From d697819781bf5acaf00543d5feb174a589ceb1dc Mon Sep 17 00:00:00 2001
From: Dong Kim <donghakim@cheyenne4.cheyenne.ucar.edu>
Date: Tue, 8 Nov 2022 12:46:25 -0700
Subject: [PATCH 1/7] working version 1

---
 src/troute-network/troute/nhd_io.py           |  33 +-
 .../channel_forcing/nex-10236_output.csv      | 720 ++++++++++++++++++
 .../channel_forcing/nex-10237_output.csv      | 720 ++++++++++++++++++
 .../channel_forcing/nex-10238_output.csv      | 720 ++++++++++++++++++
 .../channel_forcing/schout_1.nc               | Bin 0 -> 25915 bytes
 .../domain/coastal_boundary_domain.yaml       |   4 +
 .../domain/coastal_domain.yaml                |  10 +
 .../domain/gauge_01069700.gpkg                | Bin 0 -> 184320 bytes
 .../unittest_hyfeature.yaml                   |  99 +++
 9 files changed, 2305 insertions(+), 1 deletion(-)
 create mode 100644 test/unit_test_hyfeature/channel_forcing/nex-10236_output.csv
 create mode 100644 test/unit_test_hyfeature/channel_forcing/nex-10237_output.csv
 create mode 100644 test/unit_test_hyfeature/channel_forcing/nex-10238_output.csv
 create mode 100644 test/unit_test_hyfeature/channel_forcing/schout_1.nc
 create mode 100644 test/unit_test_hyfeature/domain/coastal_boundary_domain.yaml
 create mode 100644 test/unit_test_hyfeature/domain/coastal_domain.yaml
 create mode 100644 test/unit_test_hyfeature/domain/gauge_01069700.gpkg
 create mode 100644 test/unit_test_hyfeature/unittest_hyfeature.yaml

diff --git a/src/troute-network/troute/nhd_io.py b/src/troute-network/troute/nhd_io.py
index 0f0349775..c92059645 100644
--- a/src/troute-network/troute/nhd_io.py
+++ b/src/troute-network/troute/nhd_io.py
@@ -86,7 +86,7 @@ def read_config_file(custom_input_file):
     data_assimilation_parameters (dict): Input parameters re data assimilation
 
     '''
-    
+    import pdb; pdb.set_trace()
     if custom_input_file[-4:] == "yaml":
         with open(custom_input_file) as custom_file:
             data = yaml.load(custom_file, Loader=yaml.SafeLoader)
@@ -99,6 +99,37 @@ def read_config_file(custom_input_file):
     supernetwork_parameters = network_topology_parameters.get(
         "supernetwork_parameters", None
     )
+    # add attributes when HYfeature network is selected
+    if supernetwork_parameters['geo_file_path'][-4:] == "gpkg":
+        params = {
+            "title_string":"HY_Features Test",
+            "geo_file_path":supernetwork_parameters['geo_file_path'],
+            "flowpath_edge_list": None,
+            "columns": {
+                #link????
+                "key": "id",
+                "downstream": "toid",
+                "dx": "lengthkm",
+                "n": "n",  # TODO: rename to `manningn`
+                "ncc": "nCC",  # TODO: rename to `mannningncc`
+                "s0": "So",
+                "bw": "BtmWdth",  # TODO: rename to `bottomwidth`
+                #waterbody: "NHDWaterbodyComID",
+                "tw": "TopWdth",  # TODO: rename to `topwidth`
+                "twcc": "TopWdthCC",  # TODO: rename to `topwidthcc`
+                #alt: "alt",
+                "musk": "MusK",
+                "musx": "MusX",
+                "cs": "ChSlp"  # TODO: rename to `sideslope`
+                },
+            "waterbody_null_code": -9999,
+            "terminal_code": 0,
+            "waterbody_null_code": -9999,
+            "driver_string": "NetCDF",
+            "layer_string": 0
+            }
+        supernetwork_parameters['hyfeature_params'] = params
+        
     preprocessing_parameters = network_topology_parameters.get(
         "preprocessing_parameters", {}
     )        
diff --git a/test/unit_test_hyfeature/channel_forcing/nex-10236_output.csv b/test/unit_test_hyfeature/channel_forcing/nex-10236_output.csv
new file mode 100644
index 000000000..87ab7fa89
--- /dev/null
+++ b/test/unit_test_hyfeature/channel_forcing/nex-10236_output.csv
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diff --git a/test/unit_test_hyfeature/channel_forcing/nex-10237_output.csv b/test/unit_test_hyfeature/channel_forcing/nex-10237_output.csv
new file mode 100644
index 000000000..87ab7fa89
--- /dev/null
+++ b/test/unit_test_hyfeature/channel_forcing/nex-10237_output.csv
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diff --git a/test/unit_test_hyfeature/channel_forcing/nex-10238_output.csv b/test/unit_test_hyfeature/channel_forcing/nex-10238_output.csv
new file mode 100644
index 000000000..87ab7fa89
--- /dev/null
+++ b/test/unit_test_hyfeature/channel_forcing/nex-10238_output.csv
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diff --git a/test/unit_test_hyfeature/channel_forcing/schout_1.nc b/test/unit_test_hyfeature/channel_forcing/schout_1.nc
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diff --git a/test/unit_test_hyfeature/domain/coastal_boundary_domain.yaml b/test/unit_test_hyfeature/domain/coastal_boundary_domain.yaml
new file mode 100644
index 000000000..3374cc333
--- /dev/null
+++ b/test/unit_test_hyfeature/domain/coastal_boundary_domain.yaml
@@ -0,0 +1,4 @@
+10237: 0  # Lower Colorado River
+#5781901: 252935  # Lower Colorado River
+
+
diff --git a/test/unit_test_hyfeature/domain/coastal_domain.yaml b/test/unit_test_hyfeature/domain/coastal_domain.yaml
new file mode 100644
index 000000000..9bda405ce
--- /dev/null
+++ b/test/unit_test_hyfeature/domain/coastal_domain.yaml
@@ -0,0 +1,10 @@
+10237:
+  links:
+  - 10236
+  - 10237
+  rfc:
+  - wgrfc
+  rpu:
+  - 12d
+  upstream_boundary_link_mainstem:
+  - 10236
diff --git a/test/unit_test_hyfeature/domain/gauge_01069700.gpkg b/test/unit_test_hyfeature/domain/gauge_01069700.gpkg
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z`ls7RY4=PG`$5?^Z3yLK1Wco39IjzMu4jO<NyiP^kKKfFTyYwQ7Z=BR(|F{deYf^a
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zs=}j;P=jj&QaL_EHy88aeDt9~c1H<0c`lh{+_92$!?!+vs3}3w-6Lb9u?qbe^ovaz
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zCU`iW?+`7=69RjGF=Ksv`vi|uE3f%4+Zn&$eD@<-K~4Pk9X2bMbUE7KdjsW8*N21w
z-|i?mk58oL|J+E7yM<c?Z|H>xAOeU0B7g`W0*C-2fCwN0hyWsh2p|F`0)5%8n4fW_
z$h<O?;PK1xoA<Zne3ALVoef=2yC#S}zIbw@;$A|w`p`=U7QT?s;^3D@e#op#82sAR
z>7BY8`Z`#L5fPKn_1wX~F0bqRMdq@^E0>f<A&jg6;b$uo`lXl8)lONG&}NEZ6z9gV
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SSp9pagxo3di{>qS{r><Rh@XG}

literal 0
HcmV?d00001

diff --git a/test/unit_test_hyfeature/unittest_hyfeature.yaml b/test/unit_test_hyfeature/unittest_hyfeature.yaml
new file mode 100644
index 000000000..335174f57
--- /dev/null
+++ b/test/unit_test_hyfeature/unittest_hyfeature.yaml
@@ -0,0 +1,99 @@
+# $ python -m nwm_routing -f -V3 test_AnA.yaml
+#--------------------------------------------------------------------------------
+log_parameters:
+    #----------
+    showtiming: True
+    log_level : DEBUG
+#--------------------------------------------------------------------------------
+network_topology_parameters:
+    #----------
+    supernetwork_parameters:
+        #----------
+        geo_file_path: domain/gauge_01069700.gpkg   #domain/RouteLink_NWMv2.1.nc  
+        mask_file_path: # domain/unit_test_noRS/coastal_subset.txt
+        synthetic_wb_segments:
+            #- 4800002
+            #- 4800004
+            #- 4800006
+            #- 4800007
+    waterbody_parameters:
+        #----------
+        break_network_at_waterbodies: False 
+        level_pool:
+            #----------
+            level_pool_waterbody_parameter_file_path: # domain/LAKEPARM_NWMv2.1.nc 
+        rfc:
+            #----------
+            reservoir_parameter_file                : # domain/reservoir_index_AnA.nc
+            reservoir_rfc_forecasts                 : False
+            reservoir_rfc_forecasts_time_series_path: # rfc_TimeSeries/
+            reservoir_rfc_forecasts_lookback_hours  : # 48
+#--------------------------------------------------------------------------------
+compute_parameters:
+    #----------
+    parallel_compute_method: by-subnetwork-jit-clustered #serial 
+    compute_kernel         : V02-structured
+    assume_short_ts        : True
+    subnetwork_target_size : 10000
+    cpu_pool               : 36
+    restart_parameters:
+        #----------
+        wrf_hydro_channel_restart_file: # restart/HYDRO_RST.2020-08-26_00:00_DOMAIN1
+        wrf_hydro_channel_ID_crosswalk_file: # domain/RouteLink_NWMv2.1.nc
+        wrf_hydro_waterbody_restart_file: #restart/HYDRO_RST.2020-08-26_00:00_DOMAIN1
+        wrf_hydro_waterbody_ID_crosswalk_file    : # domain/LAKEPARM_NWMv2.1.nc 
+        wrf_hydro_waterbody_crosswalk_filter_file: # domain/LAKEPARM_NWMv2.1.nc  
+    hybrid_parameters:
+        run_hybrid_routing: True
+        diffusive_domain  : domain/unit_test_noRS/coastal_domain.yaml  
+        use_natl_xsections: False
+        topobathy_domain  : # domain/final_diffusive_natural_xs.nc 
+        run_refactored_network: False
+        refactored_domain: # domain/unit_test_noRS/refactored_coastal_domain.yaml 
+        refactored_topobathy_domain: # domain/refac_final_diffusive_natural_xs.nc 
+        coastal_boundary_domain: domain/unit_test_noRS/coastal_boundary_domain.yaml
+    forcing_parameters:
+        #----------
+        qts_subdivisions            : 12
+        dt                          : 300 # [sec]
+        qlat_input_folder           :  channel_forcing/
+        qlat_file_pattern_filter    : "*.CHRTOUT_DOMAIN1"
+        coastal_boundary_input_file : channel_forcing/schout_1.nc  
+        nts                         : 48 #288 for 1day
+        max_loop_size               : 24 # [hr]  
+    data_assimilation_parameters:
+        #----------
+        usgs_timeslices_folder   : #usgs_TimeSlice/
+        usace_timeslices_folder  : #usace_TimeSlice/
+        timeslice_lookback_hours : #48 
+        qc_threshold             : #1
+        streamflow_da:
+            #----------
+            streamflow_nudging            : False
+            diffusive_streamflow_nudging  : False
+            gage_segID_crosswalk_file     : # domain/RouteLink_NWMv2.1.nc  
+            crosswalk_gage_field          : # 'gages'
+            crosswalk_segID_field         : # 'link'
+            wrf_hydro_lastobs_file        :                
+            lastobs_output_folder         : lastobs/
+        reservoir_da:
+            #----------
+            reservoir_persistence_usgs  : False
+            reservoir_persistence_usace : False
+            gage_lakeID_crosswalk_file  : # domain/reservoir_index_AnA.nc
+#--------------------------------------------------------------------------------
+output_parameters:
+    #----------
+    test_output: output/unit_test_hyfeature.pkl 
+    lite_restart:
+        #----------
+        lite_restart_output_directory: restart/
+    chrtout_output:
+        #----------
+        wrf_hydro_channel_output_source_folder: channel_forcing/
+    chanobs_output:
+        #----------
+        chanobs_output_directory: output/ 
+        chanobs_filepath        : Chanobs.nc
+    lakeout_output: lakeout/
+    
\ No newline at end of file

From 016713ccd281eab238cc6f8078b707bfd614f229 Mon Sep 17 00:00:00 2001
From: Dong Kim <donghakim@cheyenne4.cheyenne.ucar.edu>
Date: Mon, 21 Nov 2022 20:53:49 -0700
Subject: [PATCH 2/7] t-route with hyfeature: prepare channel connection,
 forcing, t0, hybrid routing network

---
 .../troute/HYFeaturesNetwork.py               | 294 ++++---
 .../troute/hyfeature_network_utilities.py     | 233 ++++++
 .../troute/hyfeature_preprocess.py            | 785 ++++++++++++++++++
 src/troute-nwm/src/nwm_routing/__main__.py    |  81 +-
 src/troute-routing/troute/routing/compute.py  |  10 +-
 .../troute/routing/fast_reach/mc_reach.pyx    |   4 +-
 .../channel_forcing/201512010000NEXOUT.csv    |   8 +
 .../channel_forcing/201512010100NEXOUT.csv    |   8 +
 .../channel_forcing/201512010200NEXOUT.csv    |   8 +
 .../channel_forcing/201512010300NEXOUT.csv    |   8 +
 .../channel_forcing/201512010400NEXOUT.csv    |   8 +
 .../channel_forcing/201512010500NEXOUT.csv    |   8 +
 .../channel_forcing/201512010600NEXOUT.csv    |   8 +
 .../channel_forcing/201512010700NEXOUT.csv    |   8 +
 .../channel_forcing/201512010800NEXOUT.csv    |   8 +
 .../channel_forcing/201512010900NEXOUT.csv    |   8 +
 .../channel_forcing/201512011000NEXOUT.csv    |   8 +
 .../channel_forcing/201512011100NEXOUT.csv    |   8 +
 .../channel_forcing/201512011200NEXOUT.csv    |   8 +
 .../channel_forcing/201512011300NEXOUT.csv    |   8 +
 .../channel_forcing/201512011400NEXOUT.csv    |   8 +
 .../channel_forcing/201512011500NEXOUT.csv    |   8 +
 .../channel_forcing/201512011600NEXOUT.csv    |   8 +
 .../channel_forcing/201512011700NEXOUT.csv    |   8 +
 .../channel_forcing/201512011800NEXOUT.csv    |   8 +
 .../channel_forcing/201512011900NEXOUT.csv    |   8 +
 .../channel_forcing/201512012000NEXOUT.csv    |   8 +
 .../channel_forcing/201512012100NEXOUT.csv    |   8 +
 .../channel_forcing/201512012200NEXOUT.csv    |   8 +
 .../channel_forcing/201512012300NEXOUT.csv    |   8 +
 .../channel_forcing/201512020000NEXOUT.csv    |   8 +
 .../channel_forcing/201512020100NEXOUT.csv    |   8 +
 .../channel_forcing/201512020200NEXOUT.csv    |   8 +
 .../channel_forcing/201512020300NEXOUT.csv    |   8 +
 .../channel_forcing/201512020400NEXOUT.csv    |   8 +
 .../channel_forcing/201512020500NEXOUT.csv    |   8 +
 .../channel_forcing/201512020600NEXOUT.csv    |   8 +
 .../channel_forcing/201512020700NEXOUT.csv    |   8 +
 .../channel_forcing/201512020800NEXOUT.csv    |   8 +
 .../channel_forcing/201512020900NEXOUT.csv    |   8 +
 .../channel_forcing/201512021000NEXOUT.csv    |   8 +
 .../channel_forcing/201512021100NEXOUT.csv    |   8 +
 .../channel_forcing/201512021200NEXOUT.csv    |   8 +
 .../channel_forcing/201512021300NEXOUT.csv    |   8 +
 .../channel_forcing/201512021400NEXOUT.csv    |   8 +
 .../channel_forcing/201512021500NEXOUT.csv    |   8 +
 .../channel_forcing/201512021600NEXOUT.csv    |   8 +
 .../channel_forcing/201512021700NEXOUT.csv    |   8 +
 .../channel_forcing/201512021800NEXOUT.csv    |   8 +
 .../channel_forcing/201512021900NEXOUT.csv    |   8 +
 .../channel_forcing/201512022000NEXOUT.csv    |   8 +
 .../channel_forcing/201512022100NEXOUT.csv    |   8 +
 .../channel_forcing/201512022200NEXOUT.csv    |   8 +
 .../channel_forcing/201512022300NEXOUT.csv    |   8 +
 .../restart/201512010000NEXOUT.csv            |   8 +
 .../unittest_hyfeature.yaml                   |  42 +-
 56 files changed, 1636 insertions(+), 205 deletions(-)
 create mode 100644 src/troute-network/troute/hyfeature_network_utilities.py
 create mode 100644 src/troute-network/troute/hyfeature_preprocess.py
 create mode 100644 test/unit_test_hyfeature/channel_forcing/201512010000NEXOUT.csv
 create mode 100644 test/unit_test_hyfeature/channel_forcing/201512010100NEXOUT.csv
 create mode 100644 test/unit_test_hyfeature/channel_forcing/201512010200NEXOUT.csv
 create mode 100644 test/unit_test_hyfeature/channel_forcing/201512010300NEXOUT.csv
 create mode 100644 test/unit_test_hyfeature/channel_forcing/201512010400NEXOUT.csv
 create mode 100644 test/unit_test_hyfeature/channel_forcing/201512010500NEXOUT.csv
 create mode 100644 test/unit_test_hyfeature/channel_forcing/201512010600NEXOUT.csv
 create mode 100644 test/unit_test_hyfeature/channel_forcing/201512010700NEXOUT.csv
 create mode 100644 test/unit_test_hyfeature/channel_forcing/201512010800NEXOUT.csv
 create mode 100644 test/unit_test_hyfeature/channel_forcing/201512010900NEXOUT.csv
 create mode 100644 test/unit_test_hyfeature/channel_forcing/201512011000NEXOUT.csv
 create mode 100644 test/unit_test_hyfeature/channel_forcing/201512011100NEXOUT.csv
 create mode 100644 test/unit_test_hyfeature/channel_forcing/201512011200NEXOUT.csv
 create mode 100644 test/unit_test_hyfeature/channel_forcing/201512011300NEXOUT.csv
 create mode 100644 test/unit_test_hyfeature/channel_forcing/201512011400NEXOUT.csv
 create mode 100644 test/unit_test_hyfeature/channel_forcing/201512011500NEXOUT.csv
 create mode 100644 test/unit_test_hyfeature/channel_forcing/201512011600NEXOUT.csv
 create mode 100644 test/unit_test_hyfeature/channel_forcing/201512011700NEXOUT.csv
 create mode 100644 test/unit_test_hyfeature/channel_forcing/201512011800NEXOUT.csv
 create mode 100644 test/unit_test_hyfeature/channel_forcing/201512011900NEXOUT.csv
 create mode 100644 test/unit_test_hyfeature/channel_forcing/201512012000NEXOUT.csv
 create mode 100644 test/unit_test_hyfeature/channel_forcing/201512012100NEXOUT.csv
 create mode 100644 test/unit_test_hyfeature/channel_forcing/201512012200NEXOUT.csv
 create mode 100644 test/unit_test_hyfeature/channel_forcing/201512012300NEXOUT.csv
 create mode 100644 test/unit_test_hyfeature/channel_forcing/201512020000NEXOUT.csv
 create mode 100644 test/unit_test_hyfeature/channel_forcing/201512020100NEXOUT.csv
 create mode 100644 test/unit_test_hyfeature/channel_forcing/201512020200NEXOUT.csv
 create mode 100644 test/unit_test_hyfeature/channel_forcing/201512020300NEXOUT.csv
 create mode 100644 test/unit_test_hyfeature/channel_forcing/201512020400NEXOUT.csv
 create mode 100644 test/unit_test_hyfeature/channel_forcing/201512020500NEXOUT.csv
 create mode 100644 test/unit_test_hyfeature/channel_forcing/201512020600NEXOUT.csv
 create mode 100644 test/unit_test_hyfeature/channel_forcing/201512020700NEXOUT.csv
 create mode 100644 test/unit_test_hyfeature/channel_forcing/201512020800NEXOUT.csv
 create mode 100644 test/unit_test_hyfeature/channel_forcing/201512020900NEXOUT.csv
 create mode 100644 test/unit_test_hyfeature/channel_forcing/201512021000NEXOUT.csv
 create mode 100644 test/unit_test_hyfeature/channel_forcing/201512021100NEXOUT.csv
 create mode 100644 test/unit_test_hyfeature/channel_forcing/201512021200NEXOUT.csv
 create mode 100644 test/unit_test_hyfeature/channel_forcing/201512021300NEXOUT.csv
 create mode 100644 test/unit_test_hyfeature/channel_forcing/201512021400NEXOUT.csv
 create mode 100644 test/unit_test_hyfeature/channel_forcing/201512021500NEXOUT.csv
 create mode 100644 test/unit_test_hyfeature/channel_forcing/201512021600NEXOUT.csv
 create mode 100644 test/unit_test_hyfeature/channel_forcing/201512021700NEXOUT.csv
 create mode 100644 test/unit_test_hyfeature/channel_forcing/201512021800NEXOUT.csv
 create mode 100644 test/unit_test_hyfeature/channel_forcing/201512021900NEXOUT.csv
 create mode 100644 test/unit_test_hyfeature/channel_forcing/201512022000NEXOUT.csv
 create mode 100644 test/unit_test_hyfeature/channel_forcing/201512022100NEXOUT.csv
 create mode 100644 test/unit_test_hyfeature/channel_forcing/201512022200NEXOUT.csv
 create mode 100644 test/unit_test_hyfeature/channel_forcing/201512022300NEXOUT.csv
 create mode 100644 test/unit_test_hyfeature/restart/201512010000NEXOUT.csv

diff --git a/src/troute-network/troute/HYFeaturesNetwork.py b/src/troute-network/troute/HYFeaturesNetwork.py
index 1883e3ba5..1d447d1b8 100644
--- a/src/troute-network/troute/HYFeaturesNetwork.py
+++ b/src/troute-network/troute/HYFeaturesNetwork.py
@@ -9,6 +9,8 @@
 from itertools import chain
 import geopandas as gpd
 from pathlib import Path
+import math
+import troute.hyfeature_preprocess as hyfeature_prep
 
