Bump cython, fixes for tests, and fixes for deprecation warnings

.github/workflows/tests.yml

@@ -13,6 +13,7 @@ on:
 jobs:
   tests:
     strategy:
+      fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
         python-version: [3.11]
@@ -36,10 +37,24 @@ jobs:
           conda install -c conda-forge pocl pyopencl
           python -c 'import pyopencl as cl'
         if: ${{ runner.os != 'Windows' }}
+      - name: Setup compyle config on MacOS to use openmp enabled clang from homebrew
+        run: |
+          brew install libomp
+          mkdir -p ~/.compyle
+          touch ~/.compyle/config.py
+          echo "import os" >> ~/.compyle/config.py
+          echo "os.environ['CC'] = '$(brew --prefix llvm@15)/bin/clang'" >> ~/.compyle/config.py
+          echo "os.environ['CXX'] = '$(brew --prefix llvm@15)/bin/clang++'" >> ~/.compyle/config.py
+          export CPPFLAGS="-I$(brew --prefix libomp)/include -I$(brew --prefix llvm@15)/include -Xclang -fopenmp"
+          export LDFLAGS="-L$(brew --prefix libomp)/lib -L$(brew --prefix llvm@15)/lib -lomp"
+          python -c "import os; OMP_CFLAGS=os.environ.get('CPPFLAGS').split(' '); print(f'{OMP_CFLAGS=}')" >> ~/.compyle/config.py
+          python -c "import os; OMP_LINK=os.environ.get('LDFLAGS').split(' '); print(f'{OMP_LINK=}')" >> ~/.compyle/config.py
+          cat ~/.compyle/config.py
+        if: ${{ runner.os == 'macOS' }}
       - name: Install dependencies
         run: |
           conda info
-          conda install -c conda-forge numpy 'cython<3.0' h5py
+          conda install -c conda-forge numpy cython h5py
           python -m pip install --upgrade pip setuptools wheel
           python -m pip install https://github.com/pypr/cyarray/zipball/master
           python -m pip install https://github.com/pypr/compyle/zipball/master
@@ -52,7 +67,7 @@ jobs:
         id: month
         run: echo "month==$(date +'%m')" >> $GITHUB_OUTPUT
       - name: Deal with auto-generated code cache
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: |
             ~/.pysph

.github/workflows/zoltan-tests.yml

@@ -40,12 +40,12 @@ jobs:
       - name: Install dependencies
         run: |
           conda info
-          conda install -c conda-forge numpy 'cython<3.0'
+          conda install -c conda-forge numpy cython
           python -m pip install --upgrade pip setuptools wheel
-          python -m pip install mpi4py
+          python -m pip install "mpi4py<4.0"
           python -m pip install https://github.com/pypr/cyarray/zipball/master
-          python -m pip install --no-build-isolation https://github.com/pypr/pyzoltan/zipball/master
           python -m pip install https://github.com/pypr/compyle/zipball/master
+          python -m pip install --no-build-isolation https://github.com/pypr/pyzoltan/zipball/master
           python -m pip install -r requirements.txt
           python -m pip install -r requirements-test.txt
           python setup.py develop
@@ -55,7 +55,7 @@ jobs:
         id: month
         run: echo "month==$(date +'%m')" >> $GITHUB_OUTPUT
       - name: Deal with auto-generated code cache
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: |
             ~/.pysph

pyproject.toml

@@ -1,11 +1,11 @@
 [build-system]
 requires = [
     "Beaker",
-    "Cython<3.0",
+    "Cython>=0.20",
     "compyle>=0.8",
     "cyarray",
     "mako",
-    "oldest-supported-numpy",
+    "numpy>=2.0,<3",
     "pytools",
     "setuptools>=42.0.0",
     "wheel>=0.29.0",

pysph/base/box_sort_nnps.pxd

@@ -1,5 +1,7 @@
 # cython: language_level=3, embedsignature=True
 # distutils: language=c++
+# distutils: define_macros=NPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION
+
 from libcpp.map cimport map
 
 from .nnps_base cimport *

pysph/base/box_sort_nnps.pyx

@@ -1,4 +1,7 @@
-# cython: language_level=3, language=c++, embedsignature=True
+# cython: language_level=3, embedsignature=True
+# distutils: language=c++
+# distutils: define_macros=NPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION
+
 # Library imports.
 import numpy as np
 cimport numpy as np
@@ -42,7 +45,7 @@ cdef class BoxSortNNPS(LinkedListNNPS):
     @cython.boundscheck(False)
     @cython.wraparound(False)
     cdef inline long _get_valid_cell_index(self, int cid_x, int cid_y, int cid_z,
-            int* ncells_per_dim, int dim, int n_cells) nogil:
+            int* ncells_per_dim, int dim, int n_cells) noexcept nogil:
         """Return the flattened index for a valid cell"""
         cdef long ncx = ncells_per_dim[0]
         cdef long ncy = ncells_per_dim[1]