Fix formatting with pre-commit

compass/ocean/tests/global_ocean/__init__.py

@@ -1,26 +1,31 @@
-from compass.testgroup import TestGroup
-
-from compass.ocean.tests.global_ocean.mesh import Mesh
-from compass.ocean.tests.global_ocean.mesh.qu240.dynamic_adjustment import \
-    QU240DynamicAdjustment
-from compass.ocean.tests.global_ocean.mesh.ec30to60.dynamic_adjustment import \
-    EC30to60DynamicAdjustment
-from compass.ocean.tests.global_ocean.mesh.arrm10to60.dynamic_adjustment \
-    import ARRM10to60DynamicAdjustment
-from compass.ocean.tests.global_ocean.mesh.so12to60.dynamic_adjustment import \
-    SO12to60DynamicAdjustment
-from compass.ocean.tests.global_ocean.mesh.wc14.dynamic_adjustment import \
-    WC14DynamicAdjustment
+from compass.ocean.tests.global_ocean.analysis_test import AnalysisTest
+from compass.ocean.tests.global_ocean.daily_output_test import DailyOutputTest
+from compass.ocean.tests.global_ocean.decomp_test import DecompTest
+from compass.ocean.tests.global_ocean.files_for_e3sm import FilesForE3SM
 from compass.ocean.tests.global_ocean.init import Init
+from compass.ocean.tests.global_ocean.mesh import Mesh
+from compass.ocean.tests.global_ocean.mesh.arrm10to60.dynamic_adjustment import (  # noqa: E501
+    ARRM10to60DynamicAdjustment,
+)
+from compass.ocean.tests.global_ocean.mesh.ec30to60.dynamic_adjustment import (
+    EC30to60DynamicAdjustment,
+)
+from compass.ocean.tests.global_ocean.mesh.qu240.dynamic_adjustment import (
+    QU240DynamicAdjustment,
+)
+from compass.ocean.tests.global_ocean.mesh.so12to60.dynamic_adjustment import (
+    SO12to60DynamicAdjustment,
+)
+from compass.ocean.tests.global_ocean.mesh.wc14.dynamic_adjustment import (
+    WC14DynamicAdjustment,
+)
+from compass.ocean.tests.global_ocean.monthly_output_test import (
+    MonthlyOutputTest,
+)
 from compass.ocean.tests.global_ocean.performance_test import PerformanceTest
 from compass.ocean.tests.global_ocean.restart_test import RestartTest
-from compass.ocean.tests.global_ocean.decomp_test import DecompTest
 from compass.ocean.tests.global_ocean.threads_test import ThreadsTest
-from compass.ocean.tests.global_ocean.analysis_test import AnalysisTest
-from compass.ocean.tests.global_ocean.daily_output_test import DailyOutputTest
-from compass.ocean.tests.global_ocean.monthly_output_test import \
-    MonthlyOutputTest
-from compass.ocean.tests.global_ocean.files_for_e3sm import FilesForE3SM
+from compass.testgroup import TestGroup
 
 
 class GlobalOcean(TestGroup):

compass/ocean/tests/global_ocean/files_for_e3sm/README

@@ -13,4 +13,4 @@ E3SM members should NOT attempt to upload these files.  The files produced here
 are only a subset of those needed to support a new mesh in E3SM and should not
 be uploaded on their own. E3SM experts who know how to produce the other
 coupling files may upload these files along with other required datasets to the
-LCRC server.
+LCRC server.

