_short = "iasi" ] || [ $obtype_short = "hirs" ] || [ $obtype_short = "sevi" ] || \
@@ -114,10 +114,10 @@ else
    radiance="NO"
 fi
 
-if [ $machine = orion || $machine = hercules ]; then
+if [[ "$machine" = "orion" || "$machine" = "hercules" ]]; then
     export Datapath='/work2/noaa/da/acollard/UFO_eval/data/gsi_geovals_l127/nofgat_feb2024/'$dataprocdate 
     FixDir=/work2/noaa/da/cmartin/GDASApp/fix
-elif [ $machine = ursa || $machine" = hera ]; then
+elif [[ "$machine" = "ursa" || "$machine" = "hera" ]]; then
     export Datapath='/scratch3/NCEPDEV/da/Andrew.Collard/UFO_eval/data/gsi_geovals_l127/nofgat_Feb2024/'$dataprocdate
     FixDir=/scratch3/NCEPDEV/da/Andrew.Collard/GDASApp/fix
 else
@@ -155,7 +155,7 @@ export GPREFIX=gdas.t${gcyc}z
 
 # Load Modules for GDASApp
 module use $GDASApp/modulefiles
-module load GDAS/$machine
+module load GDAS/$machine.intel
 export PYTHONPATH=$GDASApp/ush:$PYTHONPATH
 
 # Create and set up the working directory