Update tool names in landice framework and tests

compass/landice/mesh.py

@@ -688,22 +688,22 @@ def build_mali_mesh(self, cell_width, x1, y1, geom_points,
     logger.info('writing grid_converted.nc')
     write_netcdf(dsMesh, 'grid_converted.nc')
     levels = section.get('levels')
-    args = ['create_landice_grid_from_generic_MPAS_grid.py',
+    args = ['create_landice_grid_from_generic_mpas_grid',
             '-i', 'grid_converted.nc',
             '-o', 'grid_preCull.nc',
             '-l', levels, '-v', 'glimmer']
 
     check_call(args, logger=logger)
 
-    args = ['interpolate_to_mpasli_grid.py', '-s',
+    args = ['interpolate_to_mpasli_grid', '-s',
             gridded_dataset, '-d',
             'grid_preCull.nc', '-m', 'b', '-t']
 
     check_call(args, logger=logger)
 
     cullDistance = section.get('cull_distance')
     if float(cullDistance) > 0.:
-        args = ['define_cullMask.py', '-f',
+        args = ['define_landice_cull_mask', '-f',
                 'grid_preCull.nc', '-m',
                 'distance', '-d', cullDistance]
 
@@ -715,7 +715,7 @@ def build_mali_mesh(self, cell_width, x1, y1, geom_points,
     if geojson_file is not None:
         # This step is only necessary because the GeoJSON region
         # is defined by lat-lon.
-        args = ['set_lat_lon_fields_in_planar_grid.py', '-f',
+        args = ['set_lat_lon_fields_in_planar_grid', '-f',
                 'grid_preCull.nc', '-p', projection]
 
         check_call(args, logger=logger)
@@ -742,7 +742,7 @@ def build_mali_mesh(self, cell_width, x1, y1, geom_points,
     write_netcdf(dsMesh, 'culled.nc')
 
     logger.info('Marking horns for culling')
-    args = ['mark_horns_for_culling.py', '-f', 'culled.nc']
+    args = ['mark_horns_for_culling', '-f', 'culled.nc']
 
     check_call(args, logger=logger)
 
@@ -753,24 +753,24 @@ def build_mali_mesh(self, cell_width, x1, y1, geom_points,
     dsMesh = sort_mesh(dsMesh)
     write_netcdf(dsMesh, 'dehorned.nc')
 
-    args = ['create_landice_grid_from_generic_MPAS_grid.py', '-i',
+    args = ['create_landice_grid_from_generic_mpas_grid', '-i',
             'dehorned.nc', '-o',
             mesh_name, '-l', levels, '-v', 'glimmer',
             '--beta', '--thermal', '--obs', '--diri']
 
     check_call(args, logger=logger)
 
-    args = ['interpolate_to_mpasli_grid.py', '-s',
+    args = ['interpolate_to_mpasli_grid', '-s',
             gridded_dataset, '-d', mesh_name, '-m', 'b']
 
     check_call(args, logger=logger)
 
     logger.info('Marking domain boundaries dirichlet')
-    args = ['mark_domain_boundaries_dirichlet.py',
+    args = ['mark_domain_boundaries_dirichlet',
             '-f', mesh_name]
     check_call(args, logger=logger)
 
-    args = ['set_lat_lon_fields_in_planar_grid.py', '-f',
+    args = ['set_lat_lon_fields_in_planar_grid', '-f',
             mesh_name, '-p', projection]
     check_call(args, logger=logger)
 
@@ -1061,7 +1061,7 @@ def __guess_scrip_name(filename):
 
     logger.info('creating scrip file for source dataset')
     # Note: writing scrip file to workdir
-    args = ['create_SCRIP_file_from_planar_rectangular_grid.py',
+    args = ['create_scrip_file_from_planar_rectangular_grid',
             '-i', source_file,
             '-s', source_scrip,
             '-p', proj,
@@ -1080,8 +1080,8 @@ def __guess_scrip_name(filename):
     check_call(args, logger=logger)
 
     # Perform actual interpolation using the weights
-    logger.info('calling interpolate_to_mpasli_grid.py')
-    args = ['interpolate_to_mpasli_grid.py',
+    logger.info('calling interpolate_to_mpasli_grid')
+    args = ['interpolate_to_mpasli_grid',
             '-s', source_file,
             '-d', dest_file,
             '-m', 'e',

compass/landice/tests/antarctica/mesh.py

@@ -120,8 +120,8 @@ def run(self):
         #       Also, it should be assessed if bilinear or
         #       barycentric used here is preferred for this application.
         #       Current thinking is they are both equally appropriate.
-        logger.info('calling interpolate_to_mpasli_grid.py')
-        args = ['interpolate_to_mpasli_grid.py', '-s',
+        logger.info('calling interpolate_to_mpasli_grid')
+        args = ['interpolate_to_mpasli_grid', '-s',
                 preprocessed_gridded_dataset,
                 '-d',
                 self.mesh_filename,

compass/landice/tests/antarctica/mesh_gen/mesh_gen.cfg

@@ -61,7 +61,7 @@ bedmachine_filename = BedMachineAntarctica_2020-07-15_v02_edits_floodFill_extrap
 measures_filename = antarctica_ice_velocity_450m_v2_edits_extrap.nc
 
