diff --git a/conda_package/docs/ocean/moc.rst b/conda_package/docs/ocean/moc.rst
index 06759a939..8dd448ddb 100644
--- a/conda_package/docs/ocean/moc.rst
+++ b/conda_package/docs/ocean/moc.rst
@@ -75,14 +75,14 @@ In this example, only the ``mesh.nc`` file is required as an input.  The
 resulting ``xarray.Dataset`` contains both the basin and southern-transect
 masks.
 
-A command-line tool ``moc_southern_boundary_extractor.py`` is also available
+A command-line tool ``moc_southern_boundary_extractor`` is also available
 for this purpose:
 
 .. code-block:: none
 
-    $ moc_southern_boundary_extractor.py --help
+    $ moc_southern_boundary_extractor --help
 
-    usage: moc_southern_boundary_extractor.py [-h] -f IN_FILE -m MESH_FILE -o
+    usage: moc_southern_boundary_extractor [-h] -f IN_FILE -m MESH_FILE -o
                                               OUT_FILE
 
     This script takes a mesh file (-m flag) and a file with MOC regions masks
@@ -92,9 +92,6 @@ for this purpose:
     is applied only to vertices and edges, not cells, because the need for southern
     boundary transect data on cells is not foreseen.
 
-    Author: Xylar Asay-Davis
-    last modified: 5/22/2018
-
     optional arguments:
       -h, --help            show this help message and exit
       -f IN_FILE, --in_file IN_FILE
diff --git a/conda_package/docs/visualization.rst b/conda_package/docs/visualization.rst
index 1675bf8aa..d5e36832c 100644
--- a/conda_package/docs/visualization.rst
+++ b/conda_package/docs/visualization.rst
@@ -39,7 +39,7 @@ ParaVeiw, meaning each cell has the correct polygonal geometry and will be
 visualized with a single, constant value for a given field.  The extractor,
 which is available either through the
 :py:func:`mpas_tools.viz.paraview_extractor.extract_vtk()` function or the
-``paraview_vtk_field_extractor.py`` command-line interface, can also be used to
+``paraview_vtk_field_extractor`` command-line interface, can also be used to
 visualize data on MPAS vertices (visualized on triangles) and edges (visualized
 on quadrilaterals).
 
@@ -128,7 +128,7 @@ The same extraction could be accomplished with the command-line tool as follows:
 
 .. code-block:: none
 
-    $ paraview_vtk_field_extractor.py \
+    $ paraview_vtk_field_extractor \
          -f "analysis_members/mpaso.hist.am.timeSeriesStatsDaily.*.nc" \
          -v timeDaily_avg_activeTracers_temperature -d nVertLevels=0 \
          -m init.nc -o vtk_files --xtime=xtime_startDaily
diff --git a/conda_package/mpas_tools/ocean/coastline_alteration.py b/conda_package/mpas_tools/ocean/coastline_alteration.py
index 32318d314..cc0150d0e 100644
--- a/conda_package/mpas_tools/ocean/coastline_alteration.py
+++ b/conda_package/mpas_tools/ocean/coastline_alteration.py
@@ -1,5 +1,4 @@
-from __future__ import absolute_import, division, print_function, \
-    unicode_literals
+import argparse
 
 import numpy
 import xarray
@@ -35,10 +34,43 @@ def add_critical_land_blockages(dsMask, dsBlockages):
     return dsMask
 
