add no-remotes workaround to docker image

docker/Dockerfile

@@ -174,11 +174,9 @@ RUN dnf update -y && \
 WORKDIR /ngen
 
 # Copy necessary files from build stages
-COPY  HelloNGEN.sh /ngen/HelloNGEN.sh
-COPY --from=restructure_files /dmod /dmod
+
 COPY --from=troute_build /ngen/t-route/src/troute-*/dist/*.whl /tmp/
 
-RUN ln -s /dmod/bin/ngen /usr/local/bin/ngen
 ENV UV_INSTALL_DIR=/root/.cargo/bin
 RUN curl -LsSf https://astral.sh/uv/install.sh | sh
 ENV PATH="/root/.cargo/bin:${PATH}"
@@ -189,13 +187,14 @@ RUN uv venv && \
 RUN rm -rf /tmp/*.whl
 # DONT ADD THE VENV TO THE PATH YET
 
+COPY --from=restructure_files /dmod /dmod
+RUN ln -s /dmod/bin/ngen /usr/local/bin/ngen
 # Set up library path
 RUN echo "/dmod/shared_libs/" >> /etc/ld.so.conf.d/ngen.conf && ldconfig -v
 
 # Add mpirun to path
 ENV PATH=$PATH:/usr/lib64/mpich/bin
-RUN chmod a+x /dmod/bin/* /ngen/HelloNGEN.sh
-
+RUN chmod a+x /dmod/bin/*
 # Only here after everything else is done will the ngen binary work and provide --info
 #                                                             This mess is parsing the version number
 RUN uv pip install numpy==$(/dmod/bin/ngen --info | grep -e 'NumPy Version: ' | cut -d ':' -f 2 | uniq | xargs)
@@ -216,6 +215,9 @@ RUN uv pip install --no-cache-dir /ngen/ngen/extern/lstm --extra-index-url https
 COPY --from=troute_build /tmp/troute_url /ngen/troute_url
 COPY --from=ngen_build /tmp/ngen_url /ngen/ngen_url
 
+COPY  HelloNGEN.sh /ngen/HelloNGEN.sh
+RUN chmod a+x /ngen/HelloNGEN.sh
+
 
 RUN echo "export PS1='\u\[\033[01;32m\]@ngiab_dev\[\033[00m\]:\[\033[01;35m\]\W\[\033[00m\]\$ '" >> ~/.bashrc
 

docker/HelloNGEN.sh

@@ -45,11 +45,12 @@ echo -e "\n"
 echo -e "${CYAN}\e[4mFound these Realization files:${RESET}" && echo "$NGEN_REALIZATIONS" || echo -e "${RED}No Realization files found.${RESET}"
 echo -e "\n"
 
+no_remotes=$(grep "remotes_enabled" $selected_realization | grep false | wc -l)
+
 generate_partition() {
-    # Store the grep result (0 if "false" is found, 1 if not)
-    grep_result=$(grep "remotes_enabled" $4 | grep false | wc -l)
+    # Store the grep result (0 if "false" is found, 1 if not)    
 
-    if [ "$grep_result" -eq 0 ]; then
+    if [ "$no_remotes" -eq 0 ]; then
         # Use the original partition generator
         /dmod/bin/partitionGenerator "$1" "$2" "partitions_$3.json" "$3" '' ''
     else
@@ -58,6 +59,14 @@ generate_partition() {
     fi
 }
 
+#sed '/^[[:space:]]*"routing":/,/^[[:space:]]*},/d' realization.json >> modified.json
+
+if [ "$no_remotes" -eq 1 ]; then
+        # Use the original partition generator
+        mv $selected_realization modified_noremote.json
+        sed '/^[[:space:]]*"routing":/,/^[[:space:]]*},/d' modified_noremote.json >> $selected_realization
+fi
+
 if [ "$2" == "auto" ]
   then
     echo "AUTO MODE ENGAGED"
@@ -75,9 +84,25 @@ if [ "$2" == "auto" ]
     else
       echo "Found paritions file! "$partitions
     fi
-
+    rm -f /ngen/ngen/data/outputs/ngen/*.csv
     mpirun -n $procs /dmod/bin/ngen-parallel $selected_catchment all $selected_nexus all $selected_realization $(pwd)/partitions_$procs.json
-
+    #TODO run troute manually if remotes were disabled
+    if [ "$no_remotes" -eq 1 ]; then
+        # diff two files to check if routing is needed
+        routing_used=$(wc -l < "$selected_realization")
+        modified_lines=$(wc -l < "modified_noremote.json")
+        if [ "$routing_used" -ne "$modified_lines" ]; then
+            routing_used=1
+        else
+            routing_used=0
+        fi
+        rm $selected_realization
+        mv modified_noremote.json $selected_realization
+        ts-merger /ngen/ngen/data/outputs/ngen/ _output.csv nex-
+        if [ "$routing_used" -eq 1 ]; then
+            python -m nwm_routing -V4 -f /ngen/ngen/data/config/troute.yaml
+        fi
+    fi
     echo "Run completed successfully, exiting, have a nice day!"
     exit 0
   else
@@ -139,6 +164,25 @@ else
 fi
 command_status=$?
 
+
+#TODO run troute manually if remotes were disabled
+if [ "$no_remotes" -eq 1 ]; then
+    # diff two files to check if routing is needed
+    routing_used=$(wc -l < "$selected_realization")
+    modified_lines=$(wc -l < "modified_noremote.json")
+    if [ "$routing_used" -ne "$modified_lines" ]; then
+        routing_used=1
+    else
+        routing_used=0
+    fi
+    rm $selected_realization
+    mv modified_noremote.json $selected_realization
+    ts-merger /ngen/ngen/data/outputs/ngen/ _output.csv nex-
+    if [ "$routing_used" -eq 1 ]; then
+        python -m nwm_routing -V4 -f /ngen/ngen/data/config/troute.yaml
+    fi
+fi
+
 # Set message color based on command status
 if [ $command_status -eq 0 ]; then
     color=$GREEN