track down master refs; update help for comments searching; new startup tests for dev; update Windows reset .bat

Author: briantoby

MDhelp/docs/powdersample.md

@@ -6,7 +6,8 @@
 This window shows the various sample-dependent parameters for the selected powder pattern. Some are related to the measurement conditions, such as diffractometer setting angles, or the data collection temperature. Others, such as the histogram scale factor, adjust the fit to match the collected data. 
 The presence of a refine button indicates that a parameter can be refined (all others are fixed.) All values shown in this window can be edited. 
 
-Note that the last three parameters (named internally as `FreePrm`*X*, *X*=1,2,3), which are labeled by default as "Sample humidity", "Sample Voltage" and "Applied Load" are fields where the labels that can be changed. If changed in one histogram, the same label is used for all histograms. Thus, a minimum of three parametric variables are available in addition to temperature, pressure and time. Also, note when a label `FreePrm` is changed, the Comments tree item for each PWDR histogram is searched for a matching "Label=value" pair (differences in letter case between the two label strings is ignored). When found, the value is converted to a float and saved as the appropriate Sample Parameter. 
+Note that the last three parameters (named internally as `FreePrm`*X*, *X*=1,2,3), which are labeled by default as "Sample humidity", "Sample Voltage" and "Applied Load" are fields where the labels that can be changed. If changed in one histogram, the same label is used for all histograms. Thus, a total of six parametric variables are available,
+including the more common variable of temperature, pressure and time. Also, note when a label `FreePrm` is changed to "ParmName", the Comments tree item for each PWDR histogram is searched for a matching "\*ParmName\*=value" or "\*ParmName\*:value" pair (i.e. the string "ParmName" will be looked for within the label+value pairs in the comments, ignoring differences in letter case between the two label strings). Thus if the Sample Parameters label is specified as "focus", then a Comments string of "/Instrument/BeamFocus_at_sample=10" will be matched. When found, the value is converted to a float and saved as the value for the newly-labeled Sample Parameter. Also, note the similar action in the ["Set from comments" command](#SetFromComments), below.
 
 Be sure the correct instrument type is selected (Debye-Scherrer or Bragg-Brentano). Also, ensure the goniometer radius is correct (in mm) so that sample displacements are properly scaled (in μm).
 
@@ -46,3 +47,6 @@ Note that the first line(s) in the file can be a header, but each header line mu
 
 * **Rescale all** - Allows a series of selected PWDR histograms to be put on a common scale by integrating them over a specific two-theta region and then scaling them so that the integration range will match the first pattern.
 
+<a name="SetFromComments"></a>
+* **Set from comments** - The histogram comments section, depending on the importer used to read in the data (or image the data is derived from) often contains values that are recorded on the diffraction instrument. These are commonly recorded as "Label=value" or "Label:value". 
+  This command can be used to scan the comments and transfer them to the sample parameters. This is done by selecting a sample parameter as well as a Label found in the comments. One then specifies the histograms where the search will be performed. This is particularly of use for parametric variables and for sample setting angles. 

webdocs/compile.rst

@@ -35,14 +35,12 @@ binaries that have been distributed with GSAS-II, but they can be
 compiled by users and in some cases that will be necessary. The
 documentation here discusses these files.
 
-Note that there are two methods used for compiling GSAS-II. For Python
-3.11 and earlier, a build process with a utility called ``Scons`` was used, but this
-stopped working for GSAS-II with Python 3.12 and a new build process
-using the ``meson`` tool was implemented. At present, there are two
-branches for GSAS-II. The ``master`` branch uses Scons and the
-``main`` branch uses meson. The master branch is the current default
-branch but will eventually be retired in favor of the newer ``main``
-branch. 
+Note that GSAS-II is compiled using a utility called ``meson``.
+For Python prior to 3.10, a build process with a utility called
+``Scons`` may be needed, but this
+stopped working for GSAS-II with Python 3.12.
+The now obsolete ``master`` branch uses Scons and the
+``main`` branch uses meson.
 
