Address pre-commit issues

E3SM-Project · Oct 16, 2024 · 037a248 · 037a248
1 parent aaed0ed
commit 037a248
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Showing 34 changed files with 7,587 additions and 7,224 deletions.
diff --git a/e3sm_to_cmip/cmor_handlers/mpas_vars/mlotst.py b/e3sm_to_cmip/cmor_handlers/mpas_vars/mlotst.py
@@ -1,21 +1,23 @@
-
 """
 compute Ocean Mixed Layer Thickness Defined by Sigma T, mlotst
 """
+
 from __future__ import absolute_import, division, print_function
 
-import xarray
 import logging
 
+import xarray
+
 from e3sm_to_cmip import mpas, util
 from e3sm_to_cmip.util import print_message
+
 # 'MPAS' as a placeholder for raw variables needed
-RAW_VARIABLES = ['MPASO', 'MPAS_mesh', 'MPAS_map']
+RAW_VARIABLES = ["MPASO", "MPAS_mesh", "MPAS_map"]
 
 # output variable name
-VAR_NAME = 'mlotst'
-VAR_UNITS = 'm'
-TABLE = 'CMIP6_Omon.json'
+VAR_NAME = "mlotst"
+VAR_UNITS = "m"
+TABLE = "CMIP6_Omon.json"
 
 
 def handle(infiles, tables, user_input_path, **kwargs):
@@ -38,23 +40,26 @@ def handle(infiles, tables, user_input_path, **kwargs):
     varname : str
         the name of the processed variable after processing is complete
     """
-    if kwargs.get('simple'):
+    if kwargs.get("simple"):
         msg = f"{VAR_NAME} is not supported for simple conversion"
         print_message(msg)
         return
-        
-    msg = 'Starting {name}'.format(name=__name__)
+
+    msg = "Starting {name}".format(name=__name__)
     logging.info(msg)
 
-    meshFileName = infiles['MPAS_mesh']
-    mappingFileName = infiles['MPAS_map']
-    timeSeriesFiles = infiles['MPASO']
+    meshFileName = infiles["MPAS_mesh"]
+    mappingFileName = infiles["MPAS_map"]
+    timeSeriesFiles = infiles["MPASO"]
 
     dsMesh = xarray.open_dataset(meshFileName, mask_and_scale=False)
     cellMask2D, _ = mpas.get_mpaso_cell_masks(dsMesh)
 
-    variableList = ['timeMonthly_avg_dThreshMLD',
-                    'xtime_startMonthly', 'xtime_endMonthly']
+    variableList = [
+        "timeMonthly_avg_dThreshMLD",
+        "xtime_startMonthly",
+        "xtime_endMonthly",
+    ]
 
     ds = xarray.Dataset()
     with mpas.open_mfdataset(timeSeriesFiles, variableList) as dsIn:
@@ -64,22 +69,31 @@ def handle(infiles, tables, user_input_path, **kwargs):
         ds.compute()
 
     ds = mpas.add_mask(ds, cellMask2D)
-    ds = mpas.remap(ds, 'mpasocean', mappingFileName)
+    ds = mpas.remap(ds, "mpasocean", mappingFileName)
 
-    util.setup_cmor(var_name=VAR_NAME, table_path=tables, table_name=TABLE,
-            user_input_path=user_input_path)
+    util.setup_cmor(
+        var_name=VAR_NAME,
+        table_path=tables,
+        table_name=TABLE,
+        user_input_path=user_input_path,
+    )
 
     # create axes
-    axes = [{'table_entry': 'time',
-             'units': ds.time.units},
-            {'table_entry': 'latitude',
-             'units': 'degrees_north',
-             'coord_vals': ds.lat.values,
-             'cell_bounds': ds.lat_bnds.values},
-            {'table_entry': 'longitude',
-             'units': 'degrees_east',
-             'coord_vals': ds.lon.values,
-             'cell_bounds': ds.lon_bnds.values}]
+    axes = [
+        {"table_entry": "time", "units": ds.time.units},
+        {
+            "table_entry": "latitude",
+            "units": "degrees_north",
+            "coord_vals": ds.lat.values,
+            "cell_bounds": ds.lat_bnds.values,
+        },
+        {
+            "table_entry": "longitude",
+            "units": "degrees_east",
+            "coord_vals": ds.lon.values,
+            "cell_bounds": ds.lon_bnds.values,
+        },
+    ]
     try:
         mpas.write_cmor(axes, ds, VAR_NAME, VAR_UNITS)
     except Exception:

