Adapt wrfchem to new plugin type datastream and renaming of flux from plural...

Adapt wrfchem to new plugin type datastream and renaming of flux from plural 'fluxes' to singular 'flux'

pycif/plugins/datastreams/fluxes/wrfchem/read.py

@@ -37,10 +37,10 @@ def read(
         For each in_dates, the file where the flux is found
     comp_type: string
         Name of component in yaml, i.e. level above parameter.
-        Currently "fluxes" in my config_wrfchem_explanations.yml.
+        Currently "flux" in my config_wrfchem_explanations.yml.
         Probably won't use it.
-    tracer : Plugin fluxes
-        Full fluxes object, with everything in the yaml. Use this
+    tracer : Plugin flux
+        Full flux object, with everything in the yaml. Use this
         instead of the self in read.py because that self can be
         modified. Same with write.
     model:  model plugin

pycif/plugins/models/wrfchem/__init__.py

@@ -52,7 +52,7 @@ requirements = {
     },
     
     # Used for both reading and writing fluxes
-    "fluxes": {
+    "flux": {
         "name": "wrfchem",
         "version": "std",
         "empty": False,
@@ -65,7 +65,8 @@ requirements = {
     "latcond": {
         "name": "wrfchem",
         "version": "icbc",
-        "type": "fields",
+        "type": "datastream",
+        "subtype": "field",
         "empty": True,
         "any": False,
         "newplg": True,
@@ -74,7 +75,8 @@ requirements = {
     "inicond": {
         "name": "wrfchem",
         "version": "icbc",
-        "type": "fields",
+        "type": "datastream",
+        "subtype": "field",
         "empty": True,
         "any": False,
         "newplg": True,
@@ -91,7 +93,7 @@ input_arguments = {
                "are already present in run_dir are skipped.\n"+ \
                "namelist.input is copied separately from path " + \
                "specified in argument namelist_input_file." + \
-               "Flux files are handled by the fluxes plugin.",
+               "Flux files are handled by the flux plugin.",
         "default": None,
         "accepted": str
     },

pycif/plugins/models/wrfchem/ini_mapper.py

@@ -99,7 +99,7 @@ def ini_mapper(model, transform_type, general_mapper={}, backup_comps={},
     )
 
     emis = {
-        ("fluxes", s): dict_fluxes
+        ("flux", s): dict_fluxes
         for s in model.chemistry.emis_species.attributes
     }
     mapper["inputs"].update(emis)

pycif/plugins/models/wrfchem/io/inputs/make_fluxes.py

@@ -17,7 +17,7 @@ def make_fluxes(self, datastore, runsubdir, datei, datef, mode):
     """Write fluxes to existing WRF flux input files
 
     Args:
-        self (pycif.utils.classes.Fluxes.fluxes): Flux plugin with all
+        self (pycif.utils.classes.fluxes.Flux): Flux plugin with all
                     attributes
         datastore (dict): information on flux species
         runsubdir (str): directory to the current run
@@ -36,7 +36,7 @@ def make_fluxes(self, datastore, runsubdir, datei, datef, mode):
         trid: datastore[trid]
         for trid in datastore
         # if trid[0] in ["fluxes", "biofluxes"] # original
-        if trid[0] in ["fluxes"]
+        if trid[0] in ["flux"]
     }
     
     # List of dates for which emissions are needed
@@ -49,7 +49,7 @@ def make_fluxes(self, datastore, runsubdir, datei, datef, mode):
     # Loop on all anthropogenic and biogenic species
     # If in datastore, take data, otherwise, link to original A/B EMISSIONS
     # freum: again, no biofluxes
-    list_trid = [("fluxes", spec)
+    list_trid = [("flux", spec)
                  for spec in self.chemistry.emis_species.attributes] #\
     #     + [("biofluxes", spec)
     #        for spec in self.chemistry.bio_species.attributes]
@@ -58,7 +58,7 @@ def make_fluxes(self, datastore, runsubdir, datei, datef, mode):
         emis_type = trid[0]
         # freum: again, no biofluxes
         # flx_plg = self.fluxes if emis_type == "fluxes" else self.biofluxes
-        flx_plg = self.fluxes
+        flx_plg = self.flux
         # freum 2021-11-02: According to Antoine, can only use flx_plg
         # to access methods, not parameters in the yaml. Full plugin
         # with access to parameters in yaml would be: tracer["tracer"].

pycif/plugins/models/wrfchem/io/native2inputs.py

@@ -27,9 +27,9 @@ def native2inputs(
 
     Args:
         self: the model Plugin
-        input_type (str): one of 'fluxes', 'obs'
+        input_type (str): one of 'flux', 'obs'
         datastore: data to convert
-            if input_type == 'fluxes', a dictionary with flux maps
+            if input_type == 'flux', a dictionary with flux maps
             if input_type == 'obs', a pandas dataframe with the observations
         datei, datef: date interval of the sub-simulation
         mode (str): running mode: one of 'fwd', 'adj' and 'tl'
@@ -60,7 +60,7 @@ def native2inputs(
     if not do_simu:
         return
     
-    if input_type == "fluxes":
+    if input_type == "flux":
         # msg = "Implement fluxes here"
         # logging.info(msg)
         # pass