feat: Use Pixi, pyradiomics fork

.github/workflows/ci-cd.yml

@@ -1,54 +1,78 @@
-name: ci-cd
+name: CI-CD
 
 # only run on pushes to main or pull requests
 on:
   push:
+    # push to any branch *
     branches: ["*"]
   pull_request:
-    branches: [main]
+    branches: [main, development]
+
 
 jobs:
-  Unit-Testing:
-    # Set up operating system
-    runs-on: ubuntu-latest
+  ################################################################################################
+  # Unit-Tests: Run unit tests using pytest
+  ################################################################################################
+  Unit-Tests:
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 15 # Consider increasing timeout
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest, macos-14] # , windows-latest removed for now
+        env: ["py310", "py311", "py312"]
 
-    # Define job steps
     steps:
-      - name: Set up Python
-        uses: actions/setup-python@v4
-        with:
-          python-version: "3.9"
-
-      - name: Check-out repository
-        uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - name: Install poetry
-        uses: snok/install-poetry@v1
-
-      - name: Install package
-        run: poetry install
+      - name: Install Pixi
+        uses: prefix-dev/setup-pixi@v0.8.1
+        with:
+          environments: ${{ matrix.env }}
+          pixi-version: v0.33.0
+          cache: true
+          locked: false # wont be the same because of the tag
 
-      - name: Test with pytest
-        # Github action runners now have 4 cores
-        run: poetry run pytest -s -v -n 4 tests/
+      - name: Run pytest
+        run: |
+          pixi run -e ${{ matrix.env }} test
 
-      # Commented out until we have a repo for coverage
-      # - name: Test with pytest
-      #   run: poetry run pytest tests/ --cov=readii --cov-report=xml
+      - name: Upload coverage report artifact to be used by Codecov
+        # only upload if matrix.os is ubuntu-latest and matrix.python-version is 3.12
+        if: matrix.os == 'ubuntu-latest' && matrix.env == 'py312'
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-report
+          path: coverage-report
+
+################################################################################################
+  # Semantic-Release: Run semantic-release to automate versioning and publishing
+  ################################################################################################
+  Semantic-Release:
+    permissions:
+      # Read releases read-all
+      contents: write
+      packages: write
+      issues: write
+      pull-requests: write
+
+    needs: [Unit-Tests]
+
+    # if pulling to main, deploy to PyPI
+    if: github.ref == 'refs/heads/main'
 
-      # - name: Use Codecov to track coverage
-      #   uses: codecov/codecov-action@v3
-      #   with:
-      #     files: ./coverage.xml   # coverage report
+    env:
+      PIXI_ENV: "publish"
 
-  Continuous-Deployment:
-    needs: Unit-Testing
-
-    # # Only run this job if new work is pushed to "main"
-    if: github.ref == 'refs/heads/main'
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ["3.12"]
 
     # Set up operating system
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.os }}
+
+    # Concurrency is for preventing multiple runs of the same workflow
+    concurrency: release
 
     outputs:
       released: ${{ steps.release.outputs.released }}
@@ -57,132 +81,67 @@ jobs:
 
     # Define job steps
     steps:
-      - name: Set up Python
-        uses: actions/setup-python@v4
-        with:
-          python-version: "3.9"
-
       - name: Check-out repository
         uses: actions/checkout@v3
         with:
           fetch-depth: 0
 
-      - name: Install poetry
-        uses: snok/install-poetry@v1
-
-      - name: Install package
-        run: poetry install
-
-      # This action uses Python Semantic Release v8
-      - name: Python Semantic Release
-        id: release
-        uses: python-semantic-release/python-semantic-release@master
+      - name: Install Pixi
+        uses: prefix-dev/setup-pixi@v0.8.1
+        env:
+          RUNNER_DEBUG: true
         with:
-          github_token: ${{ secrets.GITHUB_TOKEN }}
-
+          environments: ${{ env.PIXI_ENV }}
+          pixi-version: v0.33.0
+          cache: true
+          locked: false 
+          # cache-key: pixi-ENV_${{ env.PIXI_ENV }}-
+
+      - name: Print Semver
+        env: 
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: pixi run semver
+
+      - name: Run semantic-release
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        id: release
+        run: pixi run release
+
       - name: Test Outputs of semantic release step
         run: |
           echo "${{ steps.release.outputs.released }}"
           echo "${{ steps.release.outputs.version }}"
           echo "${{ steps.release.outputs.tag }}"
 