diff --git a/e3sm_to_cmip/cmor_handlers/mpas_vars/pbo.py b/e3sm_to_cmip/cmor_handlers/mpas_vars/pbo.py
@@ -1,21 +1,23 @@
-
 """
 compute Sea Water Pressure at Sea floor, pbo
 """
+
 from __future__ import absolute_import, division, print_function
 
-import xarray
 import logging
 
+import xarray
+
 from e3sm_to_cmip import mpas, util
 from e3sm_to_cmip.util import print_message
+
 # 'MPAS' as a placeholder for raw variables needed
-RAW_VARIABLES = ['MPASO', 'MPASO_namelist', 'MPAS_mesh', 'MPAS_map', 'PSL']
+RAW_VARIABLES = ["MPASO", "MPASO_namelist", "MPAS_mesh", "MPAS_map", "PSL"]
 
 # output variable name
-VAR_NAME = 'pbo'
-VAR_UNITS = 'Pa'
-TABLE = 'CMIP6_Omon.json'
+VAR_NAME = "pbo"
+VAR_UNITS = "Pa"
+TABLE = "CMIP6_Omon.json"
 
 
 def handle(infiles, tables, user_input_path, **kwargs):
@@ -40,64 +42,78 @@ def handle(infiles, tables, user_input_path, **kwargs):
     varname : str
         the name of the processed variable after processing is complete
     """
-    if kwargs.get('simple'):
+    if kwargs.get("simple"):
         msg = f"{VAR_NAME} is not supported for simple conversion"
         print_message(msg)
         return
-        
-    msg = 'Starting {name}'.format(name=__name__)
+
+    msg = "Starting {name}".format(name=__name__)
     logging.info(msg)
 
-    namelistFileName = infiles['MPASO_namelist']
-    meshFileName = infiles['MPAS_mesh']
-    mappingFileName = infiles['MPAS_map']
-    timeSeriesFiles = infiles['MPASO']
-    pslFileNames = infiles['PSL']
+    namelistFileName = infiles["MPASO_namelist"]
+    meshFileName = infiles["MPAS_mesh"]
+    mappingFileName = infiles["MPAS_map"]
+    timeSeriesFiles = infiles["MPASO"]
+    pslFileNames = infiles["PSL"]
 
     namelist = mpas.convert_namelist_to_dict(namelistFileName)
-    config_density0 = float(namelist['config_density0'])
+    config_density0 = float(namelist["config_density0"])
     gravity = 9.80616
 
     dsMesh = xarray.open_dataset(meshFileName, mask_and_scale=False)
     cellMask2D, cellMask3D = mpas.get_mpaso_cell_masks(dsMesh)
 
-    variableList = ['timeMonthly_avg_pressureAdjustedSSH',
-                    'timeMonthly_avg_ssh', 'timeMonthly_avg_layerThickness',
-                    'timeMonthly_avg_density', 'xtime_startMonthly',
-                    'xtime_endMonthly']
+    variableList = [
+        "timeMonthly_avg_pressureAdjustedSSH",
+        "timeMonthly_avg_ssh",
+        "timeMonthly_avg_layerThickness",
+        "timeMonthly_avg_density",
+        "xtime_startMonthly",
+        "xtime_endMonthly",
+    ]
 
