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Prepare for PyPI release and documentation
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‎.github/workflows/pypi-publish.yml‎

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name: Publish Python Package
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on:
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release:
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types: [created]
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workflow_dispatch:
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jobs:
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deploy:
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runs-on: ubuntu-latest
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permissions:
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contents: read
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id-token: write # This is required for trusted publishing
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steps:
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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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python-version: '3.10'
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- name: Install build tools
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run: |
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python -m pip install --upgrade pip
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pip install build twine
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- name: Build package
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run: |
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python -m build
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- name: Publish to PyPI
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uses: pypa/gh-action-pypi-publish@release/v1
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with:
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user: __token__
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password: ${{ secrets.PYPI_API_TOKEN }}
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skip_existing: true
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verbose: true

‎.github/workflows/tests.yml‎

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name: Tests
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on:
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push:
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branches: [ main, master ]
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pull_request:
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branches: [ main, master ]
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schedule:
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- cron: '0 0 * * 0' # Weekly on Sundays
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defaults:
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run:
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shell: bash -l {0}
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jobs:
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test:
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name: Python ${{ matrix.python-version }} on ${{ matrix.os }}
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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os: [ubuntu-latest]
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python-version: ['3.8', '3.9', '3.10', '3.11']
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steps:
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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@v5
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install -e .[dev]
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- name: Run tests
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run: |
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python -m pytest tests/ -v --cov=fma_ions --cov-report=xml
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- name: Upload coverage to Codecov
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uses: codecov/codecov-action@v4
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with:
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token: ${{ secrets.CODECOV_TOKEN }}
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file: ./coverage.xml
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fail_ci_if_error: false
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- name: Run type checking
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run: |
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mypy fma_ions/
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- name: Lint with flake8
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run: |
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flake8 fma_ions/
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- name: Check formatting with black
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run: |
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black --check fma_ions/

‎.gitignore‎

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*.egg
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MANIFEST
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# Requirements files
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requirements*.txt
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!requirements-docs.txt
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# PyInstaller
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# Usually these files are written by a python script from a template
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# before PyInstaller builds the exe, so as to inject date/other infos into it.

‎.readthedocs.yaml‎

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# .readthedocs.yaml
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# Read the Docs configuration file
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# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
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version: 2
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# Build documentation in the docs/ directory with Sphinx
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sphinx:
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configuration: docs/conf.py
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fail_on_warning: true
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builder: html
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# Build documentation with MkDocs
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#mkdocs:
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# configuration: mkdocs.yml
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# Optionally build your docs in additional formats such as PDF and ePub
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formats:
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- pdf
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- epub
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# Optionally set the version of Python and requirements required to build your docs
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python:
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version: "3.10"
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install:
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- requirements: requirements-docs.txt
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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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# Optionally build documentation for specific branches and tags
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# branches:
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# main:
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# name: main
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# latest:
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# name: latest
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# stable:
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# name: stable
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# type: tag
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# Optionally include additional paths in the build
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tools:
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apt_packages:
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- graphviz
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- texlive-latex-extra
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- texlive-fonts-recommended
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- latexmk
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- dvipng
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# Build documentation with Sphinx v2 by default
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sphinx:
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configuration: docs/conf.py
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fail_on_warning: false
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# Build PDF and ePub too
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formats: all
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# Optionally set the version of Python and requirements required to build your docs
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python:
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version: 3.10
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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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# Optionally build documentation for specific branches and tags
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build:
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os: ubuntu-22.04
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tools:
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python: "3.10"
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jobs:
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post_create_environment:
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- pip install -U pip
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- pip install -U setuptools wheel
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# Optionally include additional paths in the build
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sphinx:
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configuration: docs/conf.py
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builder: html
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fail_on_warning: false
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jobs:
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post_build:
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- echo "Documentation built successfully!"
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# Optionally include additional paths in the build
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tools:
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apt_packages:
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- graphviz
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- texlive-latex-extra
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- texlive-fonts-recommended
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- latexmk
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- dvipng
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- texlive-latex-recommended
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- texlive-fonts-extra
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- texlive-latex-extra
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- latex-cjk-all
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- latex-xcolor
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- latex-ucs
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- latex-ucs-doc
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- latex-ucs-utils
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- latex-ucs-extra
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- latex-ucs-extra-doc
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- latex-ucs-extra-utils
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- latex-ucs-extra-extra
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- latex-ucs-extra-extra-doc
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- latex-ucs-extra-extra-utils

‎CHANGELOG.md‎

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# Changelog
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All notable changes to this project will be documented in this file.
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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
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and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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## [Unreleased]
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### Added
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- Initial project setup with basic structure
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- GitHub Actions workflows for testing and deployment
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- Sphinx documentation setup
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- Contribution guidelines and code of conduct
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- PyPI packaging configuration
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### Changed
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- Updated project metadata and dependencies
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- Improved code organization and documentation
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### Fixed
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- Various bug fixes and improvements
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## [0.1.0] - 2024-06-03
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### Added
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- Initial release of fma_ions
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- Basic functionality for Frequency Map Analysis of ion beams
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- Support for CERN accelerators (SPS, PS, LEIR)
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- GPU acceleration support
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- Documentation and examples

‎CODE_OF_CONDUCT.md‎

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# Contributor Covenant Code of Conduct
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## Our Pledge
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In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to make participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, gender identity and expression, level of experience, nationality, personal appearance, race, religion, or sexual identity and orientation.
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## Our Standards
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Examples of behavior that contributes to creating a positive environment include:
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* Using welcoming and inclusive language
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* Being respectful of differing viewpoints and experiences
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* Gracefully accepting constructive criticism
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* Focusing on what is best for the community
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* Showing empathy towards other community members
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Examples of unacceptable behavior by participants include:
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* The use of sexualized language or imagery and unwelcome sexual attention or advances
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* Trolling, insulting/derogatory comments, and personal or political attacks
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* Public or private harassment
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* Publishing others' private information, such as a physical or electronic address, without explicit permission
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* Other conduct which could reasonably be considered inappropriate in a professional setting
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## Our Responsibilities
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Project maintainers are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior.
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Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful.
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## Scope
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This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the project or its community. Examples of representing a project or community include using an official project e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event. Representation of a project may be further defined and clarified by project maintainers.
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## Enforcement
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Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team at [INSERT EMAIL ADDRESS]. All complaints will be reviewed and investigated and will result in a response that is deemed necessary and appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately.
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Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project's leadership.
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## Attribution
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This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, available at [http://contributor-covenant.org/version/1/4][version]
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[homepage]: http://contributor-covenant.org
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[version]: http://contributor-covenant.org/version/1/4/

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