Update Build Toolchain

.github/workflows/release.yml

@@ -0,0 +1,151 @@
+name: Build and upload to PyPI
+
+on:
+  push:
+  release:
+    types:
+      - published
+
+jobs:
+  # Build the wheels for Linux, Windows and macOS for Python 3.9 and newer
+  build_wheels:
+    name: Build wheel for cp${{ matrix.python }}-${{ matrix.platform_id }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      # Ensure that a wheel builder finishes even if another fails
+      fail-fast: false
+      matrix:
+        include:
+          # Window 64 bit
+          - os: windows-latest
+            python: 39
+            platform_id: win_amd64
+          - os: windows-latest
+            python: 310
+            platform_id: win_amd64
+          - os: windows-latest
+            python: 311
+            platform_id: win_amd64
+          - os: windows-latest
+            python: 312
+            platform_id: win_amd64
+          - os: windows-latest
+            python: 313
+            platform_id: win_amd64
+          - os: windows-latest
+            python: 313t
+            platform_id: win_amd64
+            free_threaded_support: True
+
+          # Linux 64 bit manylinux2014
+          - os: ubuntu-latest
+            python: 39
+            platform_id: manylinux_x86_64
+          - os: ubuntu-latest
+            python: 310
+            platform_id: manylinux_x86_64
+          - os: ubuntu-latest
+            python: 311
+            platform_id: manylinux_x86_64
+          - os: ubuntu-latest
+            python: 312
+            platform_id: manylinux_x86_64
+          - os: ubuntu-latest
+            python: 313
+            platform_id: manylinux_x86_64
+          - os: ubuntu-latest
+            python: 313t
+            platform_id: manylinux_x86_64
+            free_threaded_support: True
+
+          # MacOS x86_64
+          - os: macos-13
+            python: 39
+            platform_id: macosx_x86_64
+          - os: macos-13
+            python: 310
+            platform_id: macosx_x86_64
+          - os: macos-13
+            python: 311
+            platform_id: macosx_x86_64
+          - os: macos-13
+            python: 312
+            platform_id: macosx_x86_64
+          - os: macos-13
+            python: 313
+            platform_id: macosx_x86_64
+          - os: macos-13
+            python: 313t
+            platform_id: macosx_x86_64
+            free_threaded_support: True
+
+          # MacOS arm64
+          - os: macos-14
+            python: 39
+            platform_id: macosx_arm64
+          - os: macos-14
+            python: 310
+            platform_id: macosx_arm64
+          - os: macos-14
+            python: 311
+            platform_id: macosx_arm64
+          - os: macos-14
+            python: 312
+            platform_id: macosx_arm64
+          - os: macos-14
+            python: 313
+            platform_id: macosx_arm64
+          - os: macos-14
+            python: 313t
+            platform_id: macosx_arm64
+            free_threaded_support: True
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Build wheels
+        env:
+          CIBW_FREE_THREADED_SUPPORT: ${{ matrix.free_threaded_support }}
+          CIBW_BUILD: cp${{ matrix.python }}-${{ matrix.platform_id }}
+          CIBW_TEST_REQUIRES: pytest psutil
+          CIBW_TEST_COMMAND: pytest -v {project}/test
+          CIBW_ENVIRONMENT: USE_CYTHON=1
+        uses: pypa/cibuildwheel@v2.22.0
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: cibw-wheels-${{ 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:
+      name: pypi
+      url: https://pypi.org/p/stochastic-arrow
+    permissions:
+      id-token: write
+    if: github.event_name == 'release' && github.event.action == 'published'
+    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

.gitignore

@@ -10,9 +10,9 @@ profile
 /.idea/
 /tmp/
 
-stochastic_arrow/arrowhead.c
-stochastic_arrow/arrowhead.*.pyd
-stochastic_arrow/*.html
+src/stochastic_arrow/arrowhead.c
+src/stochastic_arrow/arrowhead.*.pyd
+src/stochastic_arrow/*.html
 
 arrow.egg-info/
 stochastic_arrow.egg-info/

MANIFEST.in

@@ -1,2 +1,2 @@
-include stochastic_arrow/obsidian.h
-include stochastic_arrow/mersenne.h
+include src/stochastic_arrow/obsidian.h
+include src/stochastic_arrow/mersenne.h

