add pyproject.toml to ensure pip builds have Cython and numpy

.github/dependabot.yml

@@ -0,0 +1,10 @@
+# Set update schedule for GitHub Actions
+
+version: 2
+updates:
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      # Check for updates to GitHub Actions every week
+      interval: "weekly"

.github/workflows/build_wheels.yml

@@ -0,0 +1,163 @@
+name: Build wheels and publish to pypi
+
+on:
+  push:
+    branches:
+      - master
+    tags:
+      - '*'
+
+jobs:
+  build_wheels:
+    name: ${{ matrix.os }} • ${{ matrix.python }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-15-intel, macos-latest]
+        python: [cp310, cp311, cp312, cp313, cp314, pp311]
+        exclude:
+          # Skip PyPy on Windows
+          - os: windows-latest
+            python: pp311
+    steps:
+      - uses: actions/checkout@v5
+      - name: Set version suffix for TestPyPI
+        id: set_version
+        run: |
+          if [[ ! "${{ github.ref }}" =~ ^refs/tags/ ]]; then
+            BUILD_NUM=${{ github.run_number }}
+            VERSION=$(grep '^version = ' pyproject.toml | sed -E 's/version = "(.*)"/\1/')
+            sed -i -e "s/^version = \"${VERSION}\"/version = \"${VERSION}.dev${BUILD_NUM}\"/" pyproject.toml
+          fi
+        shell: bash
+      - name: Build wheels
+        uses: pypa/cibuildwheel@v3.2
+        env:
+          CIBW_BUILD: ${{ matrix.python }}-*
+          CIBW_ARCHS_MACOS: auto
+        with:
+          package-dir: .
+          output-dir: wheelhouse
+          config-file: "{package}/pyproject.toml"
+      - name: Verify clean directory
+        if: startsWith(github.ref, 'refs/tags/')
+        run: git diff --exit-code
+        shell: bash
+      - uses: actions/upload-artifact@v5
+        with:
+          name: artifact-${{ matrix.os }}-${{ matrix.python }}
+          path: ./wheelhouse/*.whl
+
+  build_sdist:
+    name: Build source distribution
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v5
+      - name: Set version suffix for TestPyPI
+        id: set_version
+        run: |
+          if [[ ! "${{ github.ref }}" =~ ^refs/tags/ ]]; then
+            BUILD_NUM=${{ github.run_number }}
+            VERSION=$(grep '^version = ' pyproject.toml | sed -E 's/version = "(.*)"/\1/')
+            sed -i -e "s/^version = \"${VERSION}\"/version = \"${VERSION}.dev${BUILD_NUM}\"/" pyproject.toml
+          fi
+      - name: Build sdist
+        run: pipx run build --sdist
+
+      - uses: actions/upload-artifact@v5
+        with:
+          name: artifact-source
+          path: dist/*.tar.gz
+
+  merge_artifacts:
+    name: Merge artifacts
+    needs: [build_wheels, build_sdist]
+    runs-on: ubuntu-latest
+    steps:
+      - name: Merge artifacts
+        uses: actions/upload-artifact/merge@v5
+        with:
+          name: all-files
+          pattern: artifact-*
+
+  publish-to-pypi:
+    name: >-
+      Publish Python distribution to PyPI
+    if: startsWith(github.ref, 'refs/tags/')  # only publish to PyPI on tag pushes
+    needs: [merge_artifacts]
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/melizalab-pyspike
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v6
+      with:
+        name: all-files
+        path: dist/
+    - name: Publish distribution to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+
+  github-release:
+    name: >-
+      Sign the Python distribution with Sigstore
+      and to GitHub Release
+    needs: [publish-to-pypi]
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write  # IMPORTANT: mandatory for making GitHub Releases
+      id-token: write  # IMPORTANT: mandatory for sigstore
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v6
+      with:
+        name: all-files
+        path: dist/
+    - name: Sign the dists with Sigstore
+      uses: sigstore/gh-action-sigstore-python@v3.1.0
+      with:
+        inputs: >-
+          ./dist/*.tar.gz
+          ./dist/*.whl
+    - name: Create GitHub Release
+      env:
+        GITHUB_TOKEN: ${{ github.token }}
+      run: >-
+        gh release create
+        '${{ github.ref_name }}'
+        --repo '${{ github.repository }}'
+        --notes ""
+    - name: Upload artifact signatures to GitHub Release
+      env:
+        GITHUB_TOKEN: ${{ github.token }}
+      # Upload to GitHub Release using the `gh` CLI.
+      # `dist/` contains the built packages, and the
+      # sigstore-produced signatures and certificates.
+      run: >-
+        gh release upload
+        '${{ github.ref_name }}' dist/**
+        --repo '${{ github.repository }}'
+
+  publish-to-testpypi:
+    name: Publish Python distribution to TestPyPI
+    needs: [merge_artifacts]
+    runs-on: ubuntu-latest
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/p/melizalab-pyspike
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v6
+      with:
+        name: all-files
+        path: dist/
+    - name: Publish distribution 📦 to TestPyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        repository-url: https://test.pypi.org/legacy/
+        verbose: true

