Merge pull request #131 from lucasimi/develop

Develop

Author: lucasimi

.github/workflows/deploy.yml

@@ -6,11 +6,12 @@ on:
       - 'v[0-9]+.[0-9]+.[0-9]+'
 
 jobs:
-  deploy-job:
+  build_locally:
+    name: Build locally
     runs-on: ubuntu-latest
     steps:
       - name: Check out repository code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
       - name: Install Python
         uses: actions/setup-python@v4
         with:
@@ -19,19 +20,55 @@ jobs:
         run: | 
           python -m pip install twine build
           python -m pip install -e .
-      - name: Build package
+      - name: Build package locally
         run: | 
-          python -m build --sdist --wheel
+          python -m build
           python -m twine check dist/*
-      - name: Upload package to TestPyPI
-        run: | 
-          python -m twine upload -r testpypi dist/* --verbose
-        env:
-          TWINE_USERNAME: ${{ secrets.TWINE_USERNAME_TEST }}
-          TWINE_PASSWORD: ${{ secrets.TWINE_PASSWORD_TEST }}
-      - name: Upload package to PyPI
-        run: | 
-          python -m twine upload -r pypi dist/* --verbose
-        env:
-          TWINE_USERNAME: ${{ secrets.TWINE_USERNAME }}
-          TWINE_PASSWORD: ${{ secrets.TWINE_PASSWORD }}
+
+  build_wheels:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-13, macos-14]
+    steps:
+      - uses: actions/checkout@v4
+      - name: Build wheels
+        uses: pypa/cibuildwheel@v2.19.2
+      - uses: actions/upload-artifact@v4
+        with:
+          name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
+          path: ./wheelhouse/*.whl
+
+  build_sdist:
+    name: Build source distribution
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Build sdist
+        run: pipx run build --sdist
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: cibw-sdist
+          path: dist/*.tar.gz
+
+  upload_pypi:
+    needs: [build_wheels, build_sdist]
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          # unpacks all CIBW artifacts into dist/
+          pattern: cibw-*
+          path: dist
+          merge-multiple: true
+
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          # To test: 
+          repository-url: https://test.pypi.org/legacy/

pyproject.toml

@@ -19,14 +19,17 @@ keywords = ["tda", "mapper", "topology", "topological data analysis"]
 dependencies = [
     "matplotlib>=3.3.4",
     "networkx>=2.5",
-    "numpy>=1.20.1",
+    "numpy>=1.20.1, <2.0.0",
     "plotly>=4.14.3"
 ]
 requires-python = ">=3.6"
 
 [project.optional-dependencies]
 dev = ["coverage", "pandas", "scikit-learn"]
 
+[tool.setuptools.package-data]
+"tdamapper.utils" = ["_metrics.c", "_metrics.pyx"]
+
 [project.urls]
 Homepage = "https://github.com/lucasimi/tda-mapper-python"
 Documentation = "https://tda-mapper.readthedocs.io"

setup.py

@@ -3,11 +3,15 @@
 from Cython.Build import cythonize
 
 
+ext_modules = [
+    Extension(
+        name='tdamapper.utils._metrics',
+        sources=[
+            'src/tdamapper/utils/_metrics.pyx',
+        ],
+    ),
+]
+
 setup(
-    ext_modules=cythonize([
-        Extension(
-            name="tdamapper.utils._metrics",
-            sources=["src/tdamapper/utils/_metrics.pyx"],
-        ),
-    ])
+    ext_modules=cythonize(ext_modules),
 )

src/tdamapper/utils/_metrics.pyx

@@ -17,7 +17,7 @@ cpdef inline double euclidean(double[:] x, double[:] y) nogil:
     return sqrt(norm_squared)
 
 
-cdef inline double minkowski(int p, double[:] x, double[:] y) nogil:
+cpdef inline double minkowski(int p, double[:] x, double[:] y) nogil:
     cdef double norm_p = 0.0
     cdef Py_ssize_t i, n = x.shape[0]
     for i in range(n):