Fix cython3 build (#11)

* Fix cython3 build

* Fix style recommendation from flask8

* Added requirements.txt

* Added test

* Added workflow

.github/workflows/main.yml

@@ -0,0 +1,41 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Python application
+
+on:
+  push:
+  pull_request:
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.10"
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install flake8 pytest
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Install package
+      run: |
+        python setup.py install
+    - name: Test with pytest
+      run: |
+        pytest
+

docs/source/conf.py

@@ -31,11 +31,11 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = ['sphinx.ext.autodoc',
-    'sphinx.ext.napoleon',
-    'sphinx.ext.doctest',
-    'sphinx.ext.imgmath',
-    'sphinx.ext.viewcode',
-    'sphinx.ext.githubpages']
+              'sphinx.ext.napoleon',
+              'sphinx.ext.doctest',
+              'sphinx.ext.imgmath',
+              'sphinx.ext.viewcode',
+              'sphinx.ext.githubpages']
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['.templates']
@@ -171,6 +171,3 @@
      author, 'Pytetgen', 'One line description of project.',
      'Miscellaneous'),
 ]
-
-
-

pytetgen/pytetgen.pyx

@@ -1,3 +1,5 @@
+#!python
+# cython: language_level=3
 # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding: utf-8 -*-
 # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
 # distutils: language=c++
@@ -354,7 +356,7 @@ cdef class Tetgenio:
     def pointlist(self,val):
         flatval = np.ascontiguousarray(val.flatten())
         cdef int npoints = flatval.shape[0]
-        self.c_tetgenio.numberofpoints = npoints / <int>3
+        self.c_tetgenio.numberofpoints = npoints // <int>3
         cdef int size = 3*sizeof(double)*self.c_tetgenio.numberofpoints
         cdef np.float64_t[:] view = flatval
         try:

pytetgen/tests/test_simple.py

@@ -0,0 +1,15 @@
+"""
+A simple test for pytetgen
+"""
+def test_simple():
+    import pytetgen
+    import numpy as np
+    import scipy.spatial
+    N=100
+    np.random.seed(1)
+    a=np.random.random(3*N).reshape(N,3)
+    del1=pytetgen.Delaunay(a)
+    del2=scipy.spatial.Delaunay(a)
+    T1=np.sort(np.sort(del1.simplices,axis=1),axis=0)
+    T2=np.sort(np.sort(del2.simplices,axis=1),axis=0)
+    assert(np.all(T1==T2))

requirements.txt

@@ -0,0 +1,3 @@
+Cython
+numpy
+scipy

setup.py

@@ -3,9 +3,8 @@
 from distutils.core import setup
 from distutils.extension import Extension
 from Cython.Distutils import build_ext
-from Cython.Build import cythonize
 import numpy as np
-import os 
+import os
 import codecs
 
 # Get the long description from the README file
@@ -14,47 +13,40 @@
 with codecs.open(os.path.join(here, 'README.rst'), encoding='utf-8') as f:
     long_description = f.read()
 
-
-
-
-setup(	name = 'pytetgen',
-	packages=['pytetgen'],
-	version = '0.2.2',
-	description = 'wrapper for the tetgen mesh generator',
-	long_description=long_description,
-	author = 'Marcello Sega',
-	author_email = '[email protected]',
-        url='https://github.com/Marcello-Sega/pytetgen',
-   	license='AGPLv3',
-	classifiers=[
-       		# How mature is this project? Common values are
-       		#   3 - Alpha
-       		#   4 - Beta
-       		#   5 - Production/Stable
-       		'Development Status :: 4 - Beta',
-
-       		# Indicate who your project is intended for
-       		'Intended Audience :: Science/Research',
-       		'Topic :: Scientific/Engineering :: Bio-Informatics',
-       		'Topic :: Scientific/Engineering :: Chemistry',
-       		'Topic :: Scientific/Engineering :: Physics',
-       		'Topic :: Software Development :: Libraries :: Python Modules',
-
-       		# Pick your license as you wish (should match "license" above)
-   		'License :: OSI Approved :: GNU Affero General Public License v3 or later (AGPLv3+)',
-
-       		# Specify the Python versions you support here. In particular, ensure
-       		# that you indicate whether you support Python 2, Python 3 or both.
-       		'Programming Language :: Python :: 3',
-    	],
-        ext_modules=[
-              Extension('pytetgen', 
-                 sources=['pytetgen/tetgen.cxx','pytetgen/predicates.cxx','pytetgen/pytetgen.pyx'],
-                 compiler_directives={'language_level':3},
-		 include_dirs=[np.get_include()],
-		 extra_compile_args=['-g0','-O0','-DTETLIBRARY'],
-                 language='c++'),
-        ],
-        cmdclass = {'build_ext': build_ext},
-        install_requires=['triangle>=20200424'],
-)
+setup(name='pytetgen',
+      packages=['pytetgen'],
+      version='0.2.2',
+      description='wrapper for the tetgen mesh generator',
+      long_description=long_description,
+      author='Marcello Sega',
+      author_email='[email protected]',
+      url='https://github.com/Marcello-Sega/pytetgen',
+      license='AGPLv3',
+      classifiers=[
+           # How mature is this project? Common values are
+           #   3 - Alpha
+           #   4 - Beta
+           #   5 - Production/Stable
+           'Development Status :: 4 - Beta',
+            # Indicate who your project is intended for
+           'Intended Audience :: Science/Research',
+           'Topic :: Scientific/Engineering :: Bio-Informatics',
+           'Topic :: Scientific/Engineering :: Chemistry',
+           'Topic :: Scientific/Engineering :: Physics',
+           'Topic :: Software Development :: Libraries :: Python Modules',
+           # Pick your license as you wish (should match "license" above)
+           'License :: OSI Approved :: GNU Affero General Public License v3 or later (AGPLv3+)',
+           # Specify the Python versions you support here. In particular, ensure
+           # that you indicate whether you support Python 2, Python 3 or both.
+           'Programming Language :: Python :: 3',
+      ],
+      ext_modules=[
+           Extension('pytetgen',
+                     sources=['pytetgen/tetgen.cxx', 'pytetgen/predicates.cxx', 'pytetgen/pytetgen.pyx'],
+                     compiler_directives={'language_level': 3},
+                     include_dirs=[np.get_include()],
+                     extra_compile_args=['-g0', '-O0', '-DTETLIBRARY'],
+                     language='c++'),
+      ],
+      cmdclass={'build_ext': build_ext},
+      install_requires=['triangle>=20200424'])