minor tweaks when testing w/MDhelp

Author: briantoby

MDhelp/docs/index.md

@@ -1,4 +1,5 @@
 <!--- Don't change the HTML version of this file; edit the .md version -->
+<a name="HelpIntro"></a> 
 # Help for GSAS-II
 
 This and the subsequent web pages provide documentation for the
@@ -14,18 +15,24 @@ window and in other locations of the program.
 An index on the topics covered in these help pages is given below. 
 
 1. [Tutorials](./preface.md)  
-2. [GSAS-II GUI Organization](./applicationwindow.md) 
+2. [GSAS-II Window Organization](./applicationwindow.md)
     1. [Data Tree](./applicationwindow.md#Data_tree)
     2. [Data Window](./applicationwindow.md#Data_frame)
     3. [Graphics Window](./applicationwindow.md#Plots)
     4. [Console Window](./applicationwindow.md#Console)
 3. [Main menu contents](./mainmenu.md)
 4. Data tree entries and their use ([overview](./datatree.md))
     1. [Universal data tree](./commontreeitems.md) items 
+        * [Notebook](./commontreeitems.md#Notebook) 
+        * [Controls and settings](./commontreeitems.md#Controls) 
+        * [Covariance and fit results](./commontreeitems.md#Covariance) 
+        * [Constraints](./commontreeitems.md#Constraints) 
+        * [Restraints](./commontreeitems.md#Restraints) 
+        * [Rigid Bodies](./commontreeitems.md#Rigidbodies) 
     0. [Sequential results](./sequential.md)
     0. [Cluster Analysis](./cluster.md)
     2. [Phase Data Tree items (overview)](./phaseoverview.md) 
-        * [General Phase tab](./phasegeneral.md)  
+        * [General Phase tab](./phasegeneral.md)
         * [Data Phase tab](./phasedata.md) 
         * [Atoms Phase tab](./phaseatoms.md) 
         * [Draw Options tab](./phasedrawopts.md)

MDhelp/docs/powder.md

@@ -1,5 +1,5 @@
 <!--- Don't change the HTML version of this file; edit the .md version -->
-<a name="PWDR"></a>
+<a name="PWDR_overview"></a>
 #  Overview on **PWDR** data tree entries: Powder Diffraction
 
 This is where to find information on the Tree item in GSAS-II associated with powder diffraction (labeled PWDR) and its associated subitems. Note that GSAS-II uses the label of "histogram" for datasets of any type (single-crystal, powder,...) Powder diffraction histograms are added to a project using the Import/"Powder Data" menu items. After data are read, if there are phases present, you will be offered a chance to link the imported histograms to the previously imported phase(s). Likewise, if phase(s) are imported after histograms you will also be asked to link the new phase(s) to existing histograms. It is also possible to add histograms to a phase later by selecting that phase in the data tree and then selecting the "Data" tab and finally using the "Edit Phase"/"Add powder histograms" menu command. Note that there is no limit to the number of histograms that can be included in a GSAS-II project (other than as limited by available computer memory) and histograms that are not linked to at least one phase are ignored in refinements. 

MDhelp/docs/powderparent.md

@@ -1,5 +1,6 @@
 <!--- Don't change the HTML version of this file; edit the .md version -->
 <a name="PWDR_parent"></a>
+<a name="PWDR"></a>
 #  **PWDR** parent data tree (Powder Diffraction)
 
 When a powder diffraction dataset (prefix 'PWDR') is selected from the data tree or for most of the subdata tree items, the dataset is plotted. The observed data points are shown as blue crosses and where fit, the calculated pattern is shown as a green line; the background is shown as red line. The difference curve is shown as a cyan line. These colors can be changed through [configuration variables](./others.md#config) `Obs_color`, `Calc_color`, `Diff_color`, and `Bkg_color`.

MDhelp/mkdocs.yml_pdf MDhelp/mkdocs.yml_htmlMDhelp/mkdocs.yml_pdf renamed to MDhelp/mkdocs.yml_html

@@ -8,6 +8,8 @@ nav:
   - Data tree items:
     - Data tree overview: datatree.md
     - Universal items: commontreeitems.md
+    - Sequential results: sequential.md
+    - Cluster Analysis: cluster.md
     - Phases:
       - Phase overview: phaseoverview.md  
       - General tab: phasegeneral.md
@@ -42,8 +44,7 @@ nav:
     - PDF: pairdistribution.md
     - Small Angle (SASD): smallanglescattering.md
     - Reflectometry (REFD): reflectometry.md
-    - Sequential results: sequential.md
-    - Cluster Analysis: cluster.md
+    - Powder Peaks (PKS): peaks.md
 
 #    - Powder peaks (PKS): powderpeak.md
 
@@ -57,21 +58,15 @@ theme:
   logo:    images/gsas2.png
 
 plugins:
-  #- with-pdf:
-  - to-pdf:
-      author: Brian H. Toby and Robert B. Von Dreele
-      enabled_if_env: ENABLE_PDF_EXPORT
-      cover_title: GSAS-II Help information
-      cover_subtitle: A compilation of HTML pages into PDF
-      copyright: From https://advancedphotonsource.github.io/GSAS-II-tutorials/help/
-      #back_cover: true
-      output_path: GSASII-help.pdf
-#      exclude_pages:
-#        - Contents
-#        - index.md
-      render_js: true
-      headless_chrome_path: /usr/bin/google-chrome-stable
-      pdf_engine: chromium
+  # - to-pdf:
+  #     author: Brian H. Toby and Robert B. Von Dreele
+  #     enabled_if_env: ENABLE_PDF_EXPORT
+  #     cover_title: GSAS-II Help information
+  #     cover_subtitle: A compilation of HTML pages into PDF
+  #     copyright: From https://advancedphotonsource.github.io/GSAS-II-tutorials/help/
+  #     output_path: GSASII-help.pdf
+  #     render_js: true
+  #     headless_chrome_path: /usr/bin/google-chrome-stable
   - i18n:
       docs_structure: suffix
       languages:
@@ -93,11 +88,7 @@ markdown_extensions:
 extra_javascript:
   - javascripts/mathjax.js
   - https://unpkg.com/mathjax@3/es5/tex-mml-chtml.js
-
-
-#extra_javascript: 
 #  - https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML
-#  - https://unpkg.com/mathjax@3/es5/tex-mml-chtml.js # MathJax library from CDN
 
 #local build settings from https://www.mkdocs.org/user-guide/deploying-your-docs/#local-files
 

webdocs/documentation.rst

@@ -27,7 +27,15 @@ The GSAS-II GUI provides context-based help via several web files that are
 distributed with the program, as well as can be `viewed here
 <help/gsasII-index.html>`_. These help pages are not always complete,
 but do provide information on how different sections of the program
-work.  
+work.
+
+The help documentation is in the process of being reformatted and updated. The
+`new help pages can be viewed here<help-test/>`_ as web pages or
+`here as a PDF document
+<https://advancedphotonsource.github.io/GSAS-II-tutorials/docs/GSASII-help.pdf>`_.
+These files are now based in MarkDown (simple text) input files found
+`in GitHub<https://github.com/AdvancedPhotonSource/GSAS-II-tutorials/tree/main/MDhelp>`_.
+Comments, corrections, additions and issue reports are most welcome. 
 
 .. index:: Source code documentation