migrate repo

.github/workflows/build.yaml

@@ -36,7 +36,7 @@ jobs:
         id: meta
         uses: docker/metadata-action@v5.8.0
         with:
-          images: ghcr.io/${{ github.repository }}
+          images: ghcr.io/${{ vars.ORG_REPO }}/${{ github.event.repository.name }}
 
       - name: Authenticate with GHCR
         id: auth
@@ -54,9 +54,10 @@ jobs:
         id: build
         uses: docker/build-push-action@v6.18.0
         with:
+          file: ./docker/Dockerfile
           platforms: ${{ matrix.platform }}
           labels: ${{ steps.meta.outputs.labels }}
-          tags: ghcr.io/${{ github.repository }}
+          tags: ghcr.io/${{ vars.ORG_REPO }}/${{ github.event.repository.name }}
           outputs: type=image,push-by-digest=true,name-canonical=true,push=true
 
       - name: Export digest
@@ -102,7 +103,7 @@ jobs:
         id: meta
         uses: docker/metadata-action@v5.8.0
         with:
-          images: ghcr.io/${{ github.repository }}
+          images: ghcr.io/${{ vars.ORG_REPO }}/${{ github.event.repository.name }}
           tags: dev
 
       - name: Create manifest list and push
@@ -116,18 +117,18 @@ jobs:
             --annotation='index:org.opencontainers.image.created=${{ steps.timestamp.outputs.timestamp }}' \
             --annotation='index:org.opencontainers.image.url=${{ github.event.repository.url }}' \
             --annotation='index:org.opencontainers.image.source=${{ github.event.repository.url }}' \
-            $(printf 'ghcr.io/${{ github.repository }}@sha256:%s ' *)
+            $(printf 'ghcr.io/${{ vars.ORG_REPO }}/${{ github.event.repository.name }}@sha256:%s ' *)
 
       - name: Create manifest list and push without annotations
         if: steps.annotate.outcome == 'failure'
         working-directory: ${{ runner.temp }}/digests
         run: |
           docker buildx imagetools create  $(jq -cr '.tags | map("-t " + .) | join(" ")' <<< "$DOCKER_METADATA_OUTPUT_JSON") \
-            $(printf 'ghcr.io/${{ github.repository }}@sha256:%s ' *)
+            $(printf 'ghcr.io/${{ vars.ORG_REPO }}/${{ github.event.repository.name }}@sha256:%s ' *)
 
       - name: Inspect image
         run: |
-          docker buildx imagetools inspect ghcr.io/${{ github.repository }}:dev
+          docker buildx imagetools inspect ghcr.io/${{ vars.ORG_REPO }}/${{ github.event.repository.name }}:dev
 
   tests:
     strategy:
@@ -147,13 +148,9 @@ jobs:
       - name: Test notebooks
         shell: bash
         run: |
-          docker run -t ghcr.io/${{ github.repository }}:dev bash -c "\
-            bash /home/jovyan/aiida-start; \
-            jupyter nbconvert --to notebook --execute PTH2R_coarse-grained_tutorial.ipynb; \
-            sleep 300; \
-            verdi process list -a; \
-            ! verdi process list -a | grep -E '\[(3.*?)\]'; \
-            ! verdi process list -a | grep -E 'Waiting'; "
+          docker run -t ghcr.io/${{ vars.ORG_REPO }}/${{ github.event.repository.name }}:dev bash -c " \
+            pip install pytest nbmake; \
+            find . -name '*.ipynb' | pytest --nbmake --nbmake-timeout=3600; "
 
   tags:
     runs-on: ubuntu-24.04
@@ -175,14 +172,14 @@ jobs:
         shell: bash
         run: |
           docker buildx imagetools create \
-            --tag ghcr.io/${{ github.repository }}:latest \
-            --tag ghcr.io/${{ github.repository }}:${{ needs.build.outputs.tag }} \
-            ghcr.io/${{ github.repository }}:dev
+            --tag ghcr.io/${{ vars.ORG_REPO }}/${{ github.event.repository.name }}:latest \
+            --tag ghcr.io/${{ vars.ORG_REPO }}/${{ github.event.repository.name }}:${{ needs.build.outputs.tag }} \
+            ghcr.io/${{ vars.ORG_REPO }}/${{ github.event.repository.name }}:dev
 
       - name: Post version update to dash
         uses: peter-evans/repository-dispatch@v3.0.0
         with:
           token: ${{ secrets.BUILD_TOKEN }}
           repository: jimboid/biosim-workshops-dash
-          event-type: build    
+          event-type: build
           client-payload: '{"repo": "${{ github.event.repository.name }}", "tag": "${{ needs.build.outputs.tag }}"}'

Dockerfile → docker/Dockerfile

@@ -1,9 +1,9 @@
 # Start with BioSim base image.
 ARG BASE_IMAGE=latest
-FROM ghcr.io/jimboid/biosim-jupyterhub-base:$BASE_IMAGE
+FROM ghcr.io/ccpbiosim/jupyterhub-base:$BASE_IMAGE
 
 LABEL maintainer="James Gebbie-Rayet <james.gebbie@stfc.ac.uk>"
-LABEL org.opencontainers.image.source=https://github.com/jimboid/biosim-aiida-gpcr-workshop
+LABEL org.opencontainers.image.source=https://github.com/ccpbiosim/aiida-gpcr-workshop
 LABEL org.opencontainers.image.description="A container environment for the PSDI workshop on AiiDA tools for data collection."
 LABEL org.opencontainers.image.licenses=MIT
 
@@ -39,19 +39,18 @@ RUN if [ "$TARGETPLATFORM" = "linux/amd64" ]; then \
     fi
 RUN pip3 install aiida-gromacs mdtraj vermouth
 
-RUN git clone https://github.com/jimboid/aiida-gromacs.git && \
+RUN git clone https://github.com/PSDI-UK/aiida-gromacs.git && \
     mv aiida-gromacs/examples/PTH2R_coarse-grained_files . && \
     mv aiida-gromacs/notebooks/PTH2R_coarse-grained_tutorial.ipynb . && \
     rm -rf aiida-gromacs
 
-COPY --chown=1000:100 aiida-stop /home/jovyan/
-
 RUN echo "./aiida-start" >> ~/.bashrc
-COPY --chown=1000:100 default-37a8.jupyterlab-workspace /home/jovyan/.jupyter/lab/workspaces/default-37a8.jupyterlab-workspace
+COPY --chown=1000:100 docker/default-37a8.jupyterlab-workspace /home/jovyan/.jupyter/lab/workspaces/default-37a8.jupyterlab-workspace
 COPY --chown=1000:100 aiida-start /home/jovyan/
+COPY --chown=1000:100 aiida-stop /home/jovyan/
 
 # UNCOMMENT THIS LINE FOR REMOTE DEPLOYMENT
-COPY jupyter_notebook_config.py /etc/jupyter/
+COPY docker/jupyter_notebook_config.py /etc/jupyter/
 
 # Always finish with non-root user as a precaution.
 USER $NB_USER