 # projection of the source datasets, according to the dictionary keys
-# create_SCRIP_file_from_planar_rectangular_grid.py from MPAS_Tools
+# create_scrip_file_from_planar_rectangular_grid from MPAS_Tools
 src_proj = ais-bedmap2
 
 # number of processors to use for ESMF_RegridWeightGen

compass/landice/tests/circular_shelf/setup_mesh.py

@@ -1,10 +1,9 @@
 import numpy
-from netCDF4 import Dataset as NetCDFFile
-
-from mpas_tools.planar_hex import make_planar_hex_mesh
 from mpas_tools.io import write_netcdf
-from mpas_tools.mesh.conversion import convert, cull
 from mpas_tools.logging import check_call
+from mpas_tools.mesh.conversion import convert, cull
+from mpas_tools.planar_hex import make_planar_hex_mesh
+from netCDF4 import Dataset as NetCDFFile
 
 from compass.model import make_graph_file
 from compass.step import Step
@@ -60,7 +59,7 @@ def run(self):
         write_netcdf(dsMesh, 'mpas_grid.nc')
 
         levels = section.get('levels')
-        args = ['create_landice_grid_from_generic_MPAS_grid.py',
+        args = ['create_landice_grid_from_generic_mpas_grid',
                 '-i', 'mpas_grid.nc',
                 '-o', 'landice_grid.nc',
                 '-l', levels,

compass/landice/tests/dome/setup_mesh.py

@@ -1,10 +1,9 @@
 import numpy
-from netCDF4 import Dataset as NetCDFFile
-
-from mpas_tools.planar_hex import make_planar_hex_mesh
 from mpas_tools.io import write_netcdf
-from mpas_tools.mesh.conversion import convert, cull
 from mpas_tools.logging import check_call
+from mpas_tools.mesh.conversion import convert, cull
+from mpas_tools.planar_hex import make_planar_hex_mesh
+from netCDF4 import Dataset as NetCDFFile
 
 from compass.model import make_graph_file
 from compass.step import Step
@@ -71,7 +70,7 @@ def run(self):
             write_netcdf(dsMesh, 'mpas_grid.nc')
 
         levels = section.get('levels')
-        args = ['create_landice_grid_from_generic_MPAS_grid.py',
+        args = ['create_landice_grid_from_generic_mpas_grid',
                 '-i', 'mpas_grid.nc',
                 '-o', 'landice_grid.nc',
                 '-l', levels]
@@ -158,7 +157,7 @@ def _setup_dome_initial_conditions(config, logger, filename):
         thickness_field[r < r0] = h0 * (1.0 - (r[r < r0] / r0) ** 2) ** 0.5
     elif dome_type == 'halfar':
         thickness_field[r < r0] = h0 * (
-                    1.0 - (r[r < r0] / r0) ** (4.0 / 3.0)) ** (3.0 / 7.0)
+            1.0 - (r[r < r0] / r0) ** (4.0 / 3.0)) ** (3.0 / 7.0)
     else:
         raise ValueError('Unexpected dome_type: {}'.format(dome_type))
     thickness[0, :] = thickness_field

compass/landice/tests/eismint2/setup_mesh.py

@@ -1,9 +1,8 @@
 import xarray
-
-from mpas_tools.planar_hex import make_planar_hex_mesh
 from mpas_tools.io import write_netcdf
-from mpas_tools.mesh.conversion import convert, cull
 from mpas_tools.logging import check_call
+from mpas_tools.mesh.conversion import convert, cull
+from mpas_tools.planar_hex import make_planar_hex_mesh
 
 from compass.model import make_graph_file
 from compass.step import Step
@@ -48,7 +47,7 @@ def run(self):
         dsMesh.close()
 
         radius = section.get('radius')
-        args = ['define_cullMask.py',
+        args = ['define_landice_cull_mask',
                 '-f', 'mpas_grid.nc',
                 '-m', 'radius',
                 '-d', radius]
@@ -61,7 +60,7 @@ def run(self):
         write_netcdf(dsMesh, 'mpas_grid2.nc')
 