compass/ocean/tests/global_ocean/files_for_e3sm/__init__.py

@@ -1,24 +1,31 @@
 import os
 
-from compass.io import symlink, package_path
-from compass.testcase import TestCase
-from compass.ocean.tests.global_ocean.files_for_e3sm.ocean_initial_condition \
-    import OceanInitialCondition
-from compass.ocean.tests.global_ocean.files_for_e3sm.seaice_initial_condition \
-    import SeaiceInitialCondition
-from compass.ocean.tests.global_ocean.files_for_e3sm.ocean_graph_partition \
-    import OceanGraphPartition
-from compass.ocean.tests.global_ocean.files_for_e3sm.seaice_graph_partition \
-    import SeaiceGraphPartition
+from compass.io import package_path, symlink
+from compass.ocean.tests.global_ocean.configure import configure_global_ocean
+from compass.ocean.tests.global_ocean.files_for_e3sm.diagnostic_maps import (
+    DiagnosticMaps,
+)
+from compass.ocean.tests.global_ocean.files_for_e3sm.diagnostic_masks import (
+    DiagnosticMasks,
+)
+from compass.ocean.tests.global_ocean.files_for_e3sm.e3sm_to_cmip_maps import (
+    E3smToCmipMaps,
+)
+from compass.ocean.tests.global_ocean.files_for_e3sm.ocean_graph_partition import (  # noqa: E501
+    OceanGraphPartition,
+)
+from compass.ocean.tests.global_ocean.files_for_e3sm.ocean_initial_condition import (  # noqa: E501
+    OceanInitialCondition,
+)
 from compass.ocean.tests.global_ocean.files_for_e3sm.scrip import Scrip
-from compass.ocean.tests.global_ocean.files_for_e3sm.e3sm_to_cmip_maps import \
-    E3smToCmipMaps
-from compass.ocean.tests.global_ocean.files_for_e3sm.diagnostic_maps \
-    import DiagnosticMaps
-from compass.ocean.tests.global_ocean.files_for_e3sm.diagnostic_masks \
-    import DiagnosticMasks
+from compass.ocean.tests.global_ocean.files_for_e3sm.seaice_graph_partition import (  # noqa: E501
+    SeaiceGraphPartition,
+)
+from compass.ocean.tests.global_ocean.files_for_e3sm.seaice_initial_condition import (  # noqa: E501
+    SeaiceInitialCondition,
+)
 from compass.ocean.tests.global_ocean.forward import get_forward_subdir
-from compass.ocean.tests.global_ocean.configure import configure_global_ocean
+from compass.testcase import TestCase
 
 
 class FilesForE3SM(TestCase):
@@ -38,7 +45,7 @@ class FilesForE3SM(TestCase):
     dynamic_adjustment : compass.ocean.tests.global_ocean.dynamic_adjustment.DynamicAdjustment
         The test case that performs dynamic adjustment to dissipate
         fast-moving waves from the initial condition
-    """
+    """  # noqa: E501
     def __init__(self, test_group, mesh=None, init=None,
                  dynamic_adjustment=None):
         """
@@ -58,11 +65,12 @@ def __init__(self, test_group, mesh=None, init=None,
         dynamic_adjustment : compass.ocean.tests.global_ocean.dynamic_adjustment.DynamicAdjustment, optional
             The test case that performs dynamic adjustment to dissipate
             fast-moving waves from the initial condition
-        """
+        """  # noqa: E501
         name = 'files_for_e3sm'
         if dynamic_adjustment is not None:
             time_integrator = dynamic_adjustment.time_integrator
-            subdir = get_forward_subdir(init.init_subdir, time_integrator, name)
+            subdir = get_forward_subdir(
+                init.init_subdir, time_integrator, name)
         else:
             subdir = name
 

compass/ocean/tests/global_ocean/files_for_e3sm/diagnostic_maps.py

@@ -1,14 +1,19 @@
-import os
 import glob
-import pyproj
-import numpy
+import os
 
-from pyremap import get_lat_lon_descriptor, ProjectionGridDescriptor, \
-    MpasMeshDescriptor, Remapper
+import numpy
+import pyproj
+from pyremap import (
+    MpasMeshDescriptor,
+    ProjectionGridDescriptor,
+    Remapper,
+    get_lat_lon_descriptor,
+)
 
 from compass.io import symlink
-from compass.ocean.tests.global_ocean.files_for_e3sm.files_for_e3sm_step \
-    import FilesForE3SMStep
+from compass.ocean.tests.global_ocean.files_for_e3sm.files_for_e3sm_step import (  # noqa: E501
+    FilesForE3SMStep,
+)
 
 
 class DiagnosticMaps(FilesForE3SMStep):
@@ -24,7 +29,7 @@ def __init__(self, test_case):
         ----------
         test_case : compass.ocean.tests.global_ocean.files_for_e3sm.FilesForE3SM
             The test case this step belongs to
-        """
+        """  # noqa: E501
 
         super().__init__(test_case, name='diagnostics_maps', ntasks=36,
                          min_tasks=1)
@@ -206,8 +211,8 @@ def _make_mapping_file(mesh_name, out_grid_name, mesh_filename, out_descriptor,
 
     remapper = Remapper(in_descriptor, out_descriptor, mapping_file_name)
 
-    remapper.build_mapping_file(method='bilinear', mpiTasks=ntasks, tempdir='.',
-                                logger=logger,
+    remapper.build_mapping_file(method='bilinear', mpiTasks=ntasks,
+                                tempdir='.', logger=logger,
                                 esmf_parallel_exec=parallel_executable)
 