 
+def main_add_critical_land_blockages():
+    """
+    Entry point for add_critical_land_blockages command-line tool
+    """
+    description = """
+Add transects that identify critical regions where narrow strips of land block
+ocean flow.  These are, essentially, the opposite of critical passages, which
+must remain open for ocean flow.
+"""
+    parser = \
+        argparse.ArgumentParser(description=description,
+                                formatter_class=argparse.RawTextHelpFormatter)
+    parser.add_argument("-f", "--input_mask_file", dest="input_mask_filename",
+                        help="Mask file that includes cell and edge masks.",
+                        metavar="INPUTMASKFILE", required=True)
+    parser.add_argument("-o", "--output_mask_file",
+                        dest="output_mask_filename",
+                        help="Mask file that includes cell and edge masks.",
+                        metavar="OUTPUTMASKFILE", required=True)
+    parser.add_argument("-b", "--blockage_file", dest="blockage_file",
+                        help="Masks for each transect identifying critical "
+                             "land blockage.", metavar="BLOCKFILE",
+                        required=True)
+    args = parser.parse_args()
+
+    dsMask = xarray.open_dataset(args.input_mask_filename)
+
+    dsBlockages = xarray.open_dataset(args.blockage_file)
+
+    dsMask = add_critical_land_blockages(dsMask, dsBlockages)
+    dsMask.to_netcdf(args.output_mask_filename)
+
+
 def widen_transect_edge_masks(dsMask, dsMesh, latitude_threshold=43.0):
     """
-    Alter critical passages at polar latitudes to be at least two cells wide, to
-    avoid sea ice blockage
+    Alter critical passages at polar latitudes to be at least two cells wide,
+    to avoid sea ice blockage
 
     Parameters
     ----------
@@ -78,6 +110,44 @@ def widen_transect_edge_masks(dsMask, dsMesh, latitude_threshold=43.0):
     return dsMask
 
 
+def main_widen_transect_edge_masks():
+    """
+    Entry point for widen_transect_edge_masks command-line tool
+    """
+    description = """
+Alter transects to be at least two cells wide.  This is used for critical
+passages, to avoid sea ice blockage.  Specifically, mark cells on both sides
+of each transect edge mask as a water cell.
+"""
+    parser = \
+        argparse.ArgumentParser(description=description,
+                                formatter_class=argparse.RawTextHelpFormatter)
+    parser.add_argument("-f", "--mask_file", dest="mask_filename",
+                        help="Mask file with cell and edge transect masks.",
+                        metavar="MASKFILE",
+                        required=True)
+    parser.add_argument("-m", "--mesh_file", dest="mesh_filename",
+                        help="MPAS Mesh filename.", metavar="MESHFILE",
+                        required=True)
+    parser.add_argument("-o", "--out_file", dest="out_filename",
+                        help="Output mask file,different from input filename.",
+                        metavar="MASKFILE",
+                        required=True)
+    parser.add_argument("-l", "--latitude_threshold",
+                        dest="latitude_threshold",
+                        help="Minimum latitude, degrees, for transect "
+                             "widening.",
+                        required=False, type=float, default=43.0)
+    args = parser.parse_args()
+
+    dsMask = xarray.open_dataset(args.mask_filename)
+
+    dsMesh = xarray.open_dataset(args.mesh_filename)
+
+    dsMask = widen_transect_edge_masks(dsMask, dsMesh, args.latitude_threshold)
+    dsMask.to_netcdf(args.out_filename)
+
+
 def add_land_locked_cells_to_mask(dsMask, dsMesh, latitude_threshold=43.0,
                                   nSweeps=10):
     """
@@ -143,6 +213,48 @@ def add_land_locked_cells_to_mask(dsMask, dsMesh, latitude_threshold=43.0,
     return dsMask
 
