update docs

_config.html

@@ -6,12 +6,12 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>&lt;no title&gt; &#8212; xraylarch 0.9.78 documentation</title>
+    <title>&lt;no title&gt; &#8212; xraylarch 0.9.80 documentation</title>
     <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
     <link rel="stylesheet" type="text/css" href="_static/larchdoc.css?v=dfcb3266" />
 
-    <script src="_static/documentation_options.js?v=8e89ea36"></script>
-    <script src="_static/doctools.js?v=888ff710"></script>
+    <script src="_static/documentation_options.js?v=d8986006"></script>
+    <script src="_static/doctools.js?v=9a2dae69"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script async="async" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
 
@@ -68,15 +68,15 @@ <h3>This Page</h3>
             rel="nofollow">Show Source</a></li>
     </ul>
    </div>
-<div id="searchbox" style="display: none" role="search">
+<search id="searchbox" style="display: none" role="search">
   <h3 id="searchlabel">Quick search</h3>
     <div class="searchformwrapper">
     <form class="search" action="search.html" method="get">
       <input type="text" name="q" aria-labelledby="searchlabel" autocomplete="off" autocorrect="off" autocapitalize="off" spellcheck="false"/>
       <input type="submit" value="Go" />
     </form>
     </div>
-</div>
+</search>
 <script>document.getElementById('searchbox').style.display = "block"</script>
         </div>
       </div>
@@ -112,7 +112,7 @@ <h3>Navigation</h3>
     </div>
     <div class="footer" role="contentinfo">
     &#169; Copyright Matthew Newville, The University of Chicago, 2022.
-      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.2.6.
+      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.3.7.
     </div>
   </body>
 </html>

_sources/data.rst.txt

@@ -161,14 +161,14 @@ Reading Athena Project Files
 
 Notes:
      1. To limit the imported groups, use the pattern in `match`,
-	using '*' to match 'all', '?' to match any single character,
-	or [sequence] to match any of a sequence of letters.  The match
-	will always be insensitive to case.
+        using '*' to match 'all', '?' to match any single character,
+        or [sequence] to match any of a sequence of letters.  The match
+        will always be insensitive to case.
      2. `do_preedge`, `do_bkg`, and `do_fft` will attempt to reproduce the
-	pre-edge, background subtraction, and FFT from Athena by using
-	the parameters saved in the project file.
+        pre-edge, background subtraction, and FFT from Athena by using
+        the parameters saved in the project file.
      3. `use_hashkey=True` will name groups from the internal 5 character
-	string used by Athena, instead of the group label.
+        string used by Athena, instead of the group label.
 
 A simple example of reading an Athena Project file::
 
@@ -309,14 +309,14 @@ data heirarchy of the HDF5 file, and pick out the needed data::
     larch> show(g)
     == Group test.h5: 3 symbols ==
       attrs: {u'Collection Time': ': Sat Feb 4 13:29:00 2012', u'Version': '1.0.0',
-	      u'Beamline': 'GSECARS, 13-IDC / APS', u'Title': 'Epics Scan Data'}
+              u'Beamline': 'GSECARS, 13-IDC / APS', u'Title': 'Epics Scan Data'}
       data: <Group test.h5/data>
       h5_file: <HDF5 file "test.h5" (mode r)>
     larch>show(g.data)
     == Group test.h5/data: 5 symbols ==
       attrs: {u'scan_prefix': '13IDC:', u'start_time': ': Sat Feb 4 13:29:00 2012',
-	    u'correct_deadtime': 'True', u'dimension': 2,
-	    u'stop_time': ': Sat Feb 4 13:44:52 2009'}
+            u'correct_deadtime': 'True', u'dimension': 2,
+            u'stop_time': ': Sat Feb 4 13:44:52 2009'}
       environ: <Group test.h5/data/environ>
       full_xrf: <Group test.h5/data/full_xrf>
       merged_xrf: <Group test.h5/data/merged_xrf>
@@ -399,12 +399,6 @@ Reading Scan Data from APS Beamlines
 This list is minimal, but can be expanded easily to accomodate more
 facilities and beamlines.
 
