From b3ea0ae8a2420db834084637636d107c71df756f Mon Sep 17 00:00:00 2001 From: Tieqiong Zhang Date: Tue, 20 Aug 2024 07:50:28 -0400 Subject: [PATCH 1/2] build doc --- doc/source/api/diffpy.pdfgui.applications.rst | 21 + doc/source/api/diffpy.pdfgui.control.rst | 141 +++++++ .../api/diffpy.pdfgui.example_package.rst | 31 -- doc/source/api/diffpy.pdfgui.gui.design.rst | 10 + doc/source/api/diffpy.pdfgui.gui.rst | 374 ++++++++++++++++++ .../api/diffpy.pdfgui.gui.wxextensions.rst | 61 +++ doc/source/api/diffpy.pdfgui.rst | 26 +- doc/source/index.rst | 61 ++- doc/source/license.rst | 112 ++++-- doc/{TUTORIAL.rst => source/tutorial.rst} | 39 +- 10 files changed, 776 insertions(+), 100 deletions(-) create mode 100644 doc/source/api/diffpy.pdfgui.applications.rst create mode 100644 doc/source/api/diffpy.pdfgui.control.rst delete mode 100644 doc/source/api/diffpy.pdfgui.example_package.rst create mode 100644 doc/source/api/diffpy.pdfgui.gui.design.rst create mode 100644 doc/source/api/diffpy.pdfgui.gui.rst create mode 100644 doc/source/api/diffpy.pdfgui.gui.wxextensions.rst rename doc/{TUTORIAL.rst => source/tutorial.rst} (85%) diff --git a/doc/source/api/diffpy.pdfgui.applications.rst b/doc/source/api/diffpy.pdfgui.applications.rst new file mode 100644 index 00000000..29d9683d --- /dev/null +++ b/doc/source/api/diffpy.pdfgui.applications.rst @@ -0,0 +1,21 @@ +:tocdepth: -1 + +diffpy.pdfgui.applications package +================================== + +.. automodule:: diffpy.pdfgui.applications + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +diffpy.pdfgui.applications.pdfgui module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.applications.pdfgui + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/api/diffpy.pdfgui.control.rst b/doc/source/api/diffpy.pdfgui.control.rst new file mode 100644 index 00000000..89d31f0d --- /dev/null +++ b/doc/source/api/diffpy.pdfgui.control.rst @@ -0,0 +1,141 @@ +:tocdepth: -1 + +diffpy.pdfgui.control package +============================= + +.. automodule:: diffpy.pdfgui.control + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +diffpy.pdfgui.control.pdfcomponent module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.control.pdfcomponent + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.control.constraint module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.control.constraint + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.control.controlerrors module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.control.controlerrors + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.control.pdflist module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.control.pdflist + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.control.pdfguimacros module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.control.pdfguimacros + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.control.calculation module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.control.calculation + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.control.pdfstructure module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.control.pdfstructure + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.control.fitdataset module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.control.fitdataset + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.control.structureviewer module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.control.structureviewer + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.control.plotter module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.control.plotter + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.control.fitstructure module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.control.fitstructure + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.control.fitting module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.control.fitting + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.control.pdfguicontrol module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.control.pdfguicontrol + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.control.parameter module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.control.parameter + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.control.pdfdataset module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.control.pdfdataset + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.control.organizer module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.control.organizer + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/api/diffpy.pdfgui.example_package.rst b/doc/source/api/diffpy.pdfgui.example_package.rst deleted file mode 100644 index 0390b965..00000000 --- a/doc/source/api/diffpy.pdfgui.example_package.rst +++ /dev/null @@ -1,31 +0,0 @@ -.. _example_package documentation: - -|title| -======= - -.. |title| replace:: diffpy.pdfgui.example_package package - -.. automodule:: diffpy.pdfgui.example_package - :members: - :undoc-members: - :show-inheritance: - -|foo| ------ - -.. |foo| replace:: diffpy.pdfgui.example_package.foo module - -.. automodule:: diffpy.pdfgui.example_package.foo - :members: - :undoc-members: - :show-inheritance: - -|bar| ------ - -.. |bar| replace:: diffpy.pdfgui.example_package.bar module - -.. automodule:: diffpy.pdfgui.example_package.foo - :members: - :undoc-members: - :show-inheritance: diff --git a/doc/source/api/diffpy.pdfgui.gui.design.rst b/doc/source/api/diffpy.pdfgui.gui.design.rst new file mode 100644 index 00000000..6f768f65 --- /dev/null +++ b/doc/source/api/diffpy.pdfgui.gui.design.rst @@ -0,0 +1,10 @@ +:tocdepth: -1 + +diffpy.pdfgui.gui.design package +================================ + +.. automodule:: diffpy.pdfgui.gui.design + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/api/diffpy.pdfgui.gui.rst b/doc/source/api/diffpy.pdfgui.gui.rst new file mode 100644 index 00000000..67db606e --- /dev/null +++ b/doc/source/api/diffpy.pdfgui.gui.rst @@ -0,0 +1,374 @@ +:tocdepth: -1 + +diffpy.pdfgui.gui package +========================= + +.. automodule:: diffpy.pdfgui.gui + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + :titlesonly: + + diffpy.pdfgui.gui.design + diffpy.pdfgui.gui.wxextensions + +Submodules +---------- + +diffpy.pdfgui.gui.phaseresultspanel module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.gui.phaseresultspanel + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.gui.tooltips module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.gui.tooltips + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.gui.bondlengthdialog module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.gui.bondlengthdialog + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.gui.datasetresultspanel module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.gui.datasetresultspanel + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.gui.phaseconfigurepanel module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.gui.phaseconfigurepanel + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.gui.supercelldialog module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.gui.supercelldialog + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.gui.sgstructuredialog module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.gui.sgstructuredialog + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.gui.sgconstraindialog module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.gui.sgconstraindialog + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.gui.bondangledialog module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.gui.bondangledialog + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.gui.adddatapanel module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.gui.adddatapanel + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.gui.phaseconstraintspanel module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.gui.phaseconstraintspanel + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.gui.temperatureseriespanel module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.gui.temperatureseriespanel + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.gui.datasetconstraintpanel module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.gui.datasetconstraintpanel + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.gui.journalpanel module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.gui.journalpanel + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.gui.debugoptions module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.gui.debugoptions + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.gui.fittree module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.gui.fittree + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.gui.extendedplotframe module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.gui.extendedplotframe + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.gui.preferencespanel module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.gui.preferencespanel + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.gui.addphasepanel module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.gui.addphasepanel + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.gui.rseriespanel module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.gui.rseriespanel + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.gui.fitnotebookpanel module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.gui.fitnotebookpanel + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.gui.aboutdialog module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.gui.aboutdialog + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.gui.paneltest module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.gui.paneltest + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.gui.dopingseriespanel module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.gui.dopingseriespanel + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.gui.blankpanel module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.gui.blankpanel + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.gui.datasetconfigurepanel module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.gui.datasetconfigurepanel + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.gui.errorreportdialog_control_fix module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.gui.errorreportdialog_control_fix + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.gui.plotpanel module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.gui.plotpanel + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.gui.welcomepanel module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.gui.welcomepanel + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.gui.pdfpanel module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.gui.pdfpanel + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.gui.resultspanel module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.gui.resultspanel + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.gui.outputpanel module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.gui.outputpanel + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.gui.insertrowsdialog module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.gui.insertrowsdialog + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.gui.errorreportdialog module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.gui.errorreportdialog + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.gui.parameterspanel module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.gui.parameterspanel + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.gui.datasetpanel module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.gui.datasetpanel + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.gui.main