 __verbose__ = False
 __showtiming__ = False
@@ -92,6 +94,9 @@ def read_qlats(forcing_parameters, segment_index, nexus_to_downstream_flowpath_d
     qlat_df = pd.concat( (nexuses_flows_df.loc[int(k)].rename(index={int(k):v})
         for k,v in nexus_to_downstream_flowpath_dict.items() ), axis=1
         ).T
+    #qlat_df = pd.concat( (nexuses_flows_df.loc[int(k)].rename(v)
+    #    for k,v in nexus_to_downstream_flowpath_dict.items() ), axis=1
+    #    ).T
     
     # The segment_index has the full network set of segments/flowpaths. 
     # Whereas the set of flowpaths that are downstream of nexuses is a 
@@ -99,22 +104,19 @@ def read_qlats(forcing_parameters, segment_index, nexus_to_downstream_flowpath_d
     # that are not accounted for in the set of flowpaths downstream of
     # nexuses need to be added to the qlateral dataframe and padded with
     # zeros.
-
-    #tq0 = time.time()
     all_df = pd.DataFrame( np.zeros( (len(segment_index), len(qlat_df.columns)) ), index=segment_index,
             columns=qlat_df.columns )
-
     all_df.loc[ qlat_df.index ] = qlat_df
-
-    #tq1 =  time.time()
-    #print("Time to fill null qlats: {}".format(tq1-tq0))
-    # Sort qlats
     qlat_df = all_df.sort_index()
 
     # Set new nts based upon total nexus inputs
     nts = (qlat_df.shape[1]) * qts_subdivisions
-
     max_col = 1 + nts // qts_subdivisions
+    
+    #dt      = 300 # [sec]
+    #dt_qlat = 3600 # [sec]
+    #nts     = 24 # steps
+    #max_col = math.ceil(nts*dt/dt_qlat)
 
     if len(qlat_df.columns) > max_col:
         qlat_df.drop(qlat_df.columns[max_col:], axis=1, inplace=True)
@@ -178,8 +180,21 @@ class HYFeaturesNetwork(AbstractNetwork):
     """
     
     """
-    __slots__ = ["_flowpath_dict"]
-    def __init__(self, supernetwork_parameters, waterbody_parameters=None, restart_parameters=None, forcing_parameters=None, verbose=False, showtiming=False):
+    __slots__ = ["_flowpath_dict", 
+                 "segment_index", 
+                 "waterbody_type_specified",
+                 "diffusive_network_data", 
+                 "topobathy_df", 
+                 "refactored_diffusive_domain",
+                 "refactored_reaches", 
+                 "unrefactored_topobathy_df"]
+    def __init__(self, 
+                 supernetwork_parameters, 
+                 waterbody_parameters=None, 
+                 restart_parameters=None, 
+                 forcing_parameters=None, 
+                 verbose=False, 
+                 showtiming=False):
         """
         
         """
@@ -190,156 +205,97 @@ def __init__(self, supernetwork_parameters, waterbody_parameters=None, restart_p
             print("creating supernetwork connections set")
         if __showtiming__:
             start_time = time.time()
-        geo_file_path = supernetwork_parameters["geo_file_path"]
-        cols = supernetwork_parameters["columns"]
-        terminal_code = supernetwork_parameters.get("terminal_code", 0)
-        break_network_at_waterbodies = supernetwork_parameters.get(
-            "break_network_at_waterbodies", False
-        )
-        break_network_at_gages = supernetwork_parameters.get(
-            "break_network_at_gages", False
-        )
-        break_points = {"break_network_at_waterbodies": break_network_at_waterbodies,
-                        "break_network_at_gages": break_network_at_gages}
-        file_type = Path(geo_file_path).suffix
-        if(  file_type == '.gpkg' ):
-            self._dataframe = read_geopkg(geo_file_path)
-            #df["NHDWaterbodyComID"].fillna(-9999, inplace=True)
-            #df["NHDWaterbodyComID"] = df["NHDWaterbodyComID"].astype("int64")
-        elif( file_type == '.json') :
-            #df = pd.read_json(geo_file_path, orient="index")
-            #print(df)
-            #raise( "BREAK" )
-            edge_list = supernetwork_parameters['flowpath_edge_list']
-            # attribute_file_path = supernetwork_parameters['flowpath_attributes']
-            self._dataframe = read_json(geo_file_path, edge_list)
-            #df["NHDWaterbodyComID"].fillna(-9999, inplace=True)
-            #df["NHDWaterbodyComID"] = df["NHDWaterbodyComID"].astype("int64")
-        else:
-            raise RuntimeError("Unsupported file type: {}".format(file_type))
-
-        #Don't need the string prefix anymore, drop it
-        mask = ~ self._dataframe['toid'].str.startswith("tnex")
-        self._dataframe = self._dataframe.apply(numeric_id, axis=1)
-        #make the flowpath linkage, ignore the terminal nexus
-        self._flowpath_dict = dict(zip(self._dataframe.loc[mask].toid, self._dataframe.loc[mask].id))
-        self._waterbody_types_df = pd.DataFrame()
-        self._waterbody_df = pd.DataFrame()
-        #FIXME the base class constructor is finiky
-        #as it requires the _dataframe, then sets some 
-        #initial default properties...which, at the moment
-        #are used by the subclass constructor.
-        #So it needs to be called at just the right spot...
-        super().__init__(cols, terminal_code, break_points)
-        #FIXME once again, order here can hurt....to hack `alt` in, either need to
-        #put it as a column in the config, or do this AFTER the super constructor
-        #otherwise the alt column gets sliced out...
-        self._dataframe['alt'] = 1.0 #FIXME get the right value for this...
-        #Load waterbody/reservoir info
-        #For ngen HYFeatures, the reservoirs to be simulated
-        #are determined by the lake.json file
-        #we limit waterbody_connections to only the flowpaths
-        #that coincide with a lake listed in this file
-        #see `waterbody_connections`
-
-        if waterbody_parameters:
-            #FIXME later, DO ALL LAKE PARAMS BETTER
-            levelpool_params = waterbody_parameters.get('level_pool', None)
-            if not levelpool_params:
-                #FIXME should not be a hard requirement
-                raise(RuntimeError("No supplied levelpool parameters in routing config"))
-            
-            lake_id = levelpool_params.get("level_pool_waterbody_id", "wb-id")
-            self._waterbody_df = read_ngen_waterbody_df(
-                levelpool_params["level_pool_waterbody_parameter_file_path"],
-                lake_id,
-                #self.waterbody_connections.values()
-            )
-            
-            # Remove duplicate lake_ids and rows
-            self._waterbody_df = (
-                self._waterbody_df.reset_index()
-                .drop_duplicates(subset=lake_id)
-                .set_index(lake_id)
-            )
-            self._waterbody_df["qd0"] = 0.0
-            self._waterbody_df["h0"] = -1e9
-
-            hybrid_params = waterbody_parameters.get('hybrid_and_rfc', None)
-            try: #FIXME for HYFeatures/ngen this will likely be a lot different...
-                self._waterbody_types_df = nhd_io.read_reservoir_parameter_file(
-                    hybrid_params["reservoir_parameter_file"],
-                    lake_id,
-                    #self.waterbody_connections.values(),
-                )
-                # Remove duplicate lake_ids and rows
-                self._waterbody_types_df = (
-                self._waterbody_types_df.reset_index()
-                .drop_duplicates(subset=lake_id)
-                .set_index(lake_id)
-                )
-            except:
-                self._waterbody_types_df = pd.DataFrame(index=self._waterbody_df.index)
-                self._waterbody_types_df['reservoir_type'] = 1
-                #FIXME any reservoir operations requires some type
-                #So make this default to 1 (levelpool)
-                #At this point, need to adjust some waterbody/channel parameters based on lakes/reservoirs
-                #HACK for bad hydrofabric
-                def make_list(s):
-                    if isinstance(s, list):
-                        return s
-                    else:
-                        return [s]
-
-                self._waterbody_df['member_wbs'] = self._waterbody_df['member_wbs'].apply(make_list)
-                self._waterbody_df['partial_length_percent'] = self._waterbody_df['partial_length_percent'].apply(make_list)
-                adjust = [ zip(x, y) 
-                        for x, y in 
-                        zip(self._waterbody_df['member_wbs'], self._waterbody_df['partial_length_percent'])
-                        ]
-                #adjust is a generator of a list of list of tuples...use chain to flatten
-                for wb, percent in chain.from_iterable(adjust):
-                    #print(wb, percent)
-                    #FIXME not sure why some of these are 100%, if that  is the case
-                    #shouldn't they just not be in the topology???
-                    wb = node_key_func_wb(wb)
-                    #Need to adjust waterbodys/channels that  interact with this waterbody
-                    #Hack for wonky hydrofabric
-                    if percent != 'NA':
-                        self._dataframe.loc[wb, 'dx'] = self._dataframe.loc[wb, 'dx'] - self._dataframe.loc[wb, 'dx']*float(percent)
-                    #print(self._dataframe.loc[wb, 'dx'])
 
+        #------------------------------------------------
+        # Preprocess network attributes
+        #------------------------------------------------        
+        (self._dataframe,            
+         self._flowpath_dict, 
+         self._waterbody_types_df,
+         self._waterbody_df,
+         self.waterbody_type_specified,
+         cols,
+         terminal_code,
+         break_points,
+        ) = hyfeature_prep.build_hyfeature_network(
+            supernetwork_parameters,
+            waterbody_parameters
+        )
+        
+        # called to mainly initialize _waterbody_connections, _connections, _independent_networks,
+        # _reverse_network, _reaches_by_tw
+        super().__init__(cols, terminal_code, break_points)    
+        
         if __verbose__:
             print("supernetwork connections set complete")
         if __showtiming__:
             print("... in %s seconds." % (time.time() - start_time))   
-        #TODO/FIXME reservoir restart load
-        #TODO/FIXME channel restart load
-        # STEP 4: Handle Channel Initial States
+        
+   
+            
+        # list of all segments in the domain (MC + diffusive)
+        self.segment_index = self._dataframe.index
+        #if self.diffusive_network_data:
+        #    for tw in self.diffusive_network_data:
+        #        self.segment_index = self.segment_index.append(
+        #            pd.Index(self.diffusive_network_data[tw]['mainstem_segs'])
+        #        )     
+            
+        #------------------------------------------------
+        #  Handle Channel Initial States
+        #------------------------------------------------ 
+        if __verbose__:
+            print("setting waterbody and channel initial states ...")
         if __showtiming__:
             start_time = time.time()
+
+        (#self._waterbody_df,
+         self._q0,
+         self._t0,) = hyfeature_prep.hyfeature_initial_warmstate_preprocess(
+            #break_network_at_waterbodies,
+            restart_parameters,
+            #data_assimilation_parameters,
+            self.segment_index,
+            #self._waterbody_df,
+            #self.link_lake_crosswalk,
+        )
+        
         if __verbose__:
-            print("setting channel initial states ...")
-        #Get channel restarts
-        channel_restart_file = restart_parameters.get("channel_restart_file", None)
-
-        if channel_restart_file:
-            self._q0 = nhd_io.get_channel_restart_from_csv(channel_restart_file)
-            self._q0 = self._q0[self._q0.index.isin(self._dataframe.index)]
-            # TODO is this the same???
-            #self._q0 = self._q0.loc[self._dataframe.index]
-        #TODO/FIXME channel restart t0? self._t0 = ???
-        if __verbose__:
-          print("channel initial states complete")
+            print("waterbody and channel initial states complete")
         if __showtiming__:
-          print("... in %s seconds." % (time.time() - start_time))
+            print("... in %s seconds." % (time.time() - start_time))
+            start_time = time.time()
+            
+        # Create empty dataframe for coastal_boundary_depth_df. This way we can check if
+        # it exists, and only read in SCHISM data during 'assemble_forcings' if it doesn't
+        self._coastal_boundary_depth_df = pd.DataFrame()
         
-        self._qlateral = read_qlats(forcing_parameters, self._dataframe.index, self.downstream_flowpath_dict)
+    
+    def assemble_forcings(self, run, forcing_parameters, hybrid_parameters, cpu_pool):
+        """
+        Assembles model forcings for hydrological lateral inflows and coastal boundary 
+        depths (hybrid simulations). Run this function after network initialization
+        and after any iteration loop in main.
+        """
+        (self._qlateral, 
+         self._coastal_boundary_depth_df
+        ) = hyfeature_prep.hyfeature_forcing(
+            run, 
+            forcing_parameters, 
+            hybrid_parameters,
+            self._flowpath_dict,
+            self.segment_index,
+            cpu_pool,
+            self._t0,             
+            self._coastal_boundary_depth_df,
+        )
+
         #Mask out all non-simulated waterbodies
         self._dataframe['waterbody'] = self.waterbody_null
+        
         #This also remaps the initial NHDComID identity to the HY_Features Waterbody ID for the reservoir...
         self._dataframe.loc[self._waterbody_df.index, 'waterbody'] = self._waterbody_df.index.name
-
+        
         #FIXME should waterbody_df and param_df overlap IDS?  Doesn't seem like it should...
         #self._dataframe.drop(self._waterbody_df.index, axis=0, inplace=True)
         #For now, doing it in property waterbody_connections...
@@ -358,7 +314,48 @@ def extract_waterbody_connections(rows, target_col, waterbody_null=-9999):
         return (
             rows.loc[rows[target_col] != waterbody_null, target_col].astype("int").to_dict()
         )
-            
+ 
+    
+    def create_routing_network(self, 
+                               conn, 
+                               param_df, 
+                               wbody_conn, gages, 
+                               preprocessing_parameters, 
+                               compute_parameters,
+                               waterbody_parameters
+    ): 
+
+        #--------------------------------------------------------------------------
+        # Creation of routing network data objects. Logical ordering of lower-level
+        # function calls that build individual network data objects.
+        #--------------------------------------------------------------------------        
+        (self._independent_networks,
+         self._reaches_by_tw,
+         self._reverse_network,
+         self.diffusive_network_data,
+         self.topobathy_df,
+         self.refactored_diffusive_domain,
+         self.refactored_reaches,
+         self.unrefactored_topobathy_df
+        ) = hyfeature_prep.hyfeature_hybrid_routing_preprocess(
+            conn,
+            param_df,
+            wbody_conn,
+            gages,
+            preprocessing_parameters,
+            compute_parameters,
+            waterbody_parameters, 
+        )
+        return (self._independent_networks,
+                self._reaches_by_tw,
+                self._reverse_network,
+                self.diffusive_network_data,
+                self.topobathy_df,
+                self.refactored_diffusive_domain,
+                self.refactored_reaches,
+                self.unrefactored_topobathy_df)
+
+
     @property
     def downstream_flowpath_dict(self):
         return self._flowpath_dict
@@ -407,4 +404,5 @@ def gages(self):
     
