Update tool names in the docs

docs/developers_guide/framework.rst

@@ -244,7 +244,7 @@ functions.  Here is a code snippet from
         section = config['dome']
         ...
         levels = section.getfloat('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]
@@ -253,7 +253,7 @@ functions.  Here is a code snippet from
         ...
 
 
-This example calls the script ``create_landice_grid_from_generic_MPAS_grid.py``
+This example calls the script ``create_landice_grid_from_generic_mpas_grid``
 from ``mpas_tools`` with several arguments, making use of the ``logger``.
 
 .. _dev_io:

docs/developers_guide/landice/test_groups/circular_shelf.rst

@@ -30,7 +30,7 @@ constructed at runtime (using
 :py:func:`mpas_tools.planar_hex.make_planar_hex_mesh()`).
 
 A MALI grid is created with the MPAS-Tools script
-``create_landice_grid_from_generic_MPAS_grid.py`` and a graph file is created
+``create_landice_grid_from_generic_mpas_grid`` and a graph file is created
 to partition the mesh before the model run.
 
 Finally, the initial condition is defined in the private function

docs/developers_guide/landice/test_groups/dome.rst

@@ -47,7 +47,7 @@ The variable resolution mesh is downloaded from
     section of the config file.
 
 A MALI grid is created with the MPAS-Tools script
-``create_landice_grid_from_generic_MPAS_grid.py`` and a graph file is created
+``create_landice_grid_from_generic_mpas_grid`` and a graph file is created
 to partition the mesh before the model run.
 
 Finally, the initial condition is defined in the private function

docs/developers_guide/landice/test_groups/eismint2.rst

@@ -30,7 +30,7 @@ defines a step for setting up the mesh for each test case.
 The horizontal mesh is constructed at runtime (using
 :py:func:`mpas_tools.planar_hex.make_planar_hex_mesh()`). A MALI grid is
 created with the MPAS-Tools script
-``create_landice_grid_from_generic_MPAS_grid.py`` and a graph file is created
+``create_landice_grid_from_generic_mpas_grid`` and a graph file is created
 to partition the mesh before the model run.
 
 run_experiment

docs/developers_guide/landice/test_groups/enthalpy_benchmark.rst

@@ -34,7 +34,7 @@ defines a step for setting up the mesh for each test case.
 
 The horizontal mesh is constructed at runtime (using
 :py:func:`mpas_tools.planar_hex.make_planar_hex_mesh()`).  Then, a MALI grid is
-created with the MPAS-Tools script ``create_landice_grid_from_generic_MPAS_grid.py``
+created with the MPAS-Tools script ``create_landice_grid_from_generic_mpas_grid``
 and a graph file is created to partition the mesh before the model run.
 
 Finally, the initial condition is defined in the private function

docs/developers_guide/landice/test_groups/hydro_radial.rst

@@ -31,7 +31,7 @@ defines a step for setting up the mesh for each test case.
 The horizontal mesh is constructed at runtime (using
 :py:func:`mpas_tools.planar_hex.make_planar_hex_mesh()`). A MALI grid is
 created with the MPAS-Tools script
-``create_landice_grid_from_generic_MPAS_grid.py`` and a graph file is created
+``create_landice_grid_from_generic_mpas_grid`` and a graph file is created
 to partition the mesh before the model run.
 
 Finally, the initial condition is defined in the private function

docs/developers_guide/landice/test_groups/ismip6_forcing.rst

@@ -9,7 +9,7 @@ atmospheric and oceanic forcing data of the Ice Sheet Model
 Intercomparison for CMIP6 (ISMIP6) protocol from its native polarstereo grid to
 the unstructure MALI mesh. The test group includes five test cases:
 ``atmosphere``, ``ocean_basal``, ``ocean_thermal_obs``, ``ocean_thermal`` and
-``shelf_collapse``. The ``atmosphere`` test case has two steps: 
+``shelf_collapse``. The ``atmosphere`` test case has two steps:
 ``process_smb`` and ``process_smb_racmo``; the ``ocean_basal`` and ``shelf_collpase``
 test cases each have one step, ``process_basal_melt`` and ``process_shelf_collpase``
 (respectively); the ``ocean_thermal_obs`` and ``ocean_thermal``
@@ -34,15 +34,15 @@ create_mapfile
 
 The module :py:class:`compass.landice.tests.ismip6_forcing.create_mapfile` defines
 a unified framework for creating the SCRIP and mapping files from the ISMIP6
-source data files. The function 
+source data files. The function
 :py:func:`compass.landice.tests.ismip6_forcing.create_mapfile.build_mapping_file`
 is the common interface to build the SCRIP files and mapping files. The
 ``scrip_from_latlon`` keyword argument is used to call the appropriate function
 for generating the SCRIP file. If ``scrip_from_latlon`` is ``false`` the
-``create_SCRIP_file_from_planar_rectangular_grid.py`` command line executable
-from the ``MPAS_Tools`` conda package is used, otherwise the 
+``create_scrip_file_from_planar_rectangular_grid`` command line executable
+from the ``MPAS_Tools`` conda package is used, otherwise the
 :py:func:`compass.landice.tests.ismip6_forcing.create_mapfile.create_scrip_from_latlon`
-function is used. Multiple methods for creating SCRIP files are necessary due to 
+function is used. Multiple methods for creating SCRIP files are necessary due to
 inconsistent dimensions names across the different ISMIP6 datasets.
 
