try out revised help gen from CoPilot; minor docs improvements

Author: briantoby

.github/workflows/update_help.yml

@@ -1,19 +1,74 @@
 name: xfer help info from GSAS-II docs repo
 # This updates the help file to match the contents of the MDhelp directory
 # in the GSAS-II-tutorials repo. It is triggered from the builddocsite.yml
-# workflow in the GSAS-II-tutorials repo.
+# workflow in the GSAS-II-tutorials repo, or runs daily, or can be triggered manually.
 
 on:
   repository_dispatch: # run from Web API
-  workflow_dispatch:
+  workflow_dispatch: # manual trigger for testing
+  schedule:
+    - cron: '0 0 * * *' # Run daily at midnight UTC
 
 permissions:
   contents: write
   id-token: write
   pages: write
 
 jobs:
-  build:       # Build web pages
+  check_files:  # Check if files need updating
+    runs-on: ubuntu-latest
+    outputs:
+      files_changed: ${{ steps.compare.outputs.files_changed }}
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Checkout tutorials repo
+        uses: actions/checkout@v4
+        with:
+          repository: AdvancedPhotonSource/GSAS-II-tutorials.git
+          path: _docs
+          ref: main
+
+      - name: Compare files
+        id: compare
+        run: |
+          # Check if any files in _docs/MDhelp/docs are newer than GSASII/help
+          files_changed="false"
+          
+          if [ ! -d "GSASII/help" ]; then
+            echo "help directory does not exist, will build"
+            files_changed="true"
+          elif [ ! -d "_docs/MDhelp/docs" ]; then
+            echo "docs directory does not exist"
+            files_changed="false"
+          else
+            # Compare modification times of files
+            for doc_file in $(find _docs/MDhelp/docs -type f); do
+              relative_path="${doc_file#_docs/MDhelp/docs/}"
+              help_file="GSASII/help/$relative_path"
+              
+              if [ ! -f "$help_file" ]; then
+                echo "New file detected: $relative_path"
+                files_changed="true"
+                break
+              fi
+              
+              # Compare modification times
+              if [ "$doc_file" -nt "$help_file" ]; then
+                echo "File is newer: $relative_path"
+                files_changed="true"
+                break
+              fi
+            done
+          fi
+          
+          echo "files_changed=$files_changed" >> $GITHUB_OUTPUT
+          echo "Files changed: $files_changed"
+
+  build:       # Build web pages (only if files changed)
+    needs: check_files
+    if: needs.check_files.outputs.files_changed == 'true'
     runs-on: ubuntu-latest
     steps:
 

GSASII/config_example.py

@@ -33,6 +33,8 @@
     float_config = 0.0
     string_config = None (or)
     string_config = 'value'
+
+Below are the configuration settings that can be used in GSAS-II. 
 '''
 
 debug = False

docs/source/packages.rst

@@ -498,27 +498,16 @@ with GSAS-II.
 
 At the request of the program authors, other programs that can be
 accessed within GSAS-II are not included
-as part of the GSAS-II distribution and must be installed separately:
+as part of the GSAS-II distribution. These are listed below. See
+`the web installation instructions
+<https://advancedphotonsource.github.io/GSAS-II-tutorials/install-external.html>`_
+for details on how they are installed.
 
   **Dysnomia**
     Computes enhanced Fourier maps with Maximum Entropy estimated
     extension of the reflection sphere. See
     https://jp-minerals.org/dysnomia/en/.
-    The appropriate zip/dmg/tar file must be downloaded from that web
-    site and the directory Dysnomia from that download must be placed
-    in one of the following locations:
 
-      * the user's home directory (``~/.``),
-      * the directory ``~/.GSASII`` or
-      * the ``GSASII`` directory where GSAS-II has been installed
-        (this will be where the GSAS-II Python files are found).
-        
-    For Windows the home directory, ``~``, is usually
-    taken from the USERPROFILE setting or a combination of HOMEPATH
-    and HOMEDRIVE, so these directories will usually have form 
-    ``C:\\Users\\YourUsername`` or
-    ``C:\\Users\\YourUsername\\.GSASII``. 
-
   **RMCProfile**
     Provides large-box PDF & S(Q) fitting. The GSAS-II interface was originally
     written for use with release 6.7.7 of RMCProfile, but updates have
@@ -533,26 +522,12 @@ as part of the GSAS-II distribution and must be installed separately:
     open-source version of fullrmc, but rather the version 5.0 must be
     used, which is distributed only as compiled versions and only for 64-bit
     Intel-compatible processors running Windows, Linux and
-    MacOS. Download this as a single executable from website
-    https://github.com/bachiraoun/fullrmc/tree/master/standalones. GSAS-II
-    will offer to install this software into the binary directory when the fullrmc
-    option is selected on the Phase/RMC tab.
-
+    MacOS.
+    
   **PDFfit2**
     For small-box fitting of PDFs; see
     https://github.com/diffpy/diffpy.pdffit2?tab=readme-ov-file#-diffpypdffit2.
     This software is no longer developed, but it is
     being maintained with respect to new Python versions.
 
-    The PDFfit2 developers recommend installing via conda, but
-    it appears that pip installation is also possible. See
-    https://pypi.org/project/diffpy.pdffit2/ for more information.
-    It is possible to install PDFfit2 into the same
-    conda environment that GSAS-II uses and if that is done, GSAS-II
-    will use the package, but it is probably best to use a separate
-    Python environment for PDFfit2, so that there is no possibility for
-    conflict between package versions. When GSAS-II is run from a
-    Python installation that includes the conda package manager (which
-    is the case with the GSAS2MAIN installer), the GUI will offer an option to
-    install PDFfit2 via a separate environment when the
-    PDFfit2 option is selected on the Phase/RMC tab.
+