     @property
     def waterbody_null(self):
-        return np.nan#pd.NA
+        return np.nan #pd.NA
+
diff --git a/src/troute-network/troute/hyfeature_network_utilities.py b/src/troute-network/troute/hyfeature_network_utilities.py
new file mode 100644
index 000000000..5c78ccd38
--- /dev/null
+++ b/src/troute-network/troute/hyfeature_network_utilities.py
@@ -0,0 +1,233 @@
+import json
+import pathlib
+from functools import partial
+from datetime import datetime, timedelta
+import logging
+
+import pandas as pd
+import numpy as np
+import netCDF4
+from joblib import delayed, Parallel
+
+import troute.nhd_io as nhd_io
+
+
+LOG = logging.getLogger('')
+
+
+def build_forcing_sets(
+    forcing_parameters,
+    t0
+):
+
+    run_sets           = forcing_parameters.get("qlat_forcing_sets", None)
+    nexus_input_folder = forcing_parameters.get("nexus_input_folder", None)
+    nts                = forcing_parameters.get("nts", None)
+    max_loop_size      = forcing_parameters.get("max_loop_size", 12)
+    dt                 = forcing_parameters.get("dt", None)
+
+    try:
+        nexus_input_folder = pathlib.Path(nexus_input_folder)
+        assert nexus_input_folder.is_dir() == True
+    except TypeError:
+        raise TypeError("Aborting simulation because no nexus_input_folder is specified in the forcing_parameters section of the .yaml control file.") from None
+    except AssertionError:
+        raise AssertionError("Aborting simulation because the nexus_input_folder:", qlat_input_folder,"does not exist. Please check the the nexus_input_folder variable is correctly entered in the .yaml control file") from None
+
+    forcing_glob_filter = forcing_parameters.get("nexus_file_pattern_filter", "*.NEXOUT")
+  
+    # TODO: Throw errors if insufficient input data are available
+    if run_sets:        
+        #FIXME: Change it for hyfeature
+        '''
+        # append final_timestamp variable to each set_list
+        qlat_input_folder = pathlib.Path(qlat_input_folder)
+        for (s, _) in enumerate(run_sets):
+            final_chrtout = qlat_input_folder.joinpath(run_sets[s]['qlat_files'
+                    ][-1])
+            final_timestamp_str = nhd_io.get_param_str(final_chrtout,
+                    'model_output_valid_time')
+            run_sets[s]['final_timestamp'] = \
+                datetime.strptime(final_timestamp_str, '%Y-%m-%d_%H:%M:%S')
+        '''  
+    elif nexus_input_folder:        
+        # Construct run_set dictionary from user-specified parameters
+
+        # get the first and seconded files from an ordered list of all forcing files
+        nexus_input_folder = pathlib.Path(nexus_input_folder)
+        all_files          = sorted(nexus_input_folder.glob(forcing_glob_filter))
+        first_file         = all_files[0]
+        second_file        = all_files[1]
+
+        # Deduce the timeinterval of the forcing data from the output timestamps of the first
+        # two ordered CHRTOUT files
+        df     = pd.read_csv(first_file)
+        t1_str = pd.to_datetime(df.columns[1]).strftime("%Y-%m-%d_%H:%M:%S")
+        t1     = datetime.strptime(t1_str,"%Y-%m-%d_%H:%M:%S")
+        df     = pd.read_csv(second_file)
+        t2_str = pd.to_datetime(df.columns[1]).strftime("%Y-%m-%d_%H:%M:%S")
+        t2     = datetime.strptime(t2_str,"%Y-%m-%d_%H:%M:%S")
+        dt_qlat_timedelta = t2 - t1
+        dt_qlat = dt_qlat_timedelta.seconds
+
+        # determine qts_subdivisions
+        qts_subdivisions = dt_qlat / dt
+        if dt_qlat % dt == 0:
+            qts_subdivisions = dt_qlat / dt
+        # make sure that qts_subdivisions = dt_qlat / dt
+        forcing_parameters['qts_subdivisions']= qts_subdivisions
+
+        # the number of files required for the simulation
+        nfiles = int(np.ceil(nts / qts_subdivisions))
+        
+        # list of forcing file datetimes
+        #datetime_list = [t0 + dt_qlat_timedelta * (n + 1) for n in
+        #                 range(nfiles)]
+        # ** Correction ** Because qlat file at time t is constantly applied throughout [t, t+1],
+        #               ** n + 1 should be replaced by n
+        datetime_list = [t0 + dt_qlat_timedelta * (n) for n in
+                         range(nfiles)]        
+        datetime_list_str = [datetime.strftime(d, '%Y%m%d%H%M') for d in
+                             datetime_list]
+
+        # list of forcing files
+        forcing_filename_list = [d_str + "NEXOUT.csv" for d_str in
+                                 datetime_list_str]
+        
+        # check that all forcing files exist
+        for f in forcing_filename_list:
+            try:
+                J = pathlib.Path(nexus_input_folder.joinpath(f))     
+                assert J.is_file() == True
+            except AssertionError:
+                raise AssertionError("Aborting simulation because forcing file", J, "cannot be not found.") from None
+                
+        # build run sets list
+        run_sets = []
+        k = 0
+        j = 0
+        nts_accum = 0
+        nts_last = 0
+        while k < len(forcing_filename_list):
+            run_sets.append({})
+
+            if k + max_loop_size < len(forcing_filename_list):
+                run_sets[j]['nexus_files'] = forcing_filename_list[k:k
+                    + max_loop_size]
+            else:
+                run_sets[j]['nexus_files'] = forcing_filename_list[k:]
+
+            nts_accum += len(run_sets[j]['nexus_files']) * qts_subdivisions
+            if nts_accum <= nts:
+                run_sets[j]['nts'] = int(len(run_sets[j]['nexus_files'])
+                                         * qts_subdivisions)
+            else:
+                run_sets[j]['nts'] = int(nts - nts_last)
+
+            final_nexout        = nexus_input_folder.joinpath(run_sets[j]['nexus_files'
+                    ][-1])            
+            #final_timestamp_str = nhd_io.get_param_str(final_nexout,
+            #        'model_output_valid_time')
+            df                  = pd.read_csv(final_nexout)
+            final_timestamp_str = pd.to_datetime(df.columns[1]).strftime("%Y-%m-%d_%H:%M:%S")           
+            
+            run_sets[j]['final_timestamp'] = \
+                datetime.strptime(final_timestamp_str, '%Y-%m-%d_%H:%M:%S')
+
+            nts_last = nts_accum
+            k += max_loop_size
+            j += 1
+
+    return run_sets
+
+def build_qlateral_array(
+    run,
+    cpu_pool,
+    nexus_to_upstream_flowpath_dict, 
+    segment_index=pd.Index([]),
+    ts_iterator=None,
+    file_run_size=None,
+):
+    # TODO: set default/optional arguments
+    qts_subdivisions = run.get("qts_subdivisions", 1)
+    nts = run.get("nts", 1)
+    nexus_input_folder = run.get("nexus_input_folder", None)
+    qlat_input_file = run.get("qlat_input_file", None)
+
+    if nexus_input_folder:
+        nexus_input_folder = pathlib.Path(nexus_input_folder)
+        if "nexus_files" in run:
+            nexus_files = run.get("nexus_files")
+            nexus_files = [nexus_input_folder.joinpath(f) for f in nexus_files]
+        elif "nexus_file_pattern_filter" in run:
+            nexus_file_pattern_filter = run.get(
+                "nexus_file_pattern_filter", "*NEXOUT*"
+            )
+            nexus_files = sorted(nexus_input_folder.glob(nexus_file_pattern_filter))
+
+        qlat_file_index_col = run.get(
+            "qlat_file_index_col", "feature_id"
+        )
+        qlat_file_value_col = run.get("qlat_file_value_col", "q_lateral")
+        gw_bucket_col = run.get("qlat_file_gw_bucket_flux_col","qBucket")
+        terrain_ro_col = run.get("qlat_file_terrain_runoff_col","qSfcLatRunoff")
+
+
+        #nexuses_lateralflows_df = nhd_io.get_ql_from_csv(nexus_files[0])
+        '''
+        # Parallel reading of qlateral data from CHRTOUT
+        with Parallel(n_jobs=cpu_pool) as parallel:
+            jobs = []
+            for f in qlat_files:
+                jobs.append(
+                    #delayed(nhd_io.get_ql_from_chrtout)
+                    #(f, qlat_file_value_col, gw_bucket_col, terrain_ro_col)
+                    delayed(nhd_io.get_ql_from_csv)
+                    (f)                    
+                )
+            ql_list = parallel(jobs)
+
+        # get feature_id from a single CHRTOUT file
+        with netCDF4.Dataset(qlat_files[0]) as ds:
+            idx = ds.variables[qlat_file_index_col][:].filled()
+
+        # package data into a DataFrame
+        qlats_df = pd.DataFrame(
+            np.stack(ql_list).T,
+            index = idx,
+            columns = range(len(qlat_files))
+        )    
+        '''
+        dfs=[]
+        for f in nexus_files:
+            df = pd.read_csv(f).set_index(['feature_id']) 
+            dfs.append(df)
+        # lateral flows [m^3/s] are stored at NEXUS points with NEXUS ids
+        nexuses_lateralflows_df = pd.concat(dfs, axis=1)  
+        
+        # Take flowpath ids entering NEXUS and replace NEXUS ids by the upstream flowpath ids 
+        qlats_df = pd.concat( (nexuses_lateralflows_df.loc[int(k)].rename(v)
+                            for k,v in nexus_to_upstream_flowpath_dict.items() ), axis=1
+                            ).T        
+        
+        qlats_df = qlats_df[qlats_df.index.isin(segment_index)]
+    elif qlat_input_file:
+        qlats_df = nhd_io.get_ql_from_csv(qlat_input_file)
+    else:
+        qlat_const = run.get("qlat_const", 0)
+        qlats_df = pd.DataFrame(
+            qlat_const,
+            index=segment_index,
+            columns=range(nts // qts_subdivisions),
+            dtype="float32",
+        )
+
+    # TODO: Make a more sophisticated date-based filter
+    max_col = 1 + nts // qts_subdivisions
+    if len(qlats_df.columns) > max_col:
+        qlats_df.drop(qlats_df.columns[max_col:], axis=1, inplace=True)
+
+    if not segment_index.empty:
+        qlats_df = qlats_df[qlats_df.index.isin(segment_index)]
+
+    return qlats_df
\ No newline at end of file
diff --git a/src/troute-network/troute/hyfeature_preprocess.py b/src/troute-network/troute/hyfeature_preprocess.py
new file mode 100644
index 000000000..ea02a3eac
--- /dev/null
+++ b/src/troute-network/troute/hyfeature_preprocess.py
@@ -0,0 +1,785 @@
+import time
+import pathlib
+import logging
+from datetime import datetime
+from collections import defaultdict
+from pathlib import Path
+
+import pandas as pd
+import numpy as np
+import xarray as xr
+
+import troute.nhd_network_utilities_v02 as nnu
+import troute.nhd_network as nhd_network
+import troute.nhd_io as nhd_io
+from troute.nhd_network import reverse_dict
+import troute.HYFeaturesNetwork as hyf_network
+import troute.hyfeature_network_utilities as hnu
+
+LOG = logging.getLogger('')
+
+def build_hyfeature_network(supernetwork_parameters,
+                            waterbody_parameters,
+):
+    
+    geo_file_path = supernetwork_parameters["geo_file_path"]
+    cols          = supernetwork_parameters["columns"]
+    terminal_code = supernetwork_parameters.get("terminal_code", 0)
+    
+    break_network_at_waterbodies = supernetwork_parameters.get("break_network_at_waterbodies", False)        
+    break_network_at_gages       = supernetwork_parameters.get("break_network_at_gages", False)       
+    break_points                 = {"break_network_at_waterbodies": break_network_at_waterbodies,
+                                     "break_network_at_gages": break_network_at_gages}
+        
+    file_type = Path(geo_file_path).suffix
+    if(  file_type == '.gpkg' ):        
+        dataframe = hyf_network.read_geopkg(geo_file_path)
+    elif( file_type == '.json') :
+        edge_list = supernetwork_parameters['flowpath_edge_list']
+        dataframe = hyf_network.read_json(geo_file_path, edge_list) 
+    else:
+        raise RuntimeError("Unsupported file type: {}".format(file_type))
+
+    # Don't need the string prefix anymore, drop it
+    mask = ~ dataframe['toid'].str.startswith("tnex") 
+    dataframe = dataframe.apply(hyf_network.numeric_id, axis=1)
+        
+    # make the flowpath linkage, ignore the terminal nexus
+    flowpath_dict = dict(zip(dataframe.loc[mask].toid, dataframe.loc[mask].id))
+    waterbody_types_df = pd.DataFrame()
+    waterbody_df = pd.DataFrame()
+    waterbody_type_specified = False
+
+ # **********  need to be included in flowpath_attributes  *************   
+    # FIXME once again, order here can hurt....to hack `alt` in, either need to
+    # put it as a column in the config, or do this AFTER the super constructor
+    # otherwise the alt column gets sliced out...
+    dataframe['alt'] = 1.0 #FIXME get the right value for this...
+    
+    #Load waterbody/reservoir info
+    #For ngen HYFeatures, the reservoirs to be simulated
+    #are determined by the lake.json file
+    #we limit waterbody_connections to only the flowpaths
+    #that coincide with a lake listed in this file
+    #see `waterbody_connections`
+    if waterbody_parameters:
+        # FIXME later, DO ALL LAKE PARAMS BETTER
+        levelpool_params = waterbody_parameters.get('level_pool', None)
+        if not levelpool_params:
+            # FIXME should not be a hard requirement
+            raise(RuntimeError("No supplied levelpool parameters in routing config"))
+            
+        lake_id = levelpool_params.get("level_pool_waterbody_id", "wb-id")
+        waterbody_df = read_ngen_waterbody_df(
+                    levelpool_params["level_pool_waterbody_parameter_file_path"],
+                    lake_id,
+                    #self.waterbody_connections.values()
+                    )
+            
+        # Remove duplicate lake_ids and rows
+        waterbody_df = (
+                        waterbody_df.reset_index()
+                        .drop_duplicates(subset=lake_id)
+                        .set_index(lake_id)
+                        )
+        waterbody_df["qd0"] = 0.0
+        waterbody_df["h0"] = -1e9
+
+        hybrid_params = waterbody_parameters.get('hybrid_and_rfc', None)
+        try: #FIXME for HYFeatures/ngen this will likely be a lot different...
+            waterbody_types_df = nhd_io.read_reservoir_parameter_file(
+                                    hybrid_params["reservoir_parameter_file"],
+                                    lake_id,
+                                    #self.waterbody_connections.values(),
+                                    )
+            # Remove duplicate lake_ids and rows
+            waterbody_types_df =(
+                                 waterbody_types_df.reset_index()
+                                .drop_duplicates(subset=lake_id)
+                                .set_index(lake_id)
+                                )
+        except:
+            waterbody_types_df = pd.DataFrame(index=waterbody_df.index)
+            waterbody_types_df['reservoir_type'] = 1
+            #FIXME any reservoir operations requires some type
+            #So make this default to 1 (levelpool)
+            #At this point, need to adjust some waterbody/channel parameters based on lakes/reservoirs
+            #HACK for bad hydrofabric
+            def make_list(s):
+                if isinstance(s, list):
+                    return s
+                else:
+                    return [s]
+
+            waterbody_df['member_wbs'] = waterbody_df['member_wbs'].apply(make_list)
+            waterbody_df['partial_length_percent'] = waterbody_df['partial_length_percent'].apply(make_list)
+            adjust = [ zip(x, y) 
+                        for x, y in 
+                        zip(waterbody_df['member_wbs'], waterbody_df['partial_length_percent'])
+                    ]
+            #adjust is a generator of a list of list of tuples...use chain to flatten
+            for wb, percent in chain.from_iterable(adjust):
+                # FIXME not sure why some of these are 100%, if that  is the case
+                # shouldn't they just not be in the topology???
+                wb = node_key_func_wb(wb)
+                #Need to adjust waterbodys/channels that  interact with this waterbody
+                #Hack for wonky hydrofabric
+                if percent != 'NA':
+                    dataframe.loc[wb, 'dx'] = dataframe.loc[wb, 'dx'] - dataframe.loc[wb, 'dx']*float(percent)
+              
+    return (dataframe,           
+            flowpath_dict,  
+            waterbody_types_df, 
+            waterbody_df, 
+            waterbody_type_specified,
+            cols,
+            terminal_code,
+            break_points,
+           )
+
+def hyfeature_hybrid_routing_preprocess(
+    connections,
+    param_df,
+    wbody_conn,
+    gages,
+    preprocessing_parameters,
+    compute_parameters,
+    waterbody_parameters, 
+):
+    '''
+    Creation of routing network data objects. Logical ordering of lower-level
+    function calls that build individual network data objects.
+    
+    Arguments
+    ---------
+    supernetwork_parameters      (dict): user input data re network extent
+    waterbody_parameters         (dict): user input data re waterbodies
+    preprocessing_parameters     (dict): user input data re preprocessing
+    compute_parameters           (dict): user input data re compute configuration
+    data_assimilation_parameters (dict): user input data re data assimilation
+    
+    Returns
+    -------
+    connections                 (dict of int: [int]): {segment id: [downsteram adjacent segment ids]}
+    param_df                             (DataFrame): Hydraulic geometry and roughness parameters, by segment
+    wbody_conn                    (dict of int: int): {segment id: associated lake id}
+    waterbodies_df                       (DataFrame): Waterbody (reservoir) parameters
+    waterbody_types_df                   (DataFrame): Waterbody type codes (1 - levelpool, 2 - USGS, 3 - USACE, 4 - RFC)
+    break_network_at_waterbodies              (bool): If True, waterbodies occpy reaches of their own
+    waterbody_type_specified                  (bool): If True, more than just levelpool waterbodies exist
+    link_lake_crosswalk           (dict of int: int): {lake id: outlet segment id}
+    independent_networks (dict of int: {int: [int]}): {tailwater id: {segment id: [upstream adjacent segment ids]}}
+    reaches_bytw              (dict of int: [[int]]): {tailwater id: list or reach lists}
+    rconn                       (dict of int: [int]): {segment id: [upstream adjacent segment ids]}
+    pd.DataFrame.from_dict(gages)        (DataFrame): Gage ids and corresponding segment ids at which they are located
+    diffusive_network_data            (dict or None): Network data objects for diffusive domain
+    topobathy_df                         (DataFrame): Natural cross section data for diffusive domain
+    
+    Notes
+    -----
+    - waterbody_type_specified is likely an excessive return and can be removed and inferred from the 
+      contents of waterbody_types_df
+    - The values of the link_lake_crosswalk dictionary are the downstream-most segments within 
+      the waterbody extent to which waterbody data are written. They are NOT the first segments 
+      downsteram of the waterbody 
+    '''
+
+    #============================================================================
+    # Establish diffusive domain for MC/diffusive hybrid simulations
+    
+    hybrid_params = compute_parameters.get("hybrid_parameters", False)
+    if hybrid_params:
+        # switch parameters
+        # if run_hybrid = False, run MC only
+        # if run_hybrid = True, if use_topobathy = False, run MC+diffusive on RouteLink.nc
+        #    "      "      "  , if use_topobathy = True,  if run_refactored_network = False, run MC+diffusive on original hydrofabric
+        #    "      "      "  , if use_topobathy = True,  if run_refactored_network = True,  run MC+diffusive on refactored hydrofabric
+        run_hybrid             = hybrid_params.get('run_hybrid_routing', False)
+        use_topobathy          = hybrid_params.get('use_natl_xsections', False) 
+        run_refactored         = hybrid_params.get('run_refactored_network', False)
+        
+        # file path parameters of non-refactored hydrofabric defined by RouteLink.nc
+        domain_file            = hybrid_params.get("diffusive_domain",   None)
+        topobathy_file         = hybrid_params.get("topobathy_domain",   None)
+        
+        # file path parameters of refactored hydrofabric for diffusive wave channel routing 
+        refactored_domain_file    = hybrid_params.get("refactored_domain", None)
+        refactored_topobathy_file = hybrid_params.get("refactored_topobathy_domain", None)
+        #-------------------------------------------------------------------------
+        # for non-refactored hydofabric defined by RouteLink.nc
+        # TODO: By default, make diffusive available for both non-refactored and refactored hydrofabric for now. Place a switch in the future. 
+        if run_hybrid and domain_file:
+            
+            LOG.info('reading diffusive domain extent for MC/Diffusive hybrid simulation')
+            
+            # read diffusive domain dictionary from yaml or json
+            diffusive_domain = nhd_io.read_diffusive_domain(domain_file)           
+            
+            if use_topobathy and topobathy_file:
+                
+                LOG.debug('Natural cross section data on original hydrofabric are provided.')
+                
+                # read topobathy domain netcdf file, set index to 'comid'
+                # TODO: replace 'link' with a user-specified indexing variable name.
+                # ... if for whatever reason there is not a `link` variable in the 
+                # ... dataframe returned from read_netcdf, then the code would break here.
+                topobathy_df = (nhd_io.read_netcdf(topobathy_file).set_index('link'))
+                
+                # TODO: Request GID make comID variable an integer in their product, so
+                # we do not need to change variable types, here.
+                topobathy_df.index = topobathy_df.index.astype(int)
+                
+            else:
+                topobathy_df = pd.DataFrame()
+                LOG.debug('No natural cross section topobathy data provided. Hybrid simualtion will run on compound trapezoidal geometry.')
+             
+            # initialize a dictionary to hold network data for each of the diffusive domains
+            diffusive_network_data = {}
+        
+        else:
+            diffusive_domain       = None
+            diffusive_network_data = None
+            topobathy_df           = pd.DataFrame()
+            LOG.info('No diffusive domain file specified in configuration file. This is an MC-only simulation')
+        unrefactored_topobathy_df  = pd.DataFrame()    
+        #-------------------------------------------------------------------------
+        # for refactored hydofabric 
+        if run_hybrid and run_refactored and refactored_domain_file:
+            
+            LOG.info('reading refactored diffusive domain extent for MC/Diffusive hybrid simulation')
+            
+            # read diffusive domain dictionary from yaml or json
+            refactored_diffusive_domain = nhd_io.read_diffusive_domain(refactored_domain_file)           
+            
+            if use_topobathy and refactored_topobathy_file:
+                
+                LOG.debug('Natural cross section data of refactored hydrofabric are provided.')
+                
+                # read topobathy domain netcdf file, set index to 'comid'
+                # TODO: replace 'link' with a user-specified indexing variable name.
+                # ... if for whatever reason there is not a `link` variable in the 
+                # ... dataframe returned from read_netcdf, then the code would break here.
+                topobathy_df = (nhd_io.read_netcdf(refactored_topobathy_file).set_index('link'))
+
+                # unrefactored_topobaty_data is passed to diffusive kernel to provide thalweg elevation of unrefactored topobathy 
+                # for crosswalking water elevations between non-refactored and refactored hydrofabrics. 
