Merge pull request #881 from xylar/update-to-1.7.0-alpha.2

Update to 1.7.0 alpha.2

Author: xylar

.github/workflows/gis_coarse_meshgen.yml

@@ -8,8 +8,8 @@ on:
     - compass/landice/tests/greenland/mesh.py
 
 jobs:
-  setup_and_run_job:
-    name: setup_and_run_job
+  gis-coarse-meshgen:
+    name: GIS Coarse Mesh Generation
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
@@ -23,10 +23,10 @@ jobs:
           pushd compass
 
           # create the compass environment
-          ./conda/configure_compass_env.py --conda $root/mambaForge --mpi mpich
+          ./conda/configure_compass_env.py --conda $root/mambaForge --env_name compass_test --mpi mpich
 
           # enable the compass environment
-          source load_dev_compass_1.7.0-alpha.1_mpich.sh
+          source load_compass_test_mpich.sh
 
           popd
 

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)
 
@@ -1064,7 +1064,7 @@ 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,
@@ -1083,8 +1083,8 @@ 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

@@ -121,8 +121,8 @@ 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,