Merge pull request #390 from nauaneed/fix-tests

Fix build and tests

.github/workflows/tests.yml

@@ -15,17 +15,17 @@ jobs:
  strategy:
  matrix:
  os: [ubuntu-latest, macos-latest, windows-latest]
- python-version: [3.9]
+ python-version: [3.11]
 
  runs-on: ${{ matrix.os }}
  defaults:
  run:
  shell: bash -l {0}
 
  steps:
- - uses: actions/checkout@v3
+ - uses: actions/checkout@v4
  - name: Set up Python ${{ matrix.python-version }}
- uses: conda-incubator/setup-miniconda@v2
+ uses: conda-incubator/setup-miniconda@v3
  with:
  auto-update-conda: true
  python-version: ${{ matrix.python-version }}
@@ -39,7 +39,8 @@ jobs:
  - name: Install dependencies
  run: |
  conda info
- conda install -c conda-forge numpy cython h5py
+ conda install -c conda-forge numpy 'cython<3.0' h5py
+ python -m pip install --upgrade pip setuptools wheel
  python -m pip install https:/pypr/cyarray/zipball/master
  python -m pip install https:/pypr/compyle/zipball/master
  python -m pip install -r requirements.txt -r requirements-test.txt

.github/workflows/zoltan-tests.yml

@@ -12,7 +12,7 @@ jobs:
  strategy:
  matrix:
  os: [ubuntu-latest]
- python-version: [3.9]
+ python-version: [3.11]
 
  env:
  USE_TRILINOS: 1
@@ -26,22 +26,24 @@ jobs:
  shell: bash -l {0}
 
  steps:
- - uses: actions/checkout@v3
+ - uses: actions/checkout@v4
  - name: Install Linux packages ZOLTAN support
  run: |
  sudo apt-get update
  sudo apt-get install -y openmpi-bin libopenmpi-dev libtrilinos-zoltan-dev
  - name: Set up Python ${{ matrix.python-version }}
- uses: conda-incubator/setup-miniconda@v2
+ uses: conda-incubator/setup-miniconda@v3
  with:
  auto-update-conda: true
  python-version: ${{ matrix.python-version }}
  channels: conda-forge
  - name: Install dependencies
  run: |
  conda info
- conda install -c conda-forge numpy cython
- python -m pip install mpi4py cyarray
+ conda install -c conda-forge numpy 'cython<3.0'
+ python -m pip install --upgrade pip setuptools wheel
+ python -m pip install mpi4py
+ python -m pip install https:/pypr/cyarray/zipball/master
  python -m pip install --no-build-isolation https:/pypr/pyzoltan/zipball/master
  python -m pip install https:/pypr/compyle/zipball/master
  python -m pip install -r requirements.txt

pyproject.toml

@@ -1,7 +1,7 @@
 [build-system]
 requires = [
  "Beaker",
- "Cython>=0.20",
+ "Cython<3.0",
  "compyle>=0.8",
  "cyarray",
  "mako",

pysph/base/linalg3.pyx

@@ -11,7 +11,7 @@ from numpy.linalg import eigh
 cimport numpy
 import numpy
 
-cdef extern:
+cdef extern from "math.h":
  double fabs(double) nogil
 
 # this is cython substitute for const values

pysph/base/nnps_base.pyx

@@ -47,13 +47,6 @@ ELSE:
  cpdef set_number_of_threads(int n):
  print("OpenMP not available, cannot set number of threads.")
 
-
-IF UNAME_SYSNAME == "Windows":
- cdef inline double fmin(double x, double y) nogil:
- return x if x < y else y
- cdef inline double fmax(double x, double y) nogil:
- return x if x > y else y
-
 # Particle Tag information
 from cyarray.carray cimport BaseArray, aligned_malloc, aligned_free
 from .utils import ParticleTAGS

pysph/base/octree.pyx

@@ -15,12 +15,6 @@ from cython.parallel import parallel, prange, threadid
 # EPS_MAX is maximum value of eps in tree building
 DEF EPS_MAX = 1e-3
 