     # now the same on vertices (e.g. for streamfunctions)
@@ -217,6 +222,6 @@ def _make_mapping_file(mesh_name, out_grid_name, mesh_filename, out_descriptor,
 
     remapper = Remapper(in_descriptor, out_descriptor, mapping_file_name)
 
-    remapper.build_mapping_file(method='bilinear', mpiTasks=ntasks, tempdir='.',
-                                logger=logger,
+    remapper.build_mapping_file(method='bilinear', mpiTasks=ntasks,
+                                tempdir='.', logger=logger,
                                 esmf_parallel_exec=parallel_executable)

compass/ocean/tests/global_ocean/files_for_e3sm/diagnostic_masks.py

@@ -1,16 +1,17 @@
 import os
-import xarray as xr
 
+import mpas_tools.io
+import xarray as xr
 from geometric_features import GeometricFeatures
 from geometric_features.aggregation import get_aggregator_by_name
+from mpas_tools.io import write_netcdf
 from mpas_tools.logging import check_call
 from mpas_tools.ocean.moc import add_moc_southern_boundary_transects
-from mpas_tools.io import write_netcdf
-import mpas_tools.io
 
 from compass.io import symlink
-from compass.ocean.tests.global_ocean.files_for_e3sm.files_for_e3sm_step \
-    import FilesForE3SMStep
+from compass.ocean.tests.global_ocean.files_for_e3sm.files_for_e3sm_step import (  # noqa: E501
+    FilesForE3SMStep,
+)
 
 
 class DiagnosticMasks(FilesForE3SMStep):
@@ -27,7 +28,7 @@ def __init__(self, test_case):
         ----------
         test_case : compass.ocean.tests.global_ocean.files_for_e3sm.FilesForE3SM
             The test case this step belongs to
-        """
+        """  # noqa: E501
 
         super().__init__(test_case, name='diagnostics_masks', cpus_per_task=18,
                          min_cpus_per_task=1)

compass/ocean/tests/global_ocean/files_for_e3sm/e3sm_to_cmip_maps.py

@@ -1,11 +1,11 @@
 import os
-import xarray
 
 from mpas_tools.logging import check_call
 
 from compass.io import symlink
-from compass.ocean.tests.global_ocean.files_for_e3sm.files_for_e3sm_step \
-    import FilesForE3SMStep
+from compass.ocean.tests.global_ocean.files_for_e3sm.files_for_e3sm_step import (  # noqa: E501
+    FilesForE3SMStep,
+)
 
 
 class E3smToCmipMaps(FilesForE3SMStep):
@@ -21,7 +21,7 @@ def __init__(self, test_case):
         ----------
         test_case : compass.ocean.tests.global_ocean.files_for_e3sm.FilesForE3SM
             The test case this step belongs to
-        """
+        """  # noqa: E501
 
         super().__init__(test_case, name='e3sm_to_cmip_maps', ntasks=36,
                          min_tasks=1)
@@ -76,7 +76,7 @@ def make_e3sm_to_cmip_maps(config, logger, mesh_short_name, creation_date,
         The number of parallel tasks to use for remapping
     """
 
-    link_dir = f'../assembled_files/diagnostics/maps'
+    link_dir = '../assembled_files/diagnostics/maps'
 
     try:
         os.makedirs(link_dir)
@@ -86,9 +86,9 @@ def make_e3sm_to_cmip_maps(config, logger, mesh_short_name, creation_date,
     src_scrip_filename = 'ocean.scrip.nc'
     cmip6_grid_res = config.get('files_for_e3sm', 'cmip6_grid_res')
     if cmip6_grid_res == '180x360':
-        dst_scrip_filename = f'cmip6_180x360_scrip.20181001.nc'
+        dst_scrip_filename = 'cmip6_180x360_scrip.20181001.nc'
     elif cmip6_grid_res == '720x1440':
-        dst_scrip_filename = f'cmip6_720x1440_scrip.20181001.nc'
+        dst_scrip_filename = 'cmip6_720x1440_scrip.20181001.nc'
     else:
         raise ValueError(f'Unexpected cmip6_grid_res: {cmip6_grid_res}')
 
