More fixes

.github/workflows/deploy-image.yml

@@ -47,12 +47,3 @@ jobs:
           tags: ${{ steps.meta.outputs.tags }}
           labels: ${{ steps.meta.outputs.labels }}
           build-args: "PYBIOCLIP_VERSION=${{ steps.meta.outputs.version }}"
-      - uses: eWaterCycle/setup-apptainer@v2
-        with:
-          apptainer-version: 1.3.3
-      - name: print stuff
-        run: echo "${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}"
-      - name: pull an apptainer container
-        run: apptainer pull apptainer.sif docker://${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:${{ steps.meta.outputs.version }}
-      - name: push the apptainer container
-        run: apptainer push apptainer.sif oras://${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}-sif:${{ steps.meta.outputs.version }}

Dockerfile

@@ -1,7 +1,16 @@
 FROM condaforge/miniforge3:24.3.0-0
 
+# Pass -s to tini since apptainer doesn't run as PID 1
+ENTRYPOINT ["tini", "-s", "--"]
+
 ARG PYBIOCLIP_VERSION
 
 # Install pybioclip from the release archive because pypi can take a while to start working.
 RUN pip install "https://github.com/Imageomics/pybioclip/archive/refs/tags/${PYBIOCLIP_VERSION}.tar.gz" && \
     pip cache purge
+
+# Create a non-root user with a home directory to help cache pybioclip files
+RUN useradd -ms /bin/bash bcuser
+USER bcuser
+ENV PATH="$PATH:/home/bcuser/.local/bin"
+WORKDIR /home/bcuser