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Merge pull request #25 from iterorganization/release/2.0.0
Notes for release 2.0.0 =============== Breaking change ------------------- The package name was changed from ``imaspy`` to ``imas`` while porting the code to GitHub https://github.com/iterorganization/IMAS-Python. This shall only affect the import statements in your code. New features and improvements ------------------------------------ - Add `imas.util.to_xarray` to convert a full IDS or only specific paths herein to a Xarray ``Dataset``. See `Convert IMAS-Python IDSs directly to Xarray Datasets` in the documentation for more details. - Implements automatic DD version conversion on `imas.db_entry.DBEntry.get` (conversion during `imas.db_entry.DBEntry.put` is not supported as this is rarely needed and easily worked around). - Enable lazy loading when reading data from a netCDF file. - Minor performance improvement loading data from a netCDF file. - Replace versioneer by setuptools-scm to determine the version of the code. - Use `saxonche` https://pypi.org/project/saxonche/ instead of the JAR for XSL transforms (when building versions of the DD). - Updating the README, CONTRIBUTING guidelines and documentation after making the code open access.
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‎.git_archival.txt

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node: $Format:%H$
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node-date: $Format:%cI$
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describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$

‎.gitattributes

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imaspy/_version.py export-subst
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.git_archival.txt export-subst

‎.github/workflows/linting.yml

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name: linting-and-code-formatting
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on:
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push:
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pull_request:
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types: [opened, synchronize, reopened]
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jobs:
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build:
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runs-on: ubuntu-22.04
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steps:
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- name: Checkout IMAS-Python sources
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uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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# until saxonche is available in 3.13
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# https://saxonica.plan.io/issues/6561
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python-version: "<3.13"
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- name: Display Python version
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run: python -c "import sys; print(sys.version)"
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- name: Install the code linting and formatting tools
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run: pip install --upgrade 'black >=24,<25' flake8
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- name: Check formatting of code with black
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run: black --check imas
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- name: Check linting with flake8
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run: flake8 imas

‎.github/workflows/publish.yml

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name: build-wheel-and-publish-test-pypi
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on:
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push:
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pull_request:
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types: [opened, synchronize, reopened]
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jobs:
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build:
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name: Build distribution
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runs-on: ubuntu-22.04
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steps:
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- uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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# until saxonche is available in 3.13
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# https://saxonica.plan.io/issues/6561
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python-version: "<3.13"
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- name: Install pypa/build
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run: >-
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python3 -m pip install pip setuptools wheel build
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- name: Build a binary wheel and a source tarball
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run: python3 -m build .
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- name: Store the distribution packages
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uses: actions/upload-artifact@v4
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with:
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name: python-package-distributions
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path: dist/
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publish-to-pypi:
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name: Publish IMAS-Python distribution to PyPI
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if: startsWith(github.ref, 'refs/tags/') # only publish to PyPI on tag pushes
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needs:
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- build
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runs-on: ubuntu-22.04
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environment:
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name: pypi
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url: https://pypi.org/p/imas-python
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permissions:
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id-token: write # IMPORTANT: mandatory for trusted publishing
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steps:
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- name: Download all the dists
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uses: actions/download-artifact@v4
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with:
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name: python-package-distributions
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path: dist/
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- name: Publish distribution to PyPI
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uses: pypa/gh-action-pypi-publish@release/v1
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publish-to-testpypi:
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name: Publish IMAS-Python distribution to TestPyPI
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if: github.ref=='refs/heads/develop' # only publish to TestPyPI on develop pushes
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needs:
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- build
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runs-on: ubuntu-22.04
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environment:
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name: testpypi
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url: https://test.pypi.org/p/imas-python
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permissions:
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id-token: write # IMPORTANT: mandatory for trusted publishing
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steps:
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- name: Download all the dists
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uses: actions/download-artifact@v4
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with:
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name: python-package-distributions
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path: dist/
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- name: Publish distribution to TestPyPI
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uses: pypa/gh-action-pypi-publish@unstable/v1
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with:
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repository-url: https://test.pypi.org/legacy/
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verbose: true

‎.github/workflows/test_with_pytest.yml

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name: Test using pytest
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on:
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push:
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pull_request:
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types: [opened, synchronize, reopened]
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jobs:
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test:
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runs-on: ubuntu-22.04
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strategy:
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matrix:
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python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"] # Test on multiple Python versions
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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: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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with:
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# until saxonche is available in 3.13
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# https://saxonica.plan.io/issues/6561
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python-version: ${{ matrix.python-version }}
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- name: Display Python version
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run: python -c "import sys; print(sys.version)"
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- name: Install dependencies
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run: |
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python -m venv venv
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source venv/bin/activate
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pip install --upgrade pip setuptools wheel
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pip install .[test]
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- name: Run tests
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run: |
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source venv/bin/activate
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python -m pytest -n=auto --cov=imas --cov-report=term-missing --cov-report=xml:coverage.xml --cov-report=html:htmlcov --junit-xml=junit.xml
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- name: Upload coverage report ${{ matrix.python-version }}
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uses: actions/upload-artifact@v4
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with:
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name: coverage-report-${{ matrix.python-version }}
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path: htmlcov
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- name: Upload test report ${{ matrix.python-version }}
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uses: actions/upload-artifact@v4
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with:
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name: test-report-${{ matrix.python-version }}
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path: junit.xml