 
+def main_add_land_locked_cells_to_mask():
+    """
+    Entry point for add_land_locked_cells_to_mask command-line tool
+    """
+    description = """
+Find ocean cells that are land-locked, and alter the cell
+mask so that they are counted as land cells.
+"""
+    parser = \
+        argparse.ArgumentParser(description=description,
+                                formatter_class=argparse.RawTextHelpFormatter)
+    parser.add_argument("-f", "--input_mask_file", dest="input_mask_filename",
+                        help="Mask file that includes cell and edge masks.",
+                        metavar="INPUTMASKFILE", required=True)
+    parser.add_argument("-o", "--output_mask_file",
+                        dest="output_mask_filename",
+                        help="Mask file that includes cell and edge masks.",
+                        metavar="OUTPUTMASKFILE", required=True)
+    parser.add_argument("-m", "--mesh_file", dest="mesh_filename",
+                        help="MPAS Mesh filename.", metavar="MESHFILE",
+                        required=True)
+    parser.add_argument("-l", "--latitude_threshold",
+                        dest="latitude_threshold",
+                        help="Minimum latitude, in degrees, for transect "
+                             "widening.",
+                        required=False, type=float, default=43.0)
+    parser.add_argument("-n", "--number_sweeps", dest="nSweeps",
+                        help="Maximum number of sweeps to search for "
+                             "land-locked cells.",
+                        required=False, type=int, default=10)
+    args = parser.parse_args()
+
+    dsMask = xarray.open_dataset(args.input_mask_filename)
+
+    dsMesh = xarray.open_dataset(args.mesh_filename)
+
+    dsMask = add_land_locked_cells_to_mask(dsMask, dsMesh,
+                                           args.latitude_threshold,
+                                           args.nSweeps)
+    dsMask.to_netcdf(args.output_mask_filename)
+
+
 def _remove_cells_with_isolated_edges1(dsMask, dsMesh, landMask,
                                        latitude_threshold):
     print("Step 1: Searching for land-locked cells.  Remove cells that only "
@@ -307,7 +419,7 @@ def _flood_fill(dsMask, dsMesh, landMask, removable):
             filledNeighbors = numpy.logical_and(neighbors >= 0,
                                                 floodFill[neighbors] == 1)
             fillIndices = cellIndices[filledNeighbors.values]
-            if(len(fillIndices) > 0):
+            if len(fillIndices) > 0:
                 floodFill[fillIndices] = 1
                 newFloodCellsThisSweep += len(fillIndices)
 
diff --git a/conda_package/mpas_tools/ocean/moc.py b/conda_package/mpas_tools/ocean/moc.py
index cb8cdc0a7..16d2d45e1 100755
--- a/conda_package/mpas_tools/ocean/moc.py
+++ b/conda_package/mpas_tools/ocean/moc.py
@@ -1,10 +1,9 @@
-from __future__ import absolute_import, division, print_function, \
-    unicode_literals
+import argparse
+import logging
+import sys
 
 import xarray
 import numpy
-import logging
-import sys
 from geometric_features.aggregation.ocean import moc
 
 import mpas_tools.mesh.conversion
@@ -88,8 +87,8 @@ def add_moc_southern_boundary_transects(dsMask, dsMesh, logger=None):
     Returns
     -------
     dsMask : ``xarray.Dataset``
-        Region masks defining MOC basins and the corresponding southern-boundary
-        transects
+        Region masks defining MOC basins and the corresponding
+        southern-boundary transects
     """
 
     useStdout = logger is None
@@ -113,6 +112,41 @@ def add_moc_southern_boundary_transects(dsMask, dsMesh, logger=None):
     return dsMask
 
 
+def moc_southern_boundary_extractor():
+    """
+    Entry point for moc_southern_boundary_extractor command-line tool
+    """
+    description = """
+This script takes a mesh file (-m flag) and a file with MOC regions masks
+(-f flag) produce by the MPAS mask creator.  The script produces a copy of
+the contents of the MOC mask file, adding transects that mark the southern
+boundary of each region in a file indicated with the -o flag.  The transect
+is applied only to vertices and edges, not cells, because the need for southern
+boundary transect data on cells is not foreseen.
+"""
+    parser = \
+        argparse.ArgumentParser(description=description,
+                                formatter_class=argparse.RawTextHelpFormatter)
+    parser.add_argument('-f', '--in_file', dest='in_file',
+                        help='Input file with MOC masks', metavar='IN_FILE',
+                        required=True)
+    parser.add_argument('-m', '--mesh_file', dest='mesh_file',
+                        help='Input mesh file', metavar='MESH_FILE',
+                        required=True)
+    parser.add_argument('-o', '--out_file', dest='out_file',
+                        help='Output file for MOC masks and southern-boundary '
+                        'transects', metavar='OUT_FILE',
+                        required=True)
+    args = parser.parse_args()
+
+    dsMasks = xarray.open_dataset(args.in_file)
+    dsMesh = xarray.open_dataset(args.mesh_file)
+
+    dsMasksAndTransects = add_moc_southern_boundary_transects(dsMasks, dsMesh)
+
+    write_netcdf(dsMasksAndTransects, args.out_file)
+
+
 def _extract_southern_boundary(mesh, mocMask, latBuffer, logger):
     """
     Extracts the southern boundary of each region mask in mocMask.  Mesh info
@@ -125,7 +159,7 @@ def _extract_southern_boundary(mesh, mocMask, latBuffer, logger):
     nEdges = mesh.sizes['nEdges']
 