Makefile

@@ -2,16 +2,19 @@
 .DEFAULT_GOAL := compile
 
 clean:
-	### Files for older versions of stochastic_arrow are in arrow folder
+	### Files for older versions of stochastic_arrow are in arrow or stochastic_arrow folder
 	rm -rf arrow/arrowhead*.so arrow/arrowhead.c arrow/arrowhead.html
 	rm -rf stochastic_arrow/arrowhead*.so stochastic_arrow/arrowhead.c stochastic_arrow/arrowhead.html build/ dist/ MANIFEST .pytest_cache/ stochastic_arrow.egg-info/
+	### Newer versions of stochastic_arrow are in src/stochastic_arrow folder
+	rm -rf src/stochastic_arrow/arrowhead*.so src/stochastic_arrow/arrowhead.c src/stochastic_arrow/arrowhead.html src/stochastic_arrow.egg-info/
 	find . -name "*.pyc" -delete
 	find . -name "__pycache__" -delete
 
 compile:
-	USE_CYTHON=1 python setup.py build_ext --inplace
+	USE_CYTHON=1 python -m pip install -e .
+
+test: clean compile
+	pytest test
 
 dist:
-	### bdist_wheel is disabled on linux since the distribution machinery doesn't
-	### yet have a way to specify compatible linux distros.
-	USE_CYTHON=1 python setup.py sdist # bdist_wheel
+	USE_CYTHON=1 python -m build --sdist

README.md

@@ -91,37 +91,53 @@ from stochastic_arrow import reenact_events
 history = reenact_events(stoichiometric_matrix, result['events'], state)
 ```
 
-## Testing
-
-`stochastic_arrow` uses [pytest](https://docs.pytest.org/en/latest/). To test it:
+## Building
 
     > make clean compile
-    > pytest
+
+This builds the extension package and installs it in editable mode.
 
 **NOTE:** `make compile` without an explicit `clean` might not fully build the extension.
 
-There are more command line features in test_arrow:
+## Testing
+
+`stochastic_arrow` uses [pytest](https://docs.pytest.org/en/latest/).
+To run the main tests, in the source tree:
 
-    > python -m stochastic_arrow.test.test_arrow --complexation
+    > make test
 
-    > python -m stochastic_arrow.test.test_arrow --plot
+or
 
-    > python -m stochastic_arrow.test.test_arrow --obsidian
+    > pytest
 
-    > python -m stochastic_arrow.test.test_arrow --memory
+There are additional command line features in test_arrow:
 
-    > python -m stochastic_arrow.test.test_arrow --time
+    > python -m test.test_arrow --help
+    > python -m test.test_arrow --complexation
+    > python -m test.test_arrow --complexation --runs 3
+    > python -m test.test_arrow --obsidian
+    > python -m test.test_arrow --memory
+    > python -m test.test_arrow --time
+    > python -m test.test_arrow --pickle
+    > python -m test.test_arrow --test-fail-flagella
+    > python -m test.test_arrow --test-fail-stdout
+    > python -m test.test_hang
 
-More examples:
+This test requires installing a version of matplotlib that's compatible with the installed numpy:
 
-    > python -m stochastic_arrow.test.test_hang
+    > python -m test.test_arrow --plot
 
-    > pytest -m stochastic_arrow/test/test_arrow.py
+More examples:
 
     > pytest -k flagella
 
 ## Changelog
 
+### Version 1.1.0
+* Update build toolchain and automatically build/publish wheels for all
+major platforms and recent Python versions.
+* Build wheels with Numpy 2+ support
+
 ### Version 1.0.0
 
 * Rename module to `stochastic_arrow` to avoid name conflict (Issue #51). **All users must update their import statements to use `stochastic_arrow` instead of `arrow`.**

optional_requirements.txt

@@ -1 +1 @@
-matplotlib==2.2.3
+matplotlib

pyproject.toml

@@ -0,0 +1,3 @@
+[build-system]
+requires = ["setuptools", "wheel", "cython==3.1.0a1; python_version=='3.13'", "cython; python_version!='3.13'", "numpy"]
+build-backend = "setuptools.build_meta"

requirements.txt

@@ -2,6 +2,7 @@
 
 pip
 setuptools
+build
 
 Cython>=0.29.34
 numpy