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migrate infra components and tidy up
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‎.github/dependabot.yml‎

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# To get started with Dependabot version updates, you'll need to specify which
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# package ecosystems to update and where the package manifests are located.
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# Please see the documentation for all configuration options:
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# https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
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version: 2
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updates:
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- package-ecosystem: "github-actions"
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directory: "/"
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schedule:
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# Check for updates to GitHub Actions every day
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interval: "daily"
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time: "09:00"
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timezone: "UTC"
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assignees:
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- "jimboid"

‎.github/workflows/build.yaml‎

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name: ci/cd
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on:
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pull_request:
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repository_dispatch:
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types: [build]
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workflow_dispatch:
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jobs:
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build:
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strategy:
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fail-fast: false
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matrix:
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platform:
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- linux/amd64
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- linux/arm64
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runs-on: ${{ matrix.platform == 'linux/amd64' && 'ubuntu-24.04' || matrix.platform == 'linux/arm64' && 'ubuntu-24.04-arm' }}
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name: build ${{ matrix.platform }}
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outputs:
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tag: ${{ steps.envvars.outputs.tag }}
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steps:
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- name: checkout
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uses: actions/checkout@v5.0.0
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- name: Prepare env
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id: envvars
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run: |
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platform=${{ matrix.platform }}
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echo "PLATFORM_PAIR=${platform//\//-}" >> $GITHUB_ENV
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if [ ${{ github.event.client_payload.tag }} != 'null' ]; then
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echo "tag=${{ github.event.client_payload.tag }}" >> $GITHUB_OUTPUT
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else
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echo "tag=$(date +'%Y-%m-%d')" >> $GITHUB_OUTPUT
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fi
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- name: Metadata
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id: meta
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uses: docker/metadata-action@v5.8.0
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with:
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images: ghcr.io/${{ vars.ORG_REPO }}/${{ github.event.repository.name }}
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- name: Authenticate with GHCR
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id: auth
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uses: docker/login-action@v3.5.0
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with:
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registry: ghcr.io
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username: ${{github.actor}}
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password: ${{secrets.BUILD_TOKEN}}
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- name: Set up Docker Buildx
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id: buildx
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uses: docker/setup-buildx-action@v3.11.1
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- name: Build and push by digest
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id: build
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uses: docker/build-push-action@v6.18.0
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with:
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file: ./docker/Dockerfile
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platforms: ${{ matrix.platform }}
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labels: ${{ steps.meta.outputs.labels }}
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tags: ghcr.io/${{ vars.ORG_REPO }}/${{ github.event.repository.name }}
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outputs: type=image,push-by-digest=true,name-canonical=true,push=true
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- name: Export digest
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run: |
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mkdir -p ${{ runner.temp }}/digests
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digest="${{ steps.build.outputs.digest }}"
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touch "${{ runner.temp }}/digests/${digest#sha256:}"
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- name: Upload digest
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uses: actions/upload-artifact@v4.6.2
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with:
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name: digests-${{ env.PLATFORM_PAIR }}
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path: ${{ runner.temp }}/digests/*
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if-no-files-found: error
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retention-days: 1
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merge:
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runs-on: ubuntu-24.04
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name: merge into multiarch manifest
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needs:
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- build
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steps:
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- name: Download digests
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uses: actions/download-artifact@v5.0.0
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with:
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path: ${{ runner.temp }}/digests
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pattern: digests-*
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merge-multiple: true