     nRegions = mocMask.sizes['nRegions']
-    assert(mocMask.sizes['nCells'] == nCells)
+    assert mocMask.sizes['nCells'] == nCells
 
     # convert to python zero-based indices
     cellsOnEdge = mesh.variables['cellsOnEdge'].values-1
@@ -198,7 +232,7 @@ def _extract_southern_boundary(mesh, mocMask, latBuffer, logger):
         startIndices = numpy.arange(1, len(edgeSequence))[belowToAbove]
         endIndices = numpy.arange(1, len(edgeSequence))[aboveToBelow]
 
-        assert(len(startIndices) == len(endIndices))
+        assert len(startIndices) == len(endIndices)
 
         if len(startIndices) == 0:
             # the whole sequence is the southern boundary
@@ -232,7 +266,8 @@ def _extract_southern_boundary(mesh, mocMask, latBuffer, logger):
 
 
 def _add_transects_to_moc(mesh, mocMask, southernBoundaryEdges,
-                          southernBoiundaryEdgeSigns, southernBoundaryVertices):
+                          southernBoiundaryEdgeSigns,
+                          southernBoundaryVertices):
     """
     Creates transect fields in mocMask from the edges, edge signs and
     vertices defining the southern boundaries.  Mesh info (nEdges and
@@ -354,7 +389,7 @@ def _get_edge_sequence_on_boundary(startEdge, edgeSign, edgesOnVertex,
     edgeSequence = []
     vertexSequence = []
     while True:
-        assert(edgeSign[iEdge] == 1. or edgeSign[iEdge] == -1.)
+        assert edgeSign[iEdge] == 1. or edgeSign[iEdge] == -1.
         if edgeSign[iEdge] == 1.:
             v = 0
         else:
@@ -369,7 +404,7 @@ def _get_edge_sequence_on_boundary(startEdge, edgeSign, edgesOnVertex,
             if edge != -1 and edge != iEdge and edgeSign[edge] != 0:
                 nextEdge = edge
                 break
-        assert(nextEdge != -1)
+        assert nextEdge != -1
 
         edgeSequence.append(iEdge)
         vertexSequence.append(iVertex)
diff --git a/conda_package/recipe/build.sh b/conda_package/recipe/build.sh
index f9a3f135f..28f4565fa 100644
--- a/conda_package/recipe/build.sh
+++ b/conda_package/recipe/build.sh
@@ -3,13 +3,11 @@
 set -x
 set -e
 
-cp -r ocean landice visualization mesh_tools conda_package
-
 cd conda_package
 ${PYTHON} -m pip install . --no-deps --no-build-isolation -vv
 
 # build and install ocean topography smoothing tool
-cd ${SRC_DIR}/conda_package/ocean/smooth_topo
+cd ${SRC_DIR}/ocean/smooth_topo
 mkdir build
 cd build
 cmake \
@@ -20,7 +18,7 @@ cmake --build .
 cmake --install .
 
 # build and install sea ice partitioning tool
-cd ${SRC_DIR}/conda_package/mesh_tools/seaice_grid_tools
+cd ${SRC_DIR}/mesh_tools/seaice_grid_tools
 mkdir build
 cd build
 cmake \
@@ -31,7 +29,7 @@ cmake --build .
 cmake --install .
 