module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.gui.main + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.gui.pdfguiglobals module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.gui.pdfguiglobals + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.gui.phasepanelutils module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.gui.phasepanelutils + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.gui.phasenotebookpanel module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.gui.phasenotebookpanel + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.gui.errorwrapper module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.gui.errorwrapper + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.gui.windowperspective module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.gui.windowperspective + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.gui.calculationpanel module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.gui.calculationpanel + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.gui.mainframe module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.gui.mainframe + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/api/diffpy.pdfgui.gui.wxextensions.rst b/doc/source/api/diffpy.pdfgui.gui.wxextensions.rst new file mode 100644 index 00000000..eb6cc419 --- /dev/null +++ b/doc/source/api/diffpy.pdfgui.gui.wxextensions.rst @@ -0,0 +1,61 @@ +:tocdepth: -1 + +diffpy.pdfgui.gui.wxextensions package +====================================== + +.. automodule:: diffpy.pdfgui.gui.wxextensions + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +diffpy.pdfgui.gui.wxextensions.wx12 module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.gui.wxextensions.wx12 + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.gui.wxextensions.listctrls module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.gui.wxextensions.listctrls + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.gui.wxextensions.validators module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.gui.wxextensions.validators + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.gui.wxextensions.autowidthlabelsgrid module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.gui.wxextensions.autowidthlabelsgrid + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.gui.wxextensions.textctrlutils module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.gui.wxextensions.textctrlutils + :members: + :undoc-members: + :show-inheritance: + +diffpy.pdfgui.gui.wxextensions.paneldialog module +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.gui.wxextensions.paneldialog + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/api/diffpy.pdfgui.rst b/doc/source/api/diffpy.pdfgui.rst index 8166640e..eaf4bd3f 100644 --- a/doc/source/api/diffpy.pdfgui.rst +++ b/doc/source/api/diffpy.pdfgui.rst @@ -1,9 +1,7 @@ :tocdepth: -1 -|title| -======= - -.. |title| replace:: diffpy.pdfgui package +diffpy.pdfgui package +===================== .. automodule:: diffpy.pdfgui :members: @@ -14,17 +12,27 @@ Subpackages ----------- .. toctree:: - diffpy.pdfgui.example_package + :titlesonly: + + diffpy.pdfgui.gui + diffpy.pdfgui.applications + diffpy.pdfgui.control Submodules ---------- -|module| --------- +diffpy.pdfgui.utils module +^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. automodule:: diffpy.pdfgui.utils + :members: + :undoc-members: + :show-inheritance: -.. |module| replace:: diffpy.pdfgui.example_submodule module +diffpy.pdfgui.tui module +^^^^^^^^^^^^^^^^^^^^^^^^ -.. automodule:: diffpy.pdfgui.example_submodule +.. automodule:: diffpy.pdfgui.tui :members: :undoc-members: :show-inheritance: diff --git a/doc/source/index.rst b/doc/source/index.rst index 7a8854ce..f60279c9 100644 --- a/doc/source/index.rst +++ b/doc/source/index.rst @@ -4,21 +4,66 @@ .. |title| replace:: diffpy.pdfgui documentation -diffpy.pdfgui - GUI for PDF simulation and structure refinement.. +diffpy.pdfgui - GUI for PDF simulation and structure refinement. -| Software version |release|. -| Last updated |today|. +| Software version |release| +| Last updated |today| + +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 <../../manual/pdfgui.html>`_ +from the help menu or follow the `tutorial instructions `_. ======= Authors ======= -diffpy.pdfgui is developed by Billinge Group -and its community contributors. +DiffPy was initiated as part of the Distributed Data Analysis of Neutron +Scattering Experiments (DANSE) project, funded by the National Science +Foundation under grant DMR-0520547. 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 NSF. + +The main contributors to this package were + + 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, + Peng Tian + +The DiffPy team is part of the Billinge Group at Columbia University in New York, +within the Department of Applied Physics and Applied Mathematics. For a detailed list of contributors see https://github.com/diffpy/diffpy.pdfgui/graphs/contributors. +========= +Reference +========= + +If you use this program for a 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 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. + ============ Installation ============ @@ -30,7 +75,11 @@ file included with the distribution. Tutorial ======== -A tutorial for this package can be found here: `<../TUTORIAL.rst>` +The tutorial for the package can be found here: + +.. toctree:: + + tutorial ================= Table of contents diff --git a/doc/source/license.rst b/doc/source/license.rst index cfab61c2..9273f487 100644 --- a/doc/source/license.rst +++ b/doc/source/license.rst @@ -5,35 +5,83 @@ License ####### -OPEN SOURCE LICENSE AGREEMENT -============================= -BSD 3-Clause License - -Copyright (c) 2024, The Trustees of Columbia University in -the City of New York. -All Rights Reserved. - -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. - -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. - -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. - -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. +.. 