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Use the original license
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Tieqiong Aug 20, 2024
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Tieqiong Aug 20, 2024
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14 changes: 7 additions & 7 deletions AUTHORS.rst
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Expand Up @@ -15,17 +15,17 @@ This code was developed as part of the DiffPy project to create python
modules for structure investigations from diffraction data. The main
contributors to this package were

Chris Farrow
Jiwu Liu
Pavol Juhas
Chris Farrow,
Jiwu Liu,
Pavol Juhas,
Dmitriy Bryndin

Other current and former contributors of the DiffPy project include

Simon Billinge
Chris Farrow
Emil Bozin
Wenduo Zhou
Simon Billinge,
Chris Farrow,
Emil Bozin,
Wenduo Zhou,
Peng Tian

The DiffPy team is part of the Billinge Group at Columbia University in New York,
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130 changes: 67 additions & 63 deletions LICENSE.rst
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@@ -1,76 +1,80 @@
Copyright (c) 2024, The Trustees of Columbia University
in the City of New York.
All rights reserved.
.. code-block:: text

This software was originally developed by the Billinge group as part
of the Distributed Data Analysis of Neutron Scattering Experiments
(DANSE) project funded by the US National Science Foundation under
grant DMR-0520547. Developments of PDFfit2 were funded by NSF grant
DMR-0304391 in the Billinge group, and with support from Michigan State
University and Columbia University. Any opinions, findings, and conclusions
or recommendations expressed in this material are those of the author(s)
and do not necessarily reflect the views of the respective funding bodies.
Subsequent development was done in the Billinge group at Columbia University
and then in collaboration between the Billinge group at Columbia and Pavol
Juhas at Brookhaven National Laboratory. Moving forward, PDFgui will be
maintained as a community project with contributions welcomed from many people.
This software was originally developed by the Billinge group as part
of the Distributed Data Analysis of Neutron Scattering Experiments
(DANSE) project funded by the US National Science Foundation under
grant DMR-0520547. Developments of PDFfit2 were funded by NSF grant
DMR-0304391 in the Billinge group, and with support from Michigan State
University and Columbia University. Any opinions, findings, and conclusions
or recommendations expressed in this material are those of the author(s)
and do not necessarily reflect the views of the respective funding bodies.
Subsequent development was done in the Billinge group at Columbia University
and then in collaboration between the Billinge group at Columbia and Pavol
Juhas at Brookhaven National Laboratory. Moving forward, PDFgui will be
maintained as a community project with contributions welcomed from many people.

If you use this program to do productive scientific research that leads
to publication, we ask that you acknowledge use of the program by citing
the following paper in your publication:
If you use this program to do productive scientific research that leads
to publication, we ask that you acknowledge use of the program by citing
the following paper in your publication:

C. L. Farrow, P. Juhas, J. W. Liu, D. Bryndin, E. S. Bozin,
J. Bloch, Th. Proffen and S. J. L. Billinge, PDFfit2 and
PDFgui: computer programs for studying nanostructure in
crystals, J. Phys.: Condens. Matter 19, 335219 (2007)
C. L. Farrow, P. Juhas, J. W. Liu, D. Bryndin, E. S. Bozin,
J. Bloch, Th. Proffen and S. J. L. Billinge, PDFfit2 and
PDFgui: computer programs for studying nanostructure in
crystals, J. Phys.: Condens. Matter 19, 335219 (2007)

Up to the release 1.1.2 (February 2017) the copyright was held by
the institutions that hosted the work as follows:
Copyright 2006-2007, Board of Trustees of Michigan State University,
Copyright 2008-2012, Board of Trustees of Columbia University in the
city of New York.
Copyright 2013, Brookhaven National Laboratory (Copyright holder
indicated in each source file).
Up to the release 1.1.2 (February 2017) the copyright was held by
the institutions that hosted the work as follows:
Copyright 2006-2007, Board of Trustees of Michigan State University,
Copyright 2008-2012, Board of Trustees of Columbia University in the
city of New York.
Copyright 2013, Brookhaven National Laboratory (Copyright holder
indicated in each source file).

As of February 2017, and the 1.1.2 release, PDFgui has moved to a shared copyright model.
As of February 2017, and the 1.1.2 release, PDFgui has moved to a shared copyright model.

