General Improvements + bug fixes + multi scale meshing support for global meshes (#87)

feat(mesh,geodata): CRS-safe global+regional multiscale meshing & shoreline Region API
	•	Add synthetic georef fallback for ungeoreferenced DEM rasters and normalize DEM full-read orientation
	•	Centralize CRS/stereo validation, drop brittle CRS set() checks, and harden multiscale SDF (non-finite guards, KDTree fixes)
	•	Align sizing grids across mixed CRS via CRS-aware Grid.reproject_to/compute_minimum; stabilize _compute_forces and min_edge_length from positive finite values
	•	Rewrite bathymetric_gradient_sizing_function to operate on DEM lattice in physical units with bounds, coarsening, and geographic meter↔degree scaling
	•	Document and test global+regional multiscale workflow (stereo/global-first semantics, bbox containment across projections, logging/plotting, e2e Australia refinement test)
	•	Introduce Region-first shoreline API with CRS autodetect/inference, improved error guidance, and Region-based DEM initialization
	•	Replace inpoly-python with Cython inpoly backend, relax boundary consistency checks, and update CI/tox/flake8 configuration

Author: krober10nd

.github/workflows/testing.yml

@@ -12,7 +12,7 @@ jobs:
     steps:
     - uses: actions/setup-python@v2
       with:
-        python-version: "3.9"
+        python-version: "3.12"
     - uses: actions/checkout@v2
     - name: Lint with flake8
       run: |
@@ -27,7 +27,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [ 3.8, 3.9, '3.10', '3.11']
+        python-version: ['3.10','3.11','3.12','3.13']
     steps:
     - uses: actions/checkout@v2
     - name: Set up Python ${{ matrix.python-version }}
@@ -44,11 +44,36 @@ jobs:
       run: |
         sudo apt install -y libopenmpi3 libopenmpi-dev openmpi-bin
         sudo apt install -y libhdf5-dev
-    - name: pre install numpy (for inpoly)
+    - name: Install Python build dependencies
       run: |
-        pip install numpy
+        python -m pip install --upgrade pip
+        python -m pip install Cython numpy
+    - name: Verify Cython inpoly kernel is available
+      env:
+        OCEANMESH_INPOLY_ACCEL: "1"
+      run: |
+        python -m pip install -e .
+        python - << 'PY'
+        import os, importlib
+        from oceanmesh.geometry import point_in_polygon as pip
+
+        # Ensure we use the default acceleration behaviour
+        os.environ.pop("OCEANMESH_INPOLY_METHOD", None)
+        os.environ["OCEANMESH_INPOLY_ACCEL"] = "1"
+        pip = importlib.reload(pip)
+
+        if not getattr(pip, "_COMPILED_KERNEL_AVAILABLE", False):
+            raise SystemExit("Cython inpoly2 kernel not available in CI environment")
+
+        print("_COMPILED_KERNEL_AVAILABLE =", pip._COMPILED_KERNEL_AVAILABLE)
+        from oceanmesh.geometry.point_in_polygon_ import inpoly2_fast
+        print("inpoly2_fast:", inpoly2_fast)
+        PY
     - name: Test with tox
+      env:
+        OCEANMESH_INPOLY_ACCEL: "1"
+        OCEANMESH_INPOLY_METHOD: ""
       run: |
-        pip install tox
+        python -m pip install tox
         tox
     - uses: codecov/codecov-action@v1

CMakeLists.txt

@@ -1,3 +1,15 @@
+##############################################################################
+# LEGACY/UNSUPPORTED BUILD SCRIPT
+#
+# This CMake configuration is retained for historical reference only.
+# It is NOT used by the standard Python build, which uses setuptools with
+# pybind11 (see setup.py and pyproject.toml). Do not rely on this file for
+# normal development or installation. The supported build path is:
+#   - pip/setuptools (Pybind11Extension) invoked via setup.py
+# On Windows, CMake may still be required by vcpkg solely to build CGAL
+# dependencies; it is not used to build oceanmesh itself.
+##############################################################################
+
 cmake_minimum_required(VERSION 2.8.12)
 
 project(oceanmesh)

MANIFEST.in

@@ -5,3 +5,5 @@ include README.md LICENSE.txt
 global-include CMakeLists.txt
 include versioneer.py
 include oceanmesh/_version.py
+recursive-include oceanmesh/geometry *.py
+recursive-include oceanmesh/geometry *.pyx *.c