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Merge pull request #324 from astro-informatics/automatic_release
Automatic release implementation plus add new papers to readme
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‎.github/workflows/build.yml‎

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# Adapted from example at
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# https://github.com/pypa/cibuildwheel/blob/0319c431dedc020eb/examples/github-deploy.yml
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#
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# Original license:
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#
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# This project is licensed under the 'BSD 2-clause license'.
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#
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# Copyright (c) 2017-2023, Joe Rickerby and contributors. All rights reserved.
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#
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# Redistribution and use in source and binary forms, with or without
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# modification, are permitted provided that the following conditions are met:
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#
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# 1. Redistributions of source code must retain the above copyright notice, this
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# list of conditions and the following disclaimer.
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#
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# 2. Redistributions in binary form must reproduce the above copyright notice,
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# this list of conditions and the following disclaimer in the documentation
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# and/or other materials provided with the distribution.
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#
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# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
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# FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
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# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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name: Build (and upload to PyPI for published releases)
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on:
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workflow_dispatch:
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pull_request:
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push:
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branches:
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- main
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release:
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types:
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- published
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jobs:
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build_wheels:
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name: Build wheels on ${{ matrix.os }}
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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os: [ubuntu-latest, macos-latest]
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steps:
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- uses: actions/checkout@v5.0.0
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with:
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fetch-depth: 0
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fetch-tags: true
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- name: Build wheels
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uses: pypa/cibuildwheel@v3.1.4
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- uses: actions/upload-artifact@v4
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with:
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name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
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path: ./wheelhouse/*.whl
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build_sdist:
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name: Build source distribution
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v5.0.0
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with:
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fetch-depth: 0
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fetch-tags: true
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- name: Build sdist
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run: pipx run build --sdist
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- uses: actions/upload-artifact@v4
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with:
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name: cibw-sdist
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path: dist/*.tar.gz
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upload_test_pypi:
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needs: [build_wheels, build_sdist]
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runs-on: ubuntu-latest
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environment: test-pypi
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permissions:
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id-token: write
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if: |
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(github.event_name == 'release' && github.event.action == 'published') ||
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(github.event_name == 'push' && github.ref == 'refs/heads/main')
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steps:
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- uses: actions/download-artifact@v5
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with:
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# Unpack all CIBW artifacts (wheels) into dist/
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# pypa/gh-action-pypi-publish action uploads contents of dist/ unconditionally
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pattern: cibw-*
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path: dist
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merge-multiple: true
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# Try publishing to Test PyPI first - if there are issues this should
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# cause job to fail before attempting to publish on PyPI itself
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- name: Publish package distribution to Test PyPI
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uses: pypa/gh-action-pypi-publish@release/v1
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with:
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repository-url: https://test.pypi.org/legacy/
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verbose: true
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upload_pypi:
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needs: [build_wheels, build_sdist, upload_test_pypi]
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runs-on: ubuntu-latest
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environment: pypi
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permissions:
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id-token: write
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if: github.event_name == 'release' && github.event.action == 'published'
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steps:
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- uses: actions/download-artifact@v5
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with:
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pattern: cibw-*
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path: dist
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merge-multiple: true
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- name: Publish package distribution to PyPI
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uses: pypa/gh-action-pypi-publish@release/v1

‎.github/workflows/python.yml‎ renamed to ‎.github/workflows/tests.yml‎

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‎.gitignore‎

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dist/
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harmonic.egg-info/
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harmonic/examples/data/NUTS
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harmonic/_version.py

