Release v0.1.16 - Python 3.12 Support

.github/workflows/build.yml

@@ -24,12 +24,12 @@ jobs:
 
       - name: Set up QEMU (For Linux ARM)
         if: runner.os == 'Linux'
-        uses: docker/setup-qemu-action@v2
+        uses: docker/setup-qemu-action@v3
         with:
           platforms: arm64
 
       - name: Build Wheels
-        uses: pypa/cibuildwheel@v2.12.3
+        uses: pypa/cibuildwheel@v2.16.2
         with:
           package-dir: .
           output-dir: wheelhouse

.github/workflows/ci.yml

@@ -36,21 +36,21 @@ jobs:
     uses: ./.github/workflows/build.yml
 
   # Skip for now, until we sort out how to get coverage from the running Cython Tests
-  # upload_coverage:
-  #   needs: [test]
-  #   name: Upload Coverage
-  #   runs-on: ubuntu-latest
-  #   steps:
-  #     - name: Checkout ${{ github.repository }}
-  #       uses: actions/checkout@v3
-  #       with:
-  #         fetch-depth: 0
+  upload_coverage:
+    needs: [test]
+    name: Upload Coverage
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout ${{ github.repository }}
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
 
-  #     - name: Download Coverage Artifact
-  #       uses: actions/download-artifact@v3
-  #       # if `name` is not specified, all artifacts are downloaded.
+      - name: Download Coverage Artifact
+        uses: actions/download-artifact@v3
+        # if `name` is not specified, all artifacts are downloaded.
 
-  #     - name: Upload Coverage to Coveralls
-  #       uses: coverallsapp/github-action@v2
-  #       with:
-  #         github-token: ${{ secrets.GITHUB_TOKEN }}
+      - name: Upload Coverage to Coveralls
+        uses: coverallsapp/github-action@v2
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/release-drafter.yml

@@ -23,7 +23,7 @@ jobs:
       pull-requests: write # for release-drafter/release-drafter to add label to PR
     steps:
       # Drafts your next Release notes as Pull Requests are merged into "main"
-      - uses: release-drafter/release-drafter@v5.23.0
+      - uses: release-drafter/release-drafter@v5.25.0
         # Specify config name to use, relative to .github/. Default: release-drafter.yml
         with:
           config-name: release-drafter.yml

.github/workflows/test.yml

@@ -13,7 +13,7 @@ jobs:
       # Ensure that if any job fails, all jobs are cancelled.
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
         os: [ubuntu-latest, macos-latest, windows-latest]
 
     steps:
@@ -38,9 +38,9 @@ jobs:
           pytest
 
       # Skip for now, until we sort out how to get coverage from the running Cython Tests
-      # - name: Archive Coverage
-      #   uses: actions/upload-artifact@v3
-      #   with:
-      #     name: coverage-${{ join(matrix.*, '-') }}
-      #     path: |
-      #       coverage.lcov
+      - name: Archive Coverage
+        uses: actions/upload-artifact@v3
+        with:
+          name: coverage-${{ join(matrix.*, '-') }}
+          path: |
+            coverage.lcov

pyproject.toml

@@ -3,13 +3,13 @@ requires = [
     "setuptools",
     "wheel",
     "numpy>=1,<2",
-    "Cython>=0.29,<1",
-    "setuptools_scm[toml]>=6.2",
+    "Cython>=3",
+    "setuptools_scm[toml]>=8",
 ]
 build-backend = "setuptools.build_meta"
 
 [project]
-dependencies = ["Cython>=0.29,<1", "numpy>=1,<2", "scipy>=1,<2"]
+dependencies = ["Cython>=3", "numpy>=1,<2", "scipy>=1,<2"]
 name = "pyFlowSOM"
 authors = [{ name = "Angelo Lab", email = "theangelolab@gmail.com" }]
 description = "A Python implementation of the SOM training functionality of FlowSOM"
@@ -23,6 +23,7 @@ classifiers = [
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
     "License :: OSI Approved :: Apache Software License",
     "Topic :: Scientific/Engineering :: Bio-Informatics",
 ]
@@ -47,7 +48,7 @@ version_scheme = "release-branch-semver"
 local_scheme = "no-local-version"
 
 [tool.cibuildwheel]
-build = ["cp39-*", "cp310-*", "cp311-*"]
+build = ["cp39-*", "cp310-*", "cp311-*", "cp312-*"]
 skip = [
     "cp36-*",         # Python 3.6
     "cp37-*",         # Python 3.7
@@ -126,8 +127,8 @@ addopts = [
     "--durations=20",
     "--randomly-seed=42",
     "--randomly-dont-reorganize",
-    # "--cov=pyFlowSOM",
-    # "--cov-report=lcov",
+    "--cov=pyFlowSOM",
+    "--cov-report=lcov",
     "--pycodestyle",
 ]
 console_output_style = "count"