pkg_resources issue resolved, future-proof with pyproject.toml file

.github/workflows/pip-test.yml

@@ -1,4 +1,5 @@
-# Testing on linux, windows, macos, for python versions 3.7, 3.8, 3.9, 3.10, 3.11, 3.12
+# Testing on linux, windows, macos, for python versions 3.8, 3.9, 3.10, 3.11, 3.12
+# Note: Python 3.7 support was dropped as it reached End of Life (EOL) on June 27, 2023
 
 name: Test pip install
 
@@ -8,20 +9,19 @@ on:
 
 jobs:
   build:
-
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
         os: ["ubuntu-latest", "windows-latest", "macos-latest"]
     runs-on: ${{ matrix.os }}
     env:
       GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Version check
@@ -32,5 +32,6 @@ jobs:
           pip install "Cython>=0.29.23" "coveralls"
       - name: Install package
         run: |
-          python setup.py sdist
-          pip install dist/py-stringmatching-0.4.6.tar.gz
+          pip install build
+          python -m build --sdist
+          python -c "import glob, subprocess, sys; files = glob.glob('dist/*.tar.gz'); assert files, 'No .tar.gz files found in dist/'; subprocess.check_call([sys.executable, '-m', 'pip', 'install'] + files)"

.github/workflows/testing.yml

@@ -1,4 +1,5 @@
-# Testing on linux, windows, macos, for python versions 3.7, 3.8, 3.9, 3.10, 3.11, 3.12
+# Testing on linux, windows, macos, for python versions 3.8, 3.9, 3.10, 3.11, 3.12
+# Note: Python 3.7 support was dropped as it reached End of Life (EOL) on June 27, 2023
 
 name: Unit testing
 
@@ -8,20 +9,19 @@ on:
 
 jobs:
   build:
-
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
         os: ["ubuntu-latest", "windows-latest", "macos-latest"]
     runs-on: ${{ matrix.os }}
     env:
       GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Version check
@@ -31,7 +31,7 @@ jobs:
           python -m pip install --upgrade pip
           pip install "numpy<2.0" "Cython>=0.29.23" "coveralls"
       - name: Install package
-        run: python setup.py build_ext --inplace
+        run: pip install -e .
       - name: Run tests
         run: |
           python -m unittest -v

CHANGES.txt

@@ -1,3 +1,8 @@
+v0.4.7 - 2/14/2026
+  * Migrated build to pyproject.toml (PEP 517/621); setup.py retained for Cython extensions only.
+  * Dropped custom build_ext and setuptools auto-install; use numpy.get_include() for extension builds.
+  * Dropped Testing support for Python 3.7 as it reached End of Life (EOL) on June 27, 2023.
+
 v0.4.6 - 7/5/2024
   * Limited Numpy to <2.0 in setup.py, due to compatibility issues
   * Added preliminary testing of pip install to Github Actions workflow

MANIFEST.in

@@ -2,4 +2,5 @@ include README.rst
 include CHANGES.txt
 include requirements.txt
 include LICENSE
+include pyproject.toml
 recursive-include LICENSES *

README.rst

@@ -18,7 +18,8 @@ Important links
 Dependencies
 ============
 
-py_stringmatching has been tested on each Python version between 3.7 and 3.12, inclusive.
+py_stringmatching has been tested on each Python version between 3.8 and 3.12, inclusive.
+Note: Python 3.7 support was dropped as it reached End of Life (EOL) on June 27, 2023.
 
 The required dependencies to build the package are NumPy 1.7.0 or higher, but lower than 2.0,
 and a C or C++ compiler. For the development version, you will also need Cython.

docs/Installation.rst

@@ -4,7 +4,7 @@ Installation
 
 Requirements
 ------------
-    * Python 3.7-3.11
+    * Python 3.8-3.11 (Python 3.7 support was dropped as it reached End of Life (EOL) on June 27, 2023)
     * C or C++ compiler (parts of the package are in Cython for efficiency reasons, and you need C or C++ compiler to compile these parts)
 
 Platforms

py_stringmatching/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "0.4.6"
+__version__ = "0.4.7"
 