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. + + 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) + + 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. + + 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. + + 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: + + * Redistributions of source code must retain the above copyright + notice, this list of conditions and the following disclaimer. + + * 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. + + * 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 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/doc/TUTORIAL.rst b/doc/source/tutorial.rst similarity index 85% rename from doc/TUTORIAL.rst rename to doc/source/tutorial.rst index 2cb5b5ce..d8a1c035 100644 --- a/doc/TUTORIAL.rst +++ b/doc/source/tutorial.rst @@ -1,24 +1,22 @@ -=============================================================================== - Welcome to the PDFgui tutorial -=============================================================================== +:tocdepth: -1 -The latest version of this document is available online at +.. index:: tutorial -`http://danse.us/trac/diffraction/browser/diffraction/diffpy/diffpy/pdfgui/doc`_ +Tutorial +######## Please, have your co-workers or students try it out and let us know if you have any comments. We want to make it really easy for the new users to get started with PDFgui. -------------------------------------------------------------------------------- - +======================================= Lesson 1: Creating simple fit of Ni PDF ----------------------------------------- +======================================= Input files: -* ``_ - experimental X-ray PDF data -* ``_ - Ni f.c.c. structure in PDFfit format +* `Ni-xray.gr <../../tutorial/Ni-xray.gr>`_ - experimental X-ray PDF data +* `Ni.stru <../../tutorial/Ni.stru>`_ - Ni f.c.c. structure in PDFfit format Procedure: @@ -68,10 +66,9 @@ Procedure: 8. Save your project for later use. -------------------------------------------------------------------------------- - +====================================================== Lesson 2: Build structure model using crystal symmetry ------------------------------------------------------- +====================================================== In the previous example the initial structure was defined by an existing file. However, PDFgui makes it very easy to build a structure model from scratch and constrain it with arbitrary crystal symmetry. @@ -101,10 +98,9 @@ In the previous example the initial structure was defined by an existing file. H 5. Continue the fit as in Lesson 1. -------------------------------------------------------------------------------- - +============================= Lesson 3: Multi-stage fitting ------------------------------ +============================= Learn how to string together fits. @@ -136,13 +132,12 @@ Learn how to string together fits. 1. Run the fit as in Lesson 1. 2. Plot the fit as in Lesson 1, but this time hold down Control and select the data sets from "Fit 1" and "Fit 1_copy". You can change the "offset" in the plotting window to 0 to place the plots on top of each other. -------------------------------------------------------------------------------- - -References: ------------ +========== +References +========== -1. `(pdf) `_, +1. `(pdf) <../../manual/Proffen-jac-1999.pdf>`_, Th. Proffen and S. J. L. Billinge, PDFFIT a program for full profile structural refinement of the atomic pair distribution function, J. Appl. Crystallogr. 32, 572-575 (1999) -2. `(pdf) `_, +2. `(pdf) <../../manual/Farrow-jpcm-2007.pdf>`_, C. L. Farrow, P. Juhas, J. W. Liu, D. Bryndin, 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) From ee5e8929a3bfcb6baa7c1cceb47bd03d5f939828 Mon Sep 17 00:00:00 2001 From: Tieqiong Zhang Date: Tue, 20 Aug 2024 07:51:30 -0400 Subject: [PATCH 2/2] pre commit --- doc/source/api/diffpy.pdfgui.applications.rst | 1 - doc/source/api/diffpy.pdfgui.control.rst | 1 - doc/source/api/diffpy.pdfgui.gui.design.rst | 1 - doc/source/api/diffpy.pdfgui.gui.rst | 1 - doc/source/api/diffpy.pdfgui.gui.wxextensions.rst | 1 - 5 files changed, 5 deletions(-) diff --git a/doc/source/api/diffpy.pdfgui.applications.rst b/doc/source/api/diffpy.pdfgui.applications.rst index 29d9683d..c9fc29a7 100644 --- a/doc/source/api/diffpy.pdfgui.applications.rst +++ b/doc/source/api/diffpy.pdfgui.applications.rst @@ -18,4 +18,3 @@ diffpy.pdfgui.applications.pdfgui module :members: :undoc-members: :show-inheritance: - diff --git a/doc/source/api/diffpy.pdfgui.control.rst b/doc/source/api/diffpy.pdfgui.control.rst index 89d31f0d..01ed5579 100644 --- a/doc/source/api/diffpy.pdfgui.control.rst +++ b/doc/source/api/diffpy.pdfgui.control.rst @@ -138,4 +138,3 @@ diffpy.pdfgui.control.organizer module :members: :undoc-members: :show-inheritance: - diff --git a/doc/source/api/diffpy.pdfgui.gui.design.rst b/doc/source/api/diffpy.pdfgui.gui.design.rst index 6f768f65..049857ee 100644 --- a/doc/source/api/diffpy.pdfgui.gui.design.rst +++ b/doc/source/api/diffpy.pdfgui.gui.design.rst @@ -7,4 +7,3 @@ diffpy.pdfgui.gui.design package :members: :undoc-members: :show-inheritance: - diff --git a/doc/source/api/diffpy.pdfgui.gui.rst b/doc/source/api/diffpy.pdfgui.gui.rst index 67db606e..8e2c9750 100644 --- a/doc/source/api/diffpy.pdfgui.gui.rst +++ b/doc/source/api/diffpy.pdfgui.gui.rst @@ -371,4 +371,3 @@ diffpy.pdfgui.gui.mainframe module :members: :undoc-members: :show-inheritance: - diff --git a/doc/source/api/diffpy.pdfgui.gui.wxextensions.rst b/doc/source/api/diffpy.pdfgui.gui.wxextensions.rst index eb6cc419..eee1258e 100644 --- a/doc/source/api/diffpy.pdfgui.gui.wxextensions.rst +++ b/doc/source/api/diffpy.pdfgui.gui.wxextensions.rst @@ -58,4 +58,3 @@ diffpy.pdfgui.gui.wxextensions.paneldialog module :members: :undoc-members: :show-inheritance: -