Use Cython flag does not seem to be working, some builds are affected by empty fields in files

compiler_mac.sh

@@ -0,0 +1,139 @@
+#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
+build_diffusive_tulane_kernel=true
+build_reservoir_kernel=true
+build_framework=true
+build_routing=true
+build_config=true
+build_nwm=true
+build_bmi=true
+
+if [ -z "$F90" ]
+then
+    export F90="gfortran"
+    echo "using F90=${F90}"
+fi
+if [ -z "$CC" ]
+then
+    export CC="gcc"
+    echo "using CC=${CC}"
+fi
+
+#preserve old/default behavior of installing packages with -e
+WITH_EDITABLE=true
+if [ "$1" == 'no-e' ]
+then
+WITH_EDITABLE=false
+fi
+
+#if you have custom static library paths, uncomment below and export them
+export LIBRARY_PATH=/opt/local/lib/:$LIBRARY_PATH
+#if you have custom dynamic library paths, uncomment below and export them
+export LD_LIBRARY_PATHS=/opt/local/lib/:$LD_LIBRARY_PATHS
+if [ -z "$NETCDF" ]
+then
+    #export NETCDFINC=/usr/include/openmpi-x86_64/
+    export NETCDFINC=/opt/local/include/
+    # set alternative NETCDF variable include path, for example for WSL
+    # (Windows Subsystems for Linux).
+    #
+    # EXAMPLE USAGE: export NETCDFALTERNATIVE=$HOME/.conda/envs/py39/include/
+    # (before ./compiler.sh)
+    if [ -n "$NETCDFALTERNATIVE" ]
+    then
+	echo "using alternative NETCDF inc ${NETCDFALTERNATIVE}"
+	export NETCDFINC=$NETCDFALTERNATIVE
+    fi
+else
+    export NETCDFINC="${NETCDF}"
+fi
+echo "using NETCDFINC=${NETCDFINC}"
+
+if  [[ "$build_mc_kernel" == true ]]; then
+  #building reach and resevoir kernel files .o
+  cd $REPOROOT/src/kernel/muskingum/
+  make clean
+  make  || exit
+  make install || exit
+fi
+
+if  [[ "$build_diffusive_tulane_kernel" == true ]]; then
+  #building reach and resevoir kernel files .o  
+  cd $REPOROOT/src/kernel/diffusive/
+  make clean
+  make diffusive.o
+  make pydiffusive.o
+  make chxsec_lookuptable.o
+  make pychxsec_lookuptable.o
+  make install || exit
+fi
+
+if [[ "$build_reservoir_kernel" == true ]]; then
+  cd $REPOROOT/src/kernel/reservoir/
+  make clean
+  #make NETCDFINC=`nc-config --includedir` || exit
+  #make binding_lp.a
+  #make install_lp || exit
+  make
+  make install_lp || exit
+  make install_rfc || exit
+
+fi
+
+if [[ "$build_framework" == true ]]; then
+  #creates troute package
+  cd $REPOROOT/src/troute-network
+  rm -rf build
+
+  if [[ ${WITH_EDITABLE} == true ]]; then
+    pip install --no-build-isolation --config-setting='--build-option=--use-cython' --editable . --config-setting='editable_mode=compat' || exit
+  else
+    pip install --no-build-isolation --config-setting='--build-option=--use-cython' . || exit
+  fi
+fi
+
+if [[ "$build_routing" == true ]]; then
+  #updates troute package with the execution script
+  cd $REPOROOT/src/troute-routing
+  rm -rf build
+
+  if [[ ${WITH_EDITABLE} == true ]]; then
+    pip install --no-build-isolation --config-setting='--build-option=--use-cython' --editable . --config-setting='editable_mode=compat' || exit
+  else
+    pip install --no-build-isolation --config-setting='--build-option=--use-cython' . || exit
+  fi
+fi
+
+if [[ "$build_config" == true ]]; then
+  #updates troute package with the execution script
+  cd $REPOROOT/src/troute-config
+  if [[ ${WITH_EDITABLE} == true ]]; then
+    pip install --editable . || exit
+  else
+    pip install . || exit
+  fi
+fi
+
+if [[ "$build_nwm" == true ]]; then
+  #updates troute package with the execution script
+  cd $REPOROOT/src/troute-nwm
+  if [[ ${WITH_EDITABLE} == true ]]; then
+    pip install --editable . || exit
+  else
+    pip install . || exit
+  fi
+fi
+
+if [[ "$build_bmi" == true ]]; then
+  cd $REPOROOT/src/troute-bmi
+  if [[ ${WITH_EDITABLE} == true ]]; then
+    pip install --editable . || exit
+  else
+    pip install . || exit
+  fi
+fi

src/troute-network/setup.py

@@ -17,7 +17,7 @@
     sys.argv.remove("--use-cython")
 else:
     USE_CYTHON = False
-
+USE_CYTHON = True
 ext = "pyx" if USE_CYTHON else "c"
 
 # adapted from https://stackoverflow.com/a/5192738/489116 and https://stackoverflow.com/a/32192172/489116

src/troute-network/troute/HYFeaturesNetwork.py

@@ -133,8 +133,20 @@ def read_layer(layer_name):
             lakes["lake_id"] = lakes["lake_id"].astype(int)
             lakes = lakes.merge(hydro[["hl_link", "id", "hl_reference"]], left_on="lake_id", right_on="hl_link", how="left")
 
-        # add hl_uri to nexus
-        nexus = nexus.merge(hydro[["nex_id", "hl_uri"]], left_on="id", right_on="nex_id", how="left")
+        # hydrolocations may call the nexus key "nex_id" or simply "id"
+        if "nex_id" in hydro.columns:
+            right_col = "nex_id"
+        elif "id" in hydro.columns:
+            right_col = "id"
+        else:
+            raise KeyError("HYFeaturesNetwork: hydrolocations layer missing expected nexus id column. available: " + ", ".join(list(hydro.columns)))
+
+        # normalize to 'nex_id' for downstream code, then merge to get hl_uri for nexus
+        if right_col != "nex_id":
+            hydro = hydro.rename(columns={right_col: "nex_id"})
+
+        if not nexus.empty: 
+            nexus = nexus.merge(hydro[["nex_id", "hl_uri"]], left_on="id", right_on="nex_id", how="left")
 
     return flowpaths, lakes, network, nexus
 
@@ -645,7 +657,13 @@ def preprocess_waterbodies(self, lakes, nexus):
             self._duplicate_ids_df = pd.DataFrame()
             self._gl_climatology_df = pd.DataFrame()
 
-        self._dataframe = self.dataframe.drop("waterbody", axis=1).drop_duplicates()
+        # drop 'waterbody' if present; avoid KeyError when it's missing
+        if "waterbody" in self.dataframe.columns:
+            self._dataframe = self.dataframe.drop(columns=["waterbody"]).drop_duplicates()
+        else:
+            #import warnings
+            #warnings.warn("HYFeaturesNetwork: 'waterbody' column not present; skipping drop")
+            self._dataframe = self.dataframe.drop_duplicates()
 
     def preprocess_data_assimilation(self, network):
         if not network.empty:

src/troute-routing/setup.py

@@ -18,7 +18,7 @@
     sys.argv.remove("--use-cython")
 else:
     USE_CYTHON = False
-
+USE_CYTHON = True
 ext = "pyx" if USE_CYTHON else "c"
 
 # adapted from https://stackoverflow.com/a/5192738/489116 and https://stackoverflow.com/a/32192172/489116