PDFgui uses a shared copyright model. Each contributor maintains copyright over their
contributions to PDFgui. But, it is important to note that these contributions are
typically only changes to the repositories. Thus, the PDFgui source code, in its entirety,
is not the copyright of any single person or institution. Instead, it is the collective
copyright of the entire PDFgui Development Team. If individual contributors want to
maintain a record of what changes/contributions they have specific copyright on, they
should indicate their copyright in the commit message of the change, when they commit
the change to one of the PDFgui repositories.
PDFgui uses a shared copyright model. Each contributor maintains copyright over their
contributions to PDFgui. But, it is important to note that these contributions are
typically only changes to the repositories. Thus, the PDFgui source code, in its entirety,
is not the copyright of any single person or institution. Instead, it is the collective
copyright of the entire PDFgui Development Team. If individual contributors want to
maintain a record of what changes/contributions they have specific copyright on, they
should indicate their copyright in the commit message of the change, when they commit
the change to one of the PDFgui repositories.

The PDFgui Development Team is the set of all contributors to the PDFgui project.
A full list can be obtained from the git version control logs.
The PDFgui Development Team is the set of all contributors to the PDFgui project.
A full list can be obtained from the git version control logs.

For more information please visit the project web-page:
https://www.diffpy.org
or email Prof. Simon Billinge at [email protected]
For more information please visit the project web-page:
https://www.diffpy.org
or email Prof. Simon Billinge at [email protected]

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions
are met:

1. Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.

2. Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer in the
documentation and/or other materials provided with the distribution.

3. Neither the name of the copyright holder nor the names of its contributors
may be used to endorse or promote products derived from this software
without specific prior written permission.
* Neither the name of the copyright holder nor the names of its
contributors may be used to endorse or promote products derived from
this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
THIS SOFTWARE IS PROVIDED BY COPYRIGHT HOLDER "AS IS". COPYRIGHT HOLDER
EXPRESSLY DISCLAIMS ANY AND ALL WARRANTIES AND CONDITIONS, EITHER
EXPRESS OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY, TITLE, FITNESS, ADEQUACY OR SUITABILITY
FOR A PARTICULAR PURPOSE, AND ANY WARRANTIES OF FREEDOM FROM
INFRINGEMENT OF ANY DOMESTIC OR FOREIGN PATENT, COPYRIGHTS, TRADE
SECRETS OR OTHER PROPRIETARY RIGHTS OF ANY PARTY. IN NO EVENT SHALL
COPYRIGHT HOLDER BE LIABLE TO ANY PARTY FOR ANY DIRECT, INDIRECT,
INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
THIS SOFTWARE OR RELATING TO THIS AGREEMENT, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.
67 changes: 31 additions & 36 deletions README.rst
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Expand Up @@ -35,45 +35,34 @@
.. |Tracking| image:: https://img.shields.io/badge/issue_tracking-github-blue
:target: https://github.com/diffpy/diffpy.pdfgui/issues

diffpy.pdfgui
========================================================================

Graphical user interface program for structure refinements to atomic
pair distribution function.

For users who do not have the expertise or necessity for command
line analysis, PDFgui is a convenient and easy to use graphical front
end for the PDFfit2 refinement program. It is capable of full-profile
fitting of the atomic pair distribution function (PDF) derived from x-ray
or neutron diffraction data and comes with built in graphical and structure
visualization capabilities.

PDFgui is a friendly interface to the PDFfit2 refinement engine, with many
powerful extensions. To get started, please open the manual from the
help menu and follow the tutorial instructions. A detailed description
is available in the doc/Farrow-jpcm-2007.pdf paper.


Requirements
------------------------------------------------------------------------

PDFgui requires Python 3.8+ or 2.7 and several third-party
libraries that are used by PDFgui and its components.
help menu and follow the tutorial instructions. A detailed description
is available in `this paper <http://dx.doi.org/10.1088/0953-8984/19/33/335219>`_.

