Merge EDFS NHF Branch (NGWPC-9874)

.gitignore

@@ -80,4 +80,19 @@ bower_components/
 src/vendor/
 dist/
 
+# Build dirs #
+##############
 build/
+
+# .vscode files #
+#################
+.vscode/
+
+# UV lock #
+###########
+uv.lock
+
+# data #
+########
+data/
+output/

compiler.sh

@@ -1,7 +1,11 @@
+#!/bin/bash
+
 #TODO add options for clean/noclean, make/nomake, cython/nocython
 #TODO include instuctions on blowing away entire package for fresh install e.g. rm -r ~/venvs/mesh/lib/python3.6/site-packages/troute/*
+
 #set root folder of github repo (should be named t-route)
 REPOROOT=`pwd`
+
 #For each build step, you can set these to true to make it build
 #or set it to anything else (or unset) to skip that step
 build_mc_kernel=true
@@ -18,23 +22,51 @@ then
     export F90="gfortran"
     echo "using F90=${F90}"
 fi
+
 if [ -z "$CC" ]
 then
     export CC="gcc"
     echo "using CC=${CC}"
 fi
 
-#preserve old/default behavior of installing packages with -e
+# Parse command line arguments
 WITH_EDITABLE=true
-if [ "$1" == 'no-e' ]
-then
-WITH_EDITABLE=false
+USE_UV=false
+
+while [[ $# -gt 0 ]]; do
+    case $1 in
+        no-e)
+            WITH_EDITABLE=false
+            shift
+            ;;
+        --uv)
+            USE_UV=true
+            shift
+            ;;
+        *)
+            echo "Unknown option: $1"
+            echo "Usage: $0 [no-e] [--uv]"
+            echo "  no-e: Install packages without editable mode"
+            echo "  --uv: Use uv pip instead of pip"
+            exit 1
+            ;;
+    esac
+done
+
+# set pip command based on UV flag
+if [[ "$USE_UV" == true ]]; then
+    PIP_CMD="uv pip"
+    echo "Using uv pip for package installation"
+else
+    PIP_CMD="pip"
+    echo "Using standard pip for package installation"
 fi
 
 #if you have custom static library paths, uncomment below and export them
 #export LIBRARY_PATH=<paths>:$LIBRARY_PATH
 #if you have custom dynamic library paths, uncomment below and export them
 #export LD_LIBRARY_PATHS=<paths>:$LD_LIBRARY_PATHS
+
 if [ -z "$NETCDF" ]
 then
     export NETCDFINC=/usr/include/openmpi-x86_64/
@@ -45,8 +77,8 @@ then
     # (before ./compiler.sh)
     if [ -n "$NETCDFALTERNATIVE" ]
     then
-	echo "using alternative NETCDF inc ${NETCDFALTERNATIVE}"
-	export NETCDFINC=$NETCDFALTERNATIVE
+        echo "using alternative NETCDF inc ${NETCDFALTERNATIVE}"
+        export NETCDFINC=$NETCDFALTERNATIVE
     fi
 else
     export NETCDFINC="${NETCDF}"
@@ -62,27 +94,26 @@ if  [[ "$build_mc_kernel" == true ]]; then
   make install || exit
 fi
 
-if  [[ "$build_diffusive_tulane_kernel" == true ]]; then
-  #building reach and resevoir kernel files .o  
-  cd $REPOROOT/src/kernel/diffusive/
-  make clean
-  make diffusive.o
-  make pydiffusive.o
-  make chxsec_lookuptable.o
-  make pychxsec_lookuptable.o
-  make install || exit
+if [[ "$build_diffusive_tulane_kernel" == true ]]; then
+    #building reach and resevoir kernel files .o
+    cd $REPOROOT/src/kernel/diffusive/
+    make clean
+    make diffusive.o
+    make pydiffusive.o
+    make chxsec_lookuptable.o
+    make pychxsec_lookuptable.o
+    make install || exit
 fi
 
 if [[ "$build_reservoir_kernel" == true ]]; then
-  cd $REPOROOT/src/kernel/reservoir/
-  make clean
-  #make NETCDFINC=`nc-config --includedir` || exit
-  #make binding_lp.a
-  #make install_lp || exit
-  make
-  make install_lp || exit
-  make install_rfc || exit
-
+    cd $REPOROOT/src/kernel/reservoir/
+    make clean
+    #make NETCDFINC=`nc-config --includedir` || exit
+    #make binding_lp.a
+    #make install_lp || exit
+    make
+    make install_lp || exit
+    make install_rfc || exit
 fi
 