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- name: Authenticate with GHCR
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id: auth
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uses: docker/login-action@v3.5.0
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with:
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registry: ghcr.io
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username: ${{github.actor}}
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password: ${{secrets.BUILD_TOKEN}}
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- name: Set up Docker Buildx
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id: buildx
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uses: docker/setup-buildx-action@v3.11.1
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- name: Metadata
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id: meta
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uses: docker/metadata-action@v5.8.0
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with:
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images: ghcr.io/${{ vars.ORG_REPO }}/${{ github.event.repository.name }}
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tags: dev
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- name: Create manifest list and push
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id: annotate
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continue-on-error: true
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working-directory: ${{ runner.temp }}/digests
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run: |
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docker buildx imagetools create $(jq -cr '.tags | map("-t " + .) | join(" ")' <<< "$DOCKER_METADATA_OUTPUT_JSON") \
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--annotation='index:org.opencontainers.image.description=${{ github.event.repository.description }}' \
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--annotation='index:org.opencontainers.image.licenses=MIT' \
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--annotation='index:org.opencontainers.image.created=${{ steps.timestamp.outputs.timestamp }}' \
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--annotation='index:org.opencontainers.image.url=${{ github.event.repository.url }}' \
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--annotation='index:org.opencontainers.image.source=${{ github.event.repository.url }}' \
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$(printf 'ghcr.io/${{ vars.ORG_REPO }}/${{ github.event.repository.name }}@sha256:%s ' *)
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- name: Create manifest list and push without annotations
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if: steps.annotate.outcome == 'failure'
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working-directory: ${{ runner.temp }}/digests
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run: |
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docker buildx imagetools create $(jq -cr '.tags | map("-t " + .) | join(" ")' <<< "$DOCKER_METADATA_OUTPUT_JSON") \
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$(printf 'ghcr.io/${{ vars.ORG_REPO }}/${{ github.event.repository.name }}@sha256:%s ' *)
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- name: Inspect image
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run: |
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docker buildx imagetools inspect ghcr.io/${{ vars.ORG_REPO }}/${{ github.event.repository.name }}:dev
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tests:
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strategy:
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fail-fast: false
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matrix:
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platform:
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- linux/amd64
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- linux/arm64
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runs-on: ${{ matrix.platform == 'linux/amd64' && 'ubuntu-latest' || matrix.platform == 'linux/arm64' && 'ubuntu-24.04-arm' }}
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name: testing on ${{ matrix.platform }}
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timeout-minutes: 360
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needs:
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- build
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- merge
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steps:
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- name: Test notebooks
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shell: bash
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run: |
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docker run -t ghcr.io/${{ vars.ORG_REPO }}/${{ github.event.repository.name }}:dev bash -c "\
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pip install pytest nbmake; \
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find . -name '*.ipynb' | pytest --nbmake --nbmake-timeout=3600 --ignore=answers; "
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tags:
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runs-on: ubuntu-24.04
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if: github.event_name != 'pull_request'
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name: add tags
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needs:
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- build
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- tests
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steps:
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- name: Authenticate with GHCR
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id: auth
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uses: docker/login-action@v3.5.0
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with:
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registry: "ghcr.io"
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username: ${{github.actor}}
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password: ${{secrets.BUILD_TOKEN}}
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- name: tag release versions
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shell: bash
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run: |
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docker buildx imagetools create \
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--tag ghcr.io/${{ vars.ORG_REPO }}/${{ github.event.repository.name }}:latest \
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--tag ghcr.io/${{ vars.ORG_REPO }}/${{ github.event.repository.name }}:${{ needs.build.outputs.tag }} \
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ghcr.io/${{ vars.ORG_REPO }}/${{ github.event.repository.name }}:dev
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- name: Post version update to dash
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uses: peter-evans/repository-dispatch@v3.0.0
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with:
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token: ${{ secrets.BUILD_TOKEN }}
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repository: jimboid/biosim-workshops-dash
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event-type: build
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client-payload: '{"repo": "${{ github.event.repository.name }}", "tag": "${{ needs.build.outputs.tag }}"}'

‎README.md‎

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## Aimed at:
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Anyone interested in using Python for Biomodelling. The material in
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this workshop will help you get the most out of the other workshops
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run during the week.
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# CCPBioSim Basic Python Workshop
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## Requirements:
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Basic knowledge of Python e.g. as in [https://chryswoods.com/beginning_python](https://chryswoods.com/beginning_python)
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[![build](https://github.com/ccpbiosim/python-workshop/actions/workflows/build.yaml/badge.svg?branch=main)](https://github.com/ccpbiosim/python-workshop/actions/workflows/build.yaml)
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## Abstract:
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This workshop will introduce more intermediate features of Python that
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are useful for biomolecular modellers. This will include the use of
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Jupyter notebooks, how to write Python functions and classes, and
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how to properly structure, document and test code. The second
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part will introduce you to data analysis tools such as Pandas,
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NumPy and MatplotLib.
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## Docker
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## Training Material
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This container is derived from the CCPBioSim JupyterHub image. This container
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adds the necessary software packages and notebook content to form a deployable
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course container. The source content for this course can be found at
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https://github.com/CCPBioSim/python-and-data-workshop
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The workshop consists of a series of Jupyter notebooks. These are available
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below, and can be run using the
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<a href="https://notebook.biosimspace.org" target="_blank">workshop Jupyter server</a>.
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## How to Use
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Once you have started the server, navigate to the `python_and_data` directory
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and you will find all workshop material there.
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In our containers we are using the JupyterHub default port 8888, so you should
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forward this port when deploying locally::
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The workshops are numbered sequentially from `01_jupyter_howto.ipynb` to
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`17_regular_expressions.ipynb`. They cover a variety of useful Python topics,
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and are *mostly* independent. Feel free to go through them in the order you
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prefer, and to skip topics that you feel you are already comfortable with.
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There are exercises in many of the topics. You can find answers in the
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equivalent notebook in the `answers` directory.
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Below is a summary of each topic, together with links to view html versions
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of the notebooks the their answers, and to download the notebooks.
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## Contents
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### [01_jupyter_howto.ipynb](html/01_jupyter_howto.html) ([answers](html/answers/01_jupyter_howto.html))
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Introduction to Jupyter notebooks, including how to use the interface,
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how to view molecules, draw graphs, download files, and start a bash
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terminal.
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[download](01_jupyter_howto.ipynb) | [download answers](answers/01_jupyter_howto.ipynb)
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### [02_lists.ipynb](html/02_lists.html) ([answers](html/answers/02_lists.html))
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Learn how to use Python Lists
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[download](02_lists.ipynb) | [download answers](answers/02_lists.ipynb)
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### [03_dictionaries.ipynb](html/03_dictionaries.html) ([answers](html/answers/03_dictionaries.html))
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Learn how to use Python dictionaries
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[download](03_dictionaries.ipynb) | [download answers](answers/03_dictionaries.ipynb)
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### [04_functions.ipynb](html/04_functions.html) ([answers](html/answers/04_functions.html))
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Learn how to write a function in Python
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[download](04_functions.ipynb) | [download answers](answers/04_functions.ipynb)
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### [05_objects.ipynb](html/05_objects.html) ([answers](html/answers/05_objects.html))
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Learn about objects and object orientated programming
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[download](05_objects.ipynb) | [download answers](answers/05_objects.ipynb)
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### [06_classes.ipynb](html/06_classes.html) ([answers](html/answers/06_classes.html))
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Learn how to write your own Python classes
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[download](06_classes.ipynb) | [download answers](answers/06_classes.ipynb)
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### [07_documentation.ipynb](html/07_documentation.html) ([answers](html/answers/07_documentation.html))
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Learn how to add documentation to your code
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[download](07_documentation.ipynb) | [download answers](answers/07_documentation.ipynb)
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### [08_class_documentation.ipynb](html/08_class_documentation.html) ([answers](html/answers/08_class_documentation.html))
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Learn how to document Python classes, and protect hidden (private) functions
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and data from view.
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[download](08_class_documentation.ipynb) | [download answers](answers/08_class_documentation.ipynb)
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### [09_exceptions.ipynb](html/09_exceptions.html) ([answers](html/answers/09_exceptions.html))
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Learn about exceptions, and how they can be used to signify errors.
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[download](09_exceptions.ipynb) | [download answers](answers/09_exceptions.ipynb)
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### [10_error_handling.ipynb](html/10_error_handling.html) ([answers](html/answers/10_error_handling.html))
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Learn how to handle errors by catching exceptions
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[download](10_error_handling.ipynb) | [download answers](answers/10_error_handling.ipynb)
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### [11_modules.ipynb](html/11_modules.html) ([answers](html/answers/11_modules.html))
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Learn how to package and share your code as a module
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[download](11_modules.ipynb) | [download answers](answers/11_modules.ipynb)
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### [12_pandas.ipynb](html/12_pandas.html) ([answers](html/answers/12_pandas.html))
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Learn how to use the pandas library for data analysis
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[download](12_pandas.ipynb) | [download answers](answers/12_pandas.ipynb)
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### [13_basic_numpy.ipynb](html/13_basic_numpy.html) ([answers](html/answers/13_basic_numpy.html))
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Learn how to use the NumPy library for numeric calculation
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[download](13_basic_numpy.ipynb) | [download answers](answers/13_basic_numpy.ipynb)
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### [14_more_numpy.ipynb](html/14_more_numpy.html) ([answers](html/answers/14_more_numpy.html))
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Learn more about how to use NumPy, including understanding copies and views
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[download](14_more_numpy.ipynb) | [download answers](answers/14_more_numpy.ipynb)
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### [15_matplotlib.ipynb](html/15_matplotlib.html) ([answers](html/answers/15_matplotlib.html))
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Learn how to use the pandas with the MatPlotLib library to draw graphs
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[download](15_matplotlib.ipynb) | [download answers](answers/15_matplotlib.ipynb)
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### [16_viewing_molecules.ipynb](html/16_viewing_molecules.html) ([answers](html/answers/16_viewing_molecules.html))
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Learn how to use the nglview and BioSimSpace libraries to create 3D
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views of molecules.
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[download](16_viewing_molecules.ipynb) | [download answers](answers/16_viewing_molecules.ipynb)
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### [17_regular_expressions.ipynb](html/17_regular_expressions.html) ([answers](html/answers/17_regular_expressions.html))
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Learn how to understand and write regular expressions for text/pattern matching.
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[download](17_regular_expressions.ipynb) | [download answers](answers/17_regular_expressions.ipynb)
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docker run -p 8888:8888 ghcr.io/jimboid/biosim-python-workshop:latest

‎_config.yml‎

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‎docker/Dockerfile‎

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# Start with BioSim base image.
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ARG BASE_IMAGE=latest
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FROM ghcr.io/ccpbiosim/jupyterhub-base:$BASE_IMAGE
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LABEL maintainer="James Gebbie-Rayet <james.gebbie@stfc.ac.uk>"
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LABEL org.opencontainers.image.source=https://github.com/jimboid/biosim-python-workshop
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LABEL org.opencontainers.image.description="A container environment for the ccpbiosim workshop on Python."
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LABEL org.opencontainers.image.licenses=MIT
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# Switch to jovyan user.
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USER $NB_USER
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WORKDIR $HOME
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# Install workshop deps
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RUN conda install matplotlib numpy pandas nglview ipywidgets -y
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RUN pip install mdtraj
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# Get workshop files and move them to jovyan directory.
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COPY --chown=1000:100 . .
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RUN rm -r _config.yml AUTHORS README.md docker .git .github
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# Copy lab workspace
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COPY --chown=1000:100 docker/default-37a8.jupyterlab-workspace /home/jovyan/.jupyter/lab/workspaces/default-37a8.jupyterlab-workspace
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# UNCOMMENT THIS LINE FOR REMOTE DEPLOYMENT
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COPY docker/jupyter_notebook_config.py /etc/jupyter/
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# Always finish with non-root user as a precaution.
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USER $NB_USER

‎docker/default-37a8.jupyterlab-workspace‎

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{"data":{"layout-restorer:data":{"main":{"dock":{"type":"tab-area","currentIndex":0,"widgets":["notebook:01_jupyter_howto.ipynb"]},"current":"notebook:01_jupyter_howto.ipynb"},"left":{"collapsed":false,"current":"filebrowser","widgets":["filebrowser","running-sessions","@jupyterlab/toc:plugin","extensionmanager.main-view"]},"right":{"collapsed":true,"widgets":["jp-property-inspector"]}},"notebook:01_jupyter_howto.ipynb":{"data":{"path":"01_jupyter_howto.ipynb","factory":"Notebook"}}},"metadata":{"id":"default"}}

‎docker/jupyter_notebook_config.py‎

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c.JupyterHub.authenticator_class = 'tmpauthenticator.TmpAuthenticator'

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