Modernize packaging; fix pip install with build isolation (#84)

.github/workflows/python-package.yml

@@ -11,41 +11,69 @@ on:
 
 jobs:
   build:
-
+    name: Python ${{ matrix.python-version }} (${{ matrix.backend }})
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.7", "3.8", "3.9", "3.10"]
-        cython: ['python -m pip install -q cython', 'echo "No Cython"']
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+        # PySpike treats Cython as an optional accelerator. Both install paths
+        # need to work and produce a passing test suite:
+        #
+        #   cython     -- `pip install .` uses pip's isolated build env, which
+        #                 installs Cython per pyproject.toml's build-system
+        #                 requires. setup.py compiles the .pyx sources into
+        #                 .so modules and the fast path is used at runtime.
+        #
+        #   no-cython  -- `pip install --no-build-isolation .` with Cython
+        #                 deliberately absent. setup.py's `try: import Cython`
+        #                 raises ImportError, no extensions are built, and
+        #                 each pyspike module falls back to python_backend.py
+        #                 via its own `try/except ImportError`.
+        backend: [cython, no-cython]
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
+
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
+
+    - name: Install system dependencies
       run: |
         sudo apt-get update
-        sudo apt-get install libblas-dev
-        sudo apt-get install liblapack-dev
-        sudo apt-get install gfortran
-        python -m pip install --upgrade pip
-        python -m pip install flake8 pytest nose numpy scipy
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-    - name: Install Cython
-      run: |
-        ${{ matrix.cython }}
-    - name: Install package
+        sudo apt-get install -y libblas-dev liblapack-dev gfortran
+
+    - name: Upgrade pip
+      run: python -m pip install --upgrade pip
+
+    - name: Install PySpike — with Cython (build isolation)
+      if: matrix.backend == 'cython'
+      run: pip install .
+
+    - name: Install PySpike — without Cython (pure-Python fallback)
+      if: matrix.backend == 'no-cython'
       run: |
-        python SetupNoPrompt.py build_ext --inplace
-    # - 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
+        # Provide only the bare build prereqs Cython is not among them, so
+        # setup.py's `try: from Cython.Distutils import build_ext` fails and
+        # no C extensions are produced. --no-build-isolation makes pip use
+        # this env instead of provisioning a fresh one (which would install
+        # Cython per pyproject.toml).
+        pip install "setuptools>=77" wheel "numpy>=1.25"
+        pip install --no-build-isolation .
+        # Sanity check: the compiled extension must NOT be importable.
+        python -c "
+        try:
+            from pyspike.cython import cython_distances
+        except ImportError:
+            print('OK: cython_distances absent, runtime will use python_backend')
+        else:
+            raise SystemExit('FAIL: cython_distances was built despite no-cython matrix')
+        "
+
+    - name: Install test dependencies
+      run: pip install pytest scipy
+
     - name: Test with PyTest
-      run: |
-        python -m pytest
+      run: python -m pytest

MANIFEST.in

@@ -1,7 +1,13 @@
 include *.rst
 include *.txt
-include pyspike/cython/*.c
-include directionality/cython/*.c
+include License.txt
+include Changelog
+include pyproject.toml
+
+# Cython sources — required so `pip install` from sdist can regenerate
+# the .c files and build the extension modules.
+recursive-include pyspike/cython *.pyx *.pxd
+
 recursive-include examples *.py *.txt
 recursive-include test *.py *.txt
 recursive-include doc *

pyproject.toml

@@ -0,0 +1,53 @@
+[build-system]
+# setuptools >=77 supports the SPDX-string form `license = "BSD-2-Clause"`
+# in [project] (PEP 639). numpy and Cython are required because setup.py
+# calls numpy.get_include() and compiles .pyx sources for the C extensions.
+requires = [
+    "setuptools>=77",
+    "wheel",
+    "Cython>=3.0",
+    "numpy>=1.25",
+]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "pyspike"
+version = "0.8.1"
+description = "A Python library for the numerical analysis of spike train similarity"
+readme = "Readme.rst"
+requires-python = ">=3.9"
+license = "BSD-2-Clause"
+license-files = ["License.txt"]
+authors = [
+    { name = "Mario Mulansky", email = "mario.mulansky@gmx.net" },
+]
+keywords = ["data analysis", "spike", "neuroscience"]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering",
+    "Topic :: Scientific/Engineering :: Information Analysis",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+]
+dependencies = [
+    "numpy",
+]
+
+[project.urls]
+Homepage = "https://github.com/mariomulansky/PySpike"
+Repository = "https://github.com/mariomulansky/PySpike"
+Issues = "https://github.com/mariomulansky/PySpike/issues"
+
+[tool.setuptools]
+include-package-data = true
+
+[tool.setuptools.packages.find]
+exclude = ["doc*", "test*", "examples*"]
+# Cython .c files are generated at build time (.gitignore excludes them) and
+# the resulting .so files are placed automatically. No package_data needed
+# for the wheel; MANIFEST.in handles inclusion of .pyx sources in the sdist.

