move lib dir to /libvcell/lib, add cibuildwheel to Github Action

Author: jcschaff

.github/workflows/main.yml

@@ -82,7 +82,7 @@ jobs:
                "target/sbml-input"
 
           mvn --batch-mode -P shared-dll package
-          cp target/libvcell.so ../libvcell/_internal/libs
+          cp target/libvcell.so ../libvcell/lib
         if: ${{ startsWith(matrix.os, 'ubuntu') }}
 
       - name: test, record, and build/install native library (macos)
@@ -96,7 +96,7 @@ jobs:
                "target/sbml-input"
 
           mvn --batch-mode -P shared-dll package
-          cp target/libvcell.dylib ../libvcell/_internal/libs
+          cp target/libvcell.dylib ../libvcell/lib
         if: ${{ startsWith(matrix.os, 'macos') }}
 
       - name: test, record, and build/install native library (windows)
@@ -107,7 +107,7 @@ jobs:
           java -agentlib:native-image-agent=config-output-dir=target\recording -jar "target\vcell-native-1.0-SNAPSHOT.jar" "src\test\resources\TinySpacialProject_Application0.xml" "target\sbml-input"
 
           mvn --batch-mode -P shared-dll package
-          cp target/libvcell.dll ../libvcell/_internal/libs
+          cp target/libvcell.dll ../libvcell/lib
         if: ${{ startsWith(matrix.os, 'windows') }}
 
       - name: Install python dependencies

.github/workflows/on-release-main.yml

@@ -1,14 +1,16 @@
 name: release-main
 
 on:
+  workflow_dispatch:
   release:
     types: [published]
     branches: [main]
 
 jobs:
-  publish:
+  build:
     strategy:
-      matrix: #        python-version: ["3.9", "3.10", "3.11", "3.12"]
+      matrix:
+        #        python-version: ["3.9", "3.10", "3.11", "3.12"]
         python-version: ["3.11", "3.12"]
         #        os: [macos-13, windows-latest, ubuntu-latest, macos-14]
         os: [ubuntu-latest, macos-14]
@@ -17,6 +19,7 @@ jobs:
     defaults:
       run:
         shell: bash
+
     steps:
       - name: Check out
         uses: actions/checkout@v4
@@ -25,7 +28,8 @@ jobs:
           fetch-depth: 2
 
 
-      - uses: actions/setup-python@v5
+      - name: Set up Python
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -42,12 +46,12 @@ jobs:
           native-image-job-reports: "true"
           cache: "maven"
 
-      - name: build entire project
+      - name: build VCell Java project from submodule
         working-directory: vcell_submodule
         run: |
           mvn --batch-mode clean install dependency:copy-dependencies -DskipTests=true
 
-      - name: test, record, and build/install native library (ubuntu)
+      - name: test, record, and build/install native library (ubuntu or macos)
         working-directory: vcell-native
         run: |
           mvn --batch-mode clean install
@@ -58,22 +62,9 @@ jobs:
                "target/sbml-input"
 
           mvn --batch-mode -P shared-dll package
-          cp target/libvcell.so ../libvcell/_internal/libs
-        if: ${{ startsWith(matrix.os, 'ubuntu') }}
-
-      - name: test, record, and build/install native library (macos)
-        working-directory: vcell-native
-        run: |
-          mvn --batch-mode clean install
-
-          java -agentlib:native-image-agent=config-output-dir=target/recording \
-               -jar target/vcell-native-1.0-SNAPSHOT.jar \
-               "src/test/resources/TinySpacialProject_Application0.xml" \
-               "target/sbml-input"
-
-          mvn --batch-mode -P shared-dll package
-          cp target/libvcell.dylib ../libvcell/_internal/libs
-        if: ${{ startsWith(matrix.os, 'macos') }}
+          cp target/libvcell.so ../libvcell/lib || true
+          cp target/libvcell.dylib ../libvcell/lib || true
+        if: ${{ startsWith(matrix.os, 'ubuntu') || startsWith(matrix.os, 'macos') }}
 
