Merge pull request #7 from CCPBioSim/ci-update

Update build.yaml

Author: jimboid

.github/workflows/build.yaml

@@ -13,7 +13,7 @@ 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 ${{ matrix.platform }}
     outputs:
@@ -39,42 +39,67 @@ jobs:
         with:
           images: ghcr.io/${{ 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:
+          build-args: TARGETPLATFORM=${{ matrix.platform }}
+          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:
+          build-args: TARGETPLATFORM=${{ matrix.platform }}
           file: ./docker/Dockerfile
           platforms: ${{ matrix.platform }}
           labels: ${{ steps.meta.outputs.labels }}
           tags: ghcr.io/${{ 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 }}@${{ steps.build.outputs.digest }} bash -c " \
-      #      pip install pytest nbmake; \
-      #      find . -name '*.ipynb' | pytest --nbmake --nbmake-timeout=3600;"
+      - name: Run tests
+        if: github.event_name != 'pull_request'
+        shell: bash
+        run: |
+          docker run -t ghcr.io/${{ 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 }}

1-allatom_setup/1-AA_assembly.ipynb

@@ -121,6 +121,9 @@
    "execution_count": null,
    "id": "132110f0",
    "metadata": {
+    "tags": [
+      "skip-execution"
+    ],
     "vscode": {
      "languageId": "shellscript"
     }
@@ -141,6 +144,9 @@
    "execution_count": null,
    "id": "17be9184",
    "metadata": {
+    "tags": [
+      "skip-execution"
+    ],
     "vscode": {
      "languageId": "shellscript"
     }

2-allatom_sim/2-AA_simulation.ipynb

@@ -23,6 +23,9 @@
    "execution_count": null,
    "id": "e4676c05",
    "metadata": {
+    "tags": [
+      "skip-execution"
+    ],
     "vscode": {
      "languageId": "shellscript"
     }
@@ -68,6 +71,9 @@
    "execution_count": null,
    "id": "8232c4a7",
    "metadata": {
+    "tags": [
+      "skip-execution"
+    ],
     "vscode": {
      "languageId": "shellscript"
     }
@@ -120,6 +126,9 @@
    "execution_count": null,
    "id": "839435bb",
    "metadata": {
+    "tags": [
+      "skip-execution"
+    ],
     "vscode": {
      "languageId": "shellscript"
     }

4-coarsegrain_equilibration/4-CG_equilibration.ipynb

@@ -88,6 +88,9 @@
    "execution_count": 2,
    "id": "b072482e",
    "metadata": {
+    "tags": [
+      "skip-execution"
+    ],
     "vscode": {
      "languageId": "shellscript"
     }
@@ -104,11 +107,11 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Info) VMD for LINUXAMD64, version 1.9.2 (December 29, 2014)\n",
+      "Info) for LINUXAMD64, version 1.9.2 (December 29, 2014)\n",
       "Info) http://www.ks.uiuc.edu/Research/vmd/                         \n",
       "Info) Email questions and bug reports to vmd@ks.uiuc.edu           \n",
       "Info) Please include this reference in published work using VMD:   \n",
-      "Info)    Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual   \n",
+      "Info)    Humphrey, W., Dalke, A. and Schulten, K., `- Visual   \n",
       "Info)    Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.\n",
       "Info) -------------------------------------------------------------\n",
       "Info) Multithreading available, 24 CPUs detected.\n",
@@ -143,15 +146,15 @@
       "Info)    Fragments: 18062   Protein: 0   Nucleic: 0\n",
       "after#0\n",
       "Material23\n",
-      "Info) VMD for LINUXAMD64, version 1.9.2 (December 29, 2014)\n",
+      "Info) for LINUXAMD64, version 1.9.2 (December 29, 2014)\n",
       "Info) Exiting normally.\n"
      ]
     }
    ],
    "source": [
     "%%bash\n",
     "\n",
-    "vmd output_initial_state.pdb"
+    "output_initial_state.pdb"
    ]
   },
   {
@@ -3470,6 +3473,9 @@
    "execution_count": null,
    "id": "a417bb34",
    "metadata": {
+    "tags": [
+      "skip-execution"
+    ],
     "vscode": {
      "languageId": "shellscript"
     }
@@ -3821,6 +3827,9 @@
    "execution_count": null,
    "id": "5cd6e11a",
    "metadata": {
+    "tags": [
+      "skip-execution"
+    ],
     "vscode": {
      "languageId": "shellscript"
     }

docker/Dockerfile

@@ -4,12 +4,19 @@ FROM ghcr.io/ccpbiosim/jupyterhub-base:$BASE_IMAGE
 
 LABEL maintainer="James Gebbie-Rayet <james.gebbie@stfc.ac.uk>"
 
+ARG TARGETPLATFORM
+
 # Switch to jovyan user.
 USER $NB_USER
 WORKDIR $HOME
 
 # Install workshop deps
-RUN mamba install gromacs=2024.4=nompi_h5f56185_100 matplotlib=3.10.6 mdanalysis=2.9.0 numpy=2.3.3 scikit-learn=1.7.2 tqdm=4.67.1 mdtraj=1.11.0 iprogress ipywidgets salilab::dssp=3.0.0 -y
+RUN if [ "$TARGETPLATFORM" = "linux/amd64" ]; then \
+      mamba install conda-forge/linux-64::gromacs=2024.5=nompi_h5f56185_100 -y; \
+    elif [ "$TARGETPLATFORM" = "linux/arm64" ]; then \
+      mamba install conda-forge/linux-aarch64::gromacs=2024.5=nompi_h9afd374_100 -y; \
+    fi
+RUN mamba install matplotlib=3.10.6 mdanalysis=2.9.0 numpy=2.3.3 scikit-learn=1.7.2 tqdm=4.67.1 mdtraj=1.11.0 iprogress ipywidgets -y
 RUN pip install alphashape==1.3.1 click==8.3.0 click-log==0.4.0 coby==1.0.9 pbr==7.0.1 rtree==1.4.1 shapely==2.1.2 trimesh==4.8.3 vermouth==0.15.0
 
 # Get workshop files and move them to jovyan directory.