 # build and install legacy mask creator
-cd ${SRC_DIR}/conda_package/mesh_tools/mesh_conversion_tools
+cd ${SRC_DIR}/mesh_tools/mesh_conversion_tools
 mkdir build
 cd build
 cmake \
@@ -42,7 +40,7 @@ cmake --build .
 cp MpasMaskCreator.x ${PREFIX}/bin
 
 # build and install mesh conversion tools
-cd ${SRC_DIR}/conda_package/mesh_tools/mesh_conversion_tools_netcdf_c
+cd ${SRC_DIR}/mesh_tools/mesh_conversion_tools_netcdf_c
 mkdir build
 cd build
 cmake \
diff --git a/conda_package/recipe/meta.yaml b/conda_package/recipe/meta.yaml
index ecfcb7d94..e80c2bbdd 100644
--- a/conda_package/recipe/meta.yaml
+++ b/conda_package/recipe/meta.yaml
@@ -10,30 +10,6 @@ source:
 
 build:
   number: 0
-  entry_points:
-    - planar_hex = mpas_tools.planar_hex:main
-    - translate_planar_grid = mpas_tools.translate:main
-    - merge_grids = mpas_tools.merge_grids:main
-    - split_grids = mpas_tools.split_grids:main
-    - inject_bathymetry = mpas_tools.ocean.inject_bathymetry:main
-    - inject_preserve_floodplain = mpas_tools.ocean.inject_preserve_floodplain:main
-    - mpas_to_triangle = mpas_tools.mesh.creation.mpas_to_triangle:main
-    - triangle_to_netcdf = mpas_tools.mesh.creation.triangle_to_netcdf:main
-    - jigsaw_to_netcdf = mpas_tools.mesh.creation.jigsaw_to_netcdf:main
-    - scrip_from_mpas = mpas_tools.scrip.from_mpas:main
-    - ocean_add_depth = mpas_tools.ocean.depth:main_add_depth
-    - ocean_add_zmid = mpas_tools.ocean.depth:main_add_zmid
-    - ocean_write_time_varying_zmid = mpas_tools.ocean.depth:main_write_time_varying_zmid
-    - plot_ocean_transects = mpas_tools.ocean.viz.transects:main
-    - compute_mpas_region_masks = mpas_tools.mesh.mask:entry_point_compute_mpas_region_masks
-    - compute_mpas_transect_masks = mpas_tools.mesh.mask:entry_point_compute_mpas_transect_masks
-    - compute_mpas_flood_fill_mask = mpas_tools.mesh.mask:entry_point_compute_mpas_flood_fill_mask
-    - compute_lon_lat_region_masks = mpas_tools.mesh.mask:entry_point_compute_lon_lat_region_masks
-    - compute_projection_region_masks = mpas_tools.mesh.mask:entry_point_compute_projection_grid_region_masks
-    - prepare_seaice_partitions = mpas_tools.seaice.partition:prepare_partitions
-    - create_seaice_partitions = mpas_tools.seaice.partition:create_partitions
-    - simple_seaice_partitions = mpas_tools.seaice.partition:simple_partitions
-    - sort_mesh = mpas_tools.mesh.creation.sort_mesh:main
 
 requirements:
   build:
@@ -121,14 +97,14 @@ test:
     - define_cullMask.py --help
     - interpolate_to_mpasli_grid.py --help
     - mark_domain_boundaries_dirichlet.py --help
-    - add_land_locked_cells_to_mask.py --help
-    - widen_transect_edge_masks.py --help
-    - add_critical_land_blockages_to_mask.py --help
-    - moc_southern_boundary_extractor.py --help
+    - add_critical_land_blockages_to_mask --help
+    - add_land_locked_cells_to_mask --help
+    - widen_transect_edge_masks --help
+    - moc_southern_boundary_extractor --help
     - ocean_add_depth --help
     - ocean_add_zmid --help
     - ocean_write_time_varying_zmid --help
-    - paraview_vtk_field_extractor.py -f mesh_tools/mesh_conversion_tools/test/mesh.QU.1920km.151026.nc -v latCell,lonCell --ignore_time -o vtk_test
+    - paraview_vtk_field_extractor -f mesh_tools/mesh_conversion_tools/test/mesh.QU.1920km.151026.nc -v latCell,lonCell --ignore_time -o vtk_test
     - split_grids --help
     - merge_grids --help
     - inject_bathymetry mesh_tools/mesh_conversion_tools/test/mesh.QU.1920km.151026.nc
diff --git a/conda_package/setup.py b/conda_package/setup.py
index 3569f9949..b00b2dfb1 100755
--- a/conda_package/setup.py
+++ b/conda_package/setup.py
@@ -33,7 +33,7 @@
 
 os.chdir(here)
 