+                unrefactored_topobathy_df       = (nhd_io.read_netcdf(topobathy_file).set_index('link'))
+                unrefactored_topobathy_df.index = unrefactored_topobathy_df.index.astype(int)
+                
+            else:
+                topobathy_df               = pd.DataFrame()
+                LOG.debug('No natural cross section topobathy data of refactored hydrofabric provided. Hybrid simualtion will run on compound trapezoidal geometry.')
+             
+            # initialize a dictionary to hold network data for each of the diffusive domains
+            refactored_diffusive_network_data = {}
+        
+        else:
+            refactored_diffusive_domain       = None
+            refactored_diffusive_network_data = None
+            refactored_reaches                = {}
+            LOG.info('No refactored diffusive domain file specified in configuration file. This is an MC-only simulation')     
+   
+    else:
+        diffusive_domain                  = None
+        diffusive_network_data            = None
+        topobathy_df                      = pd.DataFrame()
+        unrefactored_topobathy_df         = pd.DataFrame() 
+        refactored_diffusive_domain       = None
+        refactored_diffusive_network_data = None   
+        refactored_reaches                = {}
+        LOG.info('No hybrid parameters specified in configuration file. This is an MC-only simulation')
+    
+ #============================================================================
+    # build diffusive domain data and edit MC domain data for hybrid simulation
+    
+    #
+    if diffusive_domain:
+        rconn_diff0 = nhd_network.reverse_network(connections)
+        refactored_reaches = {}
+        
+        for tw in diffusive_domain:
+            mainstem_segs = diffusive_domain[tw]['links']
+            # we want mainstem_segs start at a mainstem link right after the upstream boundary mainstem link, which is
+            # in turn not under any waterbody. This boundary mainstem link should be turned into a tributary segment.
+            upstream_boundary_mainstem_link = diffusive_domain[tw]['upstream_boundary_link_mainstem']         
+            if upstream_boundary_mainstem_link[0] in mainstem_segs:
+                mainstem_segs.remove(upstream_boundary_mainstem_link[0])
+            
+            # ===== build diffusive network data objects ==== 
+            diffusive_network_data[tw] = {}
+
+            # add diffusive domain segments
+            diffusive_network_data[tw]['mainstem_segs'] =  mainstem_segs
+
+            # diffusive domain tributary segments
+            trib_segs = []
+
+            for seg in mainstem_segs:
+                us_list = rconn_diff0[seg]
+                for u in us_list:
+                    if u not in mainstem_segs:
+                        trib_segs.append(u) 
+
+            diffusive_network_data[tw]['tributary_segments'] = trib_segs
+            # diffusive domain connections object
+            diffusive_network_data[tw]['connections'] = {k: connections[k] for k in (mainstem_segs + trib_segs)}       
+
+            # diffusive domain reaches and upstream connections. 
+            # break network at tributary segments
+            _, reaches, rconn_diff = nnu.organize_independent_networks(
+                diffusive_network_data[tw]['connections'],
+                set(trib_segs),
+                set(),
+            )
+            
+            diffusive_network_data[tw]['rconn'] = rconn_diff
+            diffusive_network_data[tw]['reaches'] = reaches[tw]
+
+            # RouteLink parameters
+            diffusive_network_data[tw]['param_df'] = param_df.filter(
+                (mainstem_segs + trib_segs),
+                axis = 0,
+            )
+            diffusive_network_data[tw]['upstream_boundary_link'] = upstream_boundary_mainstem_link
+
+            if refactored_diffusive_domain: 
+                diffusive_parameters = {'geo_file_path': refactored_topobathy_file}
+                refactored_connections = nnu.build_refac_connections(diffusive_parameters)
+
+                # list of stream segments of a single refactored diffusive domain 
+                refac_tw = refactored_diffusive_domain[tw]['refac_tw']
+                rlinks_tw = refactored_diffusive_domain[tw]['rlinks']
+                refactored_connections_tw = {}   
+
+                # Subset a connection dictionary (upstream segment as key : downstream segments as values) from refactored_connections
+                # for a single refactored diffusive domain defined by a current tw. 
+                for k in rlinks_tw:
+                    if k in refactored_connections.keys() and k != refac_tw:
+                        refactored_connections_tw[k] = refactored_connections[k]
+
+                refactored_diffusive_network_data[refac_tw] = {}                
+                refactored_diffusive_network_data[refac_tw]['tributary_segments'] = trib_segs
+                refactored_diffusive_network_data[refac_tw]['connections'] = refactored_connections_tw                 
+
+                for k in trib_segs:
+                    refactored_diffusive_network_data[refac_tw]['connections'][k]= [refactored_diffusive_domain[tw]['incoming_tribs'][k]]
+
+                # diffusive domain reaches and upstream connections. 
+                # break network at tributary segments
+                _, refactored_reaches_batch, refactored_conn_diff = nnu.organize_independent_networks(
+                                                            refactored_diffusive_network_data[refac_tw]['connections'],
+                                                            set(trib_segs),
+                                                            set(),
+                                                            )
+
+                refactored_reaches[refac_tw] = refactored_reaches_batch[refac_tw]
+                refactored_diffusive_network_data[refac_tw]['mainstem_segs'] = refactored_diffusive_domain[tw]['rlinks']
+                refactored_diffusive_network_data[refac_tw]['upstream_boundary_link'] = diffusive_network_data[tw]['upstream_boundary_link'] 
+            else:
+                refactored_reaches={}
+
+            # ==== remove diffusive domain segs from MC domain ====        
+            # drop indices from param_df
+            param_df = param_df.drop(mainstem_segs)
+
+            # remove keys from connections dictionary
+            for s in mainstem_segs:
+                connections.pop(s)
+
+            # update downstream connections of trib segs
+            for us in trib_segs:
+                connections[us] = []
+
+    #============================================================================
+    # Identify Independent Networks and Reaches by Network
+    LOG.info("organizing connections into reaches ...")
+    start_time = time.time() 
+    gage_break_segments = set()
+    wbody_break_segments = set()
+    
+    break_network_at_waterbodies = waterbody_parameters.get(
+        "break_network_at_waterbodies", False
+    )
+    
+    # if streamflow DA, then break network at gages
+    break_network_at_gages = False
+    
+    if break_network_at_waterbodies:
+        wbody_break_segments = wbody_break_segments.union(wbody_conn.values())
+        
+    if break_network_at_gages:
+        gage_break_segments = gage_break_segments.union(gages['gages'].keys())
+ 
+    independent_networks, reaches_bytw, rconn = nnu.organize_independent_networks(
+        connections,
+        wbody_break_segments,
+        gage_break_segments,
+    )
+    
+    LOG.debug("reach organization complete in %s seconds." % (time.time() - start_time))
+    '''
+    if preprocessing_parameters.get('preprocess_only', False):
+
+        LOG.debug("saving preprocessed network data to disk for future use")
+        # todo: consider a better default than None
+        destination_folder = preprocessing_parameters.get('preprocess_output_folder', None)
+        if destination_folder:
+
+            output_filename = preprocessing_parameters.get(
+                'preprocess_output_filename', 
+                'preprocess_output'
+            )
+
+            outputs = {}
+            outputs.update(
+                {'connections': connections,
+                 'param_df': param_df,
+                 'wbody_conn': wbody_conn,
+                 'waterbodies_df': waterbodies_df,
+                 'waterbody_types_df': waterbody_types_df,
+                 'break_network_at_waterbodies': break_network_at_waterbodies,
+                 'waterbody_type_specified': waterbody_type_specified,
+                 'link_lake_crosswalk': link_lake_crosswalk,
+                 'independent_networks': independent_networks,
+                 'reaches_bytw': reaches_bytw,
+                 'rconn': rconn,
+                 'link_gage_df': link_gage_df,
+                 'usgs_lake_gage_crosswalk': usgs_lake_gage_crosswalk, 
+                 'usace_lake_gage_crosswalk': usace_lake_gage_crosswalk,
+                 'diffusive_network_data': diffusive_network_data,
+                 'topobathy_data': topobathy_df,
+                }
+            )
+            try:
+                np.save(
+                    pathlib.Path(destination_folder).joinpath(output_filename),
+                    outputs
+                )
+            except:
+                LOG.critical('Canonot find %s. Aborting preprocessing routine' % pathlib.Path(destination_folder))
+                quit()
+                
+            LOG.debug(
+                "writing preprocessed network data to %s"\
+                % pathlib.Path(destination_folder).joinpath(output_filename + '.npy'))
+            LOG.critical(
+                "Preprocessed network data written to %s aborting preprocessing sequence" \
+                % pathlib.Path(destination_folder).joinpath(output_filename + '.npy'))
+            quit()
+
+        else:
+            LOG.critical(
+                "No destination folder specified for preprocessing. Please specify preprocess_output_folder in configuration file. Aborting preprocessing routine"
+            )
+            quit()
+        '''
+    return(independent_networks,
+           reaches_bytw,
+           rconn,
+           diffusive_network_data,
+           topobathy_df, 
+           refactored_diffusive_domain,
+           refactored_reaches,
+           unrefactored_topobathy_df,   
+            )
+    
+def hyfeature_initial_warmstate_preprocess(
+    # break_network_at_waterbodies,
+    restart_parameters,
+    # data_assimilation_parameters,
+    segment_index,
+    # waterbodies_df,
+    # link_lake_crosswalk,
+):
+
+    '''
+    Assemble model initial condition data:
+        - waterbody inital states (outflow and pool elevation)
+        - channel initial states (flow and depth)
+        - initial time
+    
+    Arguments
+    ---------
+    - break_network_at_waterbodies (bool): If True, waterbody initial states will
+                                           be appended to the waterbody parameter
+                                           dataframe. If False, waterbodies will
+                                           not be simulated and the waterbody
+                                           parameter datataframe wil not be changed
+    - restart_parameters           (dict): User-input simulation restart 
+                                           parameters
+    - data_assimilation_parameters (dict): User-input data assimilation 
+                                           parameters
+    - segment_index        (Pandas Index): All segment IDs in the simulation 
+                                           doamin
+    - waterbodies_df   (Pandas DataFrame): Waterbody parameters
+    - link_lake_crosswalk          (dict): Crosswalking between lake ids and the link
+                                           id of the lake outlet segment
+    
+    Returns
+    -------
+    - waterbodies_df (Pandas DataFrame): Waterbody parameters with initial
+                                         states (outflow and pool elevation)
+    - q0             (Pandas DataFrame): Initial flow and depth states for each
+                                         segment in the model domain
+    - t0                     (datetime): Datetime of the model initialization
+    
+    Notes
+    -----
+    '''
+
+    #----------------------------------------------------------------------------
+    # Assemble waterbody initial states (outflow and pool elevation
+    #----------------------------------------------------------------------------
+    '''
+    if break_network_at_waterbodies:
+
+        start_time = time.time()
+        LOG.info("setting waterbody initial states ...")
+
+        # if a lite restart file is provided, read initial states from it.
+        if restart_parameters.get("lite_waterbody_restart_file", None):
+            
+            waterbodies_initial_states_df, _ = nhd_io.read_lite_restart(
+                restart_parameters['lite_waterbody_restart_file']
+            )
+            
+        # read waterbody initial states from WRF-Hydro type restart file
+        elif restart_parameters.get("wrf_hydro_waterbody_restart_file", None):
+            waterbodies_initial_states_df = nhd_io.get_reservoir_restart_from_wrf_hydro(
+                restart_parameters["wrf_hydro_waterbody_restart_file"],
+                restart_parameters["wrf_hydro_waterbody_ID_crosswalk_file"],
+                restart_parameters.get("wrf_hydro_waterbody_ID_crosswalk_file_field_name", 'lake_id'),
+                restart_parameters["wrf_hydro_waterbody_crosswalk_filter_file"],
+                restart_parameters.get(
+                    "wrf_hydro_waterbody_crosswalk_filter_file_field_name",
+                    'NHDWaterbodyComID'
+                ),
+            )
+        
+        # if no restart file is provided, default initial states
+        else:
+            # TODO: Consider adding option to read cold state from route-link file
+            waterbodies_initial_ds_flow_const = 0.0
+            waterbodies_initial_depth_const = -1e9
+            # Set initial states from cold-state
+            waterbodies_initial_states_df = pd.DataFrame(
+                0,
+                index=waterbodies_df.index,
+                columns=[
+                    "qd0",
+                    "h0",
+                ],
+                dtype="float32",
+            )
+            # TODO: This assignment could probably by done in the above call
+            waterbodies_initial_states_df["qd0"] = waterbodies_initial_ds_flow_const
+            waterbodies_initial_states_df["h0"] = waterbodies_initial_depth_const
+            waterbodies_initial_states_df["index"] = range(
+                len(waterbodies_initial_states_df)
+            )
+
+        waterbodies_df = pd.merge(
+            waterbodies_df, waterbodies_initial_states_df, on="lake_id"
+        )
+
+        LOG.debug(
+            "waterbody initial states complete in %s seconds."\
+            % (time.time() - start_time))
+        start_time = time.time()
+    '''
+
+    #----------------------------------------------------------------------------
+    # Assemble channel initial states (flow and depth)
+    # also establish simulation initialization timestamp
+    #----------------------------------------------------------------------------    
+    start_time = time.time()
+    LOG.info("setting channel initial states ...")
+
+    # if lite restart file is provided, the read channel initial states from it
+    if restart_parameters.get("lite_channel_restart_file", None):
+        # FIXME: Change it for hyfeature!
+        '''
+        q0, t0 = nhd_io.read_lite_restart(
+            restart_parameters['lite_channel_restart_file']
+        )
+        t0_str = None
+        ''' 
+    # when a restart file for hyfeature is provied, then read initial states from it.
+    elif restart_parameters.get("hyfeature_channel_restart_file", None):        
+        q0 = nnu.build_channel_initial_state(restart_parameters, segment_index)        
+        channel_initial_states_file = restart_parameters["hyfeature_channel_restart_file"]
+        df     = pd.read_csv(channel_initial_states_file)
+        t0_str = pd.to_datetime(df.columns[1]).strftime("%Y-%m-%d_%H:%M:%S")
+        t0     = datetime.strptime(t0_str,"%Y-%m-%d_%H:%M:%S")
+
+    # build initial states from user-provided restart parameters
+    else:
+        # FIXME: Change it for hyfeature!
+        '''
+        q0 = nnu.build_channel_initial_state(restart_parameters, segment_index)       
+
+        # get initialization time from restart file
+        if restart_parameters.get("wrf_hydro_channel_restart_file", None):
+            channel_initial_states_file = restart_parameters[
+                "wrf_hydro_channel_restart_file"
+            ]
+            t0_str = nhd_io.get_param_str(
+                channel_initial_states_file, 
+                "Restart_Time"
+            )
+        else:
+            t0_str = "2015-08-16_00:00:00"
+
+        # convert timestamp from string to datetime
+        t0 = datetime.strptime(t0_str, "%Y-%m-%d_%H:%M:%S")
+        '''
+    # get initial time from user inputs
+    if restart_parameters.get("start_datetime", None):
+        t0_str = restart_parameters.get("start_datetime")
+        
+        def _try_parsing_date(text):
+            for fmt in (
+                "%Y-%m-%d_%H:%M", 
+                "%Y-%m-%d_%H:%M:%S", 
+                "%Y-%m-%d %H:%M", 
+                "%Y-%m-%d %H:%M:%S", 
+                "%Y/%m/%d %H:%M", 
+                "%Y/%m/%d %H:%M:%S"
+            ):
+                try:
+                    return datetime.strptime(text, fmt)
+                except ValueError:
+                    pass
+            LOG.error('No valid date format found for start_datetime input. Please use format YYYY-MM-DD_HH:MM')
+            quit()
+            
+        t0 = _try_parsing_date(t0_str)
+    else:
+        if t0_str == "2015-08-16_00:00:00":
+            LOG.info('No user-input start_datetime and no restart file, start time arbitrarily 2015-08-16_00:00:00')
+        else:
+            LOG.info('No user-specified start_datetime, continuing with start time from restart file: %s', t0_str)
+
+    LOG.debug(
+        "channel initial states complete in %s seconds."\
+        % (time.time() - start_time)
+    )
+    start_time = time.time()
+
+    return (
+            #waterbodies_df,
+            q0, 
+            t0,
+            )
+    # TODO: This returns a full dataframe (waterbodies_df) with the
+    # merged initial states for waterbodies, but only the
+    # initial state values (q0; not merged with the channel properties)
+    # for the channels --
+    # That is because that is how they are used downstream. Need to
+    # trace that back and decide if there is one of those two ways
+    # that is optimal and make both returns that way.
+    
+
+    
+def hyfeature_forcing(
+    run,
+    forcing_parameters,
+    hybrid_parameters,
+    nexus_to_upstream_flowpath_dict,
+    segment_index,
+    cpu_pool,
+    t0,
+    coastal_boundary_depth_df,
+):
+    """
+    Assemble model forcings. Forcings include hydrological lateral inflows (qlats)
+    and coastal boundary depths for hybrid runs
+    
+    Aguments
+    --------
+    - run                (dict): List of forcing files pertaining to a 
+                                 single run-set
+    - forcing_parameters (dict): User-input simulation forcing parameters
+    - hybrid_parameters  (dict): User-input simulation hybrid parameters
+    - segment_index     (Int64): Reach segment ids
+    - cpu_pool            (int): Number of CPUs in the process-parallel pool
+    Returns
+    -------
+    - qlats_df                 (Pandas DataFrame): Lateral inflow data, indexed by 
+                                                   segment ID
+    - coastal_bounary_depth_df (Pandas DataFrame): Coastal boundary water depths,
+                                                   indexed by segment ID
+    
+    Notes
+    -----
+    
+    """
+   
+    # Unpack user-specified forcing parameters
+    dt                           = forcing_parameters.get("dt", None)
+    qts_subdivisions             = forcing_parameters.get("qts_subdivisions", None)
+    nexus_input_folder           = forcing_parameters.get("nexus_input_folder", None)
+    qlat_file_index_col          = forcing_parameters.get("qlat_file_index_col", "feature_id")
+    qlat_file_value_col          = forcing_parameters.get("qlat_file_value_col", "q_lateral")
+    qlat_file_gw_bucket_flux_col = forcing_parameters.get("qlat_file_gw_bucket_flux_col", "qBucket")
+    qlat_file_terrain_runoff_col = forcing_parameters.get("qlat_file_terrain_runoff_col", "qSfcLatRunoff")
+
+  
+    # TODO: find a better way to deal with these defaults and overrides.
+    run["t0"]                           = run.get("t0", t0)
+    run["nts"]                          = run.get("nts")
+    run["dt"]                           = run.get("dt", dt)
+    run["qts_subdivisions"]             = run.get("qts_subdivisions", qts_subdivisions)
+    run["nexus_input_folder"]           = run.get("nexus_input_folder", nexus_input_folder)
+    run["qlat_file_index_col"]          = run.get("qlat_file_index_col", qlat_file_index_col)
+    run["qlat_file_value_col"]          = run.get("qlat_file_value_col", qlat_file_value_col)
+    run["qlat_file_gw_bucket_flux_col"] = run.get("qlat_file_gw_bucket_flux_col", qlat_file_gw_bucket_flux_col)
+    run["qlat_file_terrain_runoff_col"] = run.get("qlat_file_terrain_runoff_col", qlat_file_terrain_runoff_col)
+    
+    #---------------------------------------------------------------------------
+    # Assemble lateral inflow data
+    #---------------------------------------------------------------------------
+    
+    start_time = time.time()
+    LOG.info("Creating a DataFrame of lateral inflow forcings ...")
+
+    # Place holder, if reading qlats from a file use this.
+    # TODO: add an option for reading qlat data from BMI/model engine
+    from_file = True
+    if from_file:
+        qlats_df = hnu.build_qlateral_array(
+            run,
+            cpu_pool,
+            nexus_to_upstream_flowpath_dict,
+            segment_index,
+        )
+
+    LOG.debug(
+        "lateral inflow DataFrame creation complete in %s seconds." \
+        % (time.time() - start_time)
+    )
+
+    #---------------------------------------------------------------------
+    # Assemble coastal coupling data [WIP]
+    #---------------------------------------------------------------------
+    # Run if coastal_boundary_depth_df has not already been created:
+    if coastal_boundary_depth_df.empty:
+        coastal_boundary_elev_files = forcing_parameters.get('coastal_boundary_input_file', None) 
+        coastal_boundary_domain_files = hybrid_parameters.get('coastal_boundary_domain', None)    
+        
+        if coastal_boundary_elev_files:
+            start_time = time.time()    
+            LOG.info("creating coastal dataframe ...")
+            
+            coastal_boundary_domain   = nhd_io.read_coastal_boundary_domain(coastal_boundary_domain_files)          
+            coastal_boundary_depth_df = nhd_io.build_coastal_ncdf_dataframe(
+                coastal_boundary_elev_files,
+                coastal_boundary_domain,
+            )
+                
+            LOG.debug(
+                "coastal boundary elevation observation DataFrame creation complete in %s seconds." \
+                % (time.time() - start_time)
+            )            
+
+    return qlats_df, coastal_boundary_depth_df
\ No newline at end of file
diff --git a/src/troute-nwm/src/nwm_routing/__main__.py b/src/troute-nwm/src/nwm_routing/__main__.py
index 596261af6..9e8309a20 100644
--- a/src/troute-nwm/src/nwm_routing/__main__.py
+++ b/src/troute-nwm/src/nwm_routing/__main__.py
@@ -29,6 +29,7 @@
 import troute.nhd_io as nhd_io
 import troute.nhd_network_utilities_v02 as nnu
 import troute.routing.diffusive_utils as diff_utils
+import troute.hyfeature_network_utilities as hnu
 
