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jimboid merged 8 commits into from
Nov 12, 2025
Merged

Update build.yaml #7

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8826eaf
Update build.yaml
jimboid Oct 31, 2025
0d1328e
Update build.yaml
jimboid Nov 10, 2025
a3c7fff
Merge branch 'main' into ci-update
jimboid Nov 10, 2025
446004b
Update Dockerfile
jimboid Nov 10, 2025
5981648
Update build.yaml
jimboid Nov 10, 2025
c7c643f
Update build.yaml
jimboid Nov 10, 2025
24b162c
Update build.yaml
jimboid Nov 11, 2025
bc0dbc3
Update Setup_DNA-simulation.ipynb
jimboid Nov 11, 2025
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52 changes: 41 additions & 11 deletions .github/workflows/build.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -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

Expand All @@ -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:
Expand All @@ -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 }}
Expand Down
4 changes: 2 additions & 2 deletions Setup_DNA-simulation.ipynb
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Expand Up @@ -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": {
Expand Down
6 changes: 2 additions & 4 deletions docker/Dockerfile
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Expand Up @@ -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
Expand Down