 # Import tokenizers
 from py_stringmatching.tokenizer.alphabetic_tokenizer import AlphabeticTokenizer

pyproject.toml

@@ -0,0 +1,55 @@
+[build-system]
+requires = [
+    "setuptools>=64",
+    "wheel",
+    "Cython>=0.29",
+    "numpy>=1.7.0,<2.0"
+]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "py-stringmatching"
+version = "0.4.7"
+description = "Python library for string matching."
+readme = "README.rst"
+license = {text = "BSD"}
+authors = [
+    {name = "UW Magellan Team", email = "uwmagellan@gmail.com"}
+]
+requires-python = ">=3.7"
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Environment :: Console",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Science/Research",
+    "Intended Audience :: Education",
+    "License :: OSI Approved :: BSD License",
+    "Operating System :: POSIX",
+    "Operating System :: Unix",
+    "Operating System :: MacOS",
+    "Operating System :: Microsoft :: Windows",
+    "Programming Language :: Python",
+    "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",
+    "Topic :: Scientific/Engineering",
+    "Topic :: Utilities",
+    "Topic :: Software Development :: Libraries",
+]
+dependencies = [
+    "numpy>=1.7.0,<2.0",
+]
+
+[project.urls]
+Homepage = "https://sites.google.com/site/anhaidgroup/projects/magellan/py_stringmatching"
+
+[tool.setuptools]
+include-package-data = true
+zip-safe = false
+
+[tool.setuptools.packages.find]
+exclude = ["benchmarks", "benchmarks.custom_benchmarks"]

setup.py

@@ -1,148 +1,94 @@
-import subprocess
-import sys
+"""
+Minimal setup.py for building Cython extensions.
+Most configuration is now in pyproject.toml.
+"""
 import os
+import sys
+from setuptools import setup, Extension
 
-# check if pip is installed. If not, raise an ImportError
-PIP_INSTALLED = True
-
-try:
-    import pip
-except ImportError:
-    PIP_INSTALLED = False
-
-def install_and_import(package):
-    import importlib
-    try:
-        importlib.import_module(package)
-    except ImportError:
-        if not PIP_INSTALLED:
-            raise ImportError('pip is not installed.')
-        pip.main(['install', package])
-    finally:
-        globals()[package] = importlib.import_module(package)
-
-# check if setuptools is installed. If not, install setuptools
-# automatically using pip.
-install_and_import('setuptools')
-
-from setuptools.command.build_ext import build_ext as _build_ext
-
-class build_ext(_build_ext):
-    def build_extensions(self):
-        import pkg_resources                                                            
-        numpy_incl = pkg_resources.resource_filename('numpy', 'core/include')
-
-        for ext in self.extensions:
-            if (hasattr(ext, 'include_dirs') and
-                    not numpy_incl in ext.include_dirs):
-                ext.include_dirs.append(numpy_incl)
-        _build_ext.build_extensions(self)
 
 def generate_cython():
-
+    """Generate C files from Cython sources."""
     from Cython.Build import cythonize
 
-    module_list = ["py_stringmatching/similarity_measure/cython/cython_affine.pyx",
-                   "py_stringmatching/similarity_measure/cython/cython_jaro.pyx",
-                   "py_stringmatching/similarity_measure/cython/cython_jaro_winkler.pyx",
-                   "py_stringmatching/similarity_measure/cython/cython_levenshtein.pyx",
-                   "py_stringmatching/similarity_measure/cython/cython_needleman_wunsch.pyx",
-                   "py_stringmatching/similarity_measure/cython/cython_smith_waterman.pyx",
-                   "py_stringmatching/similarity_measure/cython/cython_utils.pyx"
-                   ]
+    module_list = [
+        "py_stringmatching/similarity_measure/cython/cython_affine.pyx",
+        "py_stringmatching/similarity_measure/cython/cython_jaro.pyx",
+        "py_stringmatching/similarity_measure/cython/cython_jaro_winkler.pyx",
+        "py_stringmatching/similarity_measure/cython/cython_levenshtein.pyx",
+        "py_stringmatching/similarity_measure/cython/cython_needleman_wunsch.pyx",
+        "py_stringmatching/similarity_measure/cython/cython_smith_waterman.pyx",
+        "py_stringmatching/similarity_measure/cython/cython_utils.pyx"
+    ]
+
     p = cythonize(module_list)
-    
+
     if not p:
         raise RuntimeError("Running cythonize failed!")
 
 
-cmdclass = {"build_ext": build_ext}
-
+def get_numpy_include():
+    """Get numpy include directory using modern approach."""
+    import numpy
+    return numpy.get_include()
 
-if __name__ == "__main__":
 