 LOG = logging.getLogger('')
 
@@ -53,7 +54,7 @@ def main_v04(argv):
         parity_parameters,
         data_assimilation_parameters,
     ) = _input_handler_v03(args)
-    
+
     run_parameters = {
         'dt': forcing_parameters.get('dt'),
         'nts': forcing_parameters.get('nts'),
@@ -75,14 +76,24 @@ def main_v04(argv):
     # perform initial warmstate preprocess.
     if showtiming:
         network_start_time = time.time()
-
-    if "ngen_nexus_file" in supernetwork_parameters:
-         network = HYFeaturesNetwork(supernetwork_parameters,
-                                    waterbody_parameters=waterbody_parameters,
-                                    restart_parameters=restart_parameters,
-                                    forcing_parameters=forcing_parameters,
-                                    verbose=verbose, showtiming=showtiming) 
-    else:
+        
+    #if "ngen_nexus_file" in supernetwork_parameters:
+    if supernetwork_parameters["geo_file_type"] == 'HYFeaturesNetwork':
+        network = HYFeaturesNetwork(supernetwork_parameters,
+                                    waterbody_parameters,
+                                    restart_parameters,
+                                    forcing_parameters,
+                                    verbose=True, showtiming=showtiming) 
+
+        network.create_routing_network(network.connections,
+                                       network.dataframe, 
+                                       network.waterbody_connections,
+                                       network.gages,
+                                       preprocessing_parameters, 
+                                       compute_parameters,
+                                       waterbody_parameters,)
+        
+    elif supernetwork_parameters["geo_file_type"] == 'NHDNetwork':
         network = NHDNetwork(supernetwork_parameters,
                              waterbody_parameters,
                              restart_parameters,
@@ -97,9 +108,12 @@ def main_v04(argv):
     if showtiming:
         network_end_time = time.time()
         task_times['network_creation_time'] = network_end_time - network_start_time
-   
+
     # Create run_sets: sets of forcing files for each loop
-    run_sets = nnu.build_forcing_sets(forcing_parameters, network.t0)
+    if supernetwork_parameters["geo_file_type"] == 'NHDNetwork':
+        run_sets = nnu.build_forcing_sets(forcing_parameters, network.t0)
+    elif supernetwork_parameters["geo_file_type"] == 'HYFeaturesNetwork':
+        run_sets = hnu.build_forcing_sets(forcing_parameters, network.t0)
 
     # Create da_sets: sets of TimeSlice files for each loop
     if "data_assimilation_parameters" in compute_parameters:
@@ -113,19 +127,21 @@ def main_v04(argv):
 
     # Create forcing data within network object for first loop iteration
     network.assemble_forcings(run_sets[0], forcing_parameters, hybrid_parameters, cpu_pool)
-
+    
     # Create data assimilation object from da_sets for first loop iteration
-    data_assimilation = AllDA(data_assimilation_parameters,
-                              run_parameters,
-                              waterbody_parameters,
-                              network,
-                              da_sets[0])
+    if supernetwork_parameters["geo_file_type"] == 'NHDNetwork':
+        data_assimilation = AllDA(data_assimilation_parameters,
+                                  run_parameters,
+                                  waterbody_parameters,
+                                  network,
+                                  da_sets[0])
+    # TODO: apply data_assimilation for hyfeature network
 
     if showtiming:
         forcing_end_time = time.time()
         task_times['forcing_time'] += forcing_end_time - network_end_time
-    
 
+   
     parallel_compute_method = compute_parameters.get("parallel_compute_method", None)
     subnetwork_target_size = compute_parameters.get("subnetwork_target_size", 1)
     qts_subdivisions = forcing_parameters.get("qts_subdivisions", 1)
@@ -137,7 +153,6 @@ def main_v04(argv):
     # on first iteration of for loop only. For additional loops this will be passed
     # to function from inital loop.     
     subnetwork_list = [None, None, None]
- 
     for run_set_iterator, run in enumerate(run_sets):
         
         t0 = run.get("t0")
@@ -150,7 +165,7 @@ def main_v04(argv):
 
         if showtiming:
             route_start_time = time.time()
-
+        import pdb; pdb.set_trace()
         run_results = nwm_route(
             network.connections, 
             network.reverse_network, 
@@ -168,13 +183,13 @@ def main_v04(argv):
             network.dataframe,
             network.q0,
             network._qlateral,
-            data_assimilation.usgs_df,
-            data_assimilation.lastobs_df,
-            data_assimilation.reservoir_usgs_df,
-            data_assimilation.reservoir_usgs_param_df,
-            data_assimilation.reservoir_usace_df,
-            data_assimilation.reservoir_usace_param_df,
-            data_assimilation.assimilation_parameters,
+            pd.DataFrame(), #data_assimilation.usgs_df,
+            pd.DataFrame(), #data_assimilation.lastobs_df,
+            pd.DataFrame(), #data_assimilation.reservoir_usgs_df,
+            pd.DataFrame(), #data_assimilation.reservoir_usgs_param_df,
+            pd.DataFrame(), #data_assimilation.reservoir_usace_df,
+            pd.DataFrame(), #data_assimilation.reservoir_usace_param_df,
+            {}, #data_assimilation.assimilation_parameters,
             assume_short_ts,
             return_courant,
             network._waterbody_df, ## check:  network._waterbody_df ?? def name is different from return self._ ..
@@ -189,11 +204,11 @@ def main_v04(argv):
             network.coastal_boundary_depth_df,
             network.unrefactored_topobathy_df,
         )
- 
+        import pdb; pdb.set_trace()        
         # returns list, first item is run result, second item is subnetwork items
         subnetwork_list = run_results[1]
         run_results = run_results[0]
-        
+
         if showtiming:
             route_end_time = time.time()
             task_times['route_time'] += route_end_time - route_start_time
@@ -210,7 +225,8 @@ def main_v04(argv):
                 t0 + timedelta(seconds = dt * nts), 
                 output_parameters['lite_restart']
             )      
-   
+
+        # Prepare input forcing for next time loop simulation when mutiple time loops are presented.
         if run_set_iterator < len(run_sets) - 1:
             # update t0
             network.new_t0(dt,nts)
@@ -253,11 +269,12 @@ def main_v04(argv):
             network.link_gage_df,
             network.link_lake_crosswalk,
         )
-        
+
         if showtiming:
             output_end_time = time.time()
             task_times['output_time'] += output_end_time - output_start_time
-            
+    # end of for run_set_iterator, run in enumerate(run_sets):
+    
     if showtiming:
         task_times['total_time'] = time.time() - main_start_time
 
diff --git a/src/troute-routing/troute/routing/compute.py b/src/troute-routing/troute/routing/compute.py
index c552e80a6..6d68f4482 100644
--- a/src/troute-routing/troute/routing/compute.py
+++ b/src/troute-routing/troute/routing/compute.py
@@ -249,7 +249,7 @@ def compute_nhd_routing_v02(
     waterbody_type_specified,
     subnetwork_list,
 ):
-
+    import pdb; pdb.set_trace()
     da_decay_coefficient = da_parameter_dict.get("da_decay_coefficient", 0)
     param_df["dt"] = dt
     param_df = param_df.astype("float32")
@@ -543,7 +543,6 @@ def compute_nhd_routing_v02(
                             return_courant,
                         )
                     )
-
                 results_subn[order] = parallel(jobs)
    
