Merge pull request #399 from xylar/add_python_mask_creator

Add python mask creator

Author: xylar

conda_package/docs/Makefile

@@ -12,10 +12,6 @@ BUILDDIR      = _build
 help:
 	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 
-clean:
-	rm -rf *obs_table.rst generated obs
-	@$(SPHINXBUILD) -M clean "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
-
 .PHONY: help Makefile
 
 # Catch-all target: route all unknown targets to Sphinx using the new

conda_package/docs/api.rst

@@ -53,6 +53,16 @@ Mesh conversion
    cull
    mask
 
+.. currentmodule:: mpas_tools.mesh.mask
+
+.. autosummary::
+   :toctree: generated/
+
+   compute_mpas_region_masks
+   compute_mpas_transect_masks
+   compute_mpas_flood_fill_mask
+   compute_lon_lat_region_masks
+
 .. currentmodule:: mpas_tools.merge_grids
 
 .. autosummary::
@@ -76,6 +86,15 @@ Mesh conversion
    center
    center_on_mesh
 
+.. currentmodule:: mpas_tools.scrip.from_mpas
+
+.. autosummary::
+   :toctree: generated/
+
+   scrip_from_mpas
+
+I/O
+---
 
 .. currentmodule:: mpas_tools.io
 
@@ -84,15 +103,18 @@ Mesh conversion
 
    write_netcdf
 
-.. currentmodule:: mpas_tools.scrip.from_mpas
+Parallelism
+-----------
+
+.. currentmodule:: mpas_tools.parallel
 
 .. autosummary::
    :toctree: generated/
 
-   scrip_from_mpas
+   create_pool
 
-Inerpolation
-------------
+Interpolation
+-------------
 
 .. currentmodule:: mpas_tools.mesh.interpolation
 
@@ -147,11 +169,11 @@ Ocean Tools
    coastal_tools.plot_coarse_coast
    coastal_tools.plot_region_box
 
-    depth.add_depth
-    depth.add_zmid
-    depth.write_time_varying_zmid
-    depth.compute_depth
-    depth.compute_zmid
+   depth.add_depth
+   depth.add_zmid
+   depth.write_time_varying_zmid
+   depth.compute_depth
+   depth.compute_zmid
 
 .. currentmodule:: mpas_tools.ocean.inject_bathymetry
 
@@ -199,6 +221,25 @@ Logging
    check_call
    LoggingContext
 
+Transects
+=========
+
+.. currentmodule:: mpas_tools.transects
+
+.. autosummary::
+   :toctree: generated/
+
+   subdivide_great_circle
+   cartesian_to_great_circle_distance
+   subdivide_planar
+   lon_lat_to_cartesian
+   cartesian_to_lon_lat
+   angular_distance
+   intersects
+   intersection
+   Vector
+
+
 Visualization
 =============
 
@@ -223,9 +264,7 @@ Visualization
 
    make_triangle_tree
    find_transect_cells_and_weights
-   subdivide_great_circle
-   cartesian_to_great_circle_distance
-
+   find_planar_transect_cells_and_weights
 
 .. currentmodule:: mpas_tools.viz.colormaps
 

conda_package/docs/conf.py

@@ -39,7 +39,8 @@
 # list
 napoleon_use_ivar = True
 # Make sure multiple variable on the same line show up right
-napoleon_use_param = False
+# Commenting this out because it messes up intersphinx
+# napoleon_use_param = False
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -182,7 +183,8 @@
 intersphinx_mapping = {
     'python': ('https://docs.python.org/', None),
     'numpy': ('http://docs.scipy.org/doc/numpy/', None),
-    'xarray': ('http://xarray.pydata.org/en/stable/', None)}
-
+    'xarray': ('http://xarray.pydata.org/en/stable/', None),
+    'geometric_features':
+        ('http://mpas-dev.github.io/geometric_features/stable/', None)}
 
 github_doc_root = 'https://github.com/rtfd/recommonmark/tree/master/doc/'

conda_package/docs/index.rst

@@ -27,6 +27,8 @@ analyzing simulations, and in other MPAS-related workflows.
 
    logging
 
+   transects
+
    visualization
 
 .. toctree::