Merge branch 'develop' into gen-1000-set-autosort

.github/workflows/ci.yml

@@ -5,15 +5,18 @@ name: build
 
 on:
   push:
-    branches:
-      - develop
+    branches: [main, develop, 'GEN*', 'gen*']
 
   pull_request:
 
   release:
     types:
       - created
 
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+
 jobs:
 
   test:
@@ -77,3 +80,51 @@ jobs:
       run: python -m build
     - name: Publish to pypi
       uses: pypa/gh-action-pypi-publish@release/v1
+
+
+  build-container:
+    needs: [test, lint]
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Setup Docker buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Log into registry ${{ env.REGISTRY }}
+        uses: docker/login-action@v3
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract Docker metadata
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+
+      - name: Format tags as registry refs
+        id: registry_refs
+        env:
+          TAGS: ${{ steps.meta.outputs.json }}
+        run: |
+          echo tags=$(echo $TAGS | jq '.tags[] | "type=registry,ref=" + . + "_cache"| @text') >> $GITHUB_OUTPUT
+
+      - name: Build and push Docker image
+        id: build-and-push
+        uses: docker/build-push-action@v5
+        if: github.event_name != 'pull_request'
+        with:
+          context: .
+          push: true
+          provenance: false
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+          cache-from: ${{ steps.registry_refs.outputs.tags }},mode=max
+          cache-to: ${{ steps.registry_refs.outputs.tags }},mode=max

Dockerfile

@@ -83,6 +83,7 @@ WORKDIR /root/
 # Must move this git clone to after the install of Genie,
 # because must update cbioportal
 RUN git clone https://github.com/cBioPortal/cbioportal.git -b v5.3.19
-RUN git clone https://github.com/Sage-Bionetworks/annotation-tools.git -b 0.0.4
+RUN git clone https://github.com/Sage-Bionetworks/annotation-tools.git -b 0.0.5
+
 
 WORKDIR /root/Genie

genie/__init__.py

@@ -7,6 +7,6 @@
 
 # create version in __init__.py
 # https://packaging.python.org/en/latest/guides/single-sourcing-package-version/
-__version__ = "16.2.0"
+__version__ = "16.3.0"
 
 __all__ = ["__version__"]