Bump cython

.github/workflows/tests.yml

@@ -7,7 +7,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python-version: ['3.10', '3.11']
+        python-version: ['3.11', '3.12']
 
     env:
       USE_TRILINOS: 1
@@ -28,9 +28,9 @@ jobs:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip setuptools wheel
-          python -m pip install numpy 'cython<3.0'
-          python -m pip install -r requirements.txt
-          python setup.py develop
+          pip install --upgrade pip setuptools wheel
+          pip install https://github.com/pypr/cyarray/zipball/master
+          pip install -r requirements.txt
+          pip install -e .[tests] -v --no-build-isolation
       - name: Run tests
         run: pytest -v pyzoltan

pyproject.toml

@@ -0,0 +1,47 @@
+[build-system]
+requires = [
+    "setuptools >= 61.0", 
+    "cython>3.0", 
+    "cyarray",
+    "mpi4py>=1.2, <4.0"
+]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "pyzoltan"
+dynamic = ["version"]
+readme = "README.rst"
+license = {file = "LICENSE.txt"}
+dependencies = ["numpy", "mpi4py>=1.2"]
+description = "Wrapper for the Zoltan data management library"
+authors = [
+  {name = "PySPH Developers", email = "[email protected]"}
+]
+keywords = ["Cython", "Zoltan", "Dynamic load balancing"]
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Environment :: Console",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: BSD License",
+    "Natural Language :: English",
+    "Operating System :: MacOS :: MacOS X",
+    "Operating System :: Microsoft :: Windows",
+    "Operating System :: POSIX",
+    "Operating System :: Unix",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Topic :: Scientific/Engineering",
+    "Topic :: Scientific/Engineering :: Physics",
+    "Topic :: Software Development :: Libraries"
+]
+
+[project.optional-dependencies]
+docs = ["sphinx"]
+tests = ["pytest>=3.0"]
+dev = ["sphinx", "pytest>=3.0", "cython>3.0", "cyarray"]
+
+[project.urls]
+Documentation = "https://pyzoltan.readthedocs.io"
+Repository = "https://github.com/pypr/pyzoltan.git"
+Issues = "https://github.com/pypr/pyzoltan/issues"

pyzoltan/core/zoltan.pxd

@@ -1,3 +1,6 @@
+# cython: language_level=3, embedsignature=True
+# distutils: language=c++
+
 cimport mpi4py.MPI as mpi
 if MPI4PY_V2:
    from mpi4py cimport libmpi as mpic

pyzoltan/core/zoltan.pyx

@@ -1,3 +1,6 @@
+# cython: language_level=3, embedsignature=True
+# distutils: language=c++
+
 """Definitions for the Zoltan wrapper
 
 This module defines the main wrapper for the Zoltan library. Users can
@@ -45,7 +48,7 @@ from cyarray.carray import DoubleArray, IntArray, UIntArray
 from warnings import warn
 
 # Local imports
-import zoltan_utils
+from . import zoltan_utils
 
 def get_zoltan_id_type_max():
     if ZOLTAN_UNSIGNED_INT:
@@ -102,7 +105,7 @@ cdef int get_number_of_objects(void* data, int* ierr):
 
 cdef void get_obj_list(void* data, int sizeGID, int sizeLID,
                        ZOLTAN_ID_PTR globalID, ZOLTAN_ID_PTR localID,
-                       int wgt_dim, float* obj_wts, int* ierr):
+                       int wgt_dim, float* obj_wts, int* ierr) noexcept:
     """Return the local and global ids of the objects.
 
     Methods: RCB, RIB, HSFC
@@ -133,7 +136,7 @@ cdef int get_num_geom(void* data, int* ierr):
 
 cdef void get_geometry_list(void* data, int sizeGID, int sizeLID, int num_obj,
                             ZOLTAN_ID_PTR globalID, ZOLTAN_ID_PTR localID,
-                            int num_dim, double* geom_vec, int* ierr):
+                            int num_dim, double* geom_vec, int* ierr) noexcept:
     """Return the coordinate locations for Zoltan.
 