         levels = section.get('levels')
-        args = ['create_landice_grid_from_generic_MPAS_grid.py',
+        args = ['create_landice_grid_from_generic_mpas_grid',
                 '-i', 'mpas_grid2.nc',
                 '-o', 'landice_grid.nc',
                 '-l', levels,

compass/landice/tests/enthalpy_benchmark/setup_mesh.py

@@ -1,9 +1,8 @@
-from netCDF4 import Dataset as NetCDFFile
-
-from mpas_tools.planar_hex import make_planar_hex_mesh
 from mpas_tools.io import write_netcdf
-from mpas_tools.mesh.conversion import convert, cull
 from mpas_tools.logging import check_call
+from mpas_tools.mesh.conversion import convert, cull
+from mpas_tools.planar_hex import make_planar_hex_mesh
+from netCDF4 import Dataset as NetCDFFile
 
 from compass.model import make_graph_file
 from compass.step import Step
@@ -49,7 +48,7 @@ def run(self):
         dsMesh = convert(dsMesh, logger=logger)
         write_netcdf(dsMesh, 'mpas_grid.nc')
 
-        args = ['create_landice_grid_from_generic_MPAS_grid.py',
+        args = ['create_landice_grid_from_generic_mpas_grid',
                 '-i', 'mpas_grid.nc',
                 '-o', 'landice_grid.nc',
                 '-l', levels,

compass/landice/tests/greenland/mesh_gen/mesh_gen.cfg

@@ -62,7 +62,7 @@ bedmachine_filename = BedMachineGreenland-v5_edits_floodFill_extrap.nc
 measures_filename = greenland_vel_mosaic500_extrap.nc
 
 # projection of the source datasets, according to the dictionary keys
-# create_SCRIP_file_from_planar_rectangular_grid.py from MPAS_Tools
+# create_scrip_file_from_planar_rectangular_grid from MPAS_Tools
 src_proj = gis-gimp
 
 # number of processors to use for ESMF_RegridWeightGen

compass/landice/tests/hydro_radial/setup_mesh.py

@@ -1,10 +1,9 @@
 import numpy as np
-from netCDF4 import Dataset as NetCDFFile
-
-from mpas_tools.planar_hex import make_planar_hex_mesh
 from mpas_tools.io import write_netcdf
-from mpas_tools.mesh.conversion import convert, cull
 from mpas_tools.logging import check_call
+from mpas_tools.mesh.conversion import convert, cull
+from mpas_tools.planar_hex import make_planar_hex_mesh
+from netCDF4 import Dataset as NetCDFFile
 
 from compass.model import make_graph_file
 from compass.step import Step
@@ -72,7 +71,7 @@ def run(self):
         write_netcdf(dsMesh, 'mpas_grid.nc')
 
         levels = section.get('levels')
-        args = ['create_landice_grid_from_generic_MPAS_grid.py',
+        args = ['create_landice_grid_from_generic_mpas_grid',
                 '-i', 'mpas_grid.nc',
                 '-o', 'landice_grid.nc',
                 '-l', levels,

compass/landice/tests/ismip6_forcing/create_mapfile.py

@@ -73,7 +73,7 @@ def build_mapping_file(config, cores, logger, ismip6_grid_file, mapping_file,
     if scrip_from_latlon:
         create_scrip_from_latlon(ismip6_grid_file, source_grid_scripfile)
     else:
-        args = ["create_SCRIP_file_from_planar_rectangular_grid.py",
+        args = ["create_scrip_file_from_planar_rectangular_grid",
                 "--input", ismip6_grid_file,
                 "--scrip", source_grid_scripfile,
                 "--proj", ismip6_projection,
@@ -89,7 +89,7 @@ def build_mapping_file(config, cores, logger, ismip6_grid_file, mapping_file,
     mali_mesh_copy = f"{mali_mesh_file}_copy"
     shutil.copy(mali_mesh_file, f"{mali_mesh_file}_copy")
 
-    args = ["set_lat_lon_fields_in_planar_grid.py",
+    args = ["set_lat_lon_fields_in_planar_grid",
             "--file", mali_mesh_copy,
             "--proj", ismip6_projection]
 
@@ -133,7 +133,7 @@ def create_scrip_from_latlon(source_grid_file, source_grid_scripfile):
     dataset.
 
