Add ci

.github/workflows/docker-publish.yml

@@ -0,0 +1,128 @@
+name: Docker Publish
+
+on:
+  push:
+    tags:
+      - "v*"
+  pull_request:
+  workflow_dispatch:
+
+env:
+  IMAGE_NAME: scop3p-toolkit
+  DOCKERFILE_PATH: docker/Dockerfile
+  DOCKER_TARGET: scop3p-toolkit
+  PYTHON_VERSION: "3.12"
+
+jobs:
+  test:
+    name: Pytest suite
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ env.PYTHON_VERSION }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -r requirements-biophysics.txt
+          python -m pip install -r requirements-shiny.txt
+          python -m pip install pytest
+
+      - name: Run tests
+        run: pytest tests/unit tests/integration
+
+  docker:
+    name: Build and publish Docker image
+    runs-on: ubuntu-latest
+    needs: test
+    permissions:
+      contents: read
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Prepare image variables
+        id: vars
+        shell: bash
+        run: |
+          namespace="${{ vars.DOCKERHUB_NAMESPACE }}"
+          if [[ -z "${namespace}" ]]; then
+            namespace="${{ secrets.DOCKERHUB_USERNAME }}"
+          fi
+          if [[ -z "${namespace}" ]]; then
+            namespace="${GITHUB_REPOSITORY_OWNER,,}"
+          fi
+          version="${GITHUB_SHA}"
+          if [[ "${GITHUB_REF_TYPE}" == "tag" ]]; then
+            version="${GITHUB_REF_NAME}"
+          fi
+          {
+            echo "image_repository=${namespace}/${IMAGE_NAME}"
+            echo "build_date=$(date -u +%Y-%m-%dT%H:%M:%SZ)"
+            echo "version=${version}"
+          } >> "${GITHUB_OUTPUT}"
+
+      - name: Log in to Docker Hub
+        if: github.event_name != 'pull_request' && github.ref_type == 'tag'
+        uses: docker/login-action@v3
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - name: Extract Docker metadata
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: docker.io/${{ steps.vars.outputs.image_repository }}
+          tags: |
+            type=raw,value=latest,enable=${{ github.ref_type == 'tag' }}
+            type=sha,format=short,prefix=sha-
+            type=ref,event=tag
+          labels: |
+            org.opencontainers.image.title=Scop3P-Toolkit
+            org.opencontainers.image.description=Scop3P toolkit container for Galaxy interactive tool deployment
+            org.opencontainers.image.licenses=Apache-2.0
+
+      - name: Build image
+        if: github.ref_type != 'tag'
+        uses: docker/build-push-action@v6
+        with:
+          context: .
+          file: ${{ env.DOCKERFILE_PATH }}
+          target: ${{ env.DOCKER_TARGET }}
+          platforms: linux/amd64
+          push: false
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
+          build-args: |
+            BUILD_DATE=${{ steps.vars.outputs.build_date }}
+            VCS_REF=${{ github.sha }}
+            VERSION=${{ steps.vars.outputs.version }}
+
+      - name: Build and push image
+        if: github.ref_type == 'tag'
+        uses: docker/build-push-action@v6
+        with:
+          context: .
+          file: ${{ env.DOCKERFILE_PATH }}
+          target: ${{ env.DOCKER_TARGET }}
+          platforms: linux/amd64
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
+          build-args: |
+            BUILD_DATE=${{ steps.vars.outputs.build_date }}
+            VCS_REF=${{ github.sha }}
+            VERSION=${{ steps.vars.outputs.version }}