       - name: test, record, and build/install native library (windows)
         working-directory: vcell-native
@@ -83,7 +74,7 @@ jobs:
           java -agentlib:native-image-agent=config-output-dir=target\recording -jar "target\vcell-native-1.0-SNAPSHOT.jar" "src\test\resources\TinySpacialProject_Application0.xml" "target\sbml-input"
 
           mvn --batch-mode -P shared-dll package
-          cp target/libvcell.dll ../libvcell/_internal/libs
+          cp target/libvcell.dll ../libvcell/lib
         if: ${{ startsWith(matrix.os, 'windows') }}
 
       - name: Install python dependencies
@@ -96,14 +87,33 @@ jobs:
         id: vars
         run: echo tag=${GITHUB_REF#refs/*/} >> $GITHUB_OUTPUT
 
-      - name: Build and publish
+      - name: Build wheels
         run: |
-          source .venv/bin/activate
-          poetry version $RELEASE_VERSION
-          make build-and-publish
-        env:
-          PYPI_TOKEN: ${{ secrets.PYPI_TOKEN }}
-          RELEASE_VERSION: ${{ steps.vars.outputs.tag }}
+          pip install cibuildwheel
+          cibuildwheel --output-dir wheelhouse
+
+      - name: Upload wheels as artifacts
+        uses: actions/upload-artifact@v3
+        with:
+          name: wheels
+          path: wheelhouse/*.whl
+
+  publish:
+    needs: build
+    runs-on: ubuntu-latest
+    steps:
+      - name: Download wheels
+        uses: actions/download-artifact@v3
+        with:
+          name: wheels
+          path: wheelhouse
+
+      - name: Publish to PyPI
+        uses: pypa/[email protected]
+        with:
+          password: ${{ secrets.PYPI_TOKEN }}
+          packages_dir: wheelhouse
+
   deploy-docs:
     needs: publish
     runs-on: ubuntu-latest

libvcell/_internal/libs/.gitignore

@@ -20,7 +20,7 @@ def _load_library(self) -> ctypes.CDLL:
         if lib_ext is None:
             raise OSError(f"Unsupported operating system: {system}")
 
-        libs_dir = files(libvcell).joinpath("_internal/libs")
+        libs_dir = files(libvcell).joinpath("lib")
         if not libs_dir.is_dir():
             raise OSError(f"Could not find the shared library directory {libs_dir}")
 

libvcell/_internal/native_utils.py

@@ -10,7 +10,7 @@ packages = [
   {include = "libvcell"}
 ]
 include = [
-    {path="libvcell/_internal/libs/*", format="wheel"}
+    {path="libvcell/lib/libvcell*", format="wheel"}
 ]
 
 [tool.poetry.dependencies]
@@ -30,6 +30,13 @@ mkdocs = "^1.6.1"
 mkdocs-material = "^9.5.50"
 mkdocstrings = {extras = ["python"], version = "^0.27.0"}
 
+[tool.cibuildwheel]
+build = "cp311-manylinux_x86_64 cp311-macosx_x86_64 cp311-macosx_arm64 cp311-win_amd64"
+skip = "cp36-* cp37-* cp38-* cp310-*"
+
+[tool.setuptools.package-data]
+libvcell = ["lib/*"]
+
 [build-system]
 requires = ["poetry-core>=1.0.0"]
 build-backend = "poetry.core.masonry.api"

pyproject.toml

@@ -40,4 +40,4 @@ java -agentlib:native-image-agent=config-output-dir=target/recording \
 mvn package -P shared-dll
 
 # install vcell-native as shared object library
-cp target/libvcell.dylib "$ROOT_DIR/libvcell/_internal/libs/libvcell.dylib"
+cp target/libvcell.dylib "$ROOT_DIR/libvcell/lib/libvcell.dylib"