Merge pull request #10 from cassidymwagner/main

Merging updates from main

Author: cassidymwagner

.github/workflows/draft-pdf.yml

@@ -0,0 +1,30 @@
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - "v*"
+  pull_request:
+    branches:
+      - main
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: joss
+          # This should be the path to the paper within your repo.
+          paper-path: paper/paper.md
+      - name: Upload
+        uses: actions/upload-artifact@v1
+        with:
+          name: paper
+          # This is the output path where Pandoc will write the compiled
+          # PDF. Note, this should be the same directory as the input
+          # paper.md
+          path: paper/paper.pdf

oceans_sf/calculate_advection.py

@@ -44,17 +44,7 @@ def calculate_advection(  # noqa: D417
             northward_advection) if scalar is not provided, otherwise returns an ndarray
             of scalar advection.
     """
-    if grid_type == "latlon":
-        xcoords = dx.cumsum()
-        ycoords = dy.cumsum()
-
-        if scalar is not None:
-            dsdy, dsdx = np.gradient(scalar, xcoords, ycoords, axis=(0, 1))
-        else:
-            dudy, dudx = np.gradient(u, xcoords, ycoords, axis=(0, 1))
-            dvdy, dvdx = np.gradient(v, xcoords, ycoords, axis=(0, 1))
-
-    else:
+    if grid_type == "uniform":
         dx = np.abs(x[0] - x[1])
         dy = np.abs(y[0] - y[1])
 
@@ -64,6 +54,16 @@ def calculate_advection(  # noqa: D417
             dudy, dudx = np.gradient(u, dx, dy, axis=(0, 1))
             dvdy, dvdx = np.gradient(v, dx, dy, axis=(0, 1))
 
+    else:
+        xcoords = dx.cumsum()
+        ycoords = dy.cumsum()
+
+        if scalar is not None:
+            dsdy, dsdx = np.gradient(scalar, xcoords, ycoords, axis=(0, 1))
+        else:
+            dudy, dudx = np.gradient(u, xcoords, ycoords, axis=(0, 1))
+            dvdy, dvdx = np.gradient(v, xcoords, ycoords, axis=(0, 1))
+
     if scalar is not None:
         advection = u * dsdx + v * dsdy
     else:

oceans_sf/calculate_structure_function.py

@@ -3,7 +3,7 @@
 from .shift_array2d import shift_array2d
 
 
-def calculate_structure_function(  # noqa: D417
+def calculate_structure_function(  # noqa: D417, C901
     u,
     v,
     adv_e,
@@ -14,7 +14,7 @@ def calculate_structure_function(  # noqa: D417
     scalar=None,
     adv_scalar=None,
     traditional_type=None,
-    boundary="Periodic",
+    boundary="periodic-all",
 ):
     """
     Calculate structure function, either advective or traditional.
@@ -50,7 +50,9 @@ def calculate_structure_function(  # noqa: D417
             Accepted types are: "LL", "LLL", "LTT", "LSS". If None,
             no traditional structure functions are calculated. Defaults to None.
         boundary: str, optional
-            Boundary condition for shifting arrays. Defaults to "Periodic".
+            Boundary condition for shifting arrays. Accepted strings
+            are "periodic-x", "periodic-y", and "periodic-all".
+            Defaults to "periodic-all".
 
     Returns
     -------

oceans_sf/generate_structure_functions.py

@@ -19,7 +19,7 @@ def generate_structure_functions(  # noqa: C901, D417
     traditional_type=None,
     dx=None,
     dy=None,
-    boundary="Periodic",
+    boundary="periodic-all",
     even="True",
     grid_type="uniform",
     nbins=10,
@@ -56,7 +56,8 @@ def generate_structure_functions(  # noqa: C901, D417
         dy: float, optional
             Grid spacing in the y-direction. Defaults to None.
         boundary: str, optional
-            Boundary condition of the data. Defaults to "Periodic".
+            Boundary condition of the data. Accepted strings are "periodic-x",
+            "periodic-y", and "periodic-all". Defaults to "periodic-all".
         even: bool, optional
             Flag indicating if the grid is evenly spaced. Defaults to True.
         grid_type:str, optional
@@ -90,10 +91,16 @@ def generate_structure_functions(  # noqa: C901, D417
 
