Merge pull request #370 from UXARRAY/philipc2/refactor

Organize Helpers and Project Structure

docs/examples/003-area-calc.ipynb

@@ -586,7 +586,7 @@
    },
    "outputs": [],
    "source": [
-    "from uxarray.utils.helpers import calculate_face_area"
+    "from uxarray.grid.area import calculate_face_area"
    ]
   },
   {

docs/examples/004-working-with-mpas-grids.ipynb

@@ -447,7 +447,7 @@
     "import matplotlib.pyplot as plt\n",
     "from matplotlib.collections import PolyCollection\n",
     "\n",
-    "from uxarray.utils.helpers import close_face_nodes"
+    "from uxarray.grid.connectivity import close_face_nodes"
    ]
   },
   {

docs/internal_api/index.rst

@@ -1,8 +1,8 @@
 .. currentmodule:: uxarray
 
-########
+############
 Internal API
-########
+############
 
 This page shows already-implemented Uxarray internal API functions. You can also
 check the draft `UXarray API
@@ -23,28 +23,27 @@ Class
 
    UxDataset
 
-
 Attributes
 ----------
 .. autosummary::
    :toctree: _autosummary
+
    UxDataset._source_datasets
    UxDataset._uxgrid
 
 
-
 Methods
 -------
 .. autosummary::
    :toctree: _autosummary
-   __getitem__
-   __setitem__
-   _calculate_binary_op
-   _construct_dataarray
-   _construct_direct
-   _copy
-   _replace
 
+   UxDataset.__getitem__
+   UxDataset.__setitem__
+   UxDataset._calculate_binary_op
+   UxDataset._construct_dataarray
+   UxDataset._construct_direct
+   UxDataset._copy
+   UxDataset._replace
 
 
 UxDataArray
@@ -73,11 +72,9 @@ Methods
 .. autosummary::
    :toctree: _autosummary
 
-   _construct_direct
-   _copy
-   _replace
-
-
+   UxDataArray._construct_direct
+   UxDataArray._copy
+   UxDataArray._replace
 
 Grid
 ===========
@@ -89,45 +86,15 @@ Class
 
    Grid
 
-
-IO
-----------
-.. autosummary::
-   :toctree: _autosummary
-
-   io._exodus._read_exodus
-   io._exodus._encode_exodus
-   io._exodus._get_element_type
-   io._mpas._dual_to_ugrid
-   io._mpas._primal_to_ugrid
-   io._mpas._replace_padding
-   io._mpas._replace_zeros
-   io._mpas._to_zero_index
-   io._mpas._set_global_attrs
-   io._mpas._read_mpas
-   io._ugrid._encode_ugrid
-   io._ugrid._read_ugrid
-   io._scrip._read_scrip
-   io._scrip._encode_scrip
-   io._scrip._to_ugrid
-
-
 Methods
 -------
 .. autosummary::
    :toctree: _autosummary
 
-   __init_grid_var_names__
-   __from_ds__
-   __from_vert__
-   __init_grid_var_attrs__
-   _build_edge_node_connectivity
-   _build_face_edges_connectivity
-   _build_nNodes_per_face
-   _populate_cartesian_xyz_coord
-   _populate_lonlat_coord
-
-
+   Grid.__init_grid_var_names__
+   Grid.__from_ds__
+   Grid.__from_vert__
+   Grid.__init_grid_var_attrs__
 
 Attributes
 ----------
@@ -140,15 +107,34 @@ Operators
 ---------
 .. autosummary::
    :toctree: _autosummary
+
    Grid.__eq__
    Grid.__ne__
 
 Helpers
 ===========
 
-.. currentmodule:: uxarray
+Connectivity
+------------
+.. autosummary::
+   :toctree: _autosummary
+
+   grid.connectivity._replace_fill_values
+   grid.connectivity._build_nNodes_per_face
+   grid.connectivity._build_edge_node_connectivity
+   grid.connectivity._build_face_edges_connectivity
+
+Coordinates
+-----------
+.. autosummary::
+   :toctree: _autosummary
+
+   grid.coordinates._populate_cartesian_xyz_coord
+   grid.coordinates._populate_lonlat_coord
+
+IO
+---
 .. autosummary::
    :toctree: _autosummary
 
-   utils.helpers._is_ugrid
-   utils.helpers._replace_fill_values
+   io.utils._parse_grid_type

docs/user_api/index.rst

@@ -9,8 +9,6 @@ check the draft `UXarray API
 <https://github.com/UXARRAY/uxarray/blob/main/docs/user_api/uxarray_api.md>`_
 documentation to see the tentative whole API and let us know if you have any feedback!
 
-
-
 UxDataset
 =========
 A ``xarray.Dataset``-like, multi-dimensional, in memory, array database.
@@ -20,7 +18,6 @@ dataset operators and attributes through the ``uxgrid`` accessor.
 Below is a list of features explicitly added to `UxDataset` to work on
 Unstructured Grids:
 
-
 Class
 -----
 .. autosummary::
@@ -33,28 +30,24 @@ IO
 .. autosummary::
    :toctree: _autosummary
 
-    open_dataset
-    open_mfdataset
-    enable_jit_cache
-    disable_jit_cache
-    enable_jit
-    disable_jit
+   open_dataset
+   open_mfdataset
 
 Attributes
 ----------
 .. autosummary::
    :toctree: _autosummary
 
-    UxDataset.uxgrid
-    UxDataset.source_datasets
+   UxDataset.uxgrid
+   UxDataset.source_datasets
 
 Methods
 -------
 .. autosummary::
    :toctree: _autosummary
 
-    UxDataset.info
-    UxDataset.integrate
+   UxDataset.info
+   UxDataset.integrate
 