-IF UNAME_SYSNAME == "Windows":
- cdef inline double fmin(double x, double y) nogil:
- return x if x < y else y
- cdef inline double fmax(double x, double y) nogil:
- return x if x > y else y
-
 ctypedef cOctreeNode* node_ptr
 ctypedef double* dbl_ptr
 

pysph/base/octree_nnps.pyx

@@ -9,13 +9,6 @@ from libc.stdlib cimport malloc, free
 cimport cython
 from cython.operator cimport dereference as deref, preincrement as inc
 
-IF UNAME_SYSNAME == "Windows":
- cdef inline double fmin(double x, double y) nogil:
- return x if x < y else y
- cdef inline double fmax(double x, double y) nogil:
- return x if x > y else y
-
-
 #############################################################################
 cdef class OctreeNNPS(NNPS):
  """Nearest neighbor search using Octree.

pysph/base/spatial_hash_nnps.pyx

@@ -8,13 +8,6 @@ from libcpp.vector cimport vector
 # Cython for compiler directives
 cimport cython
 
-IF UNAME_SYSNAME == "Windows":
- cdef inline double fmin(double x, double y) nogil:
- return x if x < y else y
- cdef inline double fmax(double x, double y) nogil:
- return x if x > y else y
-
-
 #############################################################################
 cdef class SpatialHashNNPS(NNPS):
 

pysph/base/stratified_hash_nnps.pyx

@@ -12,12 +12,6 @@ cimport cython
 
 DEF EPS = 1e-6
 
-IF UNAME_SYSNAME == "Windows":
- cdef inline double fmin(double x, double y) nogil:
- return x if x < y else y
- cdef inline double fmax(double x, double y) nogil:
- return x if x > y else y
-
 #############################################################################
 cdef class StratifiedHashNNPS(NNPS):
 

pysph/base/stratified_sfc_gpu_nnps.pyx

@@ -38,13 +38,6 @@ cdef extern from *:
  #endif
  """
 
-IF UNAME_SYSNAME == "Windows":
- cdef inline double fmin(double x, double y) nogil:
- return x if x < y else y
- cdef inline double fmax(double x, double y) nogil:
- return x if x > y else y
-
-
 cdef class StratifiedSFCGPUNNPS(GPUNNPS):
  def __init__(self, int dim, list particles, double radius_scale=2.0,
  int ghost_layers=1, domain=None, bint fixed_h=False,

pysph/base/stratified_sfc_nnps.pyx

@@ -33,13 +33,6 @@ cdef extern from *:
  #endif
  """
 
-IF UNAME_SYSNAME == "Windows":
- cdef inline double fmin(double x, double y) nogil:
- return x if x < y else y
- cdef inline double fmax(double x, double y) nogil:
- return x if x > y else y
-
-
 #############################################################################
 cdef class StratifiedSFCNNPS(NNPS):
 

pysph/base/z_order_gpu_nnps.pyx

@@ -44,13 +44,6 @@ cdef extern from *:
  #endif
  """
 
-IF UNAME_SYSNAME == "Windows":
- cdef inline double fmin(double x, double y) nogil:
- return x if x < y else y
- cdef inline double fmax(double x, double y) nogil:
- return x if x > y else y
-
-
 cdef class ZOrderGPUNNPS(GPUNNPS):
  def __init__(self, int dim, list particles, double radius_scale=2.0,
  int ghost_layers=1, domain=None, bint fixed_h=False,

requirements.txt

@@ -1,6 +1,6 @@
 numpy
 setuptools>=42.0.0
-Cython>=0.20
+Cython<3.0
 cyarray
 compyle>=0.8
 mako

setup.py

@@ -681,7 +681,7 @@ def setup_package():
 
  # The requirements.
  install_requires = [
- 'numpy', 'mako', 'cyarray', 'compyle>=0.8', 'Cython>=0.20',
+ 'numpy', 'mako', 'cyarray', 'compyle>=0.8', 'Cython<3.0',
  'setuptools>=42.0.0', 'pytools', 'Beaker'
  ]
  tests_require = ['pytest>=3.0', 'h5py', 'vtk']