+def main():
+    # Check if we need to generate Cython sources
     no_frills = (len(sys.argv) >= 2 and ('--help' in sys.argv[1:] or
                                          sys.argv[1] in ('--help-commands',
                                                          'egg_info', '--version',
                                                          'clean')))
-
+    
     cwd = os.path.abspath(os.path.dirname(__file__))
     if not os.path.exists(os.path.join(cwd, 'PKG-INFO')) and not no_frills:
         # Generate Cython sources, unless building from source release
         generate_cython()
+
+    # Get numpy include directory
+    numpy_incl = get_numpy_include()
+
+    # Define extensions
+    extensions = [
+        Extension(
+            "py_stringmatching.similarity_measure.cython.cython_levenshtein",
+            ["py_stringmatching/similarity_measure/cython/cython_levenshtein.c"],
+            include_dirs=[numpy_incl]
+        ),
+        Extension(
+            "py_stringmatching.similarity_measure.cython.cython_jaro",
+            ["py_stringmatching/similarity_measure/cython/cython_jaro.c"],
+            include_dirs=[numpy_incl]
+        ),
+        Extension(
+            "py_stringmatching.similarity_measure.cython.cython_jaro_winkler",
+            ["py_stringmatching/similarity_measure/cython/cython_jaro_winkler.c"],
+            include_dirs=[numpy_incl]
+        ),
+        Extension(
+            "py_stringmatching.similarity_measure.cython.cython_utils",
+            ["py_stringmatching/similarity_measure/cython/cython_utils.c"],
+            include_dirs=[numpy_incl]
+        ),
+        Extension(
+            "py_stringmatching.similarity_measure.cython.cython_needleman_wunsch",
+            ["py_stringmatching/similarity_measure/cython/cython_needleman_wunsch.c"],
+            include_dirs=[numpy_incl]
+        ),
+        Extension(
+            "py_stringmatching.similarity_measure.cython.cython_smith_waterman",
+            ["py_stringmatching/similarity_measure/cython/cython_smith_waterman.c"],
+            include_dirs=[numpy_incl]
+        ),
+        Extension(
+            "py_stringmatching.similarity_measure.cython.cython_affine",
+            ["py_stringmatching/similarity_measure/cython/cython_affine.c"],
+            include_dirs=[numpy_incl]
+        )
+    ]
+
+    setup(ext_modules=extensions)
 
-    # specify extensions that need to be compiled
-    extensions = [setuptools.Extension("py_stringmatching.similarity_measure.cython.cython_levenshtein",
-                                       ["py_stringmatching/similarity_measure/cython/cython_levenshtein.c"],
-                                       include_dirs=[]),
-                  setuptools.Extension("py_stringmatching.similarity_measure.cython.cython_jaro",
-                                       ["py_stringmatching/similarity_measure/cython/cython_jaro.c"],
-                                       include_dirs=[]),
-                  setuptools.Extension("py_stringmatching.similarity_measure.cython.cython_jaro_winkler",
-                                       ["py_stringmatching/similarity_measure/cython/cython_jaro_winkler.c"],
-                                       include_dirs=[]),
-                  setuptools.Extension("py_stringmatching.similarity_measure.cython.cython_utils",
-                                       ["py_stringmatching/similarity_measure/cython/cython_utils.c"],
-                                       include_dirs=[]),
-                  setuptools.Extension("py_stringmatching.similarity_measure.cython.cython_needleman_wunsch",
-                                       ["py_stringmatching/similarity_measure/cython/cython_needleman_wunsch.c"],
-                                       include_dirs=[]),
-                  setuptools.Extension("py_stringmatching.similarity_measure.cython.cython_smith_waterman",
-                                       ["py_stringmatching/similarity_measure/cython/cython_smith_waterman.c"],
-                                       include_dirs=[]),
-                  setuptools.Extension("py_stringmatching.similarity_measure.cython.cython_affine",
-                                       ["py_stringmatching/similarity_measure/cython/cython_affine.c"],
-                                       include_dirs=[])
-
-                  ]
-
-    # find packages to be included. exclude benchmarks.
-    packages = setuptools.find_packages(exclude=["benchmarks", "benchmarks.custom_benchmarks"])
-
-    with open('README.rst') as f:
-        LONG_DESCRIPTION = f.read()
 
-    setuptools.setup(
-        name='py-stringmatching',
-        version='0.4.6',
-        description='Python library for string matching.',
-        long_description=LONG_DESCRIPTION,
-        url='https://sites.google.com/site/anhaidgroup/projects/magellan/py_stringmatching',
-        author='UW Magellan Team',
-        author_email='uwmagellan@gmail.com',
-        license='BSD',
-        classifiers=[
-            'Development Status :: 4 - Beta',
-            'Environment :: Console',
-            'Intended Audience :: Developers',
-            'Intended Audience :: Science/Research',
-            'Intended Audience :: Education',
-            'License :: OSI Approved :: BSD License',
-            'Operating System :: POSIX',
-            'Operating System :: Unix',
-            'Operating System :: MacOS',
-            'Operating System :: Microsoft :: Windows',
-            'Programming Language :: Python',
-            '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',
-            'Topic :: Scientific/Engineering',
-            'Topic :: Utilities',
-            'Topic :: Software Development :: Libraries',
-        ],
-        packages=packages,
-        install_requires=[
-            'numpy >= 1.7.0,<2.0',
-        ],
-        setup_requires=[
-            'numpy >= 1.7.0,<2.0'                                                   
-        ],
-        ext_modules=extensions,
-        cmdclass=cmdclass,
-        include_package_data=True,
-        zip_safe=False
-    )
+if __name__ == "__main__":
+    main()