-.. function:: read_mda(filename, maxdim=4)
-
-   read a binary MDA (multi-Dimensional Array) file from the Epics SScan
-   Record, and return a group based on the scans it contains.  This is not
-   very well tested -- use with caution!
-
 .. function:: read_gsescan(filename)
 
    read a (old-style) GSECARS Escan data file into a group.

_sources/larix.rst.txt

@@ -7,26 +7,28 @@ Larix (was XAS Viewer)
 ===========================
 
 The `Larix` Application gives a graphical user interface (GUI) for the
-visualization and analyis of X-ray absorption spectroscopy (XAS) data, both
-XANES and EXAFS. It is deliberately patterned after the Demeter Package (Athena
-and Artemis programs), and shares many concepts and presentation ideas with
-these progrqms.  As a GUI Program, Larix should seem very "Athena-like" though
-of course there will be several differences.  We hope that many of these
-differences will be "improvements".  By using Larch for all of its analysis
-steps, Larix not only provides interactive data visualization, exploration, and
-analysis of XAS data, but also records those steps as Larch / Python commands
-that can be saved and reproduced outside of the GUI, say to enable batch
-processing of large volumes of data.
-
-Larix is still in active development with new features driving much of the
-development and releases of Larch version for the past few years. At this
-writing (October, 2023, Larch version 0.9.72), the main feature of Larix are
-met, though improvements and new featutes continue to be made, and bugs are
-being fixed as quickly as possible. Ideas for additions and improvements are
-most welcome.  If you find problems with it or unexpected or missing
-functionality, please let us know.  In addition, if you find any features from
-Athena, Artemis, Sixpack, or other analysis programs that you would like to see
-in Larix, please let us know.
+visualization and analysis of X-ray absorption spectroscopy (XAS) data, both
+XANES and EXAFS.  A primary goal is to be deliberately patterned after the
+Demeter Package (Athena and Artemis programs), and shares many concepts and
+presentation ideas with these progrqms.  As a GUI Program, Larix should seem
+very "Athena-like" though of course there will be several differences.  We hope
+that many of these differences will be "improvements".  By using Larch for all
+of its analysis steps, Larix not only provides interactive data visualization,
+exploration, and analysis of XAS data, but also records those steps as Larch /
+Python commands that can be saved and reproduced outside of the GUI, say to
+enable batch processing of large volumes of data.
+
+Larix is still in active development.  New features for Larix have been driving
+much of the development and releases of Larch version for the past few
+years. At this writing (July, 2024, Larch version 0.9.80), the main goals of
+being feature-compatible with Athena and Artemis are basically met, though
+improvements and new featutes continue to be made, and bugs are being fixed as
+quickly as possible.  Ideas for additions and improvements are most welcome.
+If you find problems with it or unexpected or missing functionality, please let
+us know.  In addition, if you find any features from Athena, Artemis, Sixpack,
+or other analysis programs that you would like to see in Larix, please let us
+know.
+
 
 
 .. toctree::

_sources/xafs_feffit.rst.txt

@@ -468,7 +468,7 @@ This simply follows the essential steps:
 
 running this example prints out the following report:
 
-.. literalinclude:: ../examples/feffit/doc_feffit1.out
+.. literalinclude:: example_outputs/doc_feffit1.out
 
 and generates the plots shown below
 
@@ -564,7 +564,7 @@ vary independently for each path.
 
 The output for this fit is a bit longer, being:
 
-.. literalinclude:: ../examples/feffit/doc_feffit2.out
+.. literalinclude:: example_outputs/doc_feffit2.out
 
 With plots of data and fits as shown below.
 