-for path in ['ocean', 'landice', 'visualization', 'mesh_tools']:
+for path in ['landice', 'mesh_tools']:
     destPath = './{}'.format(path)
     if os.path.exists(destPath):
         shutil.rmtree(destPath)
@@ -71,12 +71,7 @@
                'landice/mesh_tools_li/create_landice_grid_from_generic_MPAS_grid.py',
                'landice/mesh_tools_li/define_cullMask.py',
                'landice/mesh_tools_li/interpolate_to_mpasli_grid.py',
-               'landice/mesh_tools_li/mark_domain_boundaries_dirichlet.py',
-               'ocean/coastline_alteration/add_land_locked_cells_to_mask.py',
-               'ocean/coastline_alteration/widen_transect_edge_masks.py',
-               'ocean/coastline_alteration/add_critical_land_blockages_to_mask.py',
-               'ocean/moc_southern_boundary_extractor/moc_southern_boundary_extractor.py',
-               'visualization/paraview_vtk_field_extractor/paraview_vtk_field_extractor.py'],
+               'landice/mesh_tools_li/mark_domain_boundaries_dirichlet.py'],
       install_requires=install_requires,
       entry_points={'console_scripts':
                     ['planar_hex = mpas_tools.planar_hex:main',
@@ -102,4 +97,11 @@
                      'prepare_seaice_partitions = mpas_tools.seaice.partition:prepare_partitions',
                      'create_seaice_partitions = mpas_tools.seaice.partition:create_partitions',
                      'simple_seaice_partitions = mpas_tools.seaice.partition:simple_partitions',
-                     'vector_reconstruct = mpas_tools.vector.reconstruct:main']})
+                     'vector_reconstruct = mpas_tools.vector.reconstruct:main',
+                     'add_critical_land_blockages_to_mask = mpas_tools.ocean.coastline_alteration:main_add_critical_land_blockages',
+                     'add_land_locked_cells_to_mask = mpas_tools.ocean.coastline_alteration:main_add_land_locked_cells_to_mask',
+                     'widen_transect_edge_masks = mpas_tools.ocean.coastline_alteration:main_widen_transect_edge_masks',
+                     'moc_southern_boundary_extractor = mpas_tools.ocean.moc:moc_southern_boundary_extractor',
+                     'paraview_vtk_field_extractor = mpas_tools.viz.paraview_extractor:main',
+          ]
+      })
diff --git a/ocean/coastline_alteration/add_critical_land_blockages_to_mask.py b/ocean/coastline_alteration/add_critical_land_blockages_to_mask.py
index 76286b7a5..28fd9c6ad 100755
--- a/ocean/coastline_alteration/add_critical_land_blockages_to_mask.py
+++ b/ocean/coastline_alteration/add_critical_land_blockages_to_mask.py
@@ -1,42 +1,13 @@
 #!/usr/bin/env python
 """
-Name: add_critical_land_blockages_to_mask.py
-Author: Xylar Asay-Davis
-
 Add transects that identify critical regions where narrow strips of land block
 ocean flow.  These are, essentially, the opposite of critical passages, which
 must remain open for ocean flow.
 """
 
-from __future__ import absolute_import, division, print_function, \
-    unicode_literals
-
-import xarray
-import argparse
-
-from mpas_tools.ocean.coastline_alteration import add_critical_land_blockages
-
+from mpas_tools.ocean.coastline_alteration import (
+    main_add_critical_land_blockages
+)
 
 if __name__ == '__main__':
-    parser = \
-        argparse.ArgumentParser(description=__doc__,
-                                formatter_class=argparse.RawTextHelpFormatter)
-    parser.add_argument("-f", "--input_mask_file", dest="input_mask_filename",
-                        help="Mask file that includes cell and edge masks.",
-                        metavar="INPUTMASKFILE", required=True)
-    parser.add_argument("-o", "--output_mask_file",
-                        dest="output_mask_filename",
-                        help="Mask file that includes cell and edge masks.",
-                        metavar="OUTPUTMASKFILE", required=True)
-    parser.add_argument("-b", "--blockage_file", dest="blockage_file",
-                        help="Masks for each transect identifying critical "
-                             "land blockage.", metavar="BLOCKFILE",
-                        required=True)
-    args = parser.parse_args()
-
-    dsMask = xarray.open_dataset(args.input_mask_filename)
-
-    dsBlockages = xarray.open_dataset(args.blockage_file)
-
-    dsMask = add_critical_land_blockages(dsMask, dsBlockages)
-    dsMask.to_netcdf(args.output_mask_filename)
+    main_add_critical_land_blockages()
diff --git a/ocean/coastline_alteration/add_land_locked_cells_to_mask.py b/ocean/coastline_alteration/add_land_locked_cells_to_mask.py
index 799d211fe..9756d07f9 100755
--- a/ocean/coastline_alteration/add_land_locked_cells_to_mask.py
+++ b/ocean/coastline_alteration/add_land_locked_cells_to_mask.py
@@ -1,49 +1,12 @@
 #!/usr/bin/env python
 """
-Name: add_land_locked_cells_to_mask.py
-Author: Mark Petersen, Adrian Turner, Xylar Asay-Davis
-
 Find ocean cells that are land-locked, and alter the cell
 mask so that they are counted as land cells.
 """
-from __future__ import absolute_import, division, print_function, \
-    unicode_literals
-
-import argparse
-import xarray
 
-from mpas_tools.ocean.coastline_alteration import add_land_locked_cells_to_mask
+from mpas_tools.ocean.coastline_alteration import (
+    main_add_land_locked_cells_to_mask
+)
 
 if __name__ == '__main__':
-    parser = \
-        argparse.ArgumentParser(description=__doc__,
-                                formatter_class=argparse.RawTextHelpFormatter)
-    parser.add_argument("-f", "--input_mask_file", dest="input_mask_filename",
-                        help="Mask file that includes cell and edge masks.",
-                        metavar="INPUTMASKFILE", required=True)
-    parser.add_argument("-o", "--output_mask_file",
-                        dest="output_mask_filename",
-                        help="Mask file that includes cell and edge masks.",
-                        metavar="OUTPUTMASKFILE", required=True)
-    parser.add_argument("-m", "--mesh_file", dest="mesh_filename",
-                        help="MPAS Mesh filename.", metavar="MESHFILE",
-                        required=True)
-    parser.add_argument("-l", "--latitude_threshold",
-                        dest="latitude_threshold",
-                        help="Minimum latitude, in degrees, for transect "
-                             "widening.",
-                        required=False, type=float, default=43.0)
-    parser.add_argument("-n", "--number_sweeps", dest="nSweeps",
-                        help="Maximum number of sweeps to search for "
-                             "land-locked cells.",
-                        required=False, type=int, default=10)
-    args = parser.parse_args()
-
-    dsMask = xarray.open_dataset(args.input_mask_filename)
-
-    dsMesh = xarray.open_dataset(args.mesh_filename)
-
-    dsMask = add_land_locked_cells_to_mask(dsMask, dsMesh,
-                                           args.latitude_threshold,
-                                           args.nSweeps)
-    dsMask.to_netcdf(args.output_mask_filename)
+    main_add_land_locked_cells_to_mask()
diff --git a/ocean/coastline_alteration/widen_transect_edge_masks.py b/ocean/coastline_alteration/widen_transect_edge_masks.py
index 1d4bc067c..9632cd911 100755
--- a/ocean/coastline_alteration/widen_transect_edge_masks.py
+++ b/ocean/coastline_alteration/widen_transect_edge_masks.py
@@ -1,47 +1,12 @@
 #!/usr/bin/env python
 """
-Name: widen_transect_edge_masks.py
-Author: Mark Petersen, Xylar Asay-Davis
-
 Alter transects to be at least two cells wide.  This is used for critical
 passages, to avoid sea ice blockage.  Specifically, mark cells on both sides
 of each transect edge mask as a water cell.
 """
-from __future__ import absolute_import, division, print_function, \
-    unicode_literals
-
-import argparse
-import xarray
-
-from mpas_tools.ocean.coastline_alteration import widen_transect_edge_masks
-
+from mpas_tools.ocean.coastline_alteration import (
+    main_widen_transect_edge_masks
+)
 