                 if order > 0:  # This is not needed for the last rank of subnetworks
@@ -1180,9 +1179,10 @@ def compute_diffusive_routing(
         else:
             topobathy_bytw = pd.DataFrame()
             unrefactored_topobathy_bytw = pd.DataFrame()
-  
+
         # diffusive streamflow DA activation switch
-        if da_parameter_dict['diffusive_streamflow_nudging']==True:
+        #if da_parameter_dict['diffusive_streamflow_nudging']==True:
+        if 'diffusive_streamflow_nudging' in da_parameter_dict:
             diff_usgs_df = usgs_df
         else:
             diff_usgs_df = pd.DataFrame()
@@ -1201,7 +1201,7 @@ def compute_diffusive_routing(
             coastal_boundary_depth_bytw_df = coastal_boundary_depth_df.loc[tw].to_frame().T
         else:
             coastal_boundary_depth_bytw_df = pd.DataFrame()
-
+        import pdb; pdb.set_trace()
         # build diffusive inputs
         diffusive_inputs = diff_utils.diffusive_input_data_v02(
             tw,
diff --git a/src/troute-routing/troute/routing/fast_reach/mc_reach.pyx b/src/troute-routing/troute/routing/fast_reach/mc_reach.pyx
index 5565e2c99..248630bfd 100644
--- a/src/troute-routing/troute/routing/fast_reach/mc_reach.pyx
+++ b/src/troute-routing/troute/routing/fast_reach/mc_reach.pyx
@@ -222,8 +222,10 @@ cpdef object compute_network_structured(
     # Check shapes
     if qlat_values.shape[0] != data_idx.shape[0]:
         raise ValueError(f"Number of rows in Qlat is incorrect: expected ({data_idx.shape[0]}), got ({qlat_values.shape[0]})")
-    if qlat_values.shape[1] < nsteps:
+    
+    if qlat_values.shape[1] < nsteps/qts_subdivisions:
         raise ValueError(f"Number of columns (timesteps) in Qlat is incorrect: expected at most ({data_idx.shape[0]}), got ({qlat_values.shape[1]}). The number of columns in Qlat must be equal to or less than the number of routing timesteps")
+    
     if data_values.shape[0] != data_idx.shape[0] or data_values.shape[1] != data_cols.shape[0]:
         raise ValueError(f"data_values shape mismatch")
     #define and initialize the final output array, add one extra time step for initial conditions
diff --git a/test/unit_test_hyfeature/channel_forcing/201512010000NEXOUT.csv b/test/unit_test_hyfeature/channel_forcing/201512010000NEXOUT.csv
new file mode 100644
index 000000000..57a2a30d4
--- /dev/null
+++ b/test/unit_test_hyfeature/channel_forcing/201512010000NEXOUT.csv
@@ -0,0 +1,8 @@
+feature_id,201512010000
+10238,1097500.0
+1000000001,1097500.0
+2,1097500.0
+4,1097500.0
+10236,1097500.0
+3,1097500.0
+10237,1097500.0
diff --git a/test/unit_test_hyfeature/channel_forcing/201512010100NEXOUT.csv b/test/unit_test_hyfeature/channel_forcing/201512010100NEXOUT.csv
new file mode 100644
index 000000000..5dad6ca5b
--- /dev/null
+++ b/test/unit_test_hyfeature/channel_forcing/201512010100NEXOUT.csv
@@ -0,0 +1,8 @@
+feature_id,201512010100
+10238,9876660.0
+1000000001,9876660.0
+2,9876660.0
+4,9876660.0
+10236,9876660.0
+3,9876660.0
+10237,9876660.0
diff --git a/test/unit_test_hyfeature/channel_forcing/201512010200NEXOUT.csv b/test/unit_test_hyfeature/channel_forcing/201512010200NEXOUT.csv
new file mode 100644
index 000000000..3a28297b3
--- /dev/null
+++ b/test/unit_test_hyfeature/channel_forcing/201512010200NEXOUT.csv
@@ -0,0 +1,8 @@
+feature_id,201512010200
+10238,10868900.0
+1000000001,10868900.0
+2,10868900.0
+4,10868900.0
+10236,10868900.0
+3,10868900.0
+10237,10868900.0
diff --git a/test/unit_test_hyfeature/channel_forcing/201512010300NEXOUT.csv b/test/unit_test_hyfeature/channel_forcing/201512010300NEXOUT.csv
new file mode 100644
index 000000000..7451f590c
--- /dev/null
+++ b/test/unit_test_hyfeature/channel_forcing/201512010300NEXOUT.csv
@@ -0,0 +1,8 @@
+feature_id,201512010300
+10238,14574600.0
+1000000001,14574600.0
+2,14574600.0
+4,14574600.0
+10236,14574600.0
+3,14574600.0
+10237,14574600.0
diff --git a/test/unit_test_hyfeature/channel_forcing/201512010400NEXOUT.csv b/test/unit_test_hyfeature/channel_forcing/201512010400NEXOUT.csv
new file mode 100644
index 000000000..f993d1069
--- /dev/null
+++ b/test/unit_test_hyfeature/channel_forcing/201512010400NEXOUT.csv
@@ -0,0 +1,8 @@
+feature_id,201512010400
+10238,12557100.0
+1000000001,12557100.0
+2,12557100.0
+4,12557100.0
+10236,12557100.0
+3,12557100.0
+10237,12557100.0
diff --git a/test/unit_test_hyfeature/channel_forcing/201512010500NEXOUT.csv b/test/unit_test_hyfeature/channel_forcing/201512010500NEXOUT.csv
new file mode 100644
index 000000000..488458a0d
--- /dev/null
+++ b/test/unit_test_hyfeature/channel_forcing/201512010500NEXOUT.csv
@@ -0,0 +1,8 @@
+feature_id,201512010500
+10238,14807000.0
+1000000001,14807000.0
+2,14807000.0
+4,14807000.0
+10236,14807000.0
+3,14807000.0
+10237,14807000.0
diff --git a/test/unit_test_hyfeature/channel_forcing/201512010600NEXOUT.csv b/test/unit_test_hyfeature/channel_forcing/201512010600NEXOUT.csv
new file mode 100644
index 000000000..86f6b2186
--- /dev/null
+++ b/test/unit_test_hyfeature/channel_forcing/201512010600NEXOUT.csv
@@ -0,0 +1,8 @@
+feature_id,201512010600
+10238,12601900.0
+1000000001,12601900.0
+2,12601900.0
+4,12601900.0
+10236,12601900.0
+3,12601900.0
+10237,12601900.0
diff --git a/test/unit_test_hyfeature/channel_forcing/201512010700NEXOUT.csv b/test/unit_test_hyfeature/channel_forcing/201512010700NEXOUT.csv
new file mode 100644
index 000000000..751808c6f
--- /dev/null
+++ b/test/unit_test_hyfeature/channel_forcing/201512010700NEXOUT.csv
@@ -0,0 +1,8 @@
+feature_id,201512010700
+10238,14767200.0
+1000000001,14767200.0
+2,14767200.0
+4,14767200.0
+10236,14767200.0
+3,14767200.0
+10237,14767200.0
diff --git a/test/unit_test_hyfeature/channel_forcing/201512010800NEXOUT.csv b/test/unit_test_hyfeature/channel_forcing/201512010800NEXOUT.csv
new file mode 100644
index 000000000..2c2e3aaa6
--- /dev/null
+++ b/test/unit_test_hyfeature/channel_forcing/201512010800NEXOUT.csv
@@ -0,0 +1,8 @@
+feature_id,201512010800
+10238,12642800.0
+1000000001,12642800.0
+2,12642800.0
+4,12642800.0
+10236,12642800.0
+3,12642800.0
+10237,12642800.0
diff --git a/test/unit_test_hyfeature/channel_forcing/201512010900NEXOUT.csv b/test/unit_test_hyfeature/channel_forcing/201512010900NEXOUT.csv
new file mode 100644
index 000000000..577a50d27
--- /dev/null
+++ b/test/unit_test_hyfeature/channel_forcing/201512010900NEXOUT.csv
@@ -0,0 +1,8 @@
+feature_id,201512010900
+10238,14729800.0
+1000000001,14729800.0
+2,14729800.0
+4,14729800.0
+10236,14729800.0
+3,14729800.0
+10237,14729800.0
diff --git a/test/unit_test_hyfeature/channel_forcing/201512011000NEXOUT.csv b/test/unit_test_hyfeature/channel_forcing/201512011000NEXOUT.csv
new file mode 100644
index 000000000..98ef290ff
--- /dev/null
+++ b/test/unit_test_hyfeature/channel_forcing/201512011000NEXOUT.csv
@@ -0,0 +1,8 @@
+feature_id,201512011000
+10238,12681500.0
+1000000001,12681500.0
+2,12681500.0
+4,12681500.0
+10236,12681500.0
+3,12681500.0
+10237,12681500.0
diff --git a/test/unit_test_hyfeature/channel_forcing/201512011100NEXOUT.csv b/test/unit_test_hyfeature/channel_forcing/201512011100NEXOUT.csv
new file mode 100644
index 000000000..2e44e8b85
--- /dev/null
+++ b/test/unit_test_hyfeature/channel_forcing/201512011100NEXOUT.csv
@@ -0,0 +1,8 @@
+feature_id,201512011100
+10238,14694500.0
+1000000001,14694500.0
+2,14694500.0
+4,14694500.0
+10236,14694500.0
+3,14694500.0
+10237,14694500.0
diff --git a/test/unit_test_hyfeature/channel_forcing/201512011200NEXOUT.csv b/test/unit_test_hyfeature/channel_forcing/201512011200NEXOUT.csv
new file mode 100644
index 000000000..42197d8aa
--- /dev/null
+++ b/test/unit_test_hyfeature/channel_forcing/201512011200NEXOUT.csv
@@ -0,0 +1,8 @@
+feature_id,201512011200
+10238,12718000.0
+1000000001,12718000.0
+2,12718000.0
+4,12718000.0
+10236,12718000.0
+3,12718000.0
+10237,12718000.0
diff --git a/test/unit_test_hyfeature/channel_forcing/201512011300NEXOUT.csv b/test/unit_test_hyfeature/channel_forcing/201512011300NEXOUT.csv
new file mode 100644
index 000000000..6108b27b9
--- /dev/null
+++ b/test/unit_test_hyfeature/channel_forcing/201512011300NEXOUT.csv
@@ -0,0 +1,8 @@
+feature_id,201512011300
+10238,14661300.0
+1000000001,14661300.0
+2,14661300.0
+4,14661300.0
+10236,14661300.0
+3,14661300.0
+10237,14661300.0
diff --git a/test/unit_test_hyfeature/channel_forcing/201512011400NEXOUT.csv b/test/unit_test_hyfeature/channel_forcing/201512011400NEXOUT.csv
new file mode 100644
index 000000000..1d3f452ca
--- /dev/null
+++ b/test/unit_test_hyfeature/channel_forcing/201512011400NEXOUT.csv
@@ -0,0 +1,8 @@
+feature_id,201512011400
+10238,12752400.0
+1000000001,12752400.0
+2,12752400.0
+4,12752400.0
+10236,12752400.0
+3,12752400.0
+10237,12752400.0
diff --git a/test/unit_test_hyfeature/channel_forcing/201512011500NEXOUT.csv b/test/unit_test_hyfeature/channel_forcing/201512011500NEXOUT.csv
new file mode 100644
index 000000000..a49ac1f91
--- /dev/null
+++ b/test/unit_test_hyfeature/channel_forcing/201512011500NEXOUT.csv
@@ -0,0 +1,8 @@
+feature_id,201512011500
+10238,14630000.0
+1000000001,14630000.0
+2,14630000.0
+4,14630000.0
+10236,14630000.0
+3,14630000.0
+10237,14630000.0
diff --git a/test/unit_test_hyfeature/channel_forcing/201512011600NEXOUT.csv b/test/unit_test_hyfeature/channel_forcing/201512011600NEXOUT.csv
new file mode 100644
index 000000000..1e8e79e0f
--- /dev/null
+++ b/test/unit_test_hyfeature/channel_forcing/201512011600NEXOUT.csv
@@ -0,0 +1,8 @@
+feature_id,201512011600
+10238,12785000.0
+1000000001,12785000.0
+2,12785000.0
+4,12785000.0
+10236,12785000.0
+3,12785000.0
+10237,12785000.0
diff --git a/test/unit_test_hyfeature/channel_forcing/201512011700NEXOUT.csv b/test/unit_test_hyfeature/channel_forcing/201512011700NEXOUT.csv
new file mode 100644
index 000000000..4bb649f1e
--- /dev/null
+++ b/test/unit_test_hyfeature/channel_forcing/201512011700NEXOUT.csv
@@ -0,0 +1,8 @@
+feature_id,201512011700
+10238,14600500.0
+1000000001,14600500.0
+2,14600500.0
+4,14600500.0
+10236,14600500.0
+3,14600500.0
+10237,14600500.0
diff --git a/test/unit_test_hyfeature/channel_forcing/201512011800NEXOUT.csv b/test/unit_test_hyfeature/channel_forcing/201512011800NEXOUT.csv
new file mode 100644
index 000000000..e0e4916cb
--- /dev/null
+++ b/test/unit_test_hyfeature/channel_forcing/201512011800NEXOUT.csv
@@ -0,0 +1,8 @@
+feature_id,201512011800
+10238,12815700.0
+1000000001,12815700.0
+2,12815700.0
+4,12815700.0
+10236,12815700.0
+3,12815700.0
+10237,12815700.0
diff --git a/test/unit_test_hyfeature/channel_forcing/201512011900NEXOUT.csv b/test/unit_test_hyfeature/channel_forcing/201512011900NEXOUT.csv
new file mode 100644
index 000000000..6f929612f
--- /dev/null
+++ b/test/unit_test_hyfeature/channel_forcing/201512011900NEXOUT.csv
@@ -0,0 +1,8 @@
+feature_id,201512011900
+10238,14572700.0
+1000000001,14572700.0
+2,14572700.0
+4,14572700.0
+10236,14572700.0
+3,14572700.0
+10237,14572700.0
diff --git a/test/unit_test_hyfeature/channel_forcing/201512012000NEXOUT.csv b/test/unit_test_hyfeature/channel_forcing/201512012000NEXOUT.csv
new file mode 100644
index 000000000..285b0a092
--- /dev/null
+++ b/test/unit_test_hyfeature/channel_forcing/201512012000NEXOUT.csv
@@ -0,0 +1,8 @@
+feature_id,201512012000
+10238,12844700.0
+1000000001,12844700.0
+2,12844700.0
+4,12844700.0
+10236,12844700.0
+3,12844700.0
+10237,12844700.0
diff --git a/test/unit_test_hyfeature/channel_forcing/201512012100NEXOUT.csv b/test/unit_test_hyfeature/channel_forcing/201512012100NEXOUT.csv
new file mode 100644
index 000000000..65f61c646
--- /dev/null
+++ b/test/unit_test_hyfeature/channel_forcing/201512012100NEXOUT.csv
@@ -0,0 +1,8 @@
+feature_id,201512012100
+10238,14546400.0
+1000000001,14546400.0
+2,14546400.0
+4,14546400.0
+10236,14546400.0
+3,14546400.0
+10237,14546400.0
diff --git a/test/unit_test_hyfeature/channel_forcing/201512012200NEXOUT.csv b/test/unit_test_hyfeature/channel_forcing/201512012200NEXOUT.csv
new file mode 100644
index 000000000..c94471db1
--- /dev/null
+++ b/test/unit_test_hyfeature/channel_forcing/201512012200NEXOUT.csv
@@ -0,0 +1,8 @@
+feature_id,201512012200
+10238,12872000.0
+1000000001,12872000.0
+2,12872000.0
+4,12872000.0
+10236,12872000.0
+3,12872000.0
+10237,12872000.0
diff --git a/test/unit_test_hyfeature/channel_forcing/201512012300NEXOUT.csv b/test/unit_test_hyfeature/channel_forcing/201512012300NEXOUT.csv
new file mode 100644
index 000000000..206fd56e4
--- /dev/null
+++ b/test/unit_test_hyfeature/channel_forcing/201512012300NEXOUT.csv
@@ -0,0 +1,8 @@
+feature_id,201512012300
+10238,14521700.0
+1000000001,14521700.0
+2,14521700.0
+4,14521700.0
+10236,14521700.0
+3,14521700.0
+10237,14521700.0
diff --git a/test/unit_test_hyfeature/channel_forcing/201512020000NEXOUT.csv b/test/unit_test_hyfeature/channel_forcing/201512020000NEXOUT.csv
new file mode 100644
index 000000000..93eb82869
--- /dev/null
+++ b/test/unit_test_hyfeature/channel_forcing/201512020000NEXOUT.csv
@@ -0,0 +1,8 @@
+feature_id,201512020000
+10238,12897900.0
+1000000001,12897900.0
+2,12897900.0
+4,12897900.0
+10236,12897900.0
+3,12897900.0
+10237,12897900.0
diff --git a/test/unit_test_hyfeature/channel_forcing/201512020100NEXOUT.csv b/test/unit_test_hyfeature/channel_forcing/201512020100NEXOUT.csv
new file mode 100644
index 000000000..daf0916ba
--- /dev/null
+++ b/test/unit_test_hyfeature/channel_forcing/201512020100NEXOUT.csv
@@ -0,0 +1,8 @@
+feature_id,201512020100
+10238,14498400.0
+1000000001,14498400.0
+2,14498400.0
+4,14498400.0
+10236,14498400.0
+3,14498400.0
+10237,14498400.0
diff --git a/test/unit_test_hyfeature/channel_forcing/201512020200NEXOUT.csv b/test/unit_test_hyfeature/channel_forcing/201512020200NEXOUT.csv
new file mode 100644
index 000000000..248590030
--- /dev/null
+++ b/test/unit_test_hyfeature/channel_forcing/201512020200NEXOUT.csv
@@ -0,0 +1,8 @@
+feature_id,201512020200
+10238,12922200.0
+1000000001,12922200.0
+2,12922200.0
+4,12922200.0
+10236,12922200.0
+3,12922200.0
+10237,12922200.0
diff --git a/test/unit_test_hyfeature/channel_forcing/201512020300NEXOUT.csv b/test/unit_test_hyfeature/channel_forcing/201512020300NEXOUT.csv
new file mode 100644
index 000000000..229cea278
--- /dev/null
+++ b/test/unit_test_hyfeature/channel_forcing/201512020300NEXOUT.csv
@@ -0,0 +1,8 @@
+feature_id,201512020300
+10238,14476500.0
+1000000001,14476500.0
+2,14476500.0
+4,14476500.0
+10236,14476500.0
+3,14476500.0
+10237,14476500.0
diff --git a/test/unit_test_hyfeature/channel_forcing/201512020400NEXOUT.csv b/test/unit_test_hyfeature/channel_forcing/201512020400NEXOUT.csv
new file mode 100644
index 000000000..3f185b6a3
--- /dev/null
+++ b/test/unit_test_hyfeature/channel_forcing/201512020400NEXOUT.csv
@@ -0,0 +1,8 @@
+feature_id,201512020400
+10238,12945200.0
+1000000001,12945200.0
+2,12945200.0
+4,12945200.0
+10236,12945200.0
+3,12945200.0
+10237,12945200.0
diff --git a/test/unit_test_hyfeature/channel_forcing/201512020500NEXOUT.csv b/test/unit_test_hyfeature/channel_forcing/201512020500NEXOUT.csv
new file mode 100644
index 000000000..04742804f
--- /dev/null
+++ b/test/unit_test_hyfeature/channel_forcing/201512020500NEXOUT.csv
@@ -0,0 +1,8 @@
+feature_id,201512020500
+10238,14455800.0
+1000000001,14455800.0
+2,14455800.0
+4,14455800.0
+10236,14455800.0
+3,14455800.0
+10237,14455800.0
diff --git a/test/unit_test_hyfeature/channel_forcing/201512020600NEXOUT.csv b/test/unit_test_hyfeature/channel_forcing/201512020600NEXOUT.csv
new file mode 100644
index 000000000..ef66c1536
--- /dev/null
+++ b/test/unit_test_hyfeature/channel_forcing/201512020600NEXOUT.csv
@@ -0,0 +1,8 @@
+feature_id,201512020600
+10238,12966900.0
+1000000001,12966900.0
+2,12966900.0
+4,12966900.0
+10236,12966900.0
+3,12966900.0
+10237,12966900.0
diff --git a/test/unit_test_hyfeature/channel_forcing/201512020700NEXOUT.csv b/test/unit_test_hyfeature/channel_forcing/201512020700NEXOUT.csv
new file mode 100644
index 000000000..1dc872679
--- /dev/null
+++ b/test/unit_test_hyfeature/channel_forcing/201512020700NEXOUT.csv
@@ -0,0 +1,8 @@
+feature_id,201512020700
+10238,14436200.0
+1000000001,14436200.0
+2,14436200.0
+4,14436200.0
+10236,14436200.0
+3,14436200.0
+10237,14436200.0
diff --git a/test/unit_test_hyfeature/channel_forcing/201512020800NEXOUT.csv b/test/unit_test_hyfeature/channel_forcing/201512020800NEXOUT.csv
new file mode 100644
index 000000000..2f305c40d
--- /dev/null
+++ b/test/unit_test_hyfeature/channel_forcing/201512020800NEXOUT.csv
@@ -0,0 +1,8 @@
+feature_id,201512020800
+10238,12987400.0
+1000000001,12987400.0
+2,12987400.0
+4,12987400.0
+10236,12987400.0
+3,12987400.0
+10237,12987400.0
diff --git a/test/unit_test_hyfeature/channel_forcing/201512020900NEXOUT.csv b/test/unit_test_hyfeature/channel_forcing/201512020900NEXOUT.csv
new file mode 100644
index 000000000..539eae71a
--- /dev/null
+++ b/test/unit_test_hyfeature/channel_forcing/201512020900NEXOUT.csv
@@ -0,0 +1,8 @@
+feature_id,201512020900
+10238,14417800.0
+1000000001,14417800.0
+2,14417800.0
+4,14417800.0
+10236,14417800.0
+3,14417800.0
+10237,14417800.0
diff --git a/test/unit_test_hyfeature/channel_forcing/201512021000NEXOUT.csv b/test/unit_test_hyfeature/channel_forcing/201512021000NEXOUT.csv
new file mode 100644
index 000000000..73f650e00
--- /dev/null
+++ b/test/unit_test_hyfeature/channel_forcing/201512021000NEXOUT.csv
@@ -0,0 +1,8 @@
+feature_id,201512021000
+10238,13006700.0
+1000000001,13006700.0
+2,13006700.0
+4,13006700.0
+10236,13006700.0
+3,13006700.0
+10237,13006700.0
diff --git a/test/unit_test_hyfeature/channel_forcing/201512021100NEXOUT.csv b/test/unit_test_hyfeature/channel_forcing/201512021100NEXOUT.csv
new file mode 100644
index 000000000..204dbbabf
--- /dev/null
+++ b/test/unit_test_hyfeature/channel_forcing/201512021100NEXOUT.csv
@@ -0,0 +1,8 @@
+feature_id,201512021100
+10238,14400400.0
+1000000001,14400400.0
+2,14400400.0
+4,14400400.0
+10236,14400400.0
+3,14400400.0
+10237,14400400.0
diff --git a/test/unit_test_hyfeature/channel_forcing/201512021200NEXOUT.csv b/test/unit_test_hyfeature/channel_forcing/201512021200NEXOUT.csv
new file mode 100644
index 000000000..243e6b73f
--- /dev/null
+++ b/test/unit_test_hyfeature/channel_forcing/201512021200NEXOUT.csv
@@ -0,0 +1,8 @@
+feature_id,201512021200
+10238,13024900.0
+1000000001,13024900.0
+2,13024900.0
+4,13024900.0
+10236,13024900.0
+3,13024900.0
+10237,13024900.0
diff --git a/test/unit_test_hyfeature/channel_forcing/201512021300NEXOUT.csv b/test/unit_test_hyfeature/channel_forcing/201512021300NEXOUT.csv
new file mode 100644
index 000000000..841508ecc
--- /dev/null
+++ b/test/unit_test_hyfeature/channel_forcing/201512021300NEXOUT.csv
@@ -0,0 +1,8 @@
+feature_id,201512021300
+10238,14384000.0
+1000000001,14384000.0
+2,14384000.0
+4,14384000.0
+10236,14384000.0
+3,14384000.0
+10237,14384000.0
diff --git a/test/unit_test_hyfeature/channel_forcing/201512021400NEXOUT.csv b/test/unit_test_hyfeature/channel_forcing/201512021400NEXOUT.csv
new file mode 100644
index 000000000..abde31155
--- /dev/null
+++ b/test/unit_test_hyfeature/channel_forcing/201512021400NEXOUT.csv
@@ -0,0 +1,8 @@
+feature_id,201512021400
+10238,13042100.0
+1000000001,13042100.0
+2,13042100.0
+4,13042100.0
+10236,13042100.0
+3,13042100.0
+10237,13042100.0
diff --git a/test/unit_test_hyfeature/channel_forcing/201512021500NEXOUT.csv b/test/unit_test_hyfeature/channel_forcing/201512021500NEXOUT.csv
new file mode 100644
index 000000000..20c1492f2
--- /dev/null
+++ b/test/unit_test_hyfeature/channel_forcing/201512021500NEXOUT.csv
@@ -0,0 +1,8 @@
+feature_id,201512021500
+10238,14368600.0
+1000000001,14368600.0
+2,14368600.0
+4,14368600.0
+10236,14368600.0
+3,14368600.0
+10237,14368600.0
diff --git a/test/unit_test_hyfeature/channel_forcing/201512021600NEXOUT.csv b/test/unit_test_hyfeature/channel_forcing/201512021600NEXOUT.csv
new file mode 100644
index 000000000..4b0552cf6
--- /dev/null
+++ b/test/unit_test_hyfeature/channel_forcing/201512021600NEXOUT.csv
@@ -0,0 +1,8 @@
+feature_id,201512021600
+10238,13058300.0
+1000000001,13058300.0
+2,13058300.0
+4,13058300.0
+10236,13058300.0
+3,13058300.0
+10237,13058300.0
diff --git a/test/unit_test_hyfeature/channel_forcing/201512021700NEXOUT.csv b/test/unit_test_hyfeature/channel_forcing/201512021700NEXOUT.csv
new file mode 100644
index 000000000..0851c11b8
--- /dev/null
+++ b/test/unit_test_hyfeature/channel_forcing/201512021700NEXOUT.csv
@@ -0,0 +1,8 @@
+feature_id,201512021700
+10238,14354000.0
+1000000001,14354000.0
+2,14354000.0
+4,14354000.0
+10236,14354000.0
+3,14354000.0
+10237,14354000.0
diff --git a/test/unit_test_hyfeature/channel_forcing/201512021800NEXOUT.csv b/test/unit_test_hyfeature/channel_forcing/201512021800NEXOUT.csv
new file mode 100644
index 000000000..8a25f3b88
--- /dev/null
+++ b/test/unit_test_hyfeature/channel_forcing/201512021800NEXOUT.csv
@@ -0,0 +1,8 @@
+feature_id,201512021800
+10238,13073600.0
+1000000001,13073600.0
+2,13073600.0
+4,13073600.0
+10236,13073600.0
+3,13073600.0
+10237,13073600.0
diff --git a/test/unit_test_hyfeature/channel_forcing/201512021900NEXOUT.csv b/test/unit_test_hyfeature/channel_forcing/201512021900NEXOUT.csv
new file mode 100644
index 000000000..b32fa7211
--- /dev/null
+++ b/test/unit_test_hyfeature/channel_forcing/201512021900NEXOUT.csv
@@ -0,0 +1,8 @@
+feature_id,201512021900
+10238,14340200.0
+1000000001,14340200.0
+2,14340200.0
+4,14340200.0
+10236,14340200.0
+3,14340200.0
+10237,14340200.0
diff --git a/test/unit_test_hyfeature/channel_forcing/201512022000NEXOUT.csv b/test/unit_test_hyfeature/channel_forcing/201512022000NEXOUT.csv
new file mode 100644
index 000000000..5e633fbcb
--- /dev/null
+++ b/test/unit_test_hyfeature/channel_forcing/201512022000NEXOUT.csv
@@ -0,0 +1,8 @@
+feature_id,201512022000
+10238,13088000.0
+1000000001,13088000.0
+2,13088000.0
+4,13088000.0
+10236,13088000.0
+3,13088000.0
+10237,13088000.0
diff --git a/test/unit_test_hyfeature/channel_forcing/201512022100NEXOUT.csv b/test/unit_test_hyfeature/channel_forcing/201512022100NEXOUT.csv
new file mode 100644
index 000000000..53708f36f
--- /dev/null
+++ b/test/unit_test_hyfeature/channel_forcing/201512022100NEXOUT.csv
@@ -0,0 +1,8 @@
+feature_id,201512022100
+10238,14327200.0
+1000000001,14327200.0
+2,14327200.0
+4,14327200.0
+10236,14327200.0
+3,14327200.0
+10237,14327200.0
diff --git a/test/unit_test_hyfeature/channel_forcing/201512022200NEXOUT.csv b/test/unit_test_hyfeature/channel_forcing/201512022200NEXOUT.csv
new file mode 100644
index 000000000..dfd4684d4
--- /dev/null
+++ b/test/unit_test_hyfeature/channel_forcing/201512022200NEXOUT.csv
@@ -0,0 +1,8 @@
+feature_id,201512022200
+10238,13101600.0
+1000000001,13101600.0
+2,13101600.0
+4,13101600.0
+10236,13101600.0
+3,13101600.0
+10237,13101600.0
diff --git a/test/unit_test_hyfeature/channel_forcing/201512022300NEXOUT.csv b/test/unit_test_hyfeature/channel_forcing/201512022300NEXOUT.csv
new file mode 100644
index 000000000..b184ecc70
--- /dev/null
+++ b/test/unit_test_hyfeature/channel_forcing/201512022300NEXOUT.csv
@@ -0,0 +1,8 @@
+feature_id,201512022300
+10238,14315000.0
+1000000001,14315000.0
+2,14315000.0
+4,14315000.0
+10236,14315000.0
+3,14315000.0
+10237,14315000.0
diff --git a/test/unit_test_hyfeature/restart/201512010000NEXOUT.csv b/test/unit_test_hyfeature/restart/201512010000NEXOUT.csv
new file mode 100644
index 000000000..57a2a30d4
--- /dev/null
+++ b/test/unit_test_hyfeature/restart/201512010000NEXOUT.csv
@@ -0,0 +1,8 @@
+feature_id,201512010000
+10238,1097500.0
+1000000001,1097500.0
+2,1097500.0
+4,1097500.0
+10236,1097500.0
+3,1097500.0
+10237,1097500.0
diff --git a/test/unit_test_hyfeature/unittest_hyfeature.yaml b/test/unit_test_hyfeature/unittest_hyfeature.yaml
index 335174f57..78564141f 100644
--- a/test/unit_test_hyfeature/unittest_hyfeature.yaml
+++ b/test/unit_test_hyfeature/unittest_hyfeature.yaml
@@ -9,25 +9,26 @@ network_topology_parameters:
     #----------
     supernetwork_parameters:
         #----------
-        geo_file_path: domain/gauge_01069700.gpkg   #domain/RouteLink_NWMv2.1.nc  
+        geo_file_type: HYFeaturesNetwork  #NHDNetwork        
+        geo_file_path: domain/gauge_01069700.gpkg   #domain/RouteLink_NWMv2.1.nc 
         mask_file_path: # domain/unit_test_noRS/coastal_subset.txt
         synthetic_wb_segments:
             #- 4800002
             #- 4800004
             #- 4800006
             #- 4800007
-    waterbody_parameters:
+    #waterbody_parameters:
         #----------
-        break_network_at_waterbodies: False 
-        level_pool:
+        #break_network_at_waterbodies: False 
+        #level_pool:
             #----------
-            level_pool_waterbody_parameter_file_path: # domain/LAKEPARM_NWMv2.1.nc 
-        rfc:
+            #level_pool_waterbody_parameter_file_path: domain/LAKEPARM_NWMv2.1.nc 
+        #rfc:
             #----------
-            reservoir_parameter_file                : # domain/reservoir_index_AnA.nc
-            reservoir_rfc_forecasts                 : False
-            reservoir_rfc_forecasts_time_series_path: # rfc_TimeSeries/
-            reservoir_rfc_forecasts_lookback_hours  : # 48
+            #reservoir_parameter_file                : domain/reservoir_index_AnA.nc
+            #reservoir_rfc_forecasts                 : False
+            #reservoir_rfc_forecasts_time_series_path: rfc_TimeSeries/
+            #reservoir_rfc_forecasts_lookback_hours  : 48
 #--------------------------------------------------------------------------------
 compute_parameters:
     #----------
@@ -38,29 +39,32 @@ compute_parameters:
     cpu_pool               : 36
     restart_parameters:
         #----------
-        wrf_hydro_channel_restart_file: # restart/HYDRO_RST.2020-08-26_00:00_DOMAIN1
-        wrf_hydro_channel_ID_crosswalk_file: # domain/RouteLink_NWMv2.1.nc
-        wrf_hydro_waterbody_restart_file: #restart/HYDRO_RST.2020-08-26_00:00_DOMAIN1
-        wrf_hydro_waterbody_ID_crosswalk_file    : # domain/LAKEPARM_NWMv2.1.nc 
-        wrf_hydro_waterbody_crosswalk_filter_file: # domain/LAKEPARM_NWMv2.1.nc  
+        #wrf_hydro_channel_restart_file: restart/HYDRO_RST.2020-08-26_00:00_DOMAIN1
+        #wrf_hydro_channel_ID_crosswalk_file: domain/RouteLink_NWMv2.1.nc
+        #wrf_hydro_waterbody_restart_file: restart/HYDRO_RST.2020-08-26_00:00_DOMAIN1
+        #wrf_hydro_waterbody_ID_crosswalk_file    : domain/LAKEPARM_NWMv2.1.nc 
+        #wrf_hydro_waterbody_crosswalk_filter_file: domain/LAKEPARM_NWMv2.1.nc
+        hyfeature_channel_restart_file: restart/201512010000NEXOUT.csv
     hybrid_parameters:
         run_hybrid_routing: True
-        diffusive_domain  : domain/unit_test_noRS/coastal_domain.yaml  
+        diffusive_domain  : domain/coastal_domain.yaml  
         use_natl_xsections: False
         topobathy_domain  : # domain/final_diffusive_natural_xs.nc 
         run_refactored_network: False
         refactored_domain: # domain/unit_test_noRS/refactored_coastal_domain.yaml 
         refactored_topobathy_domain: # domain/refac_final_diffusive_natural_xs.nc 
-        coastal_boundary_domain: domain/unit_test_noRS/coastal_boundary_domain.yaml
+        coastal_boundary_domain: domain/coastal_boundary_domain.yaml
     forcing_parameters:
         #----------
         qts_subdivisions            : 12
         dt                          : 300 # [sec]
-        qlat_input_folder           :  channel_forcing/
+        qlat_input_folder           : channel_forcing/ 
         qlat_file_pattern_filter    : "*.CHRTOUT_DOMAIN1"
+        nexus_input_folder           : channel_forcing/ 
+        nexus_file_pattern_filter    : "*NEXOUT.csv" 
         coastal_boundary_input_file : channel_forcing/schout_1.nc  
         nts                         : 48 #288 for 1day
-        max_loop_size               : 24 # [hr]  
+        max_loop_size               : 2 # [hr]  
     data_assimilation_parameters:
         #----------
         usgs_timeslices_folder   : #usgs_TimeSlice/