 
 UxDataArray
@@ -139,23 +132,44 @@ Attributes
    Grid.Mesh2_edge_nodes
    Grid.Mesh2_face_edges
 
-
 Helpers
 ===========
 
-.. currentmodule:: uxarray
+Face Area
+----------
+.. autosummary::
+   :toctree: _autosummary
+
+   grid.area.calculate_face_area
+   grid.area.get_all_face_area_from_coords
+   grid.area.calculate_spherical_triangle_jacobian
+   grid.area.calculate_spherical_triangle_jacobian_barycentric
+   grid.area.get_gauss_quadratureDG
+   grid.area.get_tri_quadratureDG
+
+Connectivity
+------------
+.. autosummary::
+   :toctree: _autosummary
+
+   grid.connectivity.close_face_nodes
+
+Coordinates
+-----------
+.. autosummary::
+   :toctree: _autosummary
+
+   grid.coordinates.node_lonlat_rad_to_xyz
+   grid.coordinates.node_xyz_to_lonlat_rad
+   grid.coordinates.normalize_in_place
+   grid.coordinates.grid_center_lat_lon
+
+Numba
+-----
 .. autosummary::
    :toctree: _autosummary
 
-   calculate_face_area
-   calculate_spherical_triangle_jacobian
-   calculate_spherical_triangle_jacobian_barycentric
-   close_face_nodes
-   get_all_face_area_from_coords
-   get_gauss_quadratureDG
-   get_tri_quadratureDG
-   grid_center_lat_lon
-   node_xyz_to_lonlat_rad
-   node_lonlat_rad_to_xyz
-   normalize_in_place
-   parse_grid_type
+   utils.enable_jit_cache
+   utils.disable_jit_cache
+   utils.enable_jit
+   utils.disable_jit

test/test_exodus.py

@@ -5,7 +5,7 @@
 from pathlib import Path
 
 import uxarray as ux
-from uxarray.utils.constants import INT_DTYPE, INT_FILL_VALUE
+from uxarray.constants import INT_DTYPE, INT_FILL_VALUE
 
 current_path = Path(os.path.dirname(os.path.realpath(__file__)))
 

test/test_grid.py

@@ -8,6 +8,10 @@
 
 import uxarray as ux
 
+from uxarray.grid.connectivity import _build_edge_node_connectivity, _build_face_edges_connectivity
+
+from uxarray.grid.coordinates import _populate_cartesian_xyz_coord, _populate_lonlat_coord
+
 try:
     import constants
 except ImportError:
@@ -429,7 +433,7 @@ def test_populate_cartesian_xyz_coord(self):
         verts_degree = np.stack((lon_deg, lat_deg), axis=1)
 
         vgrid = ux.open_grid(verts_degree, islatlon=False)
-        vgrid._populate_cartesian_xyz_coord()
+        _populate_cartesian_xyz_coord(vgrid)
 
         for i in range(0, vgrid.nMesh2_node):
             nt.assert_almost_equal(vgrid._ds["Mesh2_node_cart_x"].values[i],
@@ -470,7 +474,7 @@ def test_populate_lonlat_coord(self):
         verts_cart = np.stack((cart_x, cart_y, cart_z), axis=1)
 
         vgrid = ux.open_grid(verts_cart, islatlon=False)
-        vgrid._populate_lonlat_coord()
+        _populate_lonlat_coord(vgrid)
         # The connectivity in `__from_vert__()` will be formed in a reverse order
         lon_deg, lat_deg = zip(*reversed(list(zip(lon_deg, lat_deg))))
         for i in range(0, vgrid.nMesh2_node):
@@ -665,7 +669,7 @@ def test_build_face_edges_connectivity_mpas(self):
         edge_nodes_expected = np.unique(edge_nodes_expected, axis=0)
 
         # construct edge nodes
-        mpas_grid_ux._build_edge_node_connectivity(repopulate=True)
+        _build_edge_node_connectivity(mpas_grid_ux, repopulate=True)
         edge_nodes_output = mpas_grid_ux._ds['Mesh2_edge_nodes'].values
 
         self.assertTrue(np.array_equal(edge_nodes_expected, edge_nodes_output))
@@ -688,7 +692,7 @@ def test_build_face_edges_connectivity(self):
 
             mesh2_face_nodes = tgrid._ds["Mesh2_face_nodes"]
 
-            tgrid._build_face_edges_connectivity()
+            _build_face_edges_connectivity(tgrid)
             mesh2_face_edges = tgrid._ds.Mesh2_face_edges
             mesh2_edge_nodes = tgrid._ds.Mesh2_edge_nodes
 
@@ -723,7 +727,7 @@ def test_build_face_edges_connectivity_mpas(self):
 
         mesh2_face_nodes = tgrid._ds["Mesh2_face_nodes"]
 
-        tgrid._build_face_edges_connectivity()
+        _build_face_edges_connectivity(tgrid)
         mesh2_face_edges = tgrid._ds.Mesh2_face_edges
         mesh2_edge_nodes = tgrid._ds.Mesh2_edge_nodes
 
@@ -746,7 +750,7 @@ def test_build_face_edges_connectivity_fillvalues(self):
             self.f5_deg, self.f6_deg
         ]
         uds = ux.open_grid(verts)
-        uds._build_face_edges_connectivity()
+        _build_face_edges_connectivity(uds)
         n_face = len(uds._ds["Mesh2_face_edges"].values)
         n_node = uds.nMesh2_node
         n_edge = len(uds._ds["Mesh2_edge_nodes"].values)