‎.github/workflows/verify_sphinx_doc.yml

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name: verify-sphinx-doc-generation
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on:
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push:
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pull_request:
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types: [opened, synchronize, reopened]
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jobs:
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build-and-test:
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runs-on: ubuntu-22.04
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steps:
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- name: Checkout IMAS-Python sources
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uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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with:
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# until saxonche is available in 3.13
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# https://saxonica.plan.io/issues/6561
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python-version: "<3.13"
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- name: Display Python version
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run: python -c "import sys; print(sys.version)"
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- name: Set up Python virtual environment
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run: |
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python -m venv venv
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source venv/bin/activate
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- name: Install build dependencies
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run: |
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pip install --upgrade pip setuptools wheel build
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- name: Build package
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run: |
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rm -rf dist
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python -m build .
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- name: Install package and dependencies
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run: |
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pip install "$(readlink -f dist/*.whl)[docs,netcdf]"
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- name: Debug dependencies
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run: |
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pip freeze
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- name: Build Sphinx documentation
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run: |
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export SPHINXOPTS='-W -n --keep-going'
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make -C docs clean html

‎.gitignore

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*.swo
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# SCM setuptools
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imaspy/version.py
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# Saxon symlink or downloaded file
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saxon*.jar
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imas/_version.py
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# IMAS DD
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data-dictionary
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access-layer
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containers/arch/imaspy/
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containers/arch/imas/
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containers/arch/data-dictionary/
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containers/arch/access-layer/
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imaspy/assets/IDSDef.zip
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imas/assets/IDSDef.zip
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# IDS files
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*.ids
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# *.ids
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# ASV folder
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/.asv

‎.readthedocs.yml

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version: 2
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build:
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os: "ubuntu-22.04"
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tools:
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python: "3.11"
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jobs:
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post_checkout:
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- git fetch --unshallow || true
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python:
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install:
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- method: pip
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path: .
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extra_requirements:
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- docs
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- netcdf
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- h5py
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sphinx:
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builder: html
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configuration: docs/source/conf.py
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fail_on_warning: false

‎CONTRIBUTING.md

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# Contributing guidelines
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3-
We welcome any kind of contribution to `imas-python`,
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We welcome any kind of contribution to `IMAS-Python`,
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from a simple comment, a question or even a full fledged pull
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request.
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Please first make sure you read and follow the
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[Code of Conduct](CODE_OF_CONDUCT.md).
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## You think you found a bug in the code, or have a question in its use
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1. use the [issue search](https://github.com/iterorganization/imas-python/issues)
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1. use the [issue search](https://github.com/iterorganization/IMAS-Python/issues)
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to check if someone already created a similar issue;
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3. if not, make a **new issue** to describe your problem or question.
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2. if not, make a **new issue** to describe your problem or question.
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In the case of a bug suspiscion, please try to give all the relevant
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information to allow reproducing the error or identifying
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its root cause (version of the imas-python, OS and relevant
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its root cause (version of the IMAS-Python, OS and relevant
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dependencies, snippet of code);
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4. apply relevant labels to the issue.
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3. apply relevant labels to the issue.
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## You want to make or ask some change to the code
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1. use the [issue search](https://github.com/iterorganization/imas-python/issues)
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1. use the [issue search](https://github.com/iterorganization/IMAS-Python/issues)
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to check if someone already proposed a similar idea/change;
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3. if not, create a **new issue** to describe what change you would like to see
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2. if not, create a **new issue** to describe what change you would like to see
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implemented and specify it if you intend to work on it yourself or if some help
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will be needed;
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4. wait until some kind of consensus is reached about your idea being relevant,
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3. wait until some kind of consensus is reached about your idea being relevant,
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at which time the issue will be assigned (to you or someone else who can work on
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this topic);
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5. if you do the development yourself, fork the repository to your own Github
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4. if you do the development yourself, fork the repository to your own Github
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profile and create your own feature branch off of the latest develop commit.
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Make sure to regularly sync your branch with the latest commits from `develop`
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(find instructions
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[here](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/working-with-forks/syncing-a-fork));
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6. when your development is ready, create a pull request (find instructions
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5. when your development is ready, create a pull request (find instructions
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[here](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-a-pull-request-from-a-fork)).
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‎MANIFEST.in

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include imaspy/assets/IDSDef.zip
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include imaspy/assets/IDSDef2MDSpreTree.xsl
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include imaspy/assets/ITER_134173_106_equilibrium.ids
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include imaspy/assets/ITER_134173_106_core_profiles.ids
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include imaspy/assets/equilibrium.ids
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include imaspy/assets/core_profiles.ids
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include imas/assets/IDSDef.zip
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include imas/assets/IDSDef2MDSpreTree.xsl
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include imas/assets/ITER_134173_106_equilibrium.ids
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include imas/assets/ITER_134173_106_core_profiles.ids
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include imas/assets/equilibrium.ids
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include imas/assets/core_profiles.ids

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