‎README.rst‎

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:target: https://arxiv.org/abs/2307.00048
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.. |arxiv4| image:: http://img.shields.io/badge/arXiv-2405.05969-orange.svg?style=flat
2020
:target: https://arxiv.org/abs/2405.05969
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.. |arxiv5| image:: http://img.shields.io/badge/arXiv-2410.21076-orange.svg?style=flat
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:target: https://arxiv.org/abs/2410.21076
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.. |arxiv6| image:: http://img.shields.io/badge/arXiv-2506.04339-orange.svg?style=flat
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:target: https://arxiv.org/abs/2506.04339
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.. .. image:: https://img.shields.io/pypi/pyversions/harmonic.svg
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.. :target: https://pypi.python.org/pypi/harmonic/
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|github| |tests| |docs| |codecov| |pypi| |licence| |arxiv1| |arxiv2| |arxiv3| |arxiv4|
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|github| |tests| |docs| |codecov| |pypi| |licence| |arxiv1| |arxiv2| |arxiv3| |arxiv4| |arxiv5| |arxiv6|
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|logo|
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:width: 90
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=================================================================================================================
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``harmonic`` is an open source, well tested and documented Python implementation of the *learnt harmonic mean estimator* (`McEwen et al. 2021 <https://arxiv.org/abs/2111.12720>`_) to compute the marginal likelihood (Bayesian evidence), required for Bayesian model selection.
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``harmonic`` is an open source, well tested and documented Python implementation of the *learned harmonic mean estimator* (`McEwen et al. 2021 <https://arxiv.org/abs/2111.12720>`_) to compute the marginal likelihood (Bayesian evidence), required for Bayesian model selection.
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For an accessible overview of the *learnt harmonic mean estimator* please see this `Towards Data Science article <https://towardsdatascience.com/learnt-harmonic-mean-estimator-for-bayesian-model-selection-47258bb0fc2e>`_.
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For an accessible overview of the *learned harmonic mean estimator* please see this `Towards Data Science article <https://towardsdatascience.com/learnt-harmonic-mean-estimator-for-bayesian-model-selection-47258bb0fc2e>`_.
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While ``harmonic`` requires only posterior samples, and so is agnostic to the technique used to perform Markov chain Monte Carlo (MCMC) sampling, ``harmonic`` works well with MCMC sampling techniques that naturally provide samples from multiple chains by their ensemble nature, such as affine invariant ensemble samplers. For instance, ``harmonic`` can be used with the popular `emcee <https://github.com/dfm/emcee>`_ code implementing the affine invariant sampler of `Goodman & Weare (2010) <https://cims.nyu.edu/~weare/papers/d13.pdf>`_, or the `NumPyro <https://github.com/pyro-ppl/numpyro>`_ code implementing various MCMC algorithms.
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year = {2023}
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}
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Please *also* cite `Lin et al. (2025) <https://arxiv.org/abs/2506.04339>`_ if using the Savage-Dickey density ratio estimation.
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A BibTeX entry for the paper is:
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.. code-block::
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@article{spurio-mancini:harmonic_sddr,
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title={{S}avage-{D}ickey density ratio estimation with normalizing flows for {B}ayesian model comparison},
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author={Kiyam Lin and Alicja Polanska and Davide Piras and Alessio Spurio Mancini and Jason D. McEwen},
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year={2025},
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eprint={2506.04339},
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archivePrefix={arXiv},
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primaryClass={astro-ph.CO},
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url={https://arxiv.org/abs/2506.04339},
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}
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License
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=======

‎pyproject.toml‎

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[build-system]
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requires = ["setuptools", "wheel", "numpy", "Cython"]
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build-backend = "setuptools.build_meta"
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requires = ["setuptools", "setuptools-scm", "wheel", "numpy", "Cython"]
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build-backend = "setuptools.build_meta"
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[tool.setuptools_scm]
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local_scheme = "no-local-version"
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write_to = "harmonic/_version.py"

‎requirements/requirements-core.txt‎

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numpy
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setuptools==68.0.0
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setuptools-scm
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wheel==0.41.0
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cython>=0.29.30
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ipython>=8.4.0

‎setup.py‎

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setup(
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classifiers=[
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"Programming Language :: Python :: 3.9",
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"Programming Language :: Python :: 3.10",
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"Programming Language :: Python :: 3.11",
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"Programming Language :: Python :: 3.12",
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"Programming Language :: Python :: 3.13",
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"Operating System :: OS Independent",
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"Intended Audience :: Developers",
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"Intended Audience :: Science/Research",
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],
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python_requires='>=3.11, <3.14',
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name="harmonic",
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version="1.3.0",
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prefix=".",
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url="https://github.com/astro-informatics/harmonic",
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author="Jason D. McEwen, Alicja Polanska, Christopher G. R. Wallis, Matthew A. Price, Matthew M. Docherty & Contributors",
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author="Jason D. McEwen, Alicja Polanska, Christopher G. R. Wallis, Matthew A. Price, Matthew M. Docherty, Kiyam Lin, Zixiao Hu & Contributors",
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author_email="jason.mcewen@ucl.ac.uk",
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license="GNU General Public License v3 (GPLv3)",
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install_requires=required,
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include_package_data=True,
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package_data={"harmonic": ["default-logging-config.yaml"]},
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cmdclass={"build_ext": build_ext},
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dynamic = ["version",],
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ext_modules=cythonize(
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[
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Extension(

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