@@ -663,7 +663,7 @@ characteristic (here, Einstein) temperature which will determine the value of
 :math:`\sigma^2`, and two parameters for the linear temperature dependence
 of :math:`R`. The output for this fit is:
 
-.. literalinclude:: ../examples/feffit/doc_feffit3.out
+.. literalinclude:: example_outputs/doc_feffit3.out
 
 Note that an uncertainty is estimated for the Path parameters, including
 ``sigma2``, which is calculated with the :func:`sigma2_eins` function.
@@ -782,7 +782,7 @@ used in the fit.
 
 The resulting output is
 
-.. literalinclude:: ../examples/feffit/doc_feffit4.out
+.. literalinclude:: example_outputs/doc_feffit4.out
 
 with plots:
 
@@ -839,9 +839,9 @@ with::
 
 which gives
 
-.. literalinclude:: ../examples/feffit/doc_feffit5_r.out
+.. literalinclude:: example_outputs/doc_feffit5_r.out
 
-.. literalinclude:: ../examples/feffit/doc_feffit5_q.out
+.. literalinclude:: example_outputs/doc_feffit5_q.out
 
 We can see that the results are not very different -- the best fit values
 and uncertainties for the varied parameters are quite close for the fit in
@@ -858,7 +858,7 @@ Now, we can try the fit in unfiltered 'K' space::
 
 (we need to specify only one k-weight for a k-space fit) which gives:
 
-.. literalinclude:: ../examples/feffit/doc_feffit5_k.out
+.. literalinclude:: example_outputs/doc_feffit5_k.out
 
 This has pretty similar best-fit values, but dramatically larger estimates
 of the errors.  The spectrum is really very poorly fit in k-space because
@@ -876,7 +876,7 @@ of wavelet transforms (see Section :ref:`xafs-wavelet_sec`).  For this, we
 specify both k and R ranges, and the fit is done on the wavelet
 transform. This gives:
 
-.. literalinclude:: ../examples/feffit/doc_feffit5_w.out
+.. literalinclude:: example_outputs/doc_feffit5_w.out
 
 As you can see, the results are all pretty similar.
 

_sources/xrf.rst.txt

@@ -25,7 +25,6 @@ that holds energy at each point (or "channel") in the array and a `counts`
 array that holds the counts in each channel.
 
 
-
 .. _xrf_fig1:
 
 .. figure::  _images/xrf_display1.png

_sources/xrf_viewer.rst.txt

@@ -1,11 +1,21 @@
 .. _larchxrf_app:
 
 ============================
-The Larrh XRF Application
+The Larch XRF Application
 ============================
 
 .. _wxmplot:  https://newville.github.io/wxmplot
 .. _matplotlib: https://matplotlib.org/
 
 
 The Larch XRF application allows display and analysis of X-ray fluorescene spectra.
+
+
+.. _xrfviewer_fig1:
+
+.. figure::  _images/xrf_display1.png
+    :target: _images/xrf_display1.png
+    :width: 85%
+    :align: center
+
+    X-ray Fluorescence spectrum in the Larch XRF Viewing App

_static/doctools.js

@@ -4,7 +4,7 @@
  *
  * Base JavaScript utilities for all Sphinx HTML documentation.
  *
- * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */

_static/documentation_options.js

@@ -1,5 +1,5 @@
 const DOCUMENTATION_OPTIONS = {
-    VERSION: '0.9.78',
+    VERSION: '0.9.80',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

_static/language_data.js

@@ -5,15 +5,15 @@
  * This script contains the language-specific data used by searchtools.js,
  * namely the list of stopwords, stemmer, scorer and splitter.
  *
- * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
 
 var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"];
 
 
-/* Non-minified version is copied as a separate JS file, is available */
+/* Non-minified version is copied as a separate JS file, if available */
 
 /**
  * Porter Stemmer

_static/nature.css

@@ -4,7 +4,7 @@
  *
  * Sphinx stylesheet -- nature theme.
  *
- * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */