Add a step for remapping topography from MALI

MALI topogrpahy gets combined with BedMachine Antarctica/GEBCO.

For now, the masks for the grounding line, calving front, etc.
are form BedMachine, not MALI, so that the same horizontal mesh
and mapping files can be used with BedMachine and MALI topogrpahy.

compass/ocean/tests/global_ocean/__init__.py

@@ -45,6 +45,8 @@ def __init__(self, mpas_core):
         self._add_tests(mesh_names=['ARRM10to60', 'ARRMwISC10to60'])
 
         self._add_tests(mesh_names=['SO12to30', 'SOwISC12to30'])
+        self._add_tests(mesh_names=['SOwISC12to30'],
+                        mali_ais_topo='AIS_4to20km')
 
         self._add_tests(mesh_names=['WC14', 'WCwISC14'])
 
@@ -65,15 +67,16 @@ def __init__(self, mpas_core):
     def _add_tests(self, mesh_names, high_res_topography=True,
                    include_rk4=False,
                    include_regression=False, include_phc=False,
-                   include_en4_1900=False):
+                   include_en4_1900=False, mali_ais_topo=None):
         """ Add test cases for the given mesh(es) """
 
         default_ic = 'WOA23'
         default_time_int = 'split_explicit_ab2'
 
         for mesh_name in mesh_names:
             mesh_test = Mesh(test_group=self, mesh_name=mesh_name,
-                             high_res_topography=high_res_topography)
+                             high_res_topography=high_res_topography,
+                             mali_ais_topo=mali_ais_topo)
             self.add_test_case(mesh_test)
 
             init_test = Init(test_group=self, mesh=mesh_test,

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

@@ -44,9 +44,8 @@ def __init__(self, test_group, mesh, initial_condition):
             The initial condition dataset to use
         """
         name = 'init'
-        mesh_name = mesh.mesh_name
         ic_dir = initial_condition
-        self.init_subdir = os.path.join(mesh_name, ic_dir)
+        self.init_subdir = os.path.join(mesh.mesh_subdir, ic_dir)
         subdir = os.path.join(self.init_subdir, name)
         super().__init__(test_group=test_group, name=name, subdir=subdir)
 

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

@@ -1,3 +1,5 @@
+import os
+
 from compass.mesh.spherical import (
     IcosahedralMeshStep,
     QuasiUniformSphericalMeshStep,
@@ -15,6 +17,9 @@
     IcosMeshFromConfigStep,
     QUMeshFromConfigStep,
 )
+from compass.ocean.tests.global_ocean.mesh.remap_mali_topography import (
+    RemapMaliTopography,
+)
 from compass.ocean.tests.global_ocean.mesh.rrs6to18 import RRS6to18BaseMesh
 from compass.ocean.tests.global_ocean.mesh.so12to30 import SO12to30BaseMesh
 from compass.ocean.tests.global_ocean.mesh.wc14 import WC14BaseMesh
@@ -31,6 +36,13 @@ class Mesh(TestCase):
 
     Attributes
     ----------
+    mesh_name : str
+        The name of the mesh
+
+    mesh_subdir : str
+        The subdirectory within the test group for all test cases with this
+        mesh and topography
+
     package : str
         The python package for the mesh
 
@@ -43,8 +55,14 @@ class Mesh(TestCase):
     high_res_topography : bool
         Whether to remap a high resolution topography data set.  A lower
         res data set is used for low resolution meshes.
+
+    mali_ais_topo : str
+        Short name for the MALI dataset to use for Antarctic Ice Sheet
+        topography
     """
-    def __init__(self, test_group, mesh_name, high_res_topography):
+
+    def __init__(self, test_group, mesh_name,  # noqa: C901
+                 high_res_topography, mali_ais_topo=None):
         """
         Create test case for creating a global MPAS-Ocean mesh
 
@@ -59,9 +77,20 @@ def __init__(self, test_group, mesh_name, high_res_topography):
         high_res_topography : bool
             Whether to remap a high resolution topography data set.  A lower
             res data set is used for low resolution meshes.
+
+        mali_ais_topo : str, optional
+            Short name for the MALI dataset to use for Antarctic Ice Sheet
+            topography
         """
         name = 'mesh'
-        subdir = f'{mesh_name}/{name}'
+        if mali_ais_topo is None:
+            self.mesh_subdir = mesh_name
+        else:
+            self.mesh_subdir = os.path.join(mesh_name,
+                                            f'MALI_topo_{mali_ais_topo}')
+
+        subdir = os.path.join(self.mesh_subdir, name)
+
         super().__init__(test_group=test_group, name=name, subdir=subdir)
 
         with_ice_shelf_cavities = 'wISC' in mesh_name
@@ -75,6 +104,7 @@ def __init__(self, test_group, mesh_name, high_res_topography):
         self.mesh_config_filename = f'{mesh_lower}.cfg'
 
         self.mesh_name = mesh_name
+        self.mali_ais_topo = mali_ais_topo
         self.with_ice_shelf_cavities = with_ice_shelf_cavities
         self.high_res_topography = high_res_topography
 
@@ -117,9 +147,15 @@ def __init__(self, test_group, mesh_name, high_res_topography):
 
         self.add_step(base_mesh_step)
 
-        remap_step = RemapTopography(test_case=self,
-                                     base_mesh_step=base_mesh_step,
-                                     mesh_name=mesh_name)
+        if mali_ais_topo is None:
+            remap_step = RemapTopography(test_case=self,
+                                         base_mesh_step=base_mesh_step,
+                                         mesh_name=mesh_name)
+        else:
+            remap_step = RemapMaliTopography(
+                test_case=self, base_mesh_step=base_mesh_step,
+                mesh_name=mesh_name, mali_ais_topo=mali_ais_topo)
+
         self.add_step(remap_step)
 
         self.add_step(CullMeshStep(
@@ -142,6 +178,13 @@ def configure(self, config=None):
             config.add_from_package('compass.ocean.mesh',
                                     'remap_topography.cfg', exception=True)
 
+        if self.mali_ais_topo is not None:
+            package = 'compass.ocean.tests.global_ocean.mesh.' \
+                      'remap_mali_topography'
+            config.add_from_package(package,
+                                    f'{self.mali_ais_topo.lower()}.cfg',
+                                    exception=True)
+
         if not self.high_res_topography:
             filename = 'BedMachineAntarctica_v2_and_GEBCO_2022_0.05_degree_20220729.nc'  # noqa: E501
             description = 'Bathymetry is from GEBCO 2022, combined with ' \