Fix Python 3.12 and numpy 2.x compatibility

.gitignore

@@ -57,3 +57,7 @@ out/
 # C files are always generated by Cython
 *.c
 *.C
+test-env/
+*.egg-info/
+__pycache__/
+*.so

examples/distance_matrix.py

@@ -12,16 +12,23 @@
 from __future__ import print_function
 
 import matplotlib.pyplot as plt
-
+import numpy as np 
 import pyspike as spk
 
 # first load the data, interval ending time = 4000, start=0 (default)
 spike_trains = spk.load_spike_trains_from_txt("PySpike_testdata.txt", 4000)
 
 print(len(spike_trains))
 
+# plot the spike times
+plt.figure()
+for (i, spike_train) in enumerate(spike_trains):
+    plt.scatter(spike_train, i*np.ones_like(spike_train), marker='|',color='black')
+plt.title("raster plot")
+
+
 plt.figure()
-isi_distance = spk.isi_distance_matrix(spike_trains)
+isi_distance = spk.isi_distance_matrix(spike_trains,interval=(0, 1000))
 plt.imshow(isi_distance, interpolation='none')
 plt.title("ISI-distance")
 
@@ -31,8 +38,8 @@
 plt.title("SPIKE-distance, T=0-1000")
 
 plt.figure()
-spike_sync = spk.spike_sync_matrix(spike_trains, interval=(2000, 4000))
+spike_sync = spk.spike_sync_matrix(spike_trains, interval=(0, 1000))
 plt.imshow(spike_sync, interpolation='none')
-plt.title("SPIKE-Sync, T=2000-4000")
+plt.title("SPIKE-Sync, T=0-1000")
 
 plt.show()

pyproject.toml

@@ -0,0 +1,3 @@
+[build-system]
+requires = ["setuptools", "numpy", "cython"]
+build-backend = "setuptools.build_meta"

pyspike/PieceWiseConstFunc.py

@@ -157,7 +157,7 @@ def integral(self, interval=None):
         return a
 
     def avrg(self, interval=None):
-        """ Computes the average of the piece-wise const function:
+        r""" Computes the average of the piece-wise const function:
         :math:`a = 1/T \int_0^T f(x) dx` where T is the length of the interval.
 
         :param interval: averaging interval given as a pair of floats, a

pyspike/PieceWiseLinFunc.py

@@ -193,7 +193,7 @@ def intermediate_value(x0, x1, y0, y1, x):
         return integral
 
     def avrg(self, interval=None):
-        """ Computes the average of the piece-wise linear function:
+        r""" Computes the average of the piece-wise linear function:
         :math:`a = 1/T \int_0^T f(x) dx` where T is the interval length.
 
         :param interval: averaging interval given as a pair of floats, a

pyspike/__init__.py

@@ -37,22 +37,13 @@
 
 # define the __version__ following
 # http://stackoverflow.com/questions/17583443
-from pkg_resources import get_distribution, DistributionNotFound
-import os.path
+from importlib.metadata import version, PackageNotFoundError
 
 try:
-    _dist = get_distribution('pyspike')
-    # Normalize case for Windows systems
-    dist_loc = os.path.normcase(_dist.location)
-    here = os.path.normcase(__file__)
-    if not here.startswith(os.path.join(dist_loc, 'pyspike')):
-        # not installed, but there is another version that *is*
-        raise DistributionNotFound
-except DistributionNotFound:
+    __version__ = version('pyspike')
+except PackageNotFoundError:
     __version__ = 'Please install this project with setup.py'
-else:
-    __version__ = _dist.version
-
+
 disable_backend_warning = False
 
 def NoCythonWarn():

pyspike/spike_sync.py

@@ -165,7 +165,7 @@ def _spike_sync_values(spike_train1, spike_train2, interval, max_tau, **kwargs):
 # spike_sync
 ############################################################
 def spike_sync(*args, **kwargs):
-    """ Computes the spike synchronization value of the given spike
+    r""" Computes the spike synchronization value of the given spike
     trains. The spike synchronization value is the computed as the total number
     of coincidences divided by the total number of spikes:
 

setup.py

@@ -11,84 +11,40 @@
 """
 from setuptools import setup, find_packages
 from distutils.extension import Extension
+from Cython.Build import cythonize
 import os.path
 