 Most people will not need this, but some specific
 installation details are discussed in the source code documentation, 

webdocs/developers.rst

@@ -127,8 +127,42 @@ Adding startup code
 When doing repetitive testing, it can be time consuming to have to run
 the same commands from the GUI each time that GSAS-II is started. In
 debug mode, GSAS-II can run specific code when the program is started
-and a .gpx file is loaded (in routine ``GSASIIdataGUI.GSASII.StartProject``)
-by creating a file named ``debug_setup.py`` that is placed in the
+or when a .gpx file is loaded (in routine
+``GSASIIdataGUI.GSASII.StartProject``).
+
+
+Run at startup
+===============
+
+To run code at startup, creating a file named ``debug_startup.py``
+that is placed in the directory with the rest of the GSAS-II files. An
+example that tests a section of code from an exporter::
+
+  print(f'\n{70*"="}\nrunning debug_startup.py\n{70*"="}')
+  import wx
+  G2frame = wx.App.GetMainTopWindow()
+  from .imports import G2img_HDF5
+  reader = G2img_HDF5.HDF5_Reader()
+  reader.ContentsValidator('/Users/toby/Scratch/MPE_H5/test.h5')
+
+and this code loads an image file when GSAS-II starts::
+
+  print(f'\n{70*"="}\nrunning debug_startup.py\n{70*"="}')
+  import wx
+  self = G2frame = wx.App.GetMainTopWindow()
+  self.CheckNotebook()
+  rdlist = self.OnImportGeneric(None,self.ImportImageReaderlist,
+            'image',multiple=True,Preview=False,load2Tree=True,
+            filename='/tmp/MPE_H5/Cr3_Zry4_Temp_2cps_650C_016665.ge1.h5')
+  if rdlist:
+      self.GPXtree.SelectItem(GetGPXtreeItemId(self,self.Image,'Image Controls'))
+
+  
+Run after reading a project
+=============================
+
+Provide Python commands that will be run after a project is read by
+creating a file named ``debug_setup.py`` that is placed in the 
 directory with the rest of the GSAS-II files. Some examples follow.
 
 This triggers refinement of a .gpx file that is placed on the command

webdocs/help.rst

@@ -25,17 +25,24 @@ overwrite your changes with the latest GSAS-II version.
 On Windows
 ----------------
 
-At present, two windows .BAT files are created in the directory where
-GSAS-II is installed, one named ``Reset2FreshGSASII.bat`` the other
-``start_G2_bootstrap.bat``. Thus, if GSAS-II is installed in directory 
-``C:\Users\toby\gsas2main`` the files will be named
-``C:\Users\toby\gsas2main\Reset2FreshGSASII.bat`` and
-``C:\Users\toby\gsas2main\start_G2_bootstrap.bat``.
-Either will restore the GSAS-II files, but the
-``Reset2FreshGSASII`` file, will ask you to confirm before acting. The
-files can run by locating them in the Windows File Explorer and
+A Windows .BAT file is created in the directory where
+GSAS-II is installed, named ``2Reset2FreshGSASII.bat``
+Thus, if GSAS-II is installed in directory 
+``C:\Users\toby\gsas2main`` the file will be named
+``C:\Users\toby\gsas2main\2Reset2FreshGSASII.bat``.
+This file will remove any changes you have made locally to the GSAS-II
+files and will install the latest version of those files from the
+GitHub server. The
+file can run by locating them in the Windows File Explorer and
 double-clicking on it or by typing the file name into the cmd.exe
-window. 
+window.
+
+Note that the GSAS-II installers prior to 2026 did not create this
+file or created a similarly named file that would not work. If the
+file ``2Reset2FreshGSASII.bat`` is not present, download and reinstall
+GSAS-II. You can use a new location and keep the old version or delete
+the old version and install the new one in the location used
+previously. 
 
 On MacOS and Linux
 ------------------------

webdocs/index.rst

@@ -53,7 +53,7 @@ well as extensive visualization capabilities.
        codes or reference later work, with citations provided
        as they are used. *Please* cite them as well.
 
-GSAS-II is made available for free use (`see license <https://raw.githubusercontent.com/AdvancedPhotonSource/GSAS-II/master/LICENSE>`_) with open access to the `source code <https://github.com/AdvancedPhotonSource/GSAS-II>`_.  
+GSAS-II is made available for free use (`see license <https://raw.githubusercontent.com/AdvancedPhotonSource/GSAS-II/main/LICENSE>`_) with open access to the `source code <https://github.com/AdvancedPhotonSource/GSAS-II>`_.  
 
 Also, please do sign up for the GSAS-II mailing list `see below <mailinglist.html>`_.
 We add new features to GSAS-II quite frequently, so we may break

webdocs/install_dev.rst

@@ -339,7 +339,7 @@ directly editing the ``.../GSAS-II/.git/config`` file from::
 
    [remote "origin"]
 	url = https://github.com/AdvancedPhotonSource/GSAS-II.git
-	fetch = +refs/heads/master:refs/remotes/origin/master
+	fetch = +refs/heads/main:refs/remotes/origin/main
 
 to::