 if __name__ == '__main__':
-
-    parser = \
-        argparse.ArgumentParser(description=__doc__,
-                                formatter_class=argparse.RawTextHelpFormatter)
-    parser.add_argument("-f", "--mask_file", dest="mask_filename",
-                        help="Mask file with cell and edge transect masks.",
-                        metavar="MASKFILE",
-                        required=True)
-    parser.add_argument("-m", "--mesh_file", dest="mesh_filename",
-                        help="MPAS Mesh filename.", metavar="MESHFILE",
-                        required=True)
-    parser.add_argument("-o", "--out_file", dest="out_filename",
-                        help="Output mask file,different from input filename.",
-                        metavar="MASKFILE",
-                        required=True)
-    parser.add_argument("-l", "--latitude_threshold",
-                        dest="latitude_threshold",
-                        help="Minimum latitude, degrees, for transect "
-                             "widening.",
-                        required=False, type=float, default=43.0)
-    args = parser.parse_args()
-
-    dsMask = xarray.open_dataset(args.mask_filename)
-
-    dsMesh = xarray.open_dataset(args.mesh_filename)
-
-    dsMask = widen_transect_edge_masks(dsMask, dsMesh, args.latitude_threshold)
-    dsMask.to_netcdf(args.out_filename)
+    main_widen_transect_edge_masks()
diff --git a/ocean/moc_southern_boundary_extractor/moc_southern_boundary_extractor.py b/ocean/moc_southern_boundary_extractor/moc_southern_boundary_extractor.py
index 14fce2e46..5ee8f1187 100755
--- a/ocean/moc_southern_boundary_extractor/moc_southern_boundary_extractor.py
+++ b/ocean/moc_southern_boundary_extractor/moc_southern_boundary_extractor.py
@@ -7,43 +7,11 @@
 boundary of each region in a file indicated with the -o flag.  The transect
 is applied only to vertices and edges, not cells, because the need for southern
 boundary transect data on cells is not foreseen.
-
-Author: Xylar Asay-Davis
-last modified: 5/22/2018
 '''
 
-from __future__ import absolute_import, division, print_function, \
-    unicode_literals
-
-import xarray
-import argparse
-
-from mpas_tools.io import \
-    write_netcdf
-from mpas_tools.ocean.moc import \
-    add_moc_southern_boundary_transects
-
-
-if __name__ == "__main__":
-
-    parser = \
-        argparse.ArgumentParser(description=__doc__,
-                                formatter_class=argparse.RawTextHelpFormatter)
-    parser.add_argument('-f', '--in_file', dest='in_file',
-                        help='Input file with MOC masks', metavar='IN_FILE',
-                        required=True)
-    parser.add_argument('-m', '--mesh_file', dest='mesh_file',
-                        help='Input mesh file', metavar='MESH_FILE',
-                        required=True)
-    parser.add_argument('-o', '--out_file', dest='out_file',
-                        help='Output file for MOC masks and southern-boundary '
-                        'transects', metavar='OUT_FILE',
-                        required=True)
-    args = parser.parse_args()
-
-    dsMasks = xarray.open_dataset(args.in_file)
-    dsMesh = xarray.open_dataset(args.mesh_file)
-
-    dsMasksAndTransects = add_moc_southern_boundary_transects(dsMasks, dsMesh)
+from mpas_tools.ocean.moc import (
+    moc_southern_boundary_extractor
+)
 
-    write_netcdf(dsMasksAndTransects, args.out_file)
+if __name__ == '__main__':
+    moc_southern_boundary_extractor()