     This function is needed, c.f. the scrip utility in the MPAS-Tools repo
-    (i.e. `create_SCRIP_file_from_planar_rectangular_grid.py`), when a dataset
+    (i.e. `create_scrip_file_from_planar_rectangular_grid`), when a dataset
     does not have `x`/`y` coordinates to generate the scrip file from. This is
     the case for the atmospheric forcing datasets from ISMIP6
     and for RACMO products.

compass/landice/tests/ismip6_run/ismip6_ais_proj2300/create_slm_mapping_files.py

@@ -73,14 +73,14 @@ def _build_mapping_files(self, config, logger):
         args = ['ncremap',
                 '-g', slm_scripfile,
                 '-G',
-                f'latlon={nglv},{2*int(nglv)}#lat_typ=gss#lat_drc=n2s']
+                f'latlon={nglv},{2 * int(nglv)}#lat_typ=gss#lat_drc=n2s']
 
         check_call(args, logger=logger)
 
         # mali scripfile
         # first have to adjust lat-lon values as if they are on sphere
         shutil.copy(init_cond_path, mali_meshfile)
-        args = ['set_lat_lon_fields_in_planar_grid.py',
+        args = ['set_lat_lon_fields_in_planar_grid',
                 '--file', mali_meshfile,
                 '--proj', 'ais-bedmap2-sphere']
 

compass/landice/tests/mesh_modifications/subdomain_extractor/extract_region.py

@@ -144,7 +144,7 @@ def run(self):
 
         # mark horns for culling
         logger.info('Marking horns for culling')
-        args = ['mark_horns_for_culling.py', '-f',
+        args = ['mark_horns_for_culling', '-f',
                 os.path.join(tmpdir, f'{source_file_rootname}_culled.nc')]
         check_call(args, logger=logger)
 
@@ -158,8 +158,8 @@ def run(self):
         write_netcdf(ds_out, dest_mesh_only_name)
 
         # set lat/lon
-        logger.info('calling set_lat_lon_fields_in_planar_grid.py')
-        args = ['set_lat_lon_fields_in_planar_grid.py',
+        logger.info('calling set_lat_lon_fields_in_planar_grid')
+        args = ['set_lat_lon_fields_in_planar_grid',
                 '-f', dest_mesh_only_name, '-p', mesh_projection]
         check_call(args, logger=logger)
 
@@ -206,8 +206,8 @@ def run(self):
 
         elif interp_method == 'mali_interp':
             # create landice mesh
-            logger.info('calling create_landice_grid_from_generic_MPAS_grid.py')  # noqa
-            args = ['create_landice_grid_from_generic_MPAS_grid.py',
+            logger.info('calling create_landice_grid_from_generic_mpas_grid')  # noqa
+            args = ['create_landice_grid_from_generic_mpas_grid',
                     '-i', os.path.join(tmpdir, 'dest_mesh_only.nc'),
                     '-o', dest_file_name,
                     '-l', f'{levels}', '-v', 'glimmer',
@@ -216,8 +216,8 @@ def run(self):
 
             # interpolate to new mesh using nearest neighbor to ensure we get
             # identical values
-            logger.info('calling interpolate_to_mpasli_grid.py')
-            args = ['interpolate_to_mpasli_grid.py',
+            logger.info('calling interpolate_to_mpasli_grid')
+            args = ['interpolate_to_mpasli_grid',
                     '-s', source_file_path,
                     '-d', dest_file_name, '-m', 'n']
             check_call(args, logger=logger)
@@ -226,7 +226,7 @@ def run(self):
 
         # mark Dirichlet boundaries
         logger.info('Marking domain boundaries dirichlet')
-        args = ['mark_domain_boundaries_dirichlet.py',
+        args = ['mark_domain_boundaries_dirichlet',
                 '-f', dest_file_name]
         check_call(args, logger=logger)
 

compass/landice/tests/mesh_modifications/subdomain_extractor/subdomain_extractor.cfg

@@ -42,7 +42,7 @@ grow_iters = 15
 # nstd weight file and then uses ncremap to perform remapping.
 # This method supports interpolating ancillary files (below)
 # but likely needs to be run on a compute node and is more fragile.
-# 'mali_interp' uses the MALI interpolation script interpolate_to_mpasli_grid.py
+# 'mali_interp' uses the MALI interpolation script interpolate_to_mpasli_grid
 # This method does not support ancillary files but may be more robust
 # and can likely be run quickly on a login node.
 interp_method = ncremap

compass/landice/tests/mismipplus/setup_mesh.py

@@ -119,7 +119,7 @@ def run(self):
         levels = section.get('levels')
         vertMethod = section.get('vetical_layer_distribution')
 
-        args = ['create_landice_grid_from_generic_MPAS_grid.py',
+        args = ['create_landice_grid_from_generic_mpas_grid',
                 '-i', 'mpas_grid.nc',
                 '-o', 'landice_grid.nc',
                 '-l', levels,