Stop using numpy.distutils

* Stop using `numpy.distutils` since it generates deprecation warnings about removal in Python 3.12.
* Fix another `PytestReturnNotNoneWarning`.

Author: 1fish2

arrow/test/test_arrow.py

@@ -142,7 +142,7 @@ def complexation_test(make_system):
 def test_complexation():
     complexation_test(StochasticSystem)
 
-def test_obsidian():
+def check_obsidian():
     stoichiometric_matrix = np.array([
         [1, 1, -1, 0],
         [-2, 0, 0, 1],
@@ -164,6 +164,9 @@ def test_obsidian():
 
     return result
 
+def test_obsidian():
+    check_obsidian()
+
 def test_compare_runtime():
     stoichiometric_matrix, rates, initial_state, final_state = load_complexation()
     duration = 1
@@ -232,7 +235,7 @@ def test_pickle():
 
     result = arrow.evolve(1.0, np.array([50, 20, 30, 40], np.int64), rates)
 
-    straight = test_obsidian()
+    straight = check_obsidian()
 
     assert(result['steps'] == straight['steps'])
     assert((result['time'] == straight['time']).all())
@@ -320,7 +323,7 @@ def main(args):
             for run in range(args.runs):
                 complexation_test(StochasticSystem)
         if args.obsidian:
-            test_obsidian()
+            check_obsidian()
         elif args.memory:
             test_memory()
         elif args.time:

requirements.txt

@@ -1,3 +1,6 @@
+pip
+setuptools
+
 Cython
 numpy
 pytest

setup.py

@@ -1,15 +1,20 @@
+# distutils is deprecated; to be removed for Python 3.12.
+# See https://numpy.org/devdocs/reference/distutils_status_migration.html for
+# migration advice.
+# This setup.py file no longer uses numpy.distutils so it might be easy to
+# fully move to setuptools.
+
 import os
 import setuptools  # used indirectly for bdist_wheel cmd and long_description_content_type
 from distutils.core import setup
 from distutils.extension import Extension
-import numpy.distutils.misc_util
+import numpy as np
 
 with open("README.md", 'r') as readme:
     long_description = readme.read()
 
 current_dir = os.getcwd()
 arrow_dir = os.path.join(current_dir, 'arrow')
-include = [arrow_dir] + numpy.distutils.misc_util.get_numpy_include_dirs()
 
 # Compile the Cython code to C for development builds:
 #    USE_CYTHON=1 python setup.py build_ext --inplace
@@ -24,7 +29,7 @@
 cython_extensions = [
     Extension('arrow.arrowhead',
               sources=['arrow/mersenne.c', 'arrow/obsidian.c', 'arrow/arrowhead'+ext,],
-              include_dirs=['arrow'] + numpy.distutils.misc_util.get_numpy_include_dirs(),
+              include_dirs=['arrow', np.get_include()],
               define_macros=[('NPY_NO_DEPRECATED_API', 'NPY_1_7_API_VERSION')],
               )]
 
@@ -38,13 +43,13 @@
 
 setup(
     name='stochastic-arrow',
-    version='0.5.0',
+    version='0.5.1',
     packages=['arrow'],
     author='Ryan Spangler, John Mason, Jerry Morrison, Chris Skalnik, Travis Ahn-Horst',
     author_email='ryan.spangler@gmail.com',
     url='https://github.com/CovertLab/arrow',
     license='MIT',
-    include_dirs=include,
+    include_dirs=[arrow_dir, np.get_include()],
     ext_modules=cython_extensions,
     long_description=long_description,
     long_description_content_type='text/markdown',