* setuptools - tools for installing Python packages
* wxpython - graphical user interface toolkit for Python
* numpy - library for scientific computing with Python
* matplotlib - Python 2D plotting library
* diffpy.pdffit2 - computational engine for PDFgui,
https://github.com/diffpy/diffpy.pdffit2
* diffpy.structure - simple storage and manipulation of atomic
structures, https://github.com/diffpy/diffpy.structure
* diffpy.utils - shared helper utilities for wx GUI,
https://github.com/diffpy/diffpy.utils
For more information about diffpy.pdfgui, please consult our
`online documentation <https://diffpy.github.io/diffpy.pdfgui>`_.

We recommend to use `Anaconda Python <https://www.anaconda.com/download>`_
which allows to conveniently install PDFgui and all its software
dependencies with a single command.
Citation
--------

Please note that the Python3 PDFgui will read .ddp3 files. It is also
possible for it to read .ddp files that were saved by the Python2 PDFgui
but it will sometimes fail to read these. We are working on a solution
that will be available in a future version.
If you use diffpy.pdfgui in a scientific publication, we would like you to
cite this package as

diffpy.pdfgui Package, https://github.com/diffpy/diffpy.pdfgui
C L Farrow, P Juhas, J W Liu, D Bryndin, E S Božin,
J Bloch, Th Proffen and S J L Billinge, PDFfit2 and PDFgui:
computer programs for studying nanostructure in crystals, J. Phys.:
Condens. Matter 19 (2007) 335219. doi:10.1088/0953-8984/19/33/335219

Installation
------------
Expand All @@ -98,7 +87,8 @@ Then, to fully install ``diffpy.pdfgui`` in our active environment, run ::

Another option is to use ``pip`` to download and install the latest release from
`Python Package Index <https://pypi.python.org>`_.
To install using ``pip`` into your ``diffpy.pdfgui_env`` environment, we will also have to install dependencies ::
To install using ``pip`` into your ``diffpy.pdfgui_env`` environment, we will also have to
install dependencies ::

pip install -r https://raw.githubusercontent.com/diffpy/diffpy.pdfgui/main/requirements/run.txt

Expand All @@ -107,17 +97,21 @@ and then install the package ::
pip install diffpy.pdfgui

If you prefer to install from sources, after installing the dependencies, obtain the source archive from
`GitHub <https://github.com/diffpy/diffpy.pdfgui/>`_. Once installed, ``cd`` into your ``diffpy.pdfgui`` directory
and run the following ::
`GitHub <https://github.com/diffpy/diffpy.pdfgui/>`_. Once installed, ``cd`` into your ``diffpy.pdfgui``
directory and run the following ::

pip install .

Support and Contribute
----------------------

`Diffpy user group <https://groups.google.com/g/diffpy-users>`_ is the discussion forum for general questions and discussions about the use of diffpy.pdfgui. Please join the diffpy.pdfgui users community by joining the Google group. The diffpy.pdfgui project welcomes your expertise and enthusiasm!
`Diffpy user group <https://groups.google.com/g/diffpy-users>`_ is the discussion forum for general
questions and discussions about the use of diffpy.pdfgui. Please join the diffpy.pdfgui users community
by joining the Google group. The diffpy.pdfgui project welcomes your expertise and enthusiasm!

If you see a bug or want to request a feature, please `report it as an issue <https://github.com/diffpy/diffpy.pdfgui/issues>`_ and/or `submit a fix as a PR <https://github.com/diffpy/diffpy.pdfgui/pulls>`_. You can also post it to the `Diffpy user group <https://groups.google.com/g/diffpy-users>`_.
If you see a bug or want to request a feature, please `report it as an issue <https://github.com/diffpy/diffpy.pdfgui/issues>`_
and/or `submit a fix as a PR <https://github.com/diffpy/diffpy.pdfgui/pulls>`_. You can also post it to the
`Diffpy user group <https://groups.google.com/g/diffpy-users>`_.

Feel free to fork the project and contribute. To install diffpy.pdfgui
in a development mode, with its sources being directly used by Python
Expand Down Expand Up @@ -145,4 +139,5 @@ Before contribuing, please read our `Code of Conduct <https://github.com/diffpy/
Contact
-------

For more information on diffpy.pdfgui please visit the project `web-page <https://diffpy.github.io/>`_ or email Prof. Simon Billinge at [email protected].
For more information on diffpy.pdfgui please visit the project `web-page <https://diffpy.github.io/>`_ or email Prof. Simon Billinge
at [email protected].
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