Merge pull request #7 from CCPBioSim/ci-update

Update build.yaml

Author: jimboid

.github/workflows/build.yaml

@@ -13,12 +13,19 @@ jobs:
       matrix:
         platform:
           - linux/amd64
-          #- linux/arm64
+          # - linux/arm64
     runs-on: ${{ matrix.platform == 'linux/amd64' && 'ubuntu-24.04' || matrix.platform == 'linux/arm64' && 'ubuntu-24.04-arm' }}
     name: build ${{ matrix.platform }}
     outputs:
       tag: ${{ steps.envvars.outputs.tag }}
     steps:
+
+      - name: "node-cleanup"
+        run: |
+          sudo rm -rf /usr/share/dotnet /usr/local/lib/android /opt/ghc /opt/hostedtoolcache/CodeQL
+          sudo docker image prune --all --force
+          sudo docker builder prune -a
+
       - name: checkout
         uses: actions/checkout@v5.0.0
 
@@ -39,19 +46,39 @@ jobs:
         with:
           images: ghcr.io/${{ vars.ORG_REPO }}/${{ github.event.repository.name }}
 
+      - name: Set up Docker Buildx
+        id: buildx
+        uses: docker/setup-buildx-action@v3.11.1
+
+      - name: Build and push by digest
+        if: github.event_name == 'pull_request'
+        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 }}/${{ github.event.repository.name }}
+          outputs: type=docker,push-by-digest=true,name-canonical=true,push=true
+
+      - name: Run tests
+        if: github.event_name == 'pull_request'
+        shell: bash
+        run: |
+          docker run -t ghcr.io/${{ vars.ORG_REPO }}/${{ github.event.repository.name }}:latest bash -c " \
+            pip install pytest nbmake; \
+            find . -name '*.ipynb' | pytest --nbmake --nbmake-timeout=3600; "
+
       - name: Authenticate with GHCR
+        if: github.event_name != 'pull_request'
         id: auth
         uses: docker/login-action@v3.6.0
         with:
           registry: ghcr.io
           username: ${{ github.repository_owner }}
           password: ${{ secrets.BUILD_TOKEN }}
 
-      - name: Set up Docker Buildx
-        id: buildx
-        uses: docker/setup-buildx-action@v3.11.1
-
       - name: Build and push by digest
+        if: github.event_name != 'pull_request'
         id: build
         uses: docker/build-push-action@v6.18.0
         with:
@@ -61,20 +88,23 @@ jobs:
           tags: ghcr.io/${{ vars.ORG_REPO }}/${{ github.event.repository.name }}
           outputs: type=image,push-by-digest=true,name-canonical=true,push=true
 
-      #- name: Test notebooks
-      #  shell: bash
-      #  run: |
-      #    docker run -t ghcr.io/${{ vars.ORG_REPO }}/${{ github.event.repository.name }}@${{ steps.build.outputs.digest }} bash -c " \
-      #      pip install pytest nbmake; \
-      #      find ./notebooks -name '*.ipynb' | pytest --nbmake --nbmake-timeout=3600;"
+      - name: Run tests
+        if: github.event_name != 'pull_request'
+        shell: bash
+        run: |
+          docker run -t ghcr.io/${{ vars.ORG_REPO }}/${{ github.event.repository.name }}@${{ steps.build.outputs.digest }} bash -c " \
+            pip install pytest nbmake; \
+            find . -name '*.ipynb' | pytest --nbmake --nbmake-timeout=3600; "
 
       - name: Export digest
+        if: github.event_name != 'pull_request'
         run: |
           mkdir -p ${{ runner.temp }}/digests
           digest="${{ steps.build.outputs.digest }}"
           touch "${{ runner.temp }}/digests/${digest#sha256:}"
 
       - name: Upload digest
+        if: github.event_name != 'pull_request'
         uses: actions/upload-artifact@v5.0.0
         with:
           name: digests-${{ env.PLATFORM_PAIR }}

Setup_DNA-simulation.ipynb

@@ -634,9 +634,9 @@
  "metadata": {
   "anaconda-cloud": {},
   "kernelspec": {
-   "display_name": "htmd",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
-   "name": "htmd"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {

docker/Dockerfile

@@ -13,12 +13,10 @@ RUN conda install -c acellera -c conda-forge ambertools htmd matplotlib mdtraj n
 
 # Get workshop files and move them to jovyan directory.
 COPY --chown=1000:100 . .
-RUN rm -rf requirements.txt LICENSE README.md docker .git .github
+RUN rm -rf requirements.txt LICENSE README.md docker .git .github tested_files
 
 RUN wget https://www.hecbiosim.ac.uk/file-store/tw2025-dna-workshop/01_Prod-0.nc && \
-    wget https://www.hecbiosim.ac.uk/file-store/tw2025-dna-workshop/01_Prod-2.nc && \
-    cp 01_Prod-0.nc data/ && \
-    mv 01_Prod-0.nc 01_Prod-2.nc tested_files/
+    mv 01_Prod-0.nc data/
 
 # Copy updated lab workspace
 COPY --chown=1000:100 docker/default-37a8.jupyterlab-workspace /home/jovyan/.jupyter/lab/workspaces/default-37a8.jupyterlab-workspace