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Update the Readme (#301)
* Add badges * Chnage format and add badges * organise badges in line * add the short description * add usefull link * improve the short description * Add section Installation * Add section for the contribution * add conect us section * improve comments * Complete Acknowledgement section * Add section for citation * change subparagraph call * Add quick line for developement * Correct english * include a new file * fix some code example * fix some style * fix format * fix format * fix format * fix error of change extension of README * fix format * add the file how to contribute * fix error and add image * fix contribution * Update README.rst Co-authored-by: bthirion <[email protected]> * fix format in pyproject * Add angel as mainteners * Fix name of Angel * Fix for PR * fix error * change name of main workflow * Modify the badges * remove section license * remane main work flow * ange badge link to ci * move section quick start to a new file * include Contribution in documentation * fix bugs * fix error * improve contribution file * replace the file to the rigth place * Improve CONTRIBUTING --------- Co-authored-by: bthirion <[email protected]>
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‎.github/workflows/main_workflow.yml‎ renamed to ‎.github/workflows/ci.yml‎

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# Management of the action do made during a pull request
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name: 'Main_workflow'
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name: 'CI'
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on:
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pull_request_target:
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# Using 'pull_request_target' instead of 'pull_request':

‎CONTRIBUTING.rst‎

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.. ## for plotting and for examples
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#TODO Need to be updated if it's necessary
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.. |MatplotlibMinVersion| replace:: 3.9.0
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.. |SeabornMinVersion| replace:: 0.9.0
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Quick start for contributing
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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Source code
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"""""""""""
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You can check out the latest sources with the command:
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.. code-block:: sh
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git clone https://github.com/mind-inria/hidimstat.git
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Test suite
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""""""""""
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For testing, we recommend you install the test dependencies with pip:
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.. code-block:: sh
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pip install hidimstat[test]
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This will install ``pytest`` and the following extensions:
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``pytest-cov``, ``pytest-randomly``, ``pytest-xdist``, ``pytest-html``,
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``pytest-timeout``, ``pytest-durations``
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After this installation, you can launch the test suite:
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.. code-block:: sh
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pytest test
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Examples
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""""""""
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To run the examples, we recommend you install the example dependencies with pip:
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.. code-block:: sh
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pip install hidimstat[example]
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For running the examples, it's necessary to install Matplotlib >= |MatplotlibMinVersion| and seaborn >=
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|SeabornMinVersion|.
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| After this installation, you can run any example in the `examples <https://github.com/mind-inria/hidimstat/tree/main/examples>`_ folder.
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| Or you can download some of them from the `documentation <https://hidimstat.github.io/dev/auto_examples/index.html>`_.
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Documentation
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"""""""""""""
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The documentation is built with Sphinx. We recommend you install the documentation dependencies with pip:
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.. code-block:: sh
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pip install hidimstat[doc]
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After this installation, you can build the documentation from the source using the Makefile in doc_conf:
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.. code-block:: sh
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make html
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**For more information**, look at the `developer documentation <https://hidimstat.github.io/dev/dev/index.html>`_

