Upgrade NumPy and python

.github/workflows/testing.yml

@@ -12,7 +12,7 @@ jobs:
     steps:
     - uses: actions/setup-python@v2
       with:
-        python-version: "3.7"
+        python-version: "3.9"
     - uses: actions/checkout@v2
     - name: Lint with flake8
       run: |
@@ -27,7 +27,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.7, 3.8, 3.9, '3.10' ]
+        python-version: [ 3.8, 3.9, '3.10', '3.11']
     steps:
     - uses: actions/checkout@v2
     - name: Set up Python ${{ matrix.python-version }}

oceanmesh/clean.py

@@ -471,7 +471,7 @@ def _closest_node(node, nodes):
     L[L < eps] = eps
     L = L[:, None]
     for it in range(max_iter):
-        pnew = np.divide(S * np.matrix(vertices), np.hstack((W, W)))
+        pnew = np.divide(S @ np.array(vertices), np.hstack((W, W)))
         pnew[bnd, :] = vertices[bnd, :]
         vertices = pnew
         Lnew = np.sqrt(

oceanmesh/edgefx.py

@@ -7,11 +7,11 @@
 import numpy as np
 import scipy.spatial
 import skfmm
+from _HamiltonJacobi import gradient_limit
 from inpoly import inpoly2
 from shapely.geometry import LineString
 from skimage.morphology import medial_axis
 
-from _HamiltonJacobi import gradient_limit
 from oceanmesh.filterfx import filt2
 
 from . import edges

oceanmesh/fix_mesh.py

@@ -96,8 +96,10 @@ def unique_rows(A, return_index=False, return_inverse=False):
 
     orig_dtype = A.dtype
     ncolumns = A.shape[1]
-    dtype = np.dtype((np.character, orig_dtype.itemsize * ncolumns))
+    dtype = np.dtype((f"S{orig_dtype.itemsize * ncolumns}"))
     B, I, J = np.unique(A.view(dtype), return_index=True, return_inverse=True)
+    # NUMPY 2 compatibility
+    J = J.reshape(-1)
 
     B = B.view(orig_dtype).reshape((-1, ncolumns), order="C")
 

oceanmesh/geodata.py

@@ -669,7 +669,7 @@ def _read(self):
                     raise ValueError(f"Unsupported geometry type: {g.geom_type}")
 
                 poly = remove_dup(poly)
-                polys.append(np.row_stack((poly, delimiter)))
+                polys.append(np.vstack((poly, delimiter)))
 
         if len(polys) == 0:
             raise ValueError("Shoreline data does not intersect with bbox")
@@ -794,9 +794,9 @@ def __init__(self, dem, crs="EPSG:4326", bbox=None, extrapolate=False):
                     topobathy = np.transpose(topobathy, (1, 0))
             # Ensure its a floating point array
             topobathy = topobathy.astype(np.float64)
-            topobathy[
-                topobathy == nodata_value
-            ] = np.nan  # set the no-data value to nan
+            topobathy[topobathy == nodata_value] = (
+                np.nan
+            )  # set the no-data value to nan
         elif not dem.exists():
             raise FileNotFoundError(f"File {dem} could not be located.")
 

oceanmesh/idw.py

@@ -1,6 +1,7 @@
 """ invdisttree.py: inverse-distance-weighted interpolation using KDTree
     fast, solid, local
 """
+
 from __future__ import division
 
 import numpy as np

oceanmesh/mesh_generator.py

@@ -7,7 +7,6 @@
 import matplotlib.tri as tri
 import numpy as np
 import scipy.sparse as spsparse
-
 from _delaunay_class import DelaunayTriangulation as DT
 from _fast_geometry import unique_edges
 

pyproject.toml

@@ -3,4 +3,4 @@ requires = ["setuptools>=42", "wheel", "pybind11>=2.6.0", "versioneer-518"]
 build-backend = "setuptools.build_meta"
 
 [tool.black]
-target-version = ['py37']
+target-version = ['py39']

setup.cfg

@@ -28,6 +28,7 @@ install_requires =
         pyproj
         scipy
         geopandas
+        fiona
         shapely
         matplotlib
         rasterio>=1.3a1

setup.py

@@ -1,5 +1,6 @@
 import os
 import sys
+import configparser
 
 from pybind11.setup_helpers import Pybind11Extension, build_ext
 from setuptools import setup  # , find_packages
@@ -44,8 +45,26 @@
 cmdclass = versioneer.get_cmdclass()
 cmdclass.update({"build_ext": build_ext})
 
+
+def get_requirements():
+    """
+    Fix
+    """
+
+    config = configparser.ConfigParser()
+    config.read("setup.cfg")
+    requirements = config["options"]["install_requires"].split()
+
+    if sys.version_info < (3, 9):
+        requirements.remove("fiona")
+        requirements.append("fiona<1.10")
+
+    return requirements
+
+
 if __name__ == "__main__":
     setup(
+        install_requires=get_requirements(),
         cmdclass=cmdclass,
         version=versioneer.get_version(),
         ext_modules=ext_modules,

tests/test_bathymetric_gradient_function.py

@@ -1,6 +1,7 @@
 import os
 
 import pytest
+
 import oceanmesh as om
 
 fname = os.path.join(os.path.dirname(__file__), "GSHHS_i_L1.shp")