@@ -116,7 +116,7 @@ def make_e3sm_to_cmip_maps(config, logger, mesh_short_name, creation_date,
         check_call(args, logger=logger)
 
         map_filename = \
-            f'map_{mesh_short_name}_to_cmip6_{cmip6_grid_res}_{suffix}.{creation_date}.nc'
+            f'map_{mesh_short_name}_to_cmip6_{cmip6_grid_res}_{suffix}.{creation_date}.nc'  # noqa: E501
 
         symlink(os.path.abspath(local_map_filename),
                 f'{link_dir}/{map_filename}')

compass/ocean/tests/global_ocean/files_for_e3sm/files_for_e3sm_step.py

@@ -1,7 +1,8 @@
 import os
-import xarray as xr
 from datetime import datetime
 
+import xarray as xr
+
 from compass.io import symlink
 from compass.step import Step
 
@@ -94,7 +95,7 @@ def setup(self):
             self.with_ice_shelf_cavities = \
                 (with_ice_shelf_cavities.lower() == 'true')
 
-    def run(self):
+    def run(self):  # noqa: C901
         """
         Run this step of the testcase
         """
@@ -136,12 +137,11 @@ def run(self):
                                 # assume it's already YYYYMMDD
                                 pass
                             break
-
 
         if mesh_short_name == 'autodetect':
             raise ValueError(
-                'No mesh short name provided in "mesh_short_name" config option '
-                'and none found in MPAS_Mesh_Short_Name attribute.')
+                'No mesh short name provided in "mesh_short_name" config '
+                'option and none found in MPAS_Mesh_Short_Name attribute.')
 
         if creation_date == 'autodetect':
             now = datetime.now()

compass/ocean/tests/global_ocean/files_for_e3sm/ocean_graph_partition.py

@@ -1,14 +1,16 @@
 import os
-import numpy as np
 from glob import glob
 
+import numpy as np
 from mpas_tools.logging import check_call
 
 from compass.io import symlink
-from compass.ocean.tests.global_ocean.files_for_e3sm.files_for_e3sm_step \
-    import FilesForE3SMStep
-from compass.ocean.tests.global_ocean.files_for_e3sm.graph_partition import \
-    get_core_list
+from compass.ocean.tests.global_ocean.files_for_e3sm.files_for_e3sm_step import (  # noqa: E501
+    FilesForE3SMStep,
+)
+from compass.ocean.tests.global_ocean.files_for_e3sm.graph_partition import (
+    get_core_list,
+)
 
 
 class OceanGraphPartition(FilesForE3SMStep):
@@ -23,7 +25,7 @@ def __init__(self, test_case):
         ----------
         test_case : compass.ocean.tests.global_ocean.files_for_e3sm.FilesForE3SM
             The test case this step belongs to
-        """
+        """  # noqa: E501
 
         super().__init__(test_case, name='ocean_graph_partition')
 

compass/ocean/tests/global_ocean/files_for_e3sm/ocean_initial_condition.py

@@ -1,11 +1,12 @@
 import os
-import xarray
 
+import xarray
 from mpas_tools.io import write_netcdf
 
 from compass.io import symlink
-from compass.ocean.tests.global_ocean.files_for_e3sm.files_for_e3sm_step \
-    import FilesForE3SMStep
+from compass.ocean.tests.global_ocean.files_for_e3sm.files_for_e3sm_step import (  # noqa: E501
+    FilesForE3SMStep,
+)
 
 
 class OceanInitialCondition(FilesForE3SMStep):
@@ -21,7 +22,7 @@ def __init__(self, test_case):
         ----------
         test_case : compass.ocean.tests.global_ocean.files_for_e3sm.FilesForE3SM
             The test case this step belongs to
-        """
+        """  # noqa: E501
 
         super().__init__(test_case, name='ocean_initial_condition')
 

compass/ocean/tests/global_ocean/files_for_e3sm/scrip.py

@@ -1,11 +1,11 @@
 import os
-import xarray
 
 from mpas_tools.scrip.from_mpas import scrip_from_mpas
 
 from compass.io import symlink
-from compass.ocean.tests.global_ocean.files_for_e3sm.files_for_e3sm_step \
-    import FilesForE3SMStep
+from compass.ocean.tests.global_ocean.files_for_e3sm.files_for_e3sm_step import (  # noqa: E501
+    FilesForE3SMStep,
+)
 
 
 class Scrip(FilesForE3SMStep):
@@ -20,7 +20,7 @@ def __init__(self, test_case):
         ----------
         test_case : compass.ocean.tests.global_ocean.files_for_e3sm.FilesForE3SM
             The test case this step belongs to
-        """
+        """  # noqa: E501
 
         super().__init__(test_case, name='scrip')