     Methods: RCB, RIB, HSFC

pyzoltan/core/zoltan_comm.pxd

@@ -1,3 +1,6 @@
+# cython: language_level=3, embedsignature=True
+# distutils: language=c++
+
 import numpy as np
 cimport numpy as np
 

pyzoltan/core/zoltan_comm.pyx

@@ -1,3 +1,6 @@
+# cython: language_level=3, embedsignature=True
+# distutils: language=c++
+
 """Wrapper for the Zoltan Unstructured Communication Package
 
 The Unstructured Communication utilities simplifies some common

pyzoltan/core/zoltan_dd.pxd

@@ -1,3 +1,6 @@
+# cython: language_level=3, embedsignature=True
+# distutils: language=c++
+
 """Wrapper for the Zoltan Distributed Directory and routines"""
 cimport mpi4py.MPI as mpi
 if MPI4PY_V2:

pyzoltan/core/zoltan_dd.pyx

@@ -1,3 +1,6 @@
+# cython: language_level=3, embedsignature=True
+# distutils: language=c++
+
 """Example for the Zoltan Distributed data directory"""
 from pyzoltan.core.zoltan cimport _check_error
 

pyzoltan/czoltan/czoltan.pxd

@@ -1,3 +1,6 @@
+# cython: language_level=3, embedsignature=True
+# distutils: language=c++
+
 """Cython Wrapper for Zoltan. """
 
 if MPI4PY_V2:
@@ -152,7 +155,7 @@ cdef extern from "zoltan.h":
     ctypedef int ZOLTAN_NUM_OBJ_FN(
         void *data,
         int *ierr
-        )
+        ) except? -1
 
     extern int Zoltan_Set_Num_Obj_Fn(
         Zoltan_Struct *zz, ZOLTAN_NUM_OBJ_FN *fn_ptr, void *data_ptr)
@@ -217,7 +220,7 @@ cdef extern from "zoltan.h":
     ctypedef int ZOLTAN_NUM_GEOM_FN(
         void *data,
         int *ierr
-        )
+        )  except? -1
 
     extern int Zoltan_Set_Num_Geom_Fn(
         Zoltan_Struct *zz,

pyzoltan/czoltan/czoltan_comm.pxd

@@ -1,3 +1,6 @@
+# cython: language_level=3, embedsignature=True
+# distutils: language=c++
+
 """Cython wrapper for the Zoltan unstructured communication package"""
 
 if MPI4PY_V2:

pyzoltan/czoltan/czoltan_config.pxd

@@ -1,3 +1,5 @@
+# cython: language_level=3
+
 cdef extern from "Zoltan_config.h":
 
     # package string

pyzoltan/czoltan/czoltan_dd.pxd

@@ -1,3 +1,6 @@
+# cython: language_level=3, embedsignature=True
+# distutils: language=c++
+
 """Cython wrapper for the Zoltan Distributed Directory"""
 
 if MPI4PY_V2:

pyzoltan/czoltan/czoltan_types.pxd

@@ -1,3 +1,5 @@
+# cython: language_level=3
+
 cdef extern from "zoltan_types.h":
 
     # basic type used by all of Zoltan

requirements.txt

@@ -1,6 +1,6 @@
 cyarray
-Cython<3.0
+Cython
 setuptools>=6.0
 numpy
 pytest
-mpi4py>=1.2
+mpi4py>=1.2, <4.0

setup.py

@@ -269,7 +269,6 @@ def get_parallel_extensions():
             extra_link_args=mpi_link_args,
             extra_compile_args=mpi_compile_args + extra_compile_args,
             cython_compile_time_env=cython_compile_time_env,
-            language="c++",
             define_macros=MACROS,
         ),
 
@@ -287,7 +286,6 @@ def get_parallel_extensions():
             extra_link_args=mpi_link_args,
             extra_compile_args=mpi_compile_args + extra_compile_args,
             cython_compile_time_env=cython_compile_time_env,
-            language="c++",
             define_macros=MACROS,
         ),
 
@@ -304,7 +302,6 @@ def get_parallel_extensions():
             extra_link_args=mpi_link_args,
             extra_compile_args=mpi_compile_args + extra_compile_args,
             cython_compile_time_env=cython_compile_time_env,
-            language="c++",
             define_macros=MACROS,
         ),
     ]
@@ -340,9 +337,6 @@ def setup_package():
     exec(compile(open(module).read(), module, 'exec'), info)
 
     # The requirements.
-    install_requires = [
-        'cyarray', 'numpy', 'Cython<3.0', 'setuptools>=6.0', 'mpi4py>=1.2'
-    ]
     tests_require = ["pytest>=3.0"]
     docs_require = ["sphinx"]
 
@@ -391,7 +385,6 @@ def setup_package():
           ext_modules=ext_modules,
           include_package_data=True,
           cmdclass=cmdclass,
-          install_requires=install_requires,
           extras_require={
               "docs": docs_require,
               "tests": tests_require,