     # Define a list of separation distances to iterate over.
     # Periodic is half the length since the calculation will wrap the data.
-    if boundary == "Periodic":
+    if boundary == "periodic-all":
         sep_z = range(1, int(len(x) / 2))
         sep_m = range(1, int(len(y) / 2))
-    else:
+    elif boundary == "periodic-x":
+        sep_z = range(1, int(len(x) / 2))
+        sep_m = range(1, int(len(y) - 1))
+    elif boundary == "periodic-y":
+        sep_z = range(1, int(len(x) - 1))
+        sep_m = range(1, int(len(y) / 2))
+    elif boundary is None:
         sep_z = range(1, int(len(x) - 1))
         sep_m = range(1, int(len(y) - 1))
 
@@ -129,7 +136,10 @@ def generate_structure_functions(  # noqa: C901, D417
     # Iterate over separations right and down
     for down in sep_m:
         right = 1
-        yroll = shift_array1d(y, shift_by=down, boundary=boundary)
+        if boundary == "periodic-all" or boundary == "periodic-y":
+            yroll = shift_array1d(y, shift_by=down, boundary="Periodic")
+        else:
+            yroll = shift_array1d(y, shift_by=down, boundary=None)
 
         SF_dicts = calculate_structure_function(
             u,
@@ -167,7 +177,10 @@ def generate_structure_functions(  # noqa: C901, D417
 
     for right in sep_z:
         down = 1
-        xroll = shift_array1d(x, shift_by=right, boundary=boundary)
+        if boundary == "periodic-all" or boundary == "periodic-x":
+            xroll = shift_array1d(x, shift_by=right, boundary="Periodic")
+        else:
+            xroll = shift_array1d(x, shift_by=right, boundary=None)
 
         SF_dicts = calculate_structure_function(
             u,

oceans_sf/shift_array2d.py

@@ -2,7 +2,7 @@
 
 
 def shift_array2d(  # noqa: D417
-    input_array, shift_right=1, shift_down=1, boundary="Periodic"
+    input_array, shift_right=1, shift_down=1, boundary="periodic-all"
 ):
     """
     Shifts 2D array right and down by the specified integer amounts and returns
@@ -22,8 +22,9 @@ def shift_array2d(  # noqa: D417
             conditions. Defaults to 1.
         boundary: str, optional
             Boundary condition for input array. Periodic boundary conditions will wrap
-            the array, otherwise the array will be padded with NaNs. Defaults to
-            "Periodic".
+            the array, otherwise the array will be padded with NaNs. Accepted strings
+            are "periodic-x", "periodic-y", and "periodic-all".
+            Defaults to "periodic-all".
 
     Returns
     -------
@@ -35,13 +36,26 @@ def shift_array2d(  # noqa: D417
     shifted_right_array = np.full(np.shape(input_array), np.nan)
     shifted_down_array = np.full(np.shape(input_array), np.nan)
 
-    if boundary == "Periodic":
+    if boundary == "periodic-all":
         shifted_right_array[:, :shift_right] = input_array[:, -shift_right:]
         shifted_right_array[:, shift_right:] = input_array[:, :-shift_right]
 
         shifted_down_array[:shift_down, :] = input_array[-shift_down:, :]
         shifted_down_array[shift_down:, :] = input_array[:-shift_down, :]
-    else:
+
+    elif boundary == "periodic-x":
+        shifted_right_array[:, :shift_right] = input_array[:, -shift_right:]
+        shifted_right_array[:, shift_right:] = input_array[:, :-shift_right]
+
+        shifted_down_array[shift_down:, :] = input_array[:-shift_down, :]
+
+    elif boundary == "periodic-y":
+        shifted_right_array[:, shift_right:] = input_array[:, :-shift_right]
+
+        shifted_down_array[:shift_down, :] = input_array[-shift_down:, :]
+        shifted_down_array[shift_down:, :] = input_array[:-shift_down, :]
+
+    elif boundary is None:
         shifted_right_array[:, shift_right:] = input_array[:, :-shift_right]
         shifted_down_array[shift_down:, :] = input_array[:-shift_down, :]
 

