fix docker build

.github/actions/build-docker-image/action.yml

@@ -0,0 +1,86 @@
+name: 'Build Docker images'
+description: 'Build Docker images'
+
+inputs:
+  snapatac2-version:
+    description: 'SnapATAC2 version to be installed'
+    required: true
+    type: string
+
+  python-version:
+    required: false
+    default: "python:3.11-slim"
+
+  flavor:
+    required: false
+    default: "default"
+
+runs:
+  using: "composite"
+  steps:
+    # This makes some assumptions about `base-docker-image` name format so be sure to test this out if
+    # things change. For `python:3.11-slim` this should result in `PY_VER_ABBRV=py3.11` beings saved to $GITHUB_ENV
+    # See: https://docs.github.com/en/actions/using-workflows/workflow-commands-for-github-actions#setting-an-environment-variable
+    - name: Get python version shorthand
+      run: echo "PY_VER_ABBRV=py$(echo ${{ matrix.base-docker-image }} | cut -d ":" -f 2 | cut -d "-" -f 1)" >> $GITHUB_ENV
+    # Should result in something like: `IMAGE_TAG=2.5.1-default-py3.11` or `IMAGE_TAG=2.5.1-recommend-interactive-py3.11`
+    - name: Create Docker image tag
+      run: echo "IMAGE_TAG=${{ inputs.snapatac2-version }}-${{ inputs.flavor }}-${{ inputs.python-version }}" >> $GITHUB_ENV
+
+    - name: Checkout repository
+      uses: actions/checkout@v4
+      with:
+        lfs: true
+
+    - name: Set up Docker Buildx
+      uses: docker/setup-buildx-action@v3
+
+    # TODO: Has SnapATAC2 been tested for arm64? If it has and it works then uncomment the following
+    #       section and also add `linux/arm64` to `platforms` in subsequent steps:
+    # # https://github.com/docker/setup-qemu-action
+    # - name: Set up QEMU
+    #   uses: docker/setup-qemu-action@v3
+    # https://github.com/docker/build-push-action
+    # Uses github actions cache: https://docs.docker.com/build/cache/backends/gha/
+    - name: Build Dockerfile
+      uses: docker/build-push-action@v5
+      with:
+        context: docker/${{ inputs.flavor }}
+        platforms: linux/amd64
+        build-args: |
+          BASE_PYTHON_IMAGE=python:${{ inputs.python-version }}-slim
+          SNAP_ATAC_VERSION=${{ inputs.snapatac2-version }}
+        load: true
+        tags: snapatac2:TEST-${{ env.IMAGE_TAG }}
+        cache-from: type=gha
+        cache-to: type=gha,mode=max
+
+    # Mount the Github Workspace (repository root) into our test container
+    # Then install test required packages and run SnapATAC2 Python tests
+    - name: Test Docker Image
+      run: |
+        docker run --rm -t \
+          --entrypoint /bin/bash \
+          --volume "${{ github.workspace }}":"/github/workspace" \
+          snapatac2:TEST-${{ env.IMAGE_TAG }} \
+          -c "python3 -m pip install pytest hypothesis && pytest /github/workspace/snapatac2-python/tests"
+
+    - name: Login to Docker Hub
+      uses: docker/login-action@v3
+      with:
+        username: ${{ secrets.dockerhub_username }}
+        password: ${{ secrets.dockerhub_token }}
+
+    # Uses cached result from first build
+    - name: Push to Docker Hub
+      uses: docker/build-push-action@v5
+      with:
+        context: docker/${{ inputs.flavor }}
+        platforms: linux/amd64
+        build-args: |
+          BASE_PYTHON_IMAGE=python:${{ inputs.python-version }}-slim
+          SNAP_ATAC_VERSION=${{ inputs.snapatac2-version }}
+        push: true
+        tags: snapatac2:${{ env.IMAGE_TAG }}
+        cache-from: type=gha
+        cache-to: type=gha,mode=max

.github/workflows/test_python.yml

@@ -5,8 +5,6 @@ on: [push, pull_request]
 jobs:
   build-and-test:
     runs-on: ubuntu-latest
-    outputs:
-      VERSION_NUMBER: ${{ steps.get-version.outputs.VERSION_NUMBER }}
     steps:
     - name: Checkout code
       uses: nschloe/action-cached-lfs-checkout@v1
@@ -43,6 +41,12 @@ jobs:
         echo $VERSION_NUMBER
         echo "VERSION=$VERSION_NUMBER" >> $GITHUB_ENV
 
+    - name: Build docker image
+      uses: ./.github/actions/build-docker-image
+      with:
+        snapatac2-version: ${{ steps.get-version.outputs.VERSION_NUMBER }}
+        python-version: 3.11
+
     - name: Upload Coverage to Codecov
       uses: codecov/codecov-action@v3
 
@@ -52,14 +56,9 @@ jobs:
         name: wheel-files
         path: ./wheel_files/snapatac2*.whl
 
+
   build-wheel:
     if: ${{ startsWith(github.ref, 'refs/tags/') || contains(github.event.head_commit.message, 'wheel') }}
     uses: kaizhang/SnapATAC2/.github/workflows/wheels.yml@main
     with:
-      wheel: 'true'
-
-  test_docker:
-    needs: build-and-test
-    uses: kaizhang/SnapATAC2/.github/workflows/docker.yml@main
-    with:
-      version: ${{ needs.build-and-test.outputs.VERSION_NUMBER }}
+      wheel: 'true'