Merge remote-tracking branch 'origin/development' into example_notebook

.github/workflows/main.yml

@@ -31,21 +31,46 @@ jobs:
         run: |
           pip install -r requirements.txt
           poetry install
-          pytest --cov --cov-report=xml
+          pytest --cov --cov-report=xml:coverage-report/coverage.xml
+
+      - name: Build documentation
+        run: poetry run make html --directory docs/
+
+      - name: Upload coverage report
+        uses: actions/upload-artifact@v2
+        with:
+          name: coverage-report
+          path: coverage-report
+
+  Codecov:
+    needs: Continuous-Integration
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      - name: Download coverage.xml artifact
+        uses: actions/download-artifact@v2
+        with:
+          name: coverage-report
+          path: coverage-report
 
       - name: Use Codecov to track coverage
         uses: codecov/codecov-action@v3
         with:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
-          files: ./coverage.xml
-          fail_ci_if_error: true # optional (default = false)
-          verbose: true # optional (default = false)
+          files: ./coverage-report/coverage.xml
+          fail_ci_if_error: true
+          verbose: true
           name: codecov-umbrella
 
-      - name: Build documentation
-        run: poetry run make html --directory docs/
-
   Continuous-Deployment:
+    permissions:
+        contents: write
+        packages: write
+        issues: write
+        pull-requests: write
+
     # needs: Continuous-Integration
 
     # if pulling to main, deploy to PyPI
@@ -72,13 +97,6 @@ jobs:
     - name: Install package
       run: poetry install
 
-
-    # Get the last tag value (i.e 0.6.0)
-    # save to a variable called last_tag to be used later
-    - name: Get latest tag name
-      id: last_tag
-      run: echo ::set-output name=tag::$(git describe --tags --abbrev=0 | sed 's/^v//')
-
    # This action uses Python Semantic Release v8
    # What this action does:
    # - Determines the next version number based on the commit history
@@ -105,7 +123,7 @@ jobs:
       run: |
         poetry version $(git describe --tags --abbrev=0 | sed 's/^v//')
         python -m build --sdist --wheel --outdir dist/ .
-        ls dist/
+        echo "LATEST_TAG=$(poetry version | sed 's/^nbiatoolkit //')" >> "$GITHUB_ENV"
 
     - name: Publish package distributions to PyPI
       if: steps.release.outputs.released == 'true'
@@ -115,51 +133,84 @@ jobs:
         user: __token__
         password: ${{ secrets.PYPI_API_TOKEN }}
 
-    # # - name: Publish package distributions to GitHub Releases
-    # - name: Build and Publish
-    #   uses: pypa/gh-action-pypi-publish@release/v1
-    #   with:
-    #     user: __token__
-    #     password: ${{ secrets.TEST_PYPI_API_TOKEN }}
-    #     repository_url: https://test.pypi.org/legacy/
-    #     build: true
-    #     build_command: poetry build
-    #     build_command_postfix: dist/*
-
-    # - name: Publish package distributions to PyPI
-    #   id: pypi-publish
-
-
-
-    # - name: Publish package distributions to GitHub Releases
-    #   uses: python-semantic-release/upload-to-gh-release@main
-    #   if: steps.release.outputs.released == 'true'
-    #   with:
-    #     github_token: ${{ secrets.GITHUB_TOKEN }}
-    # - name: Publish to TestPyPI
-    #   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 \
-    #       nbiatoolkit
-
-    # - name: Publish to PyPI
-    #   uses: pypa/gh-action-pypi-publish@release/v1
-    #   with:
-    #     user: __token__
-    #     password: ${{ secrets.PYPI_API_TOKEN }}
-
-    # - name: Publish documentation
-    #   uses: maxheld83/ghpages@v0.2.1
-    #   with:
-    #     build_dir: docs/_build/html
-    #     target_branch: gh-pages
-    #     committer_name: "GitHub Actions"
-    #     committer_email: "jermiahjoseph98@gmail.com"
+    - name: Print latest tag name
+      run: |
+        printf "%s\n" "${LATEST_TAG}"
+
+    - name: Print branch name
+      run: |
+        printf "LATEST TAG: %s\n" "${LATEST_TAG}"
+        echo "DOCKER_IMAGE_TAG=${LATEST_TAG}" >> "$GITHUB_ENV"
+        printf "DOCKER_IMAGE_TAG: %s\n" "${DOCKER_IMAGE_TAG}"
+
+    - name: Set up QEMU
+      if: steps.release.outputs.released == 'true'
+      uses: docker/setup-qemu-action@v3
+
+    - name: Set up Docker Buildx
+      if: steps.release.outputs.released == 'true'
+      uses: docker/setup-buildx-action@v3
+
+    - name: Login to Docker Hub
+      if: steps.release.outputs.released == 'true'
+      uses: docker/login-action@v3
+      with:
+        username: ${{ secrets.DOCKERHUB_USERNAME }}
+        password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+    - name: Login to the GitHub Container Registry
+      if: steps.release.outputs.released == 'true'
+      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: |
+          ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:${{ env.DOCKER_IMAGE_TAG }}
+          ghcr.io/${{ github.repository }}/nbiatoolkit:${{ env.DOCKER_IMAGE_TAG }}
+
+    - name: Build
+      if: steps.release.outputs.released == 'true'
+      uses: docker/build-push-action@v5
+      with:
+        context: .
+        platforms: linux/amd64,linux/arm64
+        file: ./Dockerfile
+        push: true
+        tags: |
+          ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:${{ env.DOCKER_IMAGE_TAG }}
+          ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:latest
+          ghcr.io/${{ github.repository }}/nbiatoolkit:${{ env.DOCKER_IMAGE_TAG }}
+          ghcr.io/${{ github.repository }}/nbiatoolkit:latest
+        labels: ${{ steps.meta.outputs.labels }}
+
+  test_image_with_new_tag:
+    needs: Continuous-Deployment
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v2
+
+      - name: Test Image With new Tag
+        run: |
+          docker run --rm \
+            ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:${{ env.DOCKER_IMAGE_TAG }} \
+            python -c "import nbiatoolkit; print(nbiatoolkit.__version__)"
+
+  test_image_with_latest_tag:
+    needs: Continuous-Deployment
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v2
+
+      - name: Test Image with "latest" Tag
+        run: |
+          docker run --rm \
+            ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:latest \
+            python -c "import nbiatoolkit; print(nbiatoolkit.__version__)"