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chore: add docker containers for jupyterhub and daskhub
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‎.github/workflows/build_and_push_docker_images.yaml‎

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---
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name: Build and push Docker Images
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run-name: Build and push Docker Images for ${{ github.sha }} on ${{ github.ref }}
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on:
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workflow_call:
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inputs:
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version:
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description: 'Which version of the Docker image should be built?'
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required: true
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type: string
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publish:
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description: 'Should the Docker image be published to the registry?'
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required: true
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type: boolean
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env:
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REGISTRY: ghcr.io
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IMAGE: ghcr.io/3dct/image-quality-notebook
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AUTHORS: Lukas Behammer, lukas.behammer@fh-wels.at
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LICENSES: GPL-3.0-or-later
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URL: https://github.com/3dct/vIQA
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jobs:
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build-and-push-image:
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runs-on: ubuntu-latest
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strategy:
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fail-fast: false
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matrix:
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include:
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- dockerfile: ./containers/dh-image-quality-notebook/Dockerfile
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title: volumetric Image Quality Assessment Notebook - Daskhub
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description: This is a custom image for volumetric image quality assessment in daskhub.
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source: https://github.com/3dct/vIQA/tree/main/containers/dh-image-quality-notebook/Dockerfile
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documentation: https://github.com/3dct/vIQA/tree/main/containers/dh-image-quality-notebook/README.md
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prefix: dh
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- dockerfile: ./containers/jh-image-quality-notebook/Dockerfile
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title: volumetric Image Quality Assessment Notebook - JupyterHub
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description: This is a custom image for volumetric image quality assessment in jupyterhub.
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source: https://github.com/3dct/vIQA/tree/main/containers/jh-image-quality-notebook/Dockerfile
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documentation: https://github.com/3dct/vIQA/tree/main/containers/jh-image-quality-notebook/README.md
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prefix: jh
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permissions:
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contents: read
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packages: write
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steps:
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- name: Checkout repository
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uses: actions/checkout@v4
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- name: Log in to the Container registry
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uses: docker/login-action@65b78e6e13532edd9afa3aa52ac7964289d1a9c1
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with:
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registry: ${{ env.REGISTRY }}
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username: ${{ github.actor }}
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password: ${{ secrets.GITHUB_TOKEN }}
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- name: Extract metadata (tags, labels) for Docker
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id: meta
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uses: docker/metadata-action@9ec57ed1fcdbf14dcef7dfbe97b2010124a938b7
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with:
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images: ${{ env.IMAGE }}
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tags: |
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type=pep440,pattern={{version}},value=${{ inputs.version }}
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type=pep440,pattern={{major}},value=${{ inputs.version }}
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type=pep440,pattern={{major}}.{{minor}},value=${{ inputs.version }}
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labels: |
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org.opencontainers.image.created={{commit_date 'YYYY-MM-DDTHH:mm:ss.SSS[Z]'}}
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org.opencontainers.image.title=${{ matrix.title }}
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org.opencontainers.image.description=${{ matrix.description }}
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org.opencontainers.image.source=${{ matrix.source }}
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org.opencontainers.image.documentation=${{ matrix.documentation }}
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org.opencontainers.image.authors=${{ env.AUTHORS }}
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org.opencontainers.image.licenses=${{ env.LICENSES }}
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org.opencontainers.image.url=${{ env.URL }}
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org.opencontainers.image.version=${{ inputs.version }}
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flavor: |
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latest=true
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prefix=${{ matrix.prefix }},onlatest=true
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- name: Build and push Docker image
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id: push
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uses: docker/build-push-action@f2a1d5e99d037542a71f64918e516c093c6f3fc4
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if: ${{ inputs.publish }}
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with:
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context: .
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file: ${{ matrix.dockerfile }}
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push: true
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tags: ${{ steps.meta.outputs.tags }}
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labels: ${{ steps.meta.outputs.labels }}

‎.github/workflows/documentation.yaml‎

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contents: write
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jobs:
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Docs:
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docs:
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name: Build and deploy documentation
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runs-on: ubuntu-latest
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concurrency: Docs
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# if: |
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pip install -r ./requirements/docs.txt piq scipy scikit-image matplotlib nibabel tqdm
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- name: Sphinx build
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run: |
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sphinx-build docs/source _build
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sphinx-build docs/source docs/build/html
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env:
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GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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- name: Deploy to GitHub Pages
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with:
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publish_branch: gh-pages
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github_token: ${{ secrets.GITHUB_TOKEN }}
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publish_dir: _build/
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publish_dir: docs/build/html
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force_orphan: true

‎.github/workflows/release.yaml‎

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src-changes: ${{ steps.changed-files.outputs.src_any_changed }}
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test-changes: ${{ steps.changed-files.outputs.tests_any_changed }}
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lint-changes: ${{ steps.changed-files.outputs.lint_any_changed }}
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docker-changes: ${{ steps.changed-files.outputs.docker_any_changed }}
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steps:
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- uses: actions/checkout@v4
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- src/**
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- notebooks/**
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- pyproject.toml
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docker:
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- .github/workflows/build_and_push_docker_images.yaml
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- containers/**
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- notebooks/**
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- src/**
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- name: Detect if any of the combinations of file sets have changed
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id: all-changes
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[ "${{ steps.changed-files.outputs.docs_any_changed }}" == "true" ] || \
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[ "${{ steps.changed-files.outputs.src_any_changed }}" == "true" ] || \
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[ "${{ steps.changed-files.outputs.tests_any_changed }}" == "true" ] || \
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[ "${{ steps.changed-files.outputs.lint_any_changed }}" == "true" ]; then
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[ "${{ steps.changed-files.outputs.lint_any_changed }}" == "true" ] || \
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[ "${{ steps.changed-files.outputs.docker_any_changed }}" == "true" ]; then
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printf '%s\n' "any_changed=true" >> $GITHUB_OUTPUT
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fi
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with:
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github_token: ${{ secrets.GITHUB_TOKEN }}
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prepare_docs_input:
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prepare_publish_input:
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name: Check if published
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runs-on: ubuntu-latest
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if: needs.changes.outputs.doc-changes == 'true' && always()
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if: (needs.changes.outputs.doc-changes == 'true' || needs.changes.outputs.docker-changes == 'true') && always()
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outputs:
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publish: ${{ steps.check_publish.outputs.publish }}
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docs_publish: ${{ steps.check_docs_publish.outputs.publish }}
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image_publish: ${{ steps.check_image_publish.outputs.publish }}
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needs: [changes, upload_github, upload_pypi]
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steps:
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- name: Check if documentation should be published
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id: check_publish
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id: check_docs_publish
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if: needs.changes.outputs.doc-changes == 'true'
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run: |
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# If either the PyPI or GitHub release was successful, publish the docs
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if ${{ needs.upload_github.result == 'success' }} || ${{ needs.upload_pypi.result == 'success' }}; then
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echo "publish=false" >> $GITHUB_OUTPUT
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fi
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fi
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- name: Check if Docker images should be published
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id: check_image_publish
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if: needs.changes.outputs.docker-changes == 'true'
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run: |
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# If either the PyPI or GitHub release was successful, publish the Docker images
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if ${{ needs.upload_github.result == 'success' }} || ${{ needs.upload_pypi.result == 'success' }}; then
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echo "publish=true" >> $GITHUB_OUTPUT
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fi
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docs:
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name: Build and deploy documentation
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uses: ./.github/workflows/documentation.yaml
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needs: [changes, prepare_docs_input]
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needs: [changes, prepare_publish_input]
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if: github.repository == '3dct/viqa' && needs.changes.outputs.doc-changes == 'true'
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with:
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publish: ${{ needs.prepare_docs_input.outputs.publish }}
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publish: ${{ needs.prepare_publish_input.outputs.docs_publish }}
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build_and_push_docker_images:
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name: Build and push Docker Images
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uses: ./.github/workflows/build_and_push_docker_images.yaml
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needs: [changes, semantic_release, prepare_publish_input]
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if: github.repository == '3dct/viqa' && needs.changes.outputs.docker-changes == 'true'
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with:
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version: ${{ needs.semantic_release.outputs.version }}
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publish: ${{ needs.prepare_publish_input.outputs.image_publish }}

‎README.md‎

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For more examples, see the provided Jupyter notebooks and the documentation under [API Reference](https://3dct.github.io/vIQA/api_reference.html).
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## Container Images
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Container images to use this package in a JupyterHub or Daskhub environment as a single user notebook can be found under [./containers](./containers).
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<!-- ## Benchmark TODO: add benchmark results and instructions -->
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## TODO

‎containers/config/jp_app_launcher/jp_app_launcher.yaml‎

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---
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# This is the config for the jupyter_app_launcher extension to launch the vIQA notebooks
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# The notebooks are available under https://github.com/3dct/vIQA/tree/master/Notebooks
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# and have to be copied to the shared folder which might have to be mounted to the
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# singleuser pod
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- title: vIQA Documentation
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description: Example of opening a URL in a tab
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source: https://3dct.github.io/vIQA/
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type: url
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args:
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sandbox:
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- 'allow-same-origin'
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- 'allow-scripts'
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- 'allow-downloads'
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- 'allow-modals'
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- 'allow-popups'
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referrerPolicy: ['no-referrer']
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createNewWindow: false
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catalog: vIQA
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- title: vIQA Notebook
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description: vIQA template notebook
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source: /usr/share/jupyter/jupyter_app_launcher/notebooks/Image_Comparison.ipynb
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cwd: /usr/share/jupyter/jupyter_app_launcher/notebooks
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type: notebook
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catalog: vIQA
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- title: vIQA batch Notebook
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description: vIQA template notebook for batch mode
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source: /usr/share/jupyter/jupyter_app_launcher/notebooks/Image_Comparison_batch.ipynb
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cwd: /usr/share/jupyter/jupyter_app_launcher/notebooks
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type: notebook
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catalog: vIQA

‎containers/dh-image-quality-notebook/.dockerignore‎

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# Documentation
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README.md

‎containers/dh-image-quality-notebook/Dockerfile‎

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FROM pangeo/base-notebook:2024.01.15
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LABEL org.opencontainers.image.title="volumetric Image Quality Assessment Notebook - Daskhub"
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LABEL org.opencontainers.image.description="This is a custom image for volumetric image quality assessment in daskhub."
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LABEL org.opencontainers.image.authors="Lukas Behammer, lukas.behammer@fh-wels.at"
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LABEL org.opencontainers.image.source="https://github.com/3dct/vIQA/tree/main/containers/dh-image-quality-notebook/Dockerfile"
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LABEL org.opencontainers.image.documentation="https://github.com/3dct/vIQA/tree/main/containers/dh-image-quality-notebook/README.md"
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LABEL org.opencontainers.image.url="https://github.com/3dct/vIQA"
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LABEL org.opencontainers.image.licenses="GPL-3.0-or-later"
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# install git
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USER root
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RUN apt-get update
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RUN apt-get install -y git-all
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USER ${NB_UID}
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# install additional packages
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RUN pip install viqa
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RUN pip install jupyter_app_launcher
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RUN pip install jupyterlab-git
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COPY notebooks /usr/share/jupyter/jupyter_app_launcher/notebooks
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COPY containers/config/jp_app_launcher/jp_app_launcher.yaml /usr/share/jupyter/jupyter_app_launcher/jp_app_launcher.yaml

‎containers/dh-image-quality-notebook/README.md‎

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# volumetric Image Quality Assessment Notebook - Daskhub
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[![Build GH Action](https://github.com/3dct/vIQA/actions/workflows/build_and_push_docker_images.yaml/badge.svg)](https://github.com/3dct/vIQA/actions/workflows/build_and_push_docker_images.yaml)
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[![latest](https://ghcr-badge.egpl.dev/3dct/image-quality-notebook/latest_tag?label=latest&ignore=dh-*)](https://github.com/3dct/vIQA/pkgs/container/image-quality-notebook)
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[![tags](https://ghcr-badge.egpl.dev/3dct/image-quality-notebook/tags?n=3&ignore=jh-*)](https://github.com/3dct/vIQA/pkgs/container/image-quality-notebook)
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[![image size](https://ghcr-badge.egpl.dev/3dct/image-quality-notebook/size?tag=dh-latest)](https://github.com/3dct/vIQA/pkgs/container/image-quality-notebook)
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This is a single user notebook for volumetric Image Quality Assessment (vIQA) to be used with Daskhub.
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## Base Image
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[pangeo/base-notebook:2024.01.15](https://github.com/pangeo-data/pangeo-docker-images)
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## Additionally Installed Packages
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| Package | Tools | JupyterLab Extensions |
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|---------|-------|-----------------------|
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| viqa | git | jupyterlab-git |
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| | | jupyter_app_launcher |

‎containers/jh-image-quality-notebook/.dockerignore‎

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# Documentation
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README.md

‎containers/jh-image-quality-notebook/Dockerfile‎

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FROM quay.io/jupyter/base-notebook:python-3.12
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LABEL org.opencontainers.image.title="volumetric Image Quality Assessment Notebook - JupyterHub"
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LABEL org.opencontainers.image.description="This is a custom image for volumetric image quality assessment in jupyterhub."
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LABEL org.opencontainers.image.authors="Lukas Behammer, lukas.behammer@fh-wels.at"
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LABEL org.opencontainers.image.source="https://github.com/3dct/vIQA/tree/main/containers/jh-image-quality-notebook/Dockerfile"
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LABEL org.opencontainers.image.documentation="https://github.com/3dct/vIQA/tree/main/containers/jh-image-quality-notebook/README.md"
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LABEL org.opencontainers.image.url="https://github.com/3dct/vIQA"
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LABEL org.opencontainers.image.licenses="GPL-3.0-or-later"
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# install git
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USER root
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RUN apt-get update
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RUN apt-get install -y git-all
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USER ${NB_UID}
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# install additional packages
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RUN pip install viqa
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RUN pip install jupyter_app_launcher
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RUN pip install jupyterlab-git
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COPY notebooks /usr/share/jupyter/jupyter_app_launcher/notebooks
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COPY containers/config/jp_app_launcher/jp_app_launcher.yaml /usr/share/jupyter/jupyter_app_launcher/jp_app_launcher.yaml

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