‎README.md‎

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‎README.rst‎

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.. ## Define a hard line break in HTML
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.. |br| raw:: html
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<br />
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.. # Add the reference for the badges
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.. ## Reference to the CI status
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.. |Linter&Tests| image:: https://github.com/mind-inria/hidimstat/actions/workflows/ci.yml/badge.svg?branch=main
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:target: https://github.com/mind-inria/hidimstat/actions/workflows/ci.yml?query=branch%3Amain
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.. |CircleCI/Documentation| image:: https://circleci.com/gh/mind-inria/hidimstat.svg?style=shield
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:target: https://circleci.com/gh/mind-inria/hidimstat?branch=main
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.. |CodeCov| image:: https://codecov.io/github/mind-inria/hidimstat/branch/main/graph/badge.svg?token=O1YZDTFTNS
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:target: https://codecov.io/github/mind-inria/hidimstat
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.. ## Distribution python
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.. |PyPi| image:: https://img.shields.io/pypi/v/hidimstat.svg
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:target: https://pypi.org/project/hidimstat/
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.. |PyPi_download| image:: https://img.shields.io/pypi/dm/hidimstat
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:target: https://pypi.org/project/hidimstat/
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.. |PythonVersion| image:: https://img.shields.io/pypi/pyversions/hidimstat.svg?color=informational
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:target: https://pypi.org/project/hidimstat/
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.. |Latest release| image:: https://img.shields.io/github/release/mind-inria/hidimstat.svg?color=brightgreen&label=latest%20release
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.. ## Additional badge
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.. |License| image:: https://img.shields.io/github/license/mind-inria/hidimstat
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:target: https://opensource.org/license/bsd-3-clause
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.. |Black| image:: https://img.shields.io/badge/code%20style-black-000000.svg
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:target: https://github.com/psf/black
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.. # Add minimal dependecy of the main packages
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## This need to update in same time that pyproject.toml
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.. |PythonMinVersion| replace:: 3.9
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.. |JoblibMinVersion| replace:: 1.2
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.. |NumPyMinVersion| replace:: 1.25
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.. |PandasMinVersion| replace:: 2.0
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.. |SklearnMinVersion| replace:: 1.4
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.. |SciPyMinVersion| replace:: 1.6
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.. ## for plotting and for examples
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.. |MatplotlibMinVersion| replace:: 3.9.0
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.. |SeabornMinVersion| replace:: 0.9.0
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=================================================================
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HiDimStat: High-dimensional statistical inference tool for Python
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=================================================================
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.. # Add the different badge
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|Linter&Tests| |CircleCI/Documentation| |CodeCov| |Black|
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|PyPi| |PyPi_download| |PythonVersion| |Latest release|
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|License|
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.. # Short description of the library
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The HiDimStat package provides statistical inference methods to solve the problem
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of variable importance evaluation in the context of predictive model using high-dimensional and spatially structured data.
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.. # Add usefull links
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If you like the package, spread the word and ⭐ our `official repository
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<https://github.com/mind-inria/hidimstat>`_!
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Visit our website, https://hidimstat.github.io/, for more information.
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..
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## TODO: Add short citation when this will be ready
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If you use HiDimStat for your published research, we kindly ask you to :ref:`cite<citation>` our article:
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short reference
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Find your important variables in your data with the help of
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`our examples <https://hidimstat.github.io/dev/auto_examples/index.html>`_.
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If you have any problems, please report them to the `GitHub issue tracker <https://github.com/mind-inria/hidimstat/issues>`_
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or contribute to the library by opening a pull request.
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Installation
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------------
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Dependencies
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^^^^^^^^^^^^
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.. # Add dependency of the project
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TODO Need to match with pyproject.toml
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HiDimStat requires:
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- Python (>= |PythonMinVersion|)
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- joblib (>= |JoblibMinVersion|)
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- NumPy (>= |NumPyMinVersion|)
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- Pandas (>= |PandasMinVersion|)
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- Scikit-learn (>= |SklearnMinVersion|)
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- SciPy (>= |SciPyMinVersion|)
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HiDimStat's plotting capabilities require Matplotlib (>= |MatplotlibMinVersion|).
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To run the examples, Matplotlib (>= |MatplotlibMinVersion|) and seaborn (>=
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|SeabornMinVersion|) are required.
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User installation
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^^^^^^^^^^^^^^^^^
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.. # Add the instruction for installation
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TODO add conda when it will be accessible
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HiDimStat can easily be installed via ``pip``. For more installation information,
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see the `installation instructions <https://hidimstat.github.io/dev/index.html#installation>`_.
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::
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pip install -U hidimstat
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Contribute
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----------
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.. # Add short discription for contribution to the library
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The best way to support the development of HiDimStat is to spread the word!
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HiDimStat aims to be supported by an active community, and we welcome
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contributions to our code and documentation.
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For bug reports, feature requests, documentation improvements, or other issues,
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you can create a `GitHub issue <https://github.com/mind-inria/hidimstat/issues>`_.
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If you want to contribute directly to the library, check the
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`how to contribute <https://hidimstat.github.io/dev/how_to_contribute.html/>`_ page
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on the website for more information.
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Contact us
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----------
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.. # Add a way to contact maintainers
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TODO this needs to be updated when there is a change of maintainers
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Currently, this library is supported by the `INRIA <https://www.inria.fr/en>`_
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team `MIND <https://www.inria.fr/fr/mind>`_. |br|
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If you want to report a problem or suggest an enhancement, we would love for you
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to `open an issue <https://github.com/mind-inria/hidimstat/issues/new>`_ at
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this GitHub repository so we can address it quickly. |br|
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For less formal discussions or to exchange ideas, you can contact the main
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contributors:
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+-------------------+-------------------+-------------------+-------------------+
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| Lionel Kusch | Bertrand Thirion | Joseph Paillard | Angel Reyero Lobo |
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+-------------------+-------------------+-------------------+-------------------+
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| |avatar LK| | |avatar BT| | |avatar JP| | |avatar AR| |
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+-------------------+-------------------+-------------------+-------------------+
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.. |avatar LK| image:: https://avatars.githubusercontent.com/u/17182418?v=4
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:target: https://github.com/lionelkusch
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.. |avatar BT| image:: https://avatars.githubusercontent.com/u/234454?v=4
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:target: https://github.com/bthirion
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.. |avatar JP| image:: https://avatars.githubusercontent.com/u/56166877?v=4
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:target: https://github.com/jpaillard
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.. |avatar AR| image:: https://avatars.githubusercontent.com/u/79699169?v=4
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:target: https://github.com/AngelReyero
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Citation
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--------
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If you use a HiDimStat method for your research, you'll find the associated
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reference paper in the method description, and we recommend that you cite it.
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..
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TODO add the section for citing the library once a Zenodo repository is made
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or a paper is published.
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If you publish a paper using HiDimStat, please contact us or open an issue!
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We would love to hear about your work and help you promote it.
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Acknowledgments
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---------------
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This project has been funded by `Labex DigiCosme <https://anr.fr/ProjetIA-11-LABX-0045>`_
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(ANR-11-LABEX-0045-DIGICOSME) as part of the program
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`Investissement d’Avenir <https://anr.fr/ProjetIA-11-IDEX-0003>`_
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(ANR-11-IDEX-0003-02), by the `Fast Big project <https://anr.fr/Projet-ANR-17-CE23-0011>`_
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(ANR-17-CE23-0011), by the `KARAIB AI Chair <https://anr.fr/Projet-ANR-20-CHIA-0025>`_
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(ANR-20-CHIA-0025-01), and by the `VITE project <https://anr.fr/Projet-ANR-23-CE23-0016>`_ (ANR-23-CE23-0016).
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This study has also been supported by the European Union’s Horizon 2020 research and innovation program
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as part of the program `Human Brain Project SGA3 <https://cordis.europa.eu/project/id/945539>`_
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(Grant Agreement No. 945539) and `EBRAIN-Health <https://cordis.europa.eu/project/id/101058516>`_
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(Grant Agreement No. 101058516).

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