 Test cases
@@ -87,4 +87,4 @@ shelf_collapse
 ~~~~~~~~~~~~~~
 The :py:class:`compass.landice.tests.ismip6_forcing.shelf_collapse.ShelfCollapse`
 test case performs the processing of ice shelf collapse masks by remapping the
-original ISMIP6 forcing data to MALI's unstructured grid and renaming variables. 
+original ISMIP6 forcing data to MALI's unstructured grid and renaming variables.

docs/developers_guide/landice/test_groups/ismip6_run.rst

@@ -28,7 +28,7 @@ excessive subdirectories.
 
 The ``configure`` method is where the experiments to be set up are determined.
 The config option ``exp_list`` is parsed and each experiment to be included
-is set up as a step of the test case by calling the 
+is set up as a step of the test case by calling the
 ``SetUpExperiment`` constructor (``__init__``).
 All of the experiments are removed from ``steps_to_run``, because the
 experiments (steps) are not meant to be run together through the test
@@ -70,7 +70,7 @@ in the comparison of post-simulation ice mass calculations from the model output
 To address this issue, an interim solution has been made to project the southern
 polar region onto the MALI planar mesh assuming a sphere (this is done by setting
 the lat/long in the MALI mesh using the 'aid-bedmap2-sphere' projection string in
-calling the function in 'set_lat_lon_fields_in_planar_grid.py'. Thus, the resulting
+calling the function in 'set_lat_lon_fields_in_planar_grid'. Thus, the resulting
 MALI mesh for coupled MALI-SLM simulations that are setup from this testgroup have
 the lat/long values based off sphere. Once the simulation outputs are generated,
 it is necessary to calculate and apply the scaling factors to the MALI outputs

docs/developers_guide/landice/test_groups/mesh_modifications.rst

@@ -42,7 +42,7 @@ steps:
 
 * interpolate fields from source mesh to subdomain mesh using
   nearest neighbor interpolation.
-  This can be done either with the ``interpolate_to_mpasli_grid.py`` script
+  This can be done either with the ``interpolate_to_mpasli_grid`` script
   or using ``ncremap``.  The ncremap method is slower and potentially more
   fragile (depends on more external tools), but if used allows the option
   to remap additional files (e.g. forcing files).

docs/tutorials/dev_add_rrm.rst

@@ -1868,7 +1868,7 @@ run:
 
 .. code-block:: bash
 
-    paraview_vtk_field_extractor.py -m init.nc \
+    paraview_vtk_field_extractor -m init.nc \
         -f output.nc -v normalVelocity,temperature,salinity \
         -d nVertLevels=0
 

docs/users_guide/landice/test_groups/antarctica.rst

@@ -73,19 +73,19 @@ the mesh generation options are adjusted through the config file.
     # path to directory containing BedMachine and Measures datasets
     # (default value is for Perlmutter)
     data_path = /global/cfs/cdirs/fanssie/standard_datasets/AIS_datasets
-    
+
     # filename of the BedMachine thickness and bedTopography dataset
     # (default value is for Perlmutter)
     bedmachine_filename = BedMachineAntarctica_2020-07-15_v02_edits_floodFill_extrap_fillVostok.nc
-    
+
     # filename of the MEASURES ice velocity dataset
     # (default value is for Perlmutter)
     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
     nProcs = 128
 

docs/users_guide/landice/test_groups/greenland.rst

@@ -90,19 +90,19 @@ The other test cases do not use config options.
    # path to directory containing BedMachine and Measures datasets
    # (default value is for Perlmutter)
    data_path = /global/cfs/cdirs/fanssie/standard_datasets/GIS_datasets/
-   
+
    # filename of the BedMachine thickness and bedTopography dataset
    # (default value is for Perlmutter)
    bedmachine_filename = BedMachineGreenland-v5_edits_floodFill_extrap.nc
-   
+
    # filename of the MEASURES ice velocity dataset
    # (default value is for Perlmutter)
    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
    nProcs = 128
 

docs/users_guide/landice/test_groups/ismip6_run.rst

@@ -173,7 +173,7 @@ in the comparison of post-simulation ice mass calculations from the model output
 To address this issue, an interim solution has been made to project the southern
 polar region onto the MALI planar mesh assuming a sphere (this is done by setting
 the lat/long in the MALI mesh using the 'aid-bedmap2-sphere' projection string in
-calling the function in 'set_lat_lon_fields_in_planar_grid.py'. Thus, the resulting
+calling the function in 'set_lat_lon_fields_in_planar_grid'. Thus, the resulting
 MALI mesh for coupled MALI-SLM simulations that are setup from this testgroup have
 the lat/long values based off sphere. Once the simulation outputs are generated,
 it is necessary to calculate and apply the scaling factors to the MALI outputs

docs/users_guide/landice/test_groups/mesh_modifications.rst

@@ -88,7 +88,7 @@ the test case.
     # 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