 cd $REPOROOT/src/troute_ewts
@@ -93,47 +124,47 @@ else
 fi
 
 if [[ "$build_framework" == true ]]; then
-  #creates troute package
-  cd $REPOROOT/src/troute-network
-  rm -rf build
-
-  if [[ ${WITH_EDITABLE} == true ]]; then
-    pip install --no-build-isolation --config-setting='--build-option=--use-cython' --editable . --config-setting='editable_mode=compat' || exit
-  else
-    pip install --no-build-isolation --config-setting='--build-option=--use-cython' . || exit
-  fi
+    #creates troute package
+    cd $REPOROOT/src/troute-network
+    rm -rf build
+    
+    if [[ ${WITH_EDITABLE} == true ]]; then
+        $PIP_CMD install --no-build-isolation --config-setting='--build-option=--use-cython' --editable . --config-setting='editable_mode=compat' || exit
+    else
+        $PIP_CMD install --no-build-isolation --config-setting='--build-option=--use-cython' . || exit
+    fi
 fi
 
 if [[ "$build_routing" == true ]]; then
-  #updates troute package with the execution script
-  cd $REPOROOT/src/troute-routing
-  rm -rf build
-
-  if [[ ${WITH_EDITABLE} == true ]]; then
-    pip install --no-build-isolation --config-setting='--build-option=--use-cython' --editable . --config-setting='editable_mode=compat' || exit
-  else
-    pip install --no-build-isolation --config-setting='--build-option=--use-cython' . || exit
-  fi
+    #updates troute package with the execution script
+    cd $REPOROOT/src/troute-routing
+    rm -rf build
+    
+    if [[ ${WITH_EDITABLE} == true ]]; then
+        $PIP_CMD install --no-build-isolation --config-setting='--build-option=--use-cython' --editable . --config-setting='editable_mode=compat' || exit
+    else
+        $PIP_CMD install --no-build-isolation --config-setting='--build-option=--use-cython' . || exit
+    fi
 fi
 
 if [[ "$build_config" == true ]]; then
-  #updates troute package with the execution script
-  cd $REPOROOT/src/troute-config
-  if [[ ${WITH_EDITABLE} == true ]]; then
-    pip install --editable . || exit
-  else
-    pip install . || exit
-  fi
+    #updates troute package with the execution script
+    cd $REPOROOT/src/troute-config
+    if [[ ${WITH_EDITABLE} == true ]]; then
+        $PIP_CMD install --editable . || exit
+    else
+        $PIP_CMD install . || exit
+    fi
 fi
 
 if [[ "$build_nwm" == true ]]; then
-  #updates troute package with the execution script
-  cd $REPOROOT/src/troute-nwm
-  if [[ ${WITH_EDITABLE} == true ]]; then
-    pip install --editable . || exit
-  else
-    pip install . || exit
-  fi
+    #updates troute package with the execution script
+    cd $REPOROOT/src/troute-nwm
+    if [[ ${WITH_EDITABLE} == true ]]; then
+        $PIP_CMD install --editable . || exit
+    else
+        $PIP_CMD install . || exit
+    fi
 fi
 
 if [[ "$build_bmi" == true ]]; then

src/model_DAforcing.py

@@ -79,6 +79,7 @@ def __init__(self, bmi_cfg_file=None):
 
             usgs_persistence = data_assimilation_parameters.get('reservoir_da', {}).get('reservoir_persistence_da', {}).get('reservoir_persistence_usgs', False)
             usace_persistence = data_assimilation_parameters.get('reservoir_da', {}).get('reservoir_persistence_da', {}).get('reservoir_persistence_usace', False)
+            usbr_persistence = data_assimilation_parameters.get('reservoir_da', {}).get('reservoir_persistence_da', {}).get('reservoir_persistence_usbr', False)
             rfc = data_assimilation_parameters.get('reservoir_da', {}).get('reservoir_rfc_da', {}).get('reservoir_rfc_forecasts', False)
 
             qc_threshold = data_assimilation_parameters.get('qc_threshold')
@@ -135,6 +136,14 @@ def __init__(self, bmi_cfg_file=None):
                                                                  qc_threshold,
                                                                  900, #15 minutes
                                                                  cpu_pool,)
+
+            if usbr_persistence:
+                usace_timeslice_path = str(data_assimilation_parameters.get('usbr_timeslices_folder'))
+                self._reservoir_usace_df = _read_timeslice_files(usace_timeslice_path, 
+                                                                 timeslice_dates,
+                                                                 qc_threshold,
+                                                                 900, #15 minutes
+                                                                 cpu_pool,)
 
             # Produce list of datetimes to search for timeseries files
             rfc_parameters = data_assimilation_parameters.get('reservoir_da', {}).get('reservoir_rfc_da', {})