-  Publish-To-PyPI:
-    needs: Continuous-Deployment
-    if: ${{ needs.Continuous-Deployment.outputs.released == 'true' }}
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout the code with tag ${{ needs.Continuous-Deployment.outputs.tag }}
-        uses: actions/checkout@v3
-        with:
-          ref: ${{ needs.Continuous-Deployment.outputs.tag }}
-
-      - name: Set up Python
-        uses: actions/setup-python@v2
-        with:
-          python-version: "3.9"
-
-      - name: Install poetry
-        uses: snok/install-poetry@v1
-
-      - name: Install Package Building Tool
-        run: python3 -m pip install build twine
-
-      - name: Build Package
-        run: |
-          poetry version ${{ needs.Continuous-Deployment.outputs.version }}
-          python -m build --sdist --wheel --outdir dist/ .
-          ls dist/
-
-      - name: Publish to TestPyPI
-        if: steps.release.outputs.released == 'true'
-        uses: pypa/gh-action-pypi-publish@release/v1
-        with:
-          user: __token__
-          password: ${{ secrets.TEST_PYPI_API_TOKEN }}
-          repository-url: https://test.pypi.org/legacy/
-
-      - name: Test install from TestPyPI
-        run: |
-          pip install \
-          --index-url https://test.pypi.org/simple/ \
-          --extra-index-url https://pypi.org/simple \
-          readii
-
-      - name: Publish to PyPI
-        uses: pypa/gh-action-pypi-publish@release/v1
-        with:
-          verbose: true
-          user: __token__
-          password: ${{ secrets.PYPI_API_TOKEN }}
-
-  Build-Docker-Images:
-    needs: [ Continuous-Deployment, Publish-To-PyPI ]
-    if: ${{ needs.Continuous-Deployment.outputs.released == 'true' }}
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout the code with tag ${{ needs.Continuous-Deployment.outputs.tag }}
-        uses: actions/checkout@v3
-        with:
-          ref: ${{ needs.Continuous-Deployment.outputs.tag }}
-
-      - name: Set up QEMU
-        uses: docker/setup-qemu-action@v3
-
-      - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v3
-
-      - name: Login to Docker Hub
-        uses: docker/login-action@v3
-        with:
-          username: ${{ secrets.BHKLAB_DOCKERHUB_USERNAME }}
-          password: ${{ secrets.BHKLAB_DOCKERHUB_ACCESS_KEY }}
-
-      - name: Login to the GitHub Container Registry
-        uses: docker/login-action@v3
-        with:
-          registry: ghcr.io
-          username: ${{ github.actor }}
-          password: ${{ secrets.GITHUB_TOKEN }}
-
-      - name: Extract metadata (tags, labels) for Docker
-        id: meta
-        uses: docker/metadata-action@v3
-        with:
-          images: |
-            bhklab/readii:${{ needs.Continuous-Deployment.outputs.tag }}
-            ghcr.io/${{ github.repository }}/readii:${{ needs.Continuous-Deployment.outputs.tag }}
-      - name: Build
-        uses: docker/build-push-action@v5
-        with:
-          context: .
-          # platforms: macos/amd64,linux/amd64, macos/arm64, linux/arm64
-          # slim-buster only supports linux/{amd64,arm64}
-          platforms: linux/amd64
-          file: ./Dockerfile
-          push: true
-          tags: |
-            bhklab/readii:${{ needs.Continuous-Deployment.outputs.tag }}
-            bhklab/readii:latest
-            ghcr.io/${{ github.repository }}/readii:${{ needs.Continuous-Deployment.outputs.tag }}
-            ghcr.io/${{ github.repository }}/readii:latest
-          labels: ${{ steps.meta.outputs.labels }}
+  ################################################################################################
+  # Publish-To-PyPi & Test-PyPi-Installation: Publish to PyPI and test installation
+  ################################################################################################
+  # Publish-To-PyPi:
+  #   needs: Semantic-Release
+  #   env:
+  #     PIXI_ENV: "publish"
+  #     # if: needs.Semantic-Release.outputs.released == 'true'
+  #   strategy:
+  #     matrix:
+  #       os: [ubuntu-latest]
+
+  #   runs-on: ${{ matrix.os }}
+  #   steps:
+  #     - name: Checkout the code with tag ${{ needs.Semantic-Release.outputs.tag }}
+  #       uses: actions/checkout@v4
+  #       with:
+  #         ref: ${{ needs.Semantic-Release.outputs.tag }}
+
+  #     - name: Install Pixi
+  #       uses: prefix-dev/setup-pixi@v0.8.1
+  #       with:
+  #         environments: ${{ env.PIXI_ENV }}
+  #         pixi-version: v0.33.0
+  #         # cache-key: pixi-ENV_${{ env.PIXI_ENV }}-
+  #         cache: true
+  #         locked: false # wont be the same because of the tag
+
+  #     - name: Test Build
+  #       run: |
+  #           pixi run -e ${{ env.PIXI_ENV }} build