pyspike/__init__.py

@@ -35,23 +35,17 @@
     spike_train_order_bi, spike_train_order_multi, \
     optimal_spike_train_sorting, permutate_matrix
 
-# define the __version__ following
-# http://stackoverflow.com/questions/17583443
-from pkg_resources import get_distribution, DistributionNotFound
-import os.path
+# Expose the installed version via importlib.metadata (stdlib since 3.8).
+# Previously this used pkg_resources, which depends on setuptools — and from
+# Python 3.12 onwards venvs no longer ship setuptools by default, so the old
+# import would fail at runtime in fresh 3.12+ environments.
+from importlib.metadata import version as _get_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__ = 'Please install this project with setup.py'
-else:
-    __version__ = _dist.version
+    __version__ = _get_version("pyspike")
+except PackageNotFoundError:
+    # Running from a source checkout that hasn't been installed.
+    __version__ = "0.0.0+unknown"
 
 disable_backend_warning = False
 

setup.py

@@ -1,18 +1,24 @@
 """ setup.py
 
-to compile cython files:
-python setup.py build_ext --inplace
+Compile the Cython extensions for PySpike.
 
+All packaging metadata (name, version, dependencies, classifiers, ...) lives in
+pyproject.toml. This file only declares the C extension modules, because that
+still needs imperative setup() configuration.
 
-Copyright 2014-2017, Mario Mulansky <mario.mulansky@gmx.net>
+To compile cython files in-place:
+    python setup.py build_ext --inplace
+
+
+Copyright 2014-2026, Mario Mulansky <mario.mulansky@gmx.net>
 
 Distributed under the BSD License
 
 """
-from setuptools import setup, find_packages
-from distutils.extension import Extension
 import os.path
 
+from setuptools import Extension, setup
+
 try:
     from Cython.Distutils import build_ext
 except ImportError:
@@ -22,110 +28,62 @@
 
 
 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
+    """Defers import of numpy until the build environment is in place.
+
+    pyproject.toml lists numpy as a build-system requirement, so by the time
+    setup.py actually runs build_ext, numpy is importable. We can't import it
+    at module top level, though, because setuptools imports setup.py before
+    build-system requires are installed.
+    """
+
+    def __str__(self):
+        import numpy
+        return numpy.get_include()
+
+    def __fspath__(self):
+        return str(self)
+
+
+_CYTHON_MODULES = (
+    "cython_add",
+    "cython_get_tau",
+    "cython_profiles",
+    "cython_distances",
+    "cython_directionality",
+    "cython_simulated_annealing",
+)
+
+
+def _all_c_sources_present():
+    return all(
+        os.path.isfile(f"pyspike/cython/{name}.c") for name in _CYTHON_MODULES
+    )
+
+
+use_c = _all_c_sources_present()
 
 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')
+    print("Cython not installed and no pre-generated .c files found. "
+          "PySpike will fall back to the pure-Python backend (slow).")
 
 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"])
+if use_cython:  # Cython is available, compile .pyx -> .c -> binary
+    ext_modules = [
+        Extension(f"pyspike.cython.{name}", [f"pyspike/cython/{name}.pyx"])
+        for name in _CYTHON_MODULES
     ]
-    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"])
+    cmdclass["build_ext"] = build_ext
+elif use_c:  # No Cython, but pre-generated .c files are present
+    ext_modules = [
+        Extension(f"pyspike.cython.{name}", [f"pyspike/cython/{name}.c"])
+        for name in _CYTHON_MODULES
     ]
-# neither cython nor c files available -> automatic fall-back to python backend
+# else: neither Cython nor .c files — fall through to pure-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\
-train similarity',
-    author='Mario Mulansky',
-    author_email='mario.mulansky@gmx.net',
-    license='BSD',
-    url='https://github.com/mariomulansky/PySpike',
-    install_requires=['numpy'],
-    keywords=['data analysis', 'spike', 'neuroscience'],  # arbitrary keywords
-    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',
-    ],
-    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']
-    }
 )