diff --git a/AUTHORS.rst b/AUTHORS.rst index c942b8dd..99b148ea 100644 --- a/AUTHORS.rst +++ b/AUTHORS.rst @@ -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, diff --git a/LICENSE.rst b/LICENSE.rst index 0cebd08f..51d7148a 100644 --- a/LICENSE.rst +++ b/LICENSE.rst @@ -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 sb2896@columbia.edu + For more information please visit the project web-page: + https://www.diffpy.org + or email Prof. Simon Billinge at sb2896@columbia.edu -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. diff --git a/README.rst b/README.rst index b9d7da0a..3f1a9a10 100644 --- a/README.rst +++ b/README.rst @@ -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 `_. -* 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 `_. -We recommend to use `Anaconda Python `_ -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 ------------ @@ -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 `_. -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 @@ -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 `_. Once installed, ``cd`` into your ``diffpy.pdfgui`` directory -and run the following :: +`GitHub `_. Once installed, ``cd`` into your ``diffpy.pdfgui`` +directory and run the following :: pip install . Support and Contribute ---------------------- -`Diffpy user group `_ 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 `_ 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 `_ and/or `submit a fix as a PR `_. You can also post it to the `Diffpy user group `_. +If you see a bug or want to request a feature, please `report it as an issue `_ +and/or `submit a fix as a PR `_. You can also post it to the +`Diffpy user group `_. Feel free to fork the project and contribute. To install diffpy.pdfgui in a development mode, with its sources being directly used by Python @@ -145,4 +139,5 @@ Before contribuing, please read our `Code of Conduct `_ or email Prof. Simon Billinge at sb2896@columbia.edu. +For more information on diffpy.pdfgui please visit the project `web-page `_ or email Prof. Simon Billinge +at sb2896@columbia.edu.