     ds = xarray.Dataset()
     with mpas.open_mfdataset(timeSeriesFiles, variableList) as dsIn:
-        seaIcePressure = config_density0 * gravity * \
-            (dsIn.timeMonthly_avg_pressureAdjustedSSH -
-             dsIn.timeMonthly_avg_ssh)
-        ds[VAR_NAME] = seaIcePressure.where(cellMask2D) + gravity * \
-            (dsIn.timeMonthly_avg_density *
-             dsIn.timeMonthly_avg_layerThickness).where(cellMask3D).sum(
-                dim='nVertLevels')
+        seaIcePressure = (
+            config_density0
+            * gravity
+            * (dsIn.timeMonthly_avg_pressureAdjustedSSH - dsIn.timeMonthly_avg_ssh)
+        )
+        ds[VAR_NAME] = seaIcePressure.where(cellMask2D) + gravity * (
+            dsIn.timeMonthly_avg_density * dsIn.timeMonthly_avg_layerThickness
+        ).where(cellMask3D).sum(dim="nVertLevels")
 
         ds = mpas.add_time(ds, dsIn)
         ds.compute()
 
-    ds = mpas.remap(ds, 'mpasocean', mappingFileName)
+    ds = mpas.remap(ds, "mpasocean", mappingFileName)
 
-    with xarray.open_mfdataset(pslFileNames, concat_dim='time') as dsIn:
+    with xarray.open_mfdataset(pslFileNames, concat_dim="time") as dsIn:
         ds[VAR_NAME] = ds[VAR_NAME] + dsIn.PSL.values
 
-    util.setup_cmor(var_name=VAR_NAME, table_path=tables, table_name=TABLE,
-            user_input_path=user_input_path)
+    util.setup_cmor(
+        var_name=VAR_NAME,
+        table_path=tables,
+        table_name=TABLE,
+        user_input_path=user_input_path,
+    )
 
     # create axes
-    axes = [{'table_entry': 'time',
-             'units': ds.time.units},
-            {'table_entry': 'latitude',
-             'units': 'degrees_north',
-             'coord_vals': ds.lat.values,
-             'cell_bounds': ds.lat_bnds.values},
-            {'table_entry': 'longitude',
-             'units': 'degrees_east',
-             'coord_vals': ds.lon.values,
-             'cell_bounds': ds.lon_bnds.values}]
+    axes = [
+        {"table_entry": "time", "units": ds.time.units},
+        {
+            "table_entry": "latitude",
+            "units": "degrees_north",
+            "coord_vals": ds.lat.values,
+            "cell_bounds": ds.lat_bnds.values,
+        },
+        {
+            "table_entry": "longitude",
+            "units": "degrees_east",
+            "coord_vals": ds.lon.values,
+            "cell_bounds": ds.lon_bnds.values,
+        },
+    ]
     try:
         mpas.write_cmor(axes, ds, VAR_NAME, VAR_UNITS)
     except Exception:

diff --git a/e3sm_to_cmip/cmor_handlers/mpas_vars/pso.py b/e3sm_to_cmip/cmor_handlers/mpas_vars/pso.py
@@ -1,21 +1,23 @@
-
 """
 compute Sea Water Pressure at Sea Water Surface, pso
 """
+
 from __future__ import absolute_import, division, print_function
 
-import xarray
 import logging
 
+import xarray
+
 from e3sm_to_cmip import mpas, util
 from e3sm_to_cmip.util import print_message
+
 # 'MPAS' as a placeholder for raw variables needed
-RAW_VARIABLES = ['MPASO', 'MPASO_namelist', 'MPAS_mesh', 'MPAS_map', 'PSL']
+RAW_VARIABLES = ["MPASO", "MPASO_namelist", "MPAS_mesh", "MPAS_map", "PSL"]
 
 # output variable name
-VAR_NAME = 'pso'
-VAR_UNITS = 'Pa'
-TABLE = 'CMIP6_Omon.json'
+VAR_NAME = "pso"
+VAR_UNITS = "Pa"
+TABLE = "CMIP6_Omon.json"
 
 
 def handle(infiles, tables, user_input_path, **kwargs):
@@ -39,61 +41,76 @@ def handle(infiles, tables, user_input_path, **kwargs):
     varname : str
         the name of the processed variable after processing is complete
     """
-    if kwargs.get('simple'):
+    if kwargs.get("simple"):
         msg = f"{VAR_NAME} is not supported for simple conversion"
         print_message(msg)
         return
-        
-    msg = 'Starting {name}'.format(name=__name__)
+
+    msg = "Starting {name}".format(name=__name__)
     logging.info(msg)
 
-    namelistFileName = infiles['MPASO_namelist']
-    meshFileName = infiles['MPAS_mesh']
-    mappingFileName = infiles['MPAS_map']
-    timeSeriesFiles = infiles['MPASO']
-    pslFileNames = infiles['PSL']
+    namelistFileName = infiles["MPASO_namelist"]
+    meshFileName = infiles["MPAS_mesh"]
+    mappingFileName = infiles["MPAS_map"]
+    timeSeriesFiles = infiles["MPASO"]
+    pslFileNames = infiles["PSL"]
 
     namelist = mpas.convert_namelist_to_dict(namelistFileName)
-    config_density0 = float(namelist['config_density0'])
+    config_density0 = float(namelist["config_density0"])
     gravity = 9.80616
 
     dsMesh = xarray.open_dataset(meshFileName, mask_and_scale=False)
     cellMask2D, cellMask3D = mpas.get_mpaso_cell_masks(dsMesh)
 
-    variableList = ['timeMonthly_avg_pressureAdjustedSSH',
-                    'timeMonthly_avg_ssh', 'timeMonthly_avg_layerThickness',
-                    'timeMonthly_avg_density', 'xtime_startMonthly',
-                    'xtime_endMonthly']
+    variableList = [
+        "timeMonthly_avg_pressureAdjustedSSH",
+        "timeMonthly_avg_ssh",
+        "timeMonthly_avg_layerThickness",
+        "timeMonthly_avg_density",
+        "xtime_startMonthly",
+        "xtime_endMonthly",
+    ]
 
     ds = xarray.Dataset()
     with mpas.open_mfdataset(timeSeriesFiles, variableList) as dsIn:
-        seaIcePressure = config_density0 * gravity * \
-            (dsIn.timeMonthly_avg_pressureAdjustedSSH -
-             dsIn.timeMonthly_avg_ssh)
+        seaIcePressure = (
+            config_density0
+            * gravity
+            * (dsIn.timeMonthly_avg_pressureAdjustedSSH - dsIn.timeMonthly_avg_ssh)
+        )
         ds[VAR_NAME] = seaIcePressure.where(cellMask2D)
 
         ds = mpas.add_time(ds, dsIn)
         ds.compute()
 
-    ds = mpas.remap(ds, 'mpasocean', mappingFileName)
+    ds = mpas.remap(ds, "mpasocean", mappingFileName)
 
-    with xarray.open_mfdataset(pslFileNames, concat_dim='time') as dsIn:
+    with xarray.open_mfdataset(pslFileNames, concat_dim="time") as dsIn:
         ds[VAR_NAME] = ds[VAR_NAME] + dsIn.PSL.values
 
-    util.setup_cmor(var_name=VAR_NAME, table_path=tables, table_name=TABLE,
-            user_input_path=user_input_path)
+    util.setup_cmor(
+        var_name=VAR_NAME,
+        table_path=tables,
+        table_name=TABLE,
+        user_input_path=user_input_path,
+    )
 
     # create axes
-    axes = [{'table_entry': 'time',
-             'units': ds.time.units},
-            {'table_entry': 'latitude',
-             'units': 'degrees_north',
-             'coord_vals': ds.lat.values,
-             'cell_bounds': ds.lat_bnds.values},
-            {'table_entry': 'longitude',
-             'units': 'degrees_east',
-             'coord_vals': ds.lon.values,
-             'cell_bounds': ds.lon_bnds.values}]
+    axes = [
+        {"table_entry": "time", "units": ds.time.units},
+        {
+            "table_entry": "latitude",
+            "units": "degrees_north",
+            "coord_vals": ds.lat.values,
+            "cell_bounds": ds.lat_bnds.values,
+        },
+        {
+            "table_entry": "longitude",
+            "units": "degrees_east",
+            "coord_vals": ds.lon.values,
+            "cell_bounds": ds.lon_bnds.values,
+        },
+    ]
     try:
         mpas.write_cmor(axes, ds, VAR_NAME, VAR_UNITS)
     except Exception: