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RubelMozumderRubelMozumder
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Template is recooked.
1 parent 2e379e8 commit 717408f

17 files changed

Lines changed: 532 additions & 38 deletions

‎.cruft.json‎

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{
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"template": "git@github.com:FAIRmat-NFDI/pynxtools-plugin-template.git",
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"commit": "519f503945368a21d0c44125c0f34cf0d5f46e10",
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"commit": "616d3dc6584cb0f19e85310a083c7a87857c6b8d",
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"checkout": null,
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"context": {
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"cookiecutter": {
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"reader_class": "SPMReader",
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"author_name": "The NOMAD authors",
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"author_email": "fairmat@physik.hu-berlin.de",
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"github_username": "",
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"organization_name": "fairmat-nfdi",
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"license": "Apache Software License 2.0",
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"zenodo_record": "17390485",
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"vscode_settings": true,
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"include_nomad_app": true,
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"include_nomad_example_upload": true,
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"include_north_tools": true,
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"north_tool_name": "spm",
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"__package_name": "pynxtools-spm",
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"__module_name": "pynxtools_spm",
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"__nomad_example": "spm_example_upload_entry_point",
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"__nomad_app": "",
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"_copy_without_render": ["*.html"],
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"__nomad_app": "spm_app_entry_point",
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"__north_tool_EP_name": "north_tool",
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"_copy_without_render": [
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"*.html"
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],
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"_template": "git@github.com:FAIRmat-NFDI/pynxtools-plugin-template.git",
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"_commit": "519f503945368a21d0c44125c0f34cf0d5f46e10"
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"_commit": "616d3dc6584cb0f19e85310a083c7a87857c6b8d"
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}
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},
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"directory": null

‎.dockerignore‎

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# Git
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.gitignore
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.gitattributes
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# Python
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__pycache__
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*.py[cod]
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*$py.class
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*.so
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.Python
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build/
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develop-eggs/
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dist/
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downloads/
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eggs/
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.eggs/
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lib/
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lib64/
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parts/
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sdist/
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var/
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wheels/
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pip-wheel-metadata/
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share/python-wheels/
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*.egg-info/
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.installed.cfg
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*.egg
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MANIFEST
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.pytest_cache/
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# Virtual Environments
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.venv
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venv/
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ENV/
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env/
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.venv/
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# IDE
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.vscode/
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.idea/
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*.swp
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*.swo
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*~
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.DS_Store
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.project
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.pydevproject
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.settings/
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*.sublime-project
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*.sublime-workspace
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# CI/CD
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.github/
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.gitlab-ci.yml
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.travis.yml
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.circleci/
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# Testing
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.coverage
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.coverage.*
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htmlcov/
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.tox/
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.hypothesis/
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pytest.ini
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.pytest_cache/
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# Documentation
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docs/_build/
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site/
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.mkdocs.yml
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mkdocs.yml
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# Docker
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Dockerfile*
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.dockerignore
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docker/
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# Node (if used)
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node_modules/
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npm-debug.log
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package-lock.json
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# Misc
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*.md
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LICENSE
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MANIFEST.in
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*.tar.gz
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*.zip
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.tmp/
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.cache/
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# IDE configuration files
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.editorconfig
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.env
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.env.local

‎.github/workflows/cruft_update.yml‎

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jobs:
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update:
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runs-on: ubuntu-latest
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strategy:
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fail-fast: true
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matrix:
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include:
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- add-paths: .
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body: Use this to merge the changes to this repository.
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branch: cruft/update
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commit-message: "chore: accept new Cruft update"
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title: New updates detected with Cruft
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- add-paths: .cruft.json
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body: Use this to reject the changes in this repository.
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branch: cruft/reject
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commit-message: "chore: reject new Cruft update"
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title: Reject new updates detected with Cruft
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steps:
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- uses: actions/checkout@v4
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else
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echo "No .cruft.json file"
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fi
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echo "has_changes=$CHANGES" >> "$GITHUB_OUTPUT"
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- name: Run update if available
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git config --global user.name "GitHub"
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cruft update --skip-apply-ask --refresh-private-variables
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# git restore --staged .
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# --------------------------------------------------------
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# HARD BLOCK: never allow workflow updates from Cruft
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# --------------------------------------------------------
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git restore --staged .github/workflows || true
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git restore .github/workflows || true
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- name: Create pull request
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if: steps.check.outputs.has_changes == '1'
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uses: peter-evans/create-pull-request@v4
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with:
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token: ${{ secrets.GITHUB_TOKEN }}
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add-paths: ${{ matrix.add-paths }}
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commit-message: ${{ matrix.commit-message }}
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branch: ${{ matrix.branch }}
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add-paths: .
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commit-message: "chore: accept new Cruft update"
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branch: cruft/update
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delete-branch: true
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branch-suffix: timestamp
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title: ${{ matrix.title }}
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title: New updates detected with Cruft
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body: |
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This is an autogenerated PR. ${{ matrix.body }}
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This is an autogenerated PR.
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[Cruft](https://cruft.github.io/cruft/) has detected updates from the
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Cookiecutter repository.
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[Cruft](https://cruft.github.io/cruft/) has detected updates from the Cookiecutter repository.
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Changes to `.github/workflows` are intentionally excluded
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from automated updates and must be applied manually.

‎.github/workflows/nomad-requirements.yml‎

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- name: Generate (dev-)requirements.txt from modified pyproject.toml
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working-directory: ./nomad
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run: |
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uv pip compile --universal -p ${{ env.python-version }} --annotation-style=line --extra=infrastructure --extra=parsing --output-file=requirements.txt pyproject.toml
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uv pip compile --universal -p ${{ env.python-version }} --annotation-style=line --extra=dev --extra=infrastructure --extra=parsing --output-file=requirements-dev.txt requirements.txt pyproject.toml
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uv pip compile --universal -p ${{ env.python-version }} --annotation-style=line --extra=infrastructure --output-file=requirements.txt pyproject.toml
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uv pip compile --universal -p ${{ env.python-version }} --annotation-style=line --extra=dev --extra=infrastructure --output-file=requirements-dev.txt requirements.txt pyproject.toml
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uv pip compile --universal -p ${{ env.python-version }} --annotation-style=line --output-file=requirements-plugins.txt --unsafe-package nomad-lab -c requirements-dev.txt test_plugins.txt
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- name: Install NOMAD dependencies with pynxtools from current branch
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working-directory: ./nomad

‎.github/workflows/publish-north.yaml‎

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name: Build and publish docker images
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on:
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push:
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branches:
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- main
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tags:
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- "v*.*.*"
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pull_request:
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branches:
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- main
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env:
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REGISTRY: ghcr.io
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UV_VERSION: 0.9
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PYTHON_VERSION: 3.12
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JUPYTER_VERSION: 2025-12-31
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NORTH_TOOL_DIR: src/pynxtools_spm/nomad/north_tools/spm
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TEST_DATA_DIR: tests/data/north_tools/spm
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TEST_NOTEBOOKS: CommandLine.ipynb
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permissions:
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packages: write
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contents: read
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attestations: write
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id-token: write
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jobs:
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build:
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name: Build Jupyter Image
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runs-on: ubuntu-latest
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outputs:
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tags: ${{ steps.meta.outputs.tags }} # list
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labels: ${{ steps.meta.outputs.labels }} # list
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steps:
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- uses: actions/checkout@v4
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with:
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ref: ${{ github.head_ref || github.ref_name }}
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fetch-depth: 0
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show-progress: true
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submodules: true
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# Replace driver `Docker' by `Docker-container` to support cache export/import
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- name: Set up Docker Buildx
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uses: docker/setup-buildx-action@v3
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# https://github.com/docker/metadata-action
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- name: Extract Docker metadata
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id: meta
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uses: docker/metadata-action@v5
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with:
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images: ${{ env.REGISTRY }}/${{ github.repository }}
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# set latest tag for main branch and tags
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# https://github.com/docker/metadata-action?tab=readme-ov-file#image-name-and-tag-sanitization
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tags: |
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type=ref,event=tag
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type=ref,event=pr,prefix=pr-
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type=raw,value=main,enable=${{ github.ref == format('refs/heads/{0}', 'main') }}
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flavor: |
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latest=auto
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# https://docs.docker.com/build/ci/github-actions/share-image-jobs/
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# https://github.com/docker/build-push-action
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- name: Build and export to Jupyter image
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uses: docker/build-push-action@v6
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with:
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context: .
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file: ${{ env.NORTH_TOOL_DIR }}/Dockerfile
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build-args: |
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UV_VERSION=${{ env.UV_VERSION }}
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JUPYTER_TAG=${{ env.JUPYTER_VERSION }}
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cache-from: type=gha
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cache-to: type=gha,mode=max
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push: false
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tags: ${{ steps.meta.outputs.tags }}
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labels: ${{ steps.meta.outputs.labels }}
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outputs: type=docker,dest=${{ runner.temp }}/jupyter.tar.gz
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- name: Upload artifact
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uses: actions/upload-artifact@v4
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with:
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name: jupyter-image
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path: ${{ runner.temp }}/jupyter.tar.gz
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test_and_push_image:
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name: Test Jupyter Image
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needs: build
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runs-on: ubuntu-latest
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# https://docs.docker.com/build/ci/github-actions/share-image-jobs/
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steps:
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- name: Setup Repository
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uses: actions/checkout@v4
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- name: Download artifact
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uses: actions/download-artifact@v4
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with:
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name: jupyter-image
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path: ${{ runner.temp }}
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pattern: "!*.dockerbuild" # warning at https://github.com/docker/build-push-action?tab=readme-ov-file
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- name: Load and test in Jupyter container
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run: |
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docker load -i ${{ runner.temp }}/jupyter.tar.gz
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RAW_TAGS="${{ needs.build.outputs.tags }}"
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echo "Raw tags: $RAW_TAGS"
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FIRST_TAG=$(echo "$RAW_TAGS" | tr -s '[:space:]' '\n' | grep -v '^$' | head -n 1)
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echo "Using tag: $FIRST_TAG"
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for nb in ${{ env.TEST_NOTEBOOKS }}; do
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echo "Running notebook: $nb"
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docker run \
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--mount type=bind,src=./${{ env.TEST_DATA_DIR }},dst="/home/jovyan/north_test" \
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--rm "$FIRST_TAG" \
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/bin/bash -c "jupyter execute \$HOME/north_test/$nb"
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done
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- uses: docker/login-action@v3
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with:
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registry: ${{ env.REGISTRY }}
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username: ${{ github.actor }}
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password: ${{ secrets.GITHUB_TOKEN }}
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- name: Push Jupyter Image
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run: |
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RAW_TAGS="${{ needs.build.outputs.tags }}"
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for TAG in $RAW_TAGS; do
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echo "Pushing tag: $TAG"
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docker push "$TAG"
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done

‎.pre-commit-config.yaml‎

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# Run the linter.
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- id: ruff
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# Run the formatter.
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- id: ruff-format
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- id: ruff-format
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- repo: https://github.com/pre-commit/mirrors-mypy
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rev: v1.7.1
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hooks:
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- id: mypy # static type checking
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- repo: https://github.com/asottile/pyupgrade
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rev: v2.37.3
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hooks:
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- id: pyupgrade
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args: [--py36-plus] # modernizes syntax for Python 3.6+
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- repo: https://github.com/kynan/nbstripout
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rev: 0.6.0
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hooks:
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- id: nbstripout # removes notebook outputs before committing
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- repo: https://github.com/streetsidesoftware/cspell-cli
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rev: v6.31.1
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hooks:
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- id: cspell # spellchecking
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pass_filenames: false
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args:
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- --config

‎README.md‎

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.
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This `pynxtools` plugin was generated with [`cookiecutter`](https://github.com/cookiecutter/cookiecutter) using the [`pynxtools-plugin-template`](https://github.com/FAIRmat-NFDI/`pynxtools-plugin-template) template.
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This `pynxtools` plugin was generated with [`cookiecutter`](https://github.com/cookiecutter/cookiecutter) using the [`pynxtools-plugin-template`](https://github.com/FAIRmat-NFDI/pynxtools-plugin-template) template.
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## Installation
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