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Add tutorials/extension to docs nav bar, create pip.txt (#128)
* cap in description * Add news for doc nav * Install pip with pip.txt, conda with conda.txt * Overall doc paths and nav * Fix api doc table of content order * Add news on adding tutorials
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Diff for: ‎README.rst

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.. |Tracking| image:: https://img.shields.io/badge/issue_tracking-github-blue
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:target: https://github.com/diffpy/diffpy.srmise/issues
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implementation of the ParSCAPE algorithm for peak extraction from atomic pair distribution functions (PDFs)
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Implementation of the ParSCAPE algorithm for peak extraction from atomic pair distribution functions (PDFs)
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SrMise is an implementation of the `ParSCAPE algorithm
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<https://dx.doi.org/10.1107/S2053273315005276>`_ for peak extraction from

Diff for: ‎doc/source/extending.rst

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.. _extending-srmise:
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.. index:: extending-srmise
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===================
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Extending SrMise
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which need to be implemented are summarized in the source code.
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.. literalinclude:: ../../../diffpy/srmise/baselines/base.py
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.. literalinclude:: ../../src/diffpy/srmise/baselines/base.py
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:pyobject: BaselineFunction
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:end-before: __init__
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Diff for: ‎doc/source/index.rst

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Installation
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============
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See the `README <https://github.com/diffpy/diffpy.srmise#installation>`_
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See the `README <https://github.com/diffpy/diffpy.srmise/blob/main/README.rst>`_
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file included with the distribution.
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=================
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Table of contents
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=================
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.. toctree::
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:maxdepth: 1
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:titlesonly:
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license
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release
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tutorial/index
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extending
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Package API <api/diffpy.srmise>
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release
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license
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=======
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Indices

Diff for: ‎doc/source/license.rst

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=============================
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BSD 3-Clause License
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Copyright (c) 2024, The Trustees of Columbia University in
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the City of New York.
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All Rights Reserved.
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Copyright 2014-2015, Board of Trustees of Michigan State University
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Copyright 2016-2024, The Trustees of Columbia University in the City of New York.
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All rights reserved.
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If you use this program to do productive scientific research that
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leads to publication, we ask that you acknowledge use of the
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program by citing the following paper in your publication:
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L. Granlund, S.J.L. Billinge, P.M. Duxbury, Algorithm for
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systematic peak extraction from atomic pair distribution
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functions, Acta Crystallographica A 71(4), 392-409 (2015).
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doi:10.1107/S2053273315005276
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For more information please visit the diffpy web-page at
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http://www.diffpy.org
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or email Luke Granlund at [email protected], or Prof. Simon
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Billinge at [email protected].
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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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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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3. Neither the name of the copyright holder nor the names of its
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contributors may be used to endorse or promote products derived from
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this software without specific prior written permission.
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3. Neither the name of the copyright holder nor the names of its contributors
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may be used to endorse or promote products derived from this software
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without specific prior written permission.
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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

