skpkg: delete example files and standardize index.rst

Author: zmx27

doc/source/api/diffpy.morph.example_package.rst

@@ -9,13 +9,39 @@
 | Software version |release|
 | Last updated |today|.
 
-===============
-Getting started
-===============
-
-Welcome to the ``diffpy.morph`` documentation!
-
-To get started, please visit the :ref:`Getting started <getting-started>` page.
+Introduction
+++++++++++++
+
+``diffpy.morph`` is a Python package that increases the insight
+researchers can obtain from measured atomic pair distribution functions
+(PDFs) in a model-independent way. It was designed to help a
+researcher answer the question: "Has my material undergone a phase
+transition between these two measurements?"
+
+One approach is to compare the two PDFs in a plot and view the
+difference curve underneath. However, significant signal can be seen in
+the difference curve from benign effects such as thermal expansion (peak
+shifts) and increased thermal motion (peak broadening) or a change in
+scale due to differences in incident flux, for example. ``diffpy.morph`` will
+do its best to correct for these benign effects before computing and
+plotting the difference curve. One measured PDF (typically that
+collected under higher temperature) is identified as the target PDF and
+the second PDF is then morphed by "stretching" (changing the r-axis to
+simulate a uniform lattice expansion), "smearing" (broadening peaks
+through a uniform convolution to simulate increased thermal motion), and
+"scaling" (self-explanatory). ``diffpy.morph`` will vary the amplitude of the
+morphing transformations to obtain the best fit between the morphed and
+the target PDFs, then plot them on top of each other with the difference
+plotted below.
+
+There are also a few other morphing transformations in the program.
+If no morphing transformation is specified, ``diffpy.morph`` will return just
+the plotted PDFs.
+
+Finally, we note that though ``diffpy.morph`` should work on other spectra
+that are not PDFs, it has not been extensively tested beyond the PDF.
+
+To get started, please visit the :ref:`quick_start`.
 
 =======
 Authors
@@ -25,7 +51,7 @@ Authors
 Columbia University and Brookhaven National Laboratory including
 Christopher L. Farrow, Christopher J. Wright, Pavol Juhás, Chia-Hao
 (Timothy) Liu, Andrew Yang, and Simon J. L. Billinge.
-For a detailed list of contributors, see
+For a detailed list of contributors see
 https://github.com/diffpy/diffpy.morph/graphs/contributors.
 
 ============
@@ -45,12 +71,12 @@ Acknowledgements
 Table of contents
 =================
 .. toctree::
-   :maxdepth: 2
+   :titlesonly:
 
-   getting-started
-   Package API <api/diffpy.morph>
-   release
+   quickstart
    license
+   release
+   Package API <api/diffpy.morph>
 
 =======
 Indices