From d7a52885a61a01d52081ad645748a1788c7c0d13 Mon Sep 17 00:00:00 2001
From: Dong Kim <donghakim@cheyenne4.cheyenne.ucar.edu>
Date: Mon, 21 Nov 2022 21:04:13 -0700
Subject: [PATCH 3/7] add empty folders

---
 test/unit_test_hyfeature/lakeout/.gitkeep | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 test/unit_test_hyfeature/lakeout/.gitkeep

diff --git a/test/unit_test_hyfeature/lakeout/.gitkeep b/test/unit_test_hyfeature/lakeout/.gitkeep
new file mode 100644
index 000000000..e69de29bb

From 34581ef82db00826aa59c4b588b141a0f45158a9 Mon Sep 17 00:00:00 2001
From: Dong Kim <donghakim@cheyenne4.cheyenne.ucar.edu>
Date: Mon, 21 Nov 2022 21:06:12 -0700
Subject: [PATCH 4/7] add second empty folders

---
 test/unit_test_hyfeature/lastobs/.gitkeep         | 0
 test/unit_test_hyfeature/output/.gitkeep          | 0
 test/unit_test_hyfeature/rfc_TimeSeries/.gitkeep  | 0
 test/unit_test_hyfeature/usace_TimeSlice/.gitkeep | 0
 test/unit_test_hyfeature/usgs_TimeSlice/.gitkeep  | 0
 5 files changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 test/unit_test_hyfeature/lastobs/.gitkeep
 create mode 100644 test/unit_test_hyfeature/output/.gitkeep
 create mode 100644 test/unit_test_hyfeature/rfc_TimeSeries/.gitkeep
 create mode 100644 test/unit_test_hyfeature/usace_TimeSlice/.gitkeep
 create mode 100644 test/unit_test_hyfeature/usgs_TimeSlice/.gitkeep

diff --git a/test/unit_test_hyfeature/lastobs/.gitkeep b/test/unit_test_hyfeature/lastobs/.gitkeep
new file mode 100644
index 000000000..e69de29bb
diff --git a/test/unit_test_hyfeature/output/.gitkeep b/test/unit_test_hyfeature/output/.gitkeep
new file mode 100644
index 000000000..e69de29bb
diff --git a/test/unit_test_hyfeature/rfc_TimeSeries/.gitkeep b/test/unit_test_hyfeature/rfc_TimeSeries/.gitkeep
new file mode 100644
index 000000000..e69de29bb
diff --git a/test/unit_test_hyfeature/usace_TimeSlice/.gitkeep b/test/unit_test_hyfeature/usace_TimeSlice/.gitkeep
new file mode 100644
index 000000000..e69de29bb
diff --git a/test/unit_test_hyfeature/usgs_TimeSlice/.gitkeep b/test/unit_test_hyfeature/usgs_TimeSlice/.gitkeep
new file mode 100644
index 000000000..e69de29bb

From 8af5b254ad401aa8d38bbcd5f37bc89678934810 Mon Sep 17 00:00:00 2001
From: Dong Kim <donghakim@cheyenne4.cheyenne.ucar.edu>
Date: Tue, 22 Nov 2022 14:37:14 -0700
Subject: [PATCH 5/7] make hybrid routing (MC + Diffusive) run on hyfeature
 network of a unit test

---
 .../troute/HYFeaturesNetwork.py               | 29 +++++++++
 src/troute-network/troute/NHDNetwork.py       |  4 +-
 .../troute/hyfeature_network_utilities.py     |  4 +-
 .../troute/hyfeature_preprocess.py            |  1 +
 src/troute-network/troute/nhd_io.py           | 62 +++++++++----------
 .../troute/nhd_network_utilities_v02.py       | 21 ++++---
 src/troute-network/troute/nhd_preprocess.py   |  3 +-
 src/troute-nwm/src/nwm_routing/__main__.py    | 20 +++---
 src/troute-routing/troute/routing/compute.py  |  4 +-
 .../unittest_hyfeature.yaml                   |  2 +-
 10 files changed, 94 insertions(+), 56 deletions(-)

diff --git a/src/troute-network/troute/HYFeaturesNetwork.py b/src/troute-network/troute/HYFeaturesNetwork.py
index 1d447d1b8..ee0607193 100644
--- a/src/troute-network/troute/HYFeaturesNetwork.py
+++ b/src/troute-network/troute/HYFeaturesNetwork.py
@@ -11,6 +11,7 @@
 from pathlib import Path
 import math
 import troute.hyfeature_preprocess as hyfeature_prep
+from datetime import datetime, timedelta
 
 __verbose__ = False
 __showtiming__ = False
@@ -355,6 +356,34 @@ def create_routing_network(self,
                 self.refactored_reaches,
                 self.unrefactored_topobathy_df)
 
+    def new_q0(self, run_results):
+        """
+        Prepare a new q0 dataframe with initial flow and depth to act as
+        a warmstate for the next simulation chunk.
+        """
+        self._q0 = pd.concat(
+            [
+                pd.DataFrame(
+                    r[1][:, [-3, -3, -1]], index=r[0], columns=["qu0", "qd0", "h0"]
+                )
+                for r in run_results
+            ],
+            copy=False,
+        )
+        return self._q0
+    
+    def update_waterbody_water_elevation(self):           
+        """
+        Update the starting water_elevation of each lake/reservoir
+        with flow and depth values from q0
+        """
+        self._waterbody_df.update(self._q0)
+        
+    def new_t0(self, dt, nts):
+        """
+        Update t0 value for next loop iteration
+        """
+        self._t0 += timedelta(seconds = dt * nts)
 
     @property
     def downstream_flowpath_dict(self):
diff --git a/src/troute-network/troute/NHDNetwork.py b/src/troute-network/troute/NHDNetwork.py
index 61101a610..b72996a71 100644
--- a/src/troute-network/troute/NHDNetwork.py
+++ b/src/troute-network/troute/NHDNetwork.py
@@ -196,7 +196,7 @@ def __init__(
             print("setting waterbody and channel initial states ...")
         if __showtiming__:
             start_time = time.time()
-        
+
         (self._waterbody_df,
          self._q0,
          self._t0,) = nhd_prep.nhd_initial_warmstate_preprocess(
@@ -237,7 +237,7 @@ def assemble_forcings(self, run, forcing_parameters, hybrid_parameters, cpu_pool
             self._coastal_boundary_depth_df,
         )
     
-    def new_nhd_q0(self, run_results):
+    def new_q0(self, run_results):
         """
         Prepare a new q0 dataframe with initial flow and depth to act as
         a warmstate for the next simulation chunk.
diff --git a/src/troute-network/troute/hyfeature_network_utilities.py b/src/troute-network/troute/hyfeature_network_utilities.py
index 5c78ccd38..a3c603d8c 100644
--- a/src/troute-network/troute/hyfeature_network_utilities.py
+++ b/src/troute-network/troute/hyfeature_network_utilities.py
@@ -208,8 +208,8 @@ def build_qlateral_array(
         # Take flowpath ids entering NEXUS and replace NEXUS ids by the upstream flowpath ids 
         qlats_df = pd.concat( (nexuses_lateralflows_df.loc[int(k)].rename(v)
                             for k,v in nexus_to_upstream_flowpath_dict.items() ), axis=1
-                            ).T        
-        
+                            ).T 
+        qlats_df.columns=range(len(nexus_files))
         qlats_df = qlats_df[qlats_df.index.isin(segment_index)]
     elif qlat_input_file:
         qlats_df = nhd_io.get_ql_from_csv(qlat_input_file)
diff --git a/src/troute-network/troute/hyfeature_preprocess.py b/src/troute-network/troute/hyfeature_preprocess.py
index ea02a3eac..6b4485c85 100644
--- a/src/troute-network/troute/hyfeature_preprocess.py
+++ b/src/troute-network/troute/hyfeature_preprocess.py
@@ -417,6 +417,7 @@ def hyfeature_hybrid_routing_preprocess(
     )
     
     LOG.debug("reach organization complete in %s seconds." % (time.time() - start_time))
+    # FIXME: Make this commented out alive
     '''
     if preprocessing_parameters.get('preprocess_only', False):
 
diff --git a/src/troute-network/troute/nhd_io.py b/src/troute-network/troute/nhd_io.py
index c92059645..d7d344092 100644
--- a/src/troute-network/troute/nhd_io.py
+++ b/src/troute-network/troute/nhd_io.py
@@ -86,7 +86,6 @@ def read_config_file(custom_input_file):
     data_assimilation_parameters (dict): Input parameters re data assimilation
 
     '''
-    import pdb; pdb.set_trace()
     if custom_input_file[-4:] == "yaml":
         with open(custom_input_file) as custom_file:
             data = yaml.load(custom_file, Loader=yaml.SafeLoader)
@@ -101,40 +100,41 @@ def read_config_file(custom_input_file):
     )
     # add attributes when HYfeature network is selected
     if supernetwork_parameters['geo_file_path'][-4:] == "gpkg":
-        params = {
-            "title_string":"HY_Features Test",
-            "geo_file_path":supernetwork_parameters['geo_file_path'],
-            "flowpath_edge_list": None,
-            "columns": {
-                #link????
-                "key": "id",
-                "downstream": "toid",
-                "dx": "lengthkm",
-                "n": "n",  # TODO: rename to `manningn`
-                "ncc": "nCC",  # TODO: rename to `mannningncc`
-                "s0": "So",
-                "bw": "BtmWdth",  # TODO: rename to `bottomwidth`
-                #waterbody: "NHDWaterbodyComID",
-                "tw": "TopWdth",  # TODO: rename to `topwidth`
-                "twcc": "TopWdthCC",  # TODO: rename to `topwidthcc`
-                #alt: "alt",
-                "musk": "MusK",
-                "musx": "MusX",
-                "cs": "ChSlp"  # TODO: rename to `sideslope`
-                },
-            "waterbody_null_code": -9999,
-            "terminal_code": 0,
-            "waterbody_null_code": -9999,
-            "driver_string": "NetCDF",
-            "layer_string": 0
-            }
-        supernetwork_parameters['hyfeature_params'] = params
+        supernetwork_parameters["title_string"]       = "HY_Features Test"
+        supernetwork_parameters["geo_file_path"]      = supernetwork_parameters['geo_file_path']
+        supernetwork_parameters["flowpath_edge_list"] = None    
+        routelink_attr = {
+                        #link????
+                        "key": "id",
+                        "downstream": "toid",
+                        "dx": "length_m",
+                        "n": "n",  # TODO: rename to `manningn`
+                        "ncc": "nCC",  # TODO: rename to `mannningncc`
+                        "s0": "So",
+                        "bw": "BtmWdth",  # TODO: rename to `bottomwidth`
+                        #waterbody: "NHDWaterbodyComID",
+                        "tw": "TopWdth",  # TODO: rename to `topwidth`
+                        "twcc": "TopWdthCC",  # TODO: rename to `topwidthcc`
+                        "alt": "alt",
+                        "musk": "MusK",
+                        "musx": "MusX",
+                        "cs": "ChSlp"  # TODO: rename to `sideslope`
+                        }
+        supernetwork_parameters["columns"]             = routelink_attr 
+        supernetwork_parameters["waterbody_null_code"] = -9999
+        supernetwork_parameters["terminal_code"]       =  0
+        supernetwork_parameters["waterbody_null_code"] = -9999
+        supernetwork_parameters["driver_string"]       = "NetCDF"
+        supernetwork_parameters["layer_string"]        = 0
         
     preprocessing_parameters = network_topology_parameters.get(
         "preprocessing_parameters", {}
     )        
+    #waterbody_parameters = network_topology_parameters.get(
+    #    "waterbody_parameters", None
+    #)
     waterbody_parameters = network_topology_parameters.get(
-        "waterbody_parameters", None
+        "waterbody_parameters", {}
     )
     compute_parameters = data.get("compute_parameters", {})
     forcing_parameters = compute_parameters.get("forcing_parameters", {})
@@ -370,7 +370,7 @@ def read_reservoir_parameter_file(
     return df1, usgs_crosswalk, usace_crosswalk
 