-try:
-    from Cython.Distutils import build_ext
-except ImportError:
-    use_cython = False
-else:
-    use_cython = True
-
 
 class numpy_include(os.PathLike):
-     """Defers import of numpy until install_requires is through"""
-     def __str__(self):
-         import numpy
-         return numpy.get_include()
-
-     def __fspath__(self):
-         return str(self)
-
-
-if os.path.isfile("pyspike/cython/cython_add.c") and \
-   os.path.isfile("pyspike/cython/cython_get_tau.c") and \
-   os.path.isfile("pyspike/cython/cython_profiles.c") and \
-   os.path.isfile("pyspike/cython/cython_distances.c") and \
-   os.path.isfile("pyspike/cython/cython_directionality.c") and \
-   os.path.isfile("pyspike/cython/cython_simulated_annealing.c"):
-    use_c = True
-else:
-    use_c = False
-
-if not use_cython and not use_c:
-    print('Cython not installed. Programs will be slow.')
-    # Ans = input('Abort? (Y/N)\n')
-    # if len(Ans)>0 and (Ans[0]=='Y' or Ans[0]=='y'):
-    #     print("\nAborting\n")
-    #     raise RuntimeError('User termination')
+    """Defers import of numpy until install_requires is through"""
+    def __str__(self):
+        import numpy
+        return numpy.get_include()
+
+    def __fspath__(self):
+        return str(self)
+
+
+ext_modules = cythonize([
+    Extension("pyspike.cython.cython_add",
+              ["pyspike/cython/cython_add.pyx"]),
+    Extension("pyspike.cython.cython_get_tau",
+              ["pyspike/cython/cython_get_tau.pyx"]),
+    Extension("pyspike.cython.cython_profiles",
+              ["pyspike/cython/cython_profiles.pyx"]),
+    Extension("pyspike.cython.cython_distances",
+              ["pyspike/cython/cython_distances.pyx"]),
+    Extension("pyspike.cython.cython_directionality",
+              ["pyspike/cython/cython_directionality.pyx"]),
+    Extension("pyspike.cython.cython_simulated_annealing",
+              ["pyspike/cython/cython_simulated_annealing.pyx"])
+])
 
-cmdclass = {}
-ext_modules = []
-
-if use_cython:  # Cython is available, compile .pyx -> .c
-    ext_modules += [
-        Extension("pyspike.cython.cython_add",
-                  ["pyspike/cython/cython_add.pyx"]),
-        Extension("pyspike.cython.cython_get_tau",
-                  ["pyspike/cython/cython_get_tau.pyx"]),
-        Extension("pyspike.cython.cython_profiles",
-                  ["pyspike/cython/cython_profiles.pyx"]),
-        Extension("pyspike.cython.cython_distances",
-                  ["pyspike/cython/cython_distances.pyx"]),
-        Extension("pyspike.cython.cython_directionality",
-                  ["pyspike/cython/cython_directionality.pyx"]),
-        Extension("pyspike.cython.cython_simulated_annealing",
-                  ["pyspike/cython/cython_simulated_annealing.pyx"])
-    ]
-    cmdclass.update({'build_ext': build_ext})
-elif use_c:  # c files are there, compile to binaries
-    ext_modules += [
-        Extension("pyspike.cython.cython_add",
-                  ["pyspike/cython/cython_add.c"]),
-        Extension("pyspike.cython.cython_get_tau",
-                  ["pyspike/cython/cython_get_tau.c"]),
-        Extension("pyspike.cython.cython_profiles",
-                  ["pyspike/cython/cython_profiles.c"]),
-        Extension("pyspike.cython.cython_distances",
-                  ["pyspike/cython/cython_distances.c"]),
-        Extension("pyspike.cython.cython_directionality",
-                  ["pyspike/cython/cython_directionality.c"]),
-        Extension("pyspike.cython.cython_simulated_annealing",
-                  ["pyspike/cython/cython_simulated_annealing.c"])
-    ]
-# neither cython nor c files available -> automatic fall-back to python backend
 
 setup(
     name='pyspike',
     packages=find_packages(exclude=['doc', 'test*']),
     version='0.8.0',
-    cmdclass=cmdclass,
     ext_modules=ext_modules,
     include_dirs=[numpy_include()],
     description='A Python library for the numerical analysis of spike\
@@ -98,34 +54,22 @@ def __fspath__(self):
     license='BSD',
     url='https://github.com/mariomulansky/PySpike',
     install_requires=['numpy'],
-    keywords=['data analysis', 'spike', 'neuroscience'],  # arbitrary keywords
+    keywords=['data analysis', 'spike', 'neuroscience'],
     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',
         'Topic :: Scientific/Engineering :: Information Analysis',
-
         'License :: OSI Approved :: BSD License',
-
         'Programming Language :: Python :: 3',
         'Programming Language :: Python :: 3.7',
         'Programming Language :: Python :: 3.8',
         'Programming Language :: Python :: 3.9',
         'Programming Language :: Python :: 3.10',
+        'Programming Language :: Python :: 3.11',
+        'Programming Language :: Python :: 3.12',
     ],
     package_data={
-        'pyspike': ['cython/cython_add.c', 
-                    'cython/cython_profiles.c',
-                    'cython/cython_get_tau.c',
-                    'cython/cython_distances.c',
-                    'cython/cython_directionality.c',
-                    'cython/cython_simulated_annealing.c'],
         'test': ['Spike_testdata.txt']
     }
-)
+)