Fix build steps (#244)

* first attempt to fix building; sdist works; wheel misses the compiled objects
* bumps Cython version to 3.0.0; adds explicit Cython language levels and removes numpy deprecations warnings
* build.py might need to be changed in the future, but this should make the package installable as a hot fix

Author: derNarr

build.py

@@ -1,43 +1,46 @@
-from setuptools import Extension
-from setuptools.command.build_ext import build_ext as _build_ext
+import os
+import shutil
 import sys
+from distutils.core import Distribution, Extension
 
+from Cython.Build import build_ext, cythonize
+import numpy
 
-# bootstrap numpy
-# https://stackoverflow.com/questions/19919905/how-to-bootstrap-numpy-installation-in-setup-py
-class build_ext(_build_ext):
-    def finalize_options(self):
-        _build_ext.finalize_options(self)
-        # Prevent numpy from thinking it is still in its setup process:
-        #__builtins__.__NUMPY_SETUP__ = False
-        import numpy
-        self.include_dirs.append(numpy.get_include())
+cython_dir = "pyndl"
 
+ndl_parallel = Extension("pyndl.ndl_parallel",
+                         ["pyndl/ndl_parallel.pyx"],
+                         include_dirs=[numpy.get_include()])
+ndl_openmp = Extension("pyndl.ndl_openmp",
+                       ["pyndl/ndl_openmp.pyx"],
+                       extra_compile_args=['-fopenmp'],
+                       extra_link_args=['-fopenmp'],
+                       include_dirs=[numpy.get_include()])
+corr_parallel = Extension("pyndl.correlation_openmp",
+                          ["pyndl/correlation_openmp.pyx"],
+                          extra_compile_args=['-fopenmp'],
+                          extra_link_args=['-fopenmp'],
+                          include_dirs=[numpy.get_include()])
 
-ndl_parallel = Extension("pyndl.ndl_parallel", ["pyndl/ndl_parallel.pyx"])
-ndl_openmp = Extension("pyndl.ndl_openmp", ["pyndl/ndl_openmp.pyx"],
-                       extra_compile_args=['-fopenmp'], extra_link_args=['-fopenmp'])
-corr_parallel = Extension("pyndl.correlation_openmp", ["pyndl/correlation_openmp.pyx"],
-                       extra_compile_args=['-fopenmp'], extra_link_args=['-fopenmp'])
-# by giving ``cython`` as ``install_requires`` this will be ``cythonized``
-# automagically
-
-ext_modules = []
+extensions = []
+include_paths = []
 if sys.platform.startswith('linux'):
-    ext_modules = [ndl_parallel, ndl_openmp, corr_parallel]
+    extensions = [ndl_parallel, ndl_openmp, corr_parallel]
+    include_paths = [cython_dir, cython_dir, cython_dir]
 elif sys.platform.startswith('win32'):
-    ext_modules = [ndl_parallel] # skip openmp installation on windows for now
+    extensions = [ndl_parallel] # skip openmp installation on windows for now
+    include_paths = [cython_dir]
 elif sys.platform.startswith('darwin'):
-    ext_modules = [ndl_parallel]  # skip openmp installation on macos for now
+    extensions = [ndl_parallel]  # skip openmp installation on macos for now
+    include_paths = [cython_dir]
+
+ext_modules = cythonize(extensions, include_path=include_paths)
+dist = Distribution({"ext_modules": ext_modules})
+cmd = build_ext(dist)
+cmd.ensure_finalized()
+cmd.run()
 
+for output in cmd.get_outputs():
+    relative_extension = os.path.relpath(output, cmd.build_lib)
+    shutil.copyfile(output, relative_extension)
 