 
-def get_ql_from_csv(qlat_input_file, index_col=0):
+def get_ql_from_csv(nhd_input_file, index_col=0):
     """
     qlat_input_file: comma delimted file with header giving timesteps, rows for each segment
     index_col = 0: column/field in the input file with the segment/link id
diff --git a/src/troute-network/troute/nhd_network_utilities_v02.py b/src/troute-network/troute/nhd_network_utilities_v02.py
index a32b8038c..e2d353e5d 100644
--- a/src/troute-network/troute/nhd_network_utilities_v02.py
+++ b/src/troute-network/troute/nhd_network_utilities_v02.py
@@ -209,12 +209,15 @@ def build_channel_initial_state(
     wrf_hydro_channel_restart_file = restart_parameters.get(
         "wrf_hydro_channel_restart_file", None
     )
+    
+    hyfeature_channel_restart_file = restart_parameters.get(
+        "hyfeature_channel_restart_file", None
+    )
 
     if channel_restart_file:
         q0 = nhd_io.get_channel_restart_from_csv(channel_restart_file)
-
+        
     elif wrf_hydro_channel_restart_file:
-
         q0 = nhd_io.get_channel_restart_from_wrf_hydro(
             restart_parameters["wrf_hydro_channel_restart_file"],
             restart_parameters["wrf_hydro_channel_ID_crosswalk_file"],
@@ -223,6 +226,11 @@ def build_channel_initial_state(
             restart_parameters.get("wrf_hydro_channel_restart_downstream_flow_field_name", 'qlink2'),
             restart_parameters.get("wrf_hydro_channel_restart_depth_flow_field_name", 'hlink'),
         )
+    elif hyfeature_channel_restart_file: 
+        # FIXME: fix this cold start when acutal restart file for hyfeature network rolls in.
+        q0 = pd.DataFrame(
+            0, index=segment_index, columns=["qu0", "qd0", "h0"], dtype="float32",
+        )
     else:
         # Set cold initial state
         # assume to be zero
@@ -230,6 +238,7 @@ def build_channel_initial_state(
         q0 = pd.DataFrame(
             0, index=segment_index, columns=["qu0", "qd0", "h0"], dtype="float32",
         )
+  
     # TODO: If needed for performance improvement consider filtering mask file on read.
     if not segment_index.empty:
         q0 = q0[q0.index.isin(segment_index)]
@@ -247,7 +256,7 @@ def build_forcing_sets(
     nts = forcing_parameters.get("nts", None)
     max_loop_size = forcing_parameters.get("max_loop_size", 12)
     dt = forcing_parameters.get("dt", None)
-
+    
     try:
         qlat_input_folder = pathlib.Path(qlat_input_folder)
         assert qlat_input_folder.is_dir() == True
@@ -259,7 +268,6 @@ def build_forcing_sets(
     forcing_glob_filter = forcing_parameters.get("qlat_file_pattern_filter", "*.CHRTOUT_DOMAIN1")
         
     # TODO: Throw errors if insufficient input data are available
-
     if run_sets:
         
         # append final_timestamp variable to each set_list
@@ -316,7 +324,7 @@ def build_forcing_sets(
                 assert J.is_file() == True
             except AssertionError:
                 raise AssertionError("Aborting simulation because forcing file", J, "cannot be not found.") from None
-                
+ 
         # build run sets list
         run_sets = []
         k = 0
@@ -349,7 +357,6 @@ def build_forcing_sets(
             nts_last = nts_accum
             k += max_loop_size
             j += 1
-    
     return run_sets
 
 def build_qlateral_array(
@@ -382,7 +389,7 @@ def build_qlateral_array(
         qlat_file_value_col = forcing_parameters.get("qlat_file_value_col", "q_lateral")
         gw_bucket_col = forcing_parameters.get("qlat_file_gw_bucket_flux_col","qBucket")
         terrain_ro_col = forcing_parameters.get("qlat_file_terrain_runoff_col","qSfcLatRunoff")
-        
+
         # Parallel reading of qlateral data from CHRTOUT
         with Parallel(n_jobs=cpu_pool) as parallel:
 
diff --git a/src/troute-network/troute/nhd_preprocess.py b/src/troute-network/troute/nhd_preprocess.py
index c1f4c7934..dc303815b 100644
--- a/src/troute-network/troute/nhd_preprocess.py
+++ b/src/troute-network/troute/nhd_preprocess.py
@@ -735,12 +735,11 @@ def nhd_initial_warmstate_preprocess(
             "waterbody initial states complete in %s seconds."\
             % (time.time() - start_time))
         start_time = time.time()
-
+    
     #----------------------------------------------------------------------------
     # Assemble channel initial states (flow and depth)
     # also establish simulation initialization timestamp
     #----------------------------------------------------------------------------
-    
     start_time = time.time()
     LOG.info("setting channel initial states ...")
 
diff --git a/src/troute-nwm/src/nwm_routing/__main__.py b/src/troute-nwm/src/nwm_routing/__main__.py
index 9e8309a20..d3c8c6f33 100644
--- a/src/troute-nwm/src/nwm_routing/__main__.py
+++ b/src/troute-nwm/src/nwm_routing/__main__.py
@@ -129,13 +129,13 @@ def main_v04(argv):
     network.assemble_forcings(run_sets[0], forcing_parameters, hybrid_parameters, cpu_pool)
     
     # Create data assimilation object from da_sets for first loop iteration
-    if supernetwork_parameters["geo_file_type"] == 'NHDNetwork':
+    # TODO: Add data_assimilation for hyfeature network
+    if 1==2:
         data_assimilation = AllDA(data_assimilation_parameters,
                                   run_parameters,
                                   waterbody_parameters,
                                   network,
                                   da_sets[0])
-    # TODO: apply data_assimilation for hyfeature network
 
     if showtiming:
         forcing_end_time = time.time()
@@ -165,7 +165,7 @@ def main_v04(argv):
 
         if showtiming:
             route_start_time = time.time()
-        import pdb; pdb.set_trace()
+
         run_results = nwm_route(
             network.connections, 
             network.reverse_network, 
@@ -204,7 +204,7 @@ def main_v04(argv):
             network.coastal_boundary_depth_df,
             network.unrefactored_topobathy_df,
         )
-        import pdb; pdb.set_trace()        
+      
         # returns list, first item is run result, second item is subnetwork items
         subnetwork_list = run_results[1]
         run_results = run_results[0]
@@ -214,7 +214,7 @@ def main_v04(argv):
             task_times['route_time'] += route_end_time - route_start_time
 
         # create initial conditions for next loop itteration
-        network.new_nhd_q0(run_results)
+        network.new_q0(run_results)
         network.update_waterbody_water_elevation()    
         
         # TODO move the conditional call to write_lite_restart to nwm_output_generator.
@@ -238,7 +238,9 @@ def main_v04(argv):
                                       cpu_pool)
             
             # get reservoir DA initial parameters for next loop iteration
-            data_assimilation.update(run_results,
+            # TODO: Add data_assimilation for hyfeature network
+            if 1==2: 
+                data_assimilation.update(run_results,
                                      data_assimilation_parameters,
                                      run_parameters,
                                      network,
@@ -265,9 +267,9 @@ def main_v04(argv):
             network._waterbody_df,  ## check:  network._waterbody_df ?? def name is different from return self._ ..
             network._waterbody_types_df, ## check:  network._waterbody_types_df ?? def name is different from return self._ ..
             data_assimilation_parameters,
-            data_assimilation.lastobs_df,
-            network.link_gage_df,
-            network.link_lake_crosswalk,
+            pd.DataFrame(), #data_assimilation.lastobs_df,
+            pd.DataFrame(), #network.link_gage_df,
+            None, #network.link_lake_crosswalk, 
         )
 
         if showtiming:
diff --git a/src/troute-routing/troute/routing/compute.py b/src/troute-routing/troute/routing/compute.py
index 6d68f4482..a5673817c 100644
--- a/src/troute-routing/troute/routing/compute.py
+++ b/src/troute-routing/troute/routing/compute.py
@@ -249,7 +249,7 @@ def compute_nhd_routing_v02(
     waterbody_type_specified,
     subnetwork_list,
 ):
-    import pdb; pdb.set_trace()
+
     da_decay_coefficient = da_parameter_dict.get("da_decay_coefficient", 0)
     param_df["dt"] = dt
     param_df = param_df.astype("float32")
@@ -1201,7 +1201,7 @@ def compute_diffusive_routing(
             coastal_boundary_depth_bytw_df = coastal_boundary_depth_df.loc[tw].to_frame().T
         else:
             coastal_boundary_depth_bytw_df = pd.DataFrame()
-        import pdb; pdb.set_trace()
+
         # build diffusive inputs
         diffusive_inputs = diff_utils.diffusive_input_data_v02(
             tw,
diff --git a/test/unit_test_hyfeature/unittest_hyfeature.yaml b/test/unit_test_hyfeature/unittest_hyfeature.yaml
index 78564141f..151e4c36e 100644
--- a/test/unit_test_hyfeature/unittest_hyfeature.yaml
+++ b/test/unit_test_hyfeature/unittest_hyfeature.yaml
@@ -94,7 +94,7 @@ output_parameters:
         lite_restart_output_directory: restart/
     chrtout_output:
         #----------
-        wrf_hydro_channel_output_source_folder: channel_forcing/
+        #wrf_hydro_channel_output_source_folder: channel_forcing/
     chanobs_output:
         #----------
         chanobs_output_directory: output/ 

From 5f66efca728ead9b80f91557dc4e24b8ed39f349 Mon Sep 17 00:00:00 2001
From: Dong Kim <donghakim@cheyenne4.cheyenne.ucar.edu>
Date: Mon, 28 Nov 2022 11:41:07 -0700
Subject: [PATCH 6/7] waterbody dataframe updates by Sean Horvath

---
 .../troute/HYFeaturesNetwork.py               | 18 ----
 .../troute/hyfeature_preprocess.py            | 86 ++++++++++++-------
 .../unittest_hyfeature.yaml                   |  9 +-
 3 files changed, 58 insertions(+), 55 deletions(-)

diff --git a/src/troute-network/troute/HYFeaturesNetwork.py b/src/troute-network/troute/HYFeaturesNetwork.py
index ee0607193..cd1791761 100644
--- a/src/troute-network/troute/HYFeaturesNetwork.py
+++ b/src/troute-network/troute/HYFeaturesNetwork.py
@@ -29,24 +29,6 @@ def numeric_id(flowpath):
     flowpath['toid'] = int(toid)
     return flowpath
 
-def read_ngen_waterbody_df(parm_file, lake_index_field="wb-id", lake_id_mask=None):
-    """
-    Reads lake.json file and prepares a dataframe, filtered
-    to the relevant reservoirs, to provide the parameters
-    for level-pool reservoir computation.
-    """
-    def node_key_func(x):
-        return int(x[3:])
-    df = pd.read_json(parm_file, orient="index")
-
-    df.index = df.index.map(node_key_func)
-    df.index.name = lake_index_field
-    #df = df.set_index(lake_index_field, append=True).reset_index(level=0)
-    #df.rename(columns={'level_0':'wb-id'}, inplace=True)
-    if lake_id_mask:
-        df = df.loc[lake_id_mask]
-    return df
-
 def read_qlats(forcing_parameters, segment_index, nexus_to_downstream_flowpath_dict):
     # STEP 5: Read (or set) QLateral Inputs
     if __showtiming__:
diff --git a/src/troute-network/troute/hyfeature_preprocess.py b/src/troute-network/troute/hyfeature_preprocess.py
index 6b4485c85..446f356df 100644
--- a/src/troute-network/troute/hyfeature_preprocess.py
+++ b/src/troute-network/troute/hyfeature_preprocess.py
@@ -4,10 +4,12 @@
 from datetime import datetime
 from collections import defaultdict
 from pathlib import Path
+import os
 
 import pandas as pd
 import numpy as np
 import xarray as xr
+import geopandas as gpd
 
 import troute.nhd_network_utilities_v02 as nnu
 import troute.nhd_network as nhd_network
@@ -85,10 +87,9 @@ def build_hyfeature_network(supernetwork_parameters,
         waterbody_df["qd0"] = 0.0
         waterbody_df["h0"] = -1e9
 
-        hybrid_params = waterbody_parameters.get('hybrid_and_rfc', None)
-        try: #FIXME for HYFeatures/ngen this will likely be a lot different...
-            waterbody_types_df = nhd_io.read_reservoir_parameter_file(
-                                    hybrid_params["reservoir_parameter_file"],
+        try:
+            waterbody_types_df = read_ngen_waterbody_type_df(
+                                    levelpool_params["reservoir_parameter_file"],
                                     lake_id,
                                     #self.waterbody_connections.values(),
                                     )
@@ -98,34 +99,12 @@ def build_hyfeature_network(supernetwork_parameters,
                                 .drop_duplicates(subset=lake_id)
                                 .set_index(lake_id)
                                 )
-        except:
-            waterbody_types_df = pd.DataFrame(index=waterbody_df.index)
-            waterbody_types_df['reservoir_type'] = 1
+
+        except ValueError:
             #FIXME any reservoir operations requires some type
             #So make this default to 1 (levelpool)
-            #At this point, need to adjust some waterbody/channel parameters based on lakes/reservoirs
-            #HACK for bad hydrofabric
-            def make_list(s):
-                if isinstance(s, list):
-                    return s
-                else:
-                    return [s]
-
-            waterbody_df['member_wbs'] = waterbody_df['member_wbs'].apply(make_list)
-            waterbody_df['partial_length_percent'] = waterbody_df['partial_length_percent'].apply(make_list)
-            adjust = [ zip(x, y) 
-                        for x, y in 
-                        zip(waterbody_df['member_wbs'], waterbody_df['partial_length_percent'])
-                    ]
-            #adjust is a generator of a list of list of tuples...use chain to flatten
-            for wb, percent in chain.from_iterable(adjust):
-                # FIXME not sure why some of these are 100%, if that  is the case
-                # shouldn't they just not be in the topology???
-                wb = node_key_func_wb(wb)
-                #Need to adjust waterbodys/channels that  interact with this waterbody
-                #Hack for wonky hydrofabric
-                if percent != 'NA':
-                    dataframe.loc[wb, 'dx'] = dataframe.loc[wb, 'dx'] - dataframe.loc[wb, 'dx']*float(percent)
+            waterbody_types_df = pd.DataFrame(index=waterbody_df.index)
+            waterbody_types_df['reservoir_type'] = 1        
               
     return (dataframe,           
             flowpath_dict,  
@@ -679,9 +658,7 @@ def _try_parsing_date(text):
     # That is because that is how they are used downstream. Need to
     # trace that back and decide if there is one of those two ways
     # that is optimal and make both returns that way.
-    
 
-    
 def hyfeature_forcing(
     run,
     forcing_parameters,
@@ -783,4 +760,47 @@ def hyfeature_forcing(
                 % (time.time() - start_time)
             )            
 
-    return qlats_df, coastal_boundary_depth_df
\ No newline at end of file
+    return qlats_df, coastal_boundary_depth_df
+
+def read_ngen_waterbody_df(parm_file, lake_index_field="wb-id", lake_id_mask=None):
+    """
+    Reads lake.json file and prepares a dataframe, filtered
+    to the relevant reservoirs, to provide the parameters
+    for level-pool reservoir computation.
+    """
+    def node_key_func(x):
+        return int(x[3:])
+    if os.path.splitext(parm_file)[1]=='.gpkg':
+        df = gpd.read_file(parm_file, layer="lake_attributes").set_index('id')
+    elif os.path.splitext(parm_file)[1]=='.json':
+        df = pd.read_json(parm_file, orient="index")
+
+    df.index = df.index.map(node_key_func)
+    df.index.name = lake_index_field
+    #df = df.set_index(lake_index_field, append=True).reset_index(level=0)
+    #df.rename(columns={'level_0':'wb-id'}, inplace=True)
+    if lake_id_mask:
+        df = df.loc[lake_id_mask]
+    return df
+
+def read_ngen_waterbody_type_df(parm_file, lake_index_field="wb-id", lake_id_mask=None):
+    """
+    """
+    #FIXME: this function is likely not correct. Unclear how we will get 
+    # reservoir type from the gpkg files. Information should be in 'crosswalk'
+    # layer, but as of now (Nov 22, 2022) there doesn't seem to be a differentiation
+    # between USGS reservoirs, USACE reservoirs, or RFC reservoirs...
+    def node_key_func(x):
+        return int(x[3:])
+    
+    if os.path.splitext(parm_file)[1]=='.gpkg':
+        df = gpd.read_file(parm_file, layer="crosswalk").set_index('id')
+    elif os.path.splitext(parm_file)[1]=='.json':
+        df = pd.read_json(parm_file, orient="index")
+
+    df.index = df.index.map(node_key_func)
+    df.index.name = lake_index_field
+    if lake_id_mask:
+        df = df.loc[lake_id_mask]
+        
+    return df
\ No newline at end of file
diff --git a/test/unit_test_hyfeature/unittest_hyfeature.yaml b/test/unit_test_hyfeature/unittest_hyfeature.yaml
index 151e4c36e..a74b827be 100644
--- a/test/unit_test_hyfeature/unittest_hyfeature.yaml
+++ b/test/unit_test_hyfeature/unittest_hyfeature.yaml
@@ -17,12 +17,13 @@ network_topology_parameters:
             #- 4800004
             #- 4800006
             #- 4800007
-    #waterbody_parameters:
+    waterbody_parameters:
         #----------
-        #break_network_at_waterbodies: False 
-        #level_pool:
+        break_network_at_waterbodies: False 
+        level_pool:
             #----------
-            #level_pool_waterbody_parameter_file_path: domain/LAKEPARM_NWMv2.1.nc 
+            level_pool_waterbody_parameter_file_path: domain/gauge_01069700.gpkg #domain/LAKEPARM_NWMv2.1.nc 
+            reservoir_parameter_file                : domain/gauge_01069700.gpkg #domain/reservoir_index_AnA.nc
         #rfc:
             #----------
             #reservoir_parameter_file                : domain/reservoir_index_AnA.nc

From b03bf627e73055d5bca5db9a97fa3cf07fe2d205 Mon Sep 17 00:00:00 2001
From: Dong Kim <donghakim@cheyenne4.cheyenne.ucar.edu>
Date: Tue, 29 Nov 2022 08:07:01 -0700
Subject: [PATCH 7/7] remove redundant line in nhd_io.py

---
 src/troute-network/troute/nhd_io.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/troute-network/troute/nhd_io.py b/src/troute-network/troute/nhd_io.py
index d7d344092..3515cd2d6 100644
--- a/src/troute-network/troute/nhd_io.py
+++ b/src/troute-network/troute/nhd_io.py
@@ -123,7 +123,6 @@ def read_config_file(custom_input_file):
         supernetwork_parameters["columns"]             = routelink_attr 
         supernetwork_parameters["waterbody_null_code"] = -9999
         supernetwork_parameters["terminal_code"]       =  0
-        supernetwork_parameters["waterbody_null_code"] = -9999
         supernetwork_parameters["driver_string"]       = "NetCDF"
         supernetwork_parameters["layer_string"]        = 0