fix filtertabular build

.github/workflows/build-and-push.yaml

@@ -1,27 +1,17 @@
 name: Build and Push Docker Images
-
 on:
-  push:
+  pull_request:
     branches:
       - main
-  #pull_request:
-  #  branches:
-  #    - main
   workflow_dispatch:
     inputs:
       package:
         description: 'Package name to build (leave empty for all)'
         required: false
         default: ''
-      urgap_wheel_url:
-        description: 'URL to urgap wheel (for pre-release testing)'
-        required: false
-        default: ''
-
 env:
   REGISTRY: ghcr.io
   IMAGE_PREFIX: ghcr.io/urgap
-
 jobs:
   build-matrix:
     name: Generate Build Matrix
@@ -32,12 +22,10 @@ jobs:
     steps:
       - name: Checkout repository
         uses: actions/checkout@v4
-
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
           python-version: '3.11'
-
       - name: Generate matrix
         id: set-matrix
         run: |
@@ -55,7 +43,6 @@ jobs:
           else
             echo "has_packages=false" >> $GITHUB_OUTPUT
           fi
-
   build-test-push:
     name: Build ${{ matrix.name }}:${{ matrix.version }}
     needs: build-matrix
@@ -70,35 +57,14 @@ jobs:
     steps:
       - name: Checkout repository
         uses: actions/checkout@v4
-
       - name: Set up Docker Buildx
         uses: docker/setup-buildx-action@v3
-
       - name: Log in to GitHub Container Registry
         uses: docker/login-action@v3
         with:
           registry: ${{ env.REGISTRY }}
           username: ${{ github.actor }}
           password: ${{ secrets.GITHUB_TOKEN }}
-
-      - name: Download urgap wheel from PyPI
-        id: download-wheel
-        run: |
-          mkdir -p ${{ matrix.name }}/wheel
-
-          if [ -n "${{ github.event.inputs.urgap_wheel_url }}" ]; then
-            # Use provided wheel URL
-            curl -L -o ${{ matrix.name }}/wheel/urgap.whl "${{ github.event.inputs.urgap_wheel_url }}"
-          else
-            # Download from PyPI
-            pip download urgap==${{ matrix.urgap_version }} --no-deps -d ${{ matrix.name }}/wheel/ || \
-            pip download urgap --no-deps -d ${{ matrix.name }}/wheel/
-          fi
-
-          WHEEL_FILE=$(ls ${{ matrix.name }}/wheel/*.whl | head -1)
-          WHEEL_NAME=$(basename "$WHEEL_FILE")
-          echo "wheel_name=$WHEEL_NAME" >> $GITHUB_OUTPUT
-
       - name: Prepare Docker tags
         id: tags
         run: |
@@ -110,7 +76,6 @@ jobs:
           fi
 
           echo "tags=$TAGS" >> $GITHUB_OUTPUT
-
       - name: Build Docker image
         uses: docker/build-push-action@v5
         with:
@@ -124,12 +89,14 @@ jobs:
             URGAP=wheel/${{ steps.download-wheel.outputs.wheel_name }}
           cache-from: type=gha
           cache-to: type=gha,mode=max
-
       - name: Run tests
         run: |
           IMAGE_TAG="${{ env.IMAGE_PREFIX }}/${{ matrix.name }}:${{ matrix.version }}"
           CONTAINER_NAME="${{ matrix.name }}-test-$$"
 
+          # Start container
+          docker run -d --name "$CONTAINER_NAME" "$IMAGE_TAG"
+
           # Copy tests into container
           docker cp ${{ matrix.name }}/tests "$CONTAINER_NAME":/home/nonroot/tests
 
@@ -145,9 +112,7 @@ jobs:
           # Cleanup
           docker stop "$CONTAINER_NAME"
           docker rm "$CONTAINER_NAME"
-
       - name: Push Docker image
-        if: github.event_name == 'push' && github.ref == 'refs/heads/main'
         uses: docker/build-push-action@v5
         with:
           context: ${{ matrix.name }}

filtertabular/Dockerfile

@@ -2,16 +2,12 @@ ARG BASEIMAGE
 
 FROM ${BASEIMAGE}
 
-ARG URGAP
-
 RUN addgroup --system nonroot && \
     adduser --system \
       --ingroup nonroot \
       --home /home/nonroot \
       nonroot
 
-COPY ${URGAP} /home/nonroot
-
 ENV HOME=/home/nonroot
 ENV VENV_PATH=$HOME/venv
 ENV PATH=$VENV_PATH/bin:$PATH
@@ -20,7 +16,7 @@ USER nonroot
 RUN python -m venv "$VENV_PATH" --system-site-packages
 
 RUN pip install uv
-RUN uv pip install /home/nonroot/${URGAP}["all"]
+RUN uv pip install urgap["all"]
 
 WORKDIR $HOME
 

package-information.json

@@ -1,5 +1,5 @@
 {
-    "urgap": "3.2.18",
+    "urgap": "3.3.5",
     "packages": [
         {
             "name": "plink",
@@ -11,7 +11,7 @@
         {
             "name": "filtertabular",
             "versions": ["1.0.0"],
-            "base_image": "python:3.10",
+            "base_image": "python:3.13-slim-trixie",
             "gh_url": "urgap/urgap.git",
             "separate_venv": false
         }

plink/Dockerfile

@@ -8,8 +8,6 @@ RUN cp $(which plink2 || which plink) /tmp/plink2
 # Stage 2: Build final image with Python 3.11 + plink
 FROM python:3.11-slim
 
-ARG URGAP
-
 # Copy plink binary from base image
 COPY --from=plink-source /tmp/plink2 /usr/local/bin/plink2
 
@@ -18,14 +16,9 @@ RUN useradd -m -s /bin/bash nonroot
 USER nonroot
 WORKDIR /home/nonroot
 
-RUN python -m venv /home/nonroot/venv
-
-# Copy and install urgap wheel into venv
-COPY --chown=nonroot:nonroot ${URGAP} /tmp/
-RUN /home/nonroot/venv/bin/pip install --upgrade pip && \
-    WHEEL=$(ls /tmp/*.whl) && \
-    /home/nonroot/venv/bin/pip install "${WHEEL}[all]" && \
-    rm /tmp/*.whl
+RUN python -m venv /home/nonroot/venv && \
+    /home/nonroot/venv/bin/pip install --upgrade pip && \
+    /home/nonroot/venv/bin/pip install urgap["all"]
 
 # Add venv to PATH
 ENV PATH="/home/nonroot/venv/bin:$PATH"