From 5fcbd65dc0dc85bf5a87956f251e6e3ec2c29334 Mon Sep 17 00:00:00 2001 From: James Gebbie-Rayet Date: Tue, 16 Sep 2025 23:18:45 +0100 Subject: [PATCH 1/2] additional tweaks after migration --- .github/workflows/build.yaml | 1 + Dockerfile => docker/Dockerfile | 11 +++-------- .../default-37a8.jupyterlab-workspace | 0 .../jupyter_notebook_config.py | 0 4 files changed, 4 insertions(+), 8 deletions(-) rename Dockerfile => docker/Dockerfile (67%) rename default-37a8.jupyterlab-workspace => docker/default-37a8.jupyterlab-workspace (100%) rename jupyter_notebook_config.py => docker/jupyter_notebook_config.py (100%) diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml index 741d093..e6c2218 100644 --- a/.github/workflows/build.yaml +++ b/.github/workflows/build.yaml @@ -54,6 +54,7 @@ jobs: id: build uses: docker/build-push-action@v6.18.0 with: + file: ./docker/Dockerfile platforms: ${{ matrix.platform }} labels: ${{ steps.meta.outputs.labels }} tags: ghcr.io/${{ vars.ORG_REPO }}/${{ github.event.repository.name }} diff --git a/Dockerfile b/docker/Dockerfile similarity index 67% rename from Dockerfile rename to docker/Dockerfile index b834419..27b19c8 100644 --- a/Dockerfile +++ b/docker/Dockerfile @@ -1,6 +1,6 @@ # Start with BioSim base image. ARG BASE_IMAGE=latest -FROM ghcr.io/jimboid/biosim-jupyterhub-base:$BASE_IMAGE +FROM ghcr.io/ccpbiosim/jupyterhub-base:$BASE_IMAGE LABEL maintainer="James Gebbie-Rayet " LABEL org.opencontainers.image.source=https://github.com/jimboid/biosim-structure-validation-workshop @@ -14,13 +14,8 @@ WORKDIR $HOME # Install workshop deps RUN pip install requests -COPY --chown=1000:100 exercise1.ipynb /home/jovyan -COPY --chown=1000:100 exercise2.ipynb /home/jovyan - -COPY --chown=1000:100 coot_dens.png /home/jovyan -COPY --chown=1000:100 errb4_validation_report.png /home/jovyan -COPY --chown=1000:100 pdbekb_structures.png /home/jovyan -COPY --chown=1000:100 RNApol_in_uglymol.png /home/jovyan +COPY --chown=1000:100 . . +RUN rm -rf LICENSE README.md docker .git .github # Copy lab workspace COPY --chown=1000:100 default-37a8.jupyterlab-workspace /home/jovyan/.jupyter/lab/workspaces/default-37a8.jupyterlab-workspace diff --git a/default-37a8.jupyterlab-workspace b/docker/default-37a8.jupyterlab-workspace similarity index 100% rename from default-37a8.jupyterlab-workspace rename to docker/default-37a8.jupyterlab-workspace diff --git a/jupyter_notebook_config.py b/docker/jupyter_notebook_config.py similarity index 100% rename from jupyter_notebook_config.py rename to docker/jupyter_notebook_config.py From 34a846429341958a36a4518b414323346a02ab69 Mon Sep 17 00:00:00 2001 From: James Gebbie-Rayet Date: Tue, 16 Sep 2025 23:22:40 +0100 Subject: [PATCH 2/2] Update Dockerfile --- docker/Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docker/Dockerfile b/docker/Dockerfile index 27b19c8..118f8f8 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -18,10 +18,10 @@ COPY --chown=1000:100 . . RUN rm -rf LICENSE README.md docker .git .github # Copy lab workspace -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 # 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