-def build(setup_kwargs):
-    """
-    This function is mandatory in order to build the extensions.
-    """
-    setup_kwargs.update({
-        'ext_modules': ext_modules,
-        'cmdclass': {
-            'build_ext': build_ext
-        }
-    })

pyndl/correlation_openmp.pyx

@@ -1,3 +1,6 @@
+# cython: language_level=3
+# distutils: define_macros=NPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION
+
 import numpy as np
 cimport numpy as np
 

pyndl/error_codes.pxd

@@ -1,3 +1,5 @@
+# cython: language_level=3
+
 cdef enum ErrorCode:
     NO_ERROR = 0
     MAGIC_NUMBER_DOES_NOT_MATCH = 1

pyndl/ndl_openmp.pyx

@@ -1,21 +1,24 @@
+# cython: language_level=3
+# distutils: define_macros=NPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION
+
 import numpy as np
 import math
 cimport numpy as np
 ctypedef np.float64_t dtype_t
 cimport cython
 from cython.parallel cimport parallel, prange
 
-from ndl_parallel cimport (learn_inplace_binary_to_binary_ptr,
-                           learn_inplace_binary_to_real_ptr,
-                           learn_inplace_real_to_real_ptr,
-                           learn_inplace_real_to_binary_ptr)
-from error_codes cimport (ErrorCode,
-                          NO_ERROR,
-                          MAGIC_NUMBER_DOES_NOT_MATCH,
-                          VERSION_NUMBER_DOES_NOT_MATCH,
-                          INITIAL_ERROR_CODE,
-                          ONLY_ONE_OUTCOME_PER_EVENT,
-                          ERROR_CODES)
+from .ndl_parallel cimport (learn_inplace_binary_to_binary_ptr,
+                            learn_inplace_binary_to_real_ptr,
+                            learn_inplace_real_to_real_ptr,
+                            learn_inplace_real_to_binary_ptr)
+from .error_codes cimport (ErrorCode,
+                           NO_ERROR,
+                           MAGIC_NUMBER_DOES_NOT_MATCH,
+                           VERSION_NUMBER_DOES_NOT_MATCH,
+                           INITIAL_ERROR_CODE,
+                           ONLY_ONE_OUTCOME_PER_EVENT,
+                           ERROR_CODES)
 
 
 def learn_inplace_binary_to_binary(binary_file_paths,

pyndl/ndl_parallel.pxd

@@ -1,3 +1,6 @@
+# cython: language_level=3
+# distutils: define_macros=NPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION
+
 cimport numpy as np
 ctypedef np.float64_t dtype_t
 from error_codes cimport ErrorCode

pyndl/ndl_parallel.pyx

@@ -1,3 +1,6 @@
+# cython: language_level=3
+# distutils: define_macros=NPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION
+
 import numpy as np
 import math
 from libc.stdlib cimport abort, malloc, free

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pyndl"
-version = "1.1.1"
+version = "1.1.2"
 description = "Naive discriminative learning implements learning and classification models based on the Rescorla-Wagner equations."
 
 license = "MIT"
@@ -27,16 +27,14 @@ classifiers = ['Development Status :: 5 - Production/Stable',
                'Topic :: Scientific/Engineering :: Artificial Intelligence',
                'Topic :: Scientific/Engineering :: Information Analysis',]
 
-build = "build.py"
-
 [tool.poetry.dependencies]
 python = ">=3.8,<3.12"  # Compatible python versions must be declared here
 numpy = "^1.23.1"
 scipy = "^1.9.0"
 pandas = "^1.4.3"
 xarray = "^2022.6.0"
 netCDF4 = "^1.6.0"
-Cython = "^0.29.32"
+Cython = "^3.0.0"
 
 [tool.poetry.dev-dependencies]
 pytest = "^7.0"
@@ -70,5 +68,10 @@ addopts = '--doctest-glob "*.rst"'
   disable = "E1101"
 
 [build-system]
-requires = ["poetry>=1.0.0", "setuptools", "Cython", "numpy"]
-build-backend = "poetry.masonry.api"
+requires = ["poetry-core", "setuptools", "Cython", "numpy"]
+build-backend = "poetry.core.masonry.api"
+
+[tool.poetry.build]
+generate-setup-file = false
+script = 'build.py'
+