tests/test_calculate_structure_function.py

@@ -8,7 +8,7 @@
 
 @pytest.mark.parametrize(
     "u, v, adv_e, adv_n, down, right, skip_velocity_sf, scalar, "
-    "adv_scalar, traditional_order, boundary, expected_result",
+    "adv_scalar, traditional_type, boundary, expected_result",
     [
         # Test 1: velocity and scalar no traditional
         (
@@ -21,8 +21,8 @@
             False,  # skip_velocity_sf
             np.array([[1, 2], [3, 4]]),  # scalar
             np.array([[3, -2], [-3, 12]]),  # adv_scalar
-            0,  # traditional_order
-            "Periodic",  # boundary
+            None,  # traditional_type
+            "periodic-all",  # boundary
             {
                 "SF_velocity_right": 88,
                 "SF_velocity_down": 138,
@@ -42,17 +42,15 @@
             False,
             np.array([[1, 2], [3, 4]]),
             np.array([[3, -2], [-3, 12]]),
-            2,
-            "Periodic",
+            ["LL"],
+            "periodic-all",
             {
                 "SF_velocity_right": 88,
-                "SF_trad_velocity_right": 1,
+                "SF_LL_right": 1,
                 "SF_scalar_right": 5,
-                "SF_trad_scalar_right": 1,
                 "SF_velocity_down": 138,
-                "SF_trad_velocity_down": 4,
+                "SF_LL_down": 4,
                 "SF_scalar_down": 8,
-                "SF_trad_scalar_down": 4,
             },
         ),
         # Test 3: all but skip velocity and no traditional
@@ -66,8 +64,8 @@
             True,
             np.array([[1, 2], [3, 4]]),
             np.array([[3, -2], [-3, 12]]),
-            0,
-            "Periodic",
+            None,
+            "periodic-all",
             {
                 "SF_scalar_right": 5,
                 "SF_scalar_down": 8,
@@ -84,8 +82,8 @@
             False,
             None,
             None,
-            0,
-            "Periodic",
+            None,
+            "periodic-all",
             {
                 "SF_velocity_right": 88,
                 "SF_velocity_down": 138,
@@ -102,7 +100,7 @@
             False,
             np.array([[1, 2], [3, 4]]),
             np.array([[3, -2], [-3, 12]]),
-            0,
+            None,
             None,
             {
                 "SF_velocity_right": 88,
@@ -122,17 +120,15 @@
             False,
             np.array([[1, 2], [3, 4]]),
             np.array([[3, -2], [-3, 12]]),
-            2,
+            ["LL"],
             None,
             {
                 "SF_velocity_right": 88,
-                "SF_trad_velocity_right": 1,
+                "SF_LL_right": 1,
                 "SF_scalar_right": 5,
-                "SF_trad_scalar_right": 1,
                 "SF_velocity_down": 138,
-                "SF_trad_velocity_down": 4,
+                "SF_LL_down": 4,
                 "SF_scalar_down": 8,
-                "SF_trad_scalar_down": 4,
             },
         ),
         # Test 7: all but skip velocity and no traditional non-periodic
@@ -146,7 +142,7 @@
             True,
             np.array([[1, 2], [3, 4]]),
             np.array([[3, -2], [-3, 12]]),
-            0,
+            None,
             None,
             {
                 "SF_scalar_right": 5,
@@ -164,7 +160,7 @@
             False,
             None,
             None,
-            0,
+            None,
             None,
             {
                 "SF_velocity_right": 88,
@@ -183,7 +179,7 @@ def test_calculate_structure_function_parameterized(
     skip_velocity_sf,
     scalar,
     adv_scalar,
-    traditional_order,
+    traditional_type,
     boundary,
     expected_result,
 ):
@@ -198,7 +194,7 @@ def test_calculate_structure_function_parameterized(
         skip_velocity_sf,
         scalar,
         adv_scalar,
-        traditional_order,
+        traditional_type,
         boundary,
     )