Diff for: ‎doc/source/tutorial/abbreviations.txt

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.. |tar.gz| replace:: :source-release:`tar.gz`
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.. Image substitutions
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.. |images/extract_single_peak1.png| image:: ../../../examples/images/extract_single_peak1.png
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.. |images/extract_single_peak2.png| image:: ../../../examples/images/extract_single_peak2.png
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.. |images/extract_single_peak3.png| image:: ../../../examples/images/extract_single_peak3.png
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.. |images/parameter_summary1.png| image:: ../../../examples/images/parameter_summary1.png
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.. |images/parameter_summary2.png| image:: ../../../examples/images/parameter_summary2.png
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.. |images/parameter_summary3.png| image:: ../../../examples/images/parameter_summary3.png
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.. |images/parameter_summary4.png| image:: ../../../examples/images/parameter_summary4.png
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.. |images/fit_initial1.png| image:: ../../../examples/images/fit_initial1.png
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.. |images/fit_initial2.png| image:: ../../../examples/images/fit_initial2.png
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.. |images/query_results1.png| image:: ../../../examples/images/query_results1.png
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.. |images/query_results2.png| image:: ../../../examples/images/query_results2.png
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.. |images/query_results3.png| image:: ../../../examples/images/query_results3.png
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.. Links to non-tutorial parts of documentation.
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.. |Extending SrMise| replace:: :ref:`extending-srmise`
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.. |images/extract_single_peak1.png| ge:: ../../examples/images/extract_single_peak1.png
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.. |images/extract_single_peak2.png| image:: ../../examples/images/extract_single_peak2.png
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.. |images/extract_single_peak3.png| image:: ../../examples/images/extract_single_peak3.png
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.. |images/parameter_summary1.png| image:: ../../examples/images/parameter_summary1.png
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.. |images/parameter_summary2.png| image:: ../../examples/images/parameter_summary2.png
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.. |images/parameter_summary3.png| image:: ../../examples/images/parameter_summary3.png
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.. |images/parameter_summary4.png| image:: ../../examples/images/parameter_summary4.png
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.. |images/fit_initial1.png| image:: ../../examples/images/fit_initial1.png
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.. |images/fit_initial2.png| image:: ../../examples/images/fit_initial2.png
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.. |images/query_results1.png| image:: ../../examples/images/query_results1.png
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.. |images/query_results2.png| image:: ../../examples/images/query_results2.png
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.. |images/query_results3.png| image:: ../../examples/images/query_results3.png
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.. External links
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.. _ParSCAPE algorithm: https://dx.doi.org/10.1107/S2053273315005276
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.. |pi/Qmax| replace:: π/Q\ :sub:`max`
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.. Links to PDF information defined in sample_links.txt
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.. |Extending SrMise| replace:: :ref:`extending-srmise`

Diff for: ‎doc/source/tutorial/extract_single_peak.rst

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.. include:: sample_links.txt
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.. include:: ../../../examples/README
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.. include:: ../../examples/README.rst
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:start-after: ~Example 1~
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Script (extract_single_peak.py)
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-------------------------------
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.. literalinclude:: ../../../examples/extract_single_peak.py
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.. literalinclude:: ../../examples/extract_single_peak.py

Diff for: ‎doc/source/tutorial/fit_initial.rst

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.. include:: sample_links.txt
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.. include:: ../../../examples/README
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.. include:: ../../examples/README.rst
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:start-after: ~Example 3~
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Script (fit_initial.py)
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---------------------------
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.. literalinclude:: ../../../examples/fit_initial.py
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.. literalinclude:: ../../examples/fit_initial.py

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.. include:: abbreviations.txt
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.. _tutorial:
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===================
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Tutorial
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===================
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.. include:: ../../../examples/README
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.. include:: ../../examples/README.rst
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:end-before: ~List of Examples~
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.. Replace bare list from README
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Examples
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========
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:maxdepth: 1
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extract_single_peak.rst
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parameter_summary.rst
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fit_initial.rst
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query_results.rst
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multimodel_known_uncertainties.rst
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multimodel_unknown_uncertainties.rst
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extract_single_peak
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parameter_summary
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fit_initial
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query_results
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multimodel_known_uncertainties
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multimodel_unknown_uncertainties
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.. Now add information about the samples
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.. include:: ../../../examples/README
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.. include:: ../../examples/README
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:start-after: ~PDF Info~

Diff for: ‎doc/source/tutorial/multimodel_known_uncertainties.rst

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.. include:: ../../examples/README.rst
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Extraction Script (multimodel_known_dG1.py)
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.. literalinclude:: ../../examples/multimodel_known_dG1.py
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.. literalinclude:: ../../../examples/multimodel_known_dG2.py
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.. literalinclude:: ../../examples/multimodel_known_dG2.py

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.. literalinclude:: ../../examples/multimodel_unknown_dG2.py

Diff for: ‎doc/source/tutorial/parameter_summary.rst

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.. literalinclude:: ../../examples/parameter_summary.py

Diff for: ‎doc/source/tutorial/query_results.rst

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.. literalinclude:: ../../examples/query_results.py

Diff for: ‎news/add-nav.rst

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**Added:**
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* <news item>
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**Changed:**
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* <news item>
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**Deprecated:**
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* <news item>
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**Removed:**
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* <news item>
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**Fixed:**
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* add pip dependencies under pip.txt, conda dependencies under conda.txt
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* add tutorial and extending examples to docs
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**Security:**
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* <news item>

Diff for: ‎pyproject.toml

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dependencies = {file = ["requirements/run.txt"]}
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dependencies = {file = ["requirements/pip.txt"]}
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[tool.black]
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line-length = 115

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Diff for: ‎requirements/pip.txt

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numpy
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scipy
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matplotlib

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