.github/workflows/python_tests.yml

@@ -0,0 +1,28 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Python tests
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [macos-15-intel, macos-latest, ubuntu-latest, windows-latest]
+        python-version: ["3.10", "3.11", "3.12", "3.13", "3.14", "pypy3.10", "pypy3.11"]
+    runs-on: ${{ matrix.os }}
+
+    steps:
+    - uses: actions/checkout@v5
+    - name: Install uv
+      uses: astral-sh/setup-uv@v7
+      with:
+        enable-cache: true
+        version: "latest"
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: uv sync --frozen
+    - name: Run tests on python ${{ matrix.python-version }}
+      run: uv run pytest        

.gitignore

@@ -1,59 +1,8 @@
-HELP.md
-.gradle
-build/
-!gradle/wrapper/gradle-wrapper.jar
-!**/src/main/**/build/
-!**/src/test/**/build/
-
-### STS ###
-.apt_generated
-.classpath
-.factorypath
-.project
-.settings
-.springBeans
-.sts4-cache
-bin/
-!**/src/main/**/bin/
-!**/src/test/**/bin/
-
-### IntelliJ IDEA ###
-.idea
-*.iws
-*.iml
-*.ipr
-out/
-!**/src/main/**/out/
-!**/src/test/**/out/
-
-### NetBeans ###
-/nbproject/private/
-/nbbuild/
-/dist/
-/nbdist/
-/.nb-gradle/
-
-### VS Code ###
-.vscode/
-
-# Emacs backups
-*~
-.#*
-\#*
-
-# Log files
-*.log
-
-# MacOS does this
-.DS_Store
-~*
-
-# Jacoco generated
-*.exec
-
-# KDiff3 backup files
-*.orig
-
-# C files are always generated by Cython
 *.c
-*.C
+*.so
+.DS_Store
+.coverage
+__pycache__/
+build/
+dist/
+melizalab_pyspike.egg-info/

MANIFEST.in

@@ -1,7 +1,6 @@
 include *.rst
 include *.txt
-include pyspike/cython/*.c
-include directionality/cython/*.c
+recursive-include pyspike *.pyx *.pxd
 recursive-include examples *.py *.txt
 recursive-include test *.py *.txt
 recursive-include doc *

Readme.rst

@@ -1,10 +1,22 @@
 PySpike
 =======
 
-.. image:: https://badge.fury.io/py/pyspike.png
-    :target: http://badge.fury.io/py/pyspike
-.. image:: https://travis-ci.org/mariomulansky/PySpike.svg?branch=master
-    :target: https://travis-ci.org/mariomulansky/PySpike
+|ProjectStatus|_ |Version|_ |BuildStatus|_ |License|_ |PythonVersions|_
+
+.. |ProjectStatus| image:: https://www.repostatus.org/badges/latest/active.svg
+.. _ProjectStatus: https://www.repostatus.org/#active
+
+.. |Version| image:: https://img.shields.io/pypi/v/melizalab-pyspike.svg
+.. _Version: https://pypi.python.org/pypi/melizalab-pyspike/
+
+.. |BuildStatus| image:: https://github.com/melizalab/melizalab-pyspike/actions/workflows/python_tests.yml/badge.svg
+.. _BuildStatus: https://github.com/melizalab/melizalab-pyspike/actions/workflows/python_tests.yml
+
+.. |License| image:: https://img.shields.io/pypi/l/melizalab-pyspike.svg
+.. _License: https://opensource.org/license/bsd-3-clause/
+
+.. |PythonVersions| image:: https://img.shields.io/pypi/pyversions/melizalab-pyspike.svg
+.. _PythonVersions: https://pypi.python.org/pypi/melizalab-pyspike/
 
 PySpike is a Python library for the numerical analysis of spike train similarity. 
 Its core functionality is the implementation of the ISI_\-distance [#]_ and SPIKE_\-distance [#]_, SPIKE-Synchronization_ [#]_, as well as their adaptive generalizations [#]_.
@@ -13,7 +25,7 @@ All computation intensive parts are implemented in C via cython_ to reach a comp
 
 PySpike provides the same fundamental functionality as the SPIKY_ framework for Matlab, which additionally contains spike-train generators, more spike train distance measures and many visualization routines.
 
-All source codes are available on `Github <https://github.com/mariomulansky/PySpike>`_  and are published under the BSD_License_.
+All source codes are available on `Github <https://github.com/mariomulansky/PySpike>`_  and are published under the BSD_License_. `This fork <https://github.com/melizalab/PySpike>`_ is maintained by the Meliza Lab for PEP518-compatible builds and CI-generated `wheels <https://pypi.org/project/melizalab-pyspike/>`_.
 
 Citing PySpike
 ----------------------------