extensive but superficial changes in docs; addvance mini version to differentiate main from master

briantoby · briantoby · commit ad02d9a95908 · 2025-04-24T15:31:10.000-05:00
diff --git a/GSASII/GSASIIscriptable.py b/GSASII/GSASIIscriptable.py
@@ -5118,9 +5118,11 @@ def HAPvalue(self, param=None, newValue=None, targethistlist='all'):
           and only one histogram is selected, the value is retrieved and
           returned.
           When param='PO' then this value is interpreted as the following:
+
             if the value is 0 or an even integer, then the preferred 
             orientation model is set to "Spherical harmonics". If the value is 
             1, then "March-Dollase" is used. Any other value generates an error.
+
         :param list targethistlist: a list of histograms where each item in the
             list can be a histogram object (:class:`G2PwdrData`),
             a histogram name or the index number of the histogram.
@@ -5131,7 +5133,6 @@ def HAPvalue(self, param=None, newValue=None, targethistlist='all'):
 
             targethistlist must correspond to a single histogram if a value
             is to be returned (i.e. when argument newValue is not specified).
-        :param int order: is a value for the order when     
 
         :returns: the value of the parameter, when argument newValue is not specified.
 
diff --git a/GSASII/config_example.py b/GSASII/config_example.py
@@ -128,7 +128,7 @@
 '''
 Main_Size = (700,450)
 '''Main window size (width, height) - initially uses wx.DefaultSize but will updated
- and saved as the user changes the window.
+and saved as the user changes the window.
 This is used internally by GSAS-II and would not normally be changed by a user. 
 '''
 Main_Pos = (100,100)
diff --git a/GSASII/exports/G2export_Bracket.py b/GSASII/exports/G2export_Bracket.py
@@ -1,5 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
+'''Classes in :mod:`~GSASII.exports.G2export_Bracket` follow.
+'''
 
 # This module initially written by Conrad Gillard. For any enquiries please contact conrad.gillard@gmail.com
 # Export3col exporter adapted from Exportbracket by BHT
diff --git a/GSASII/exports/G2export_CIF.py b/GSASII/exports/G2export_CIF.py
@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-'''Classes in :mod:`G2export_CIF` follow:
+'''Classes in :mod:`~GSASII.exports.G2export_CIF` follow:
 '''
 # note documentation in docs/source/exports.rst
 #
@@ -84,13 +84,13 @@ def getCellwStrain(phasedict,seqData,pId,histname):
 
 def mkSeqResTable(mode,seqHistList,seqData,Phases,Histograms,Controls):
     '''Setup sequential results table (based on code from
-    GSASIIseqGUI.UpdateSeqResults)
+    :func:`GSASII.GSASIIseqGUI.UpdateSeqResults`)
 
     TODO: This should be merged with the table build code in
-    GSASIIseqGUI.UpdateSeqResults and moved to somewhere non-GUI
-    like GSASIIstrIO to create a single routine that can be used
+    :func:`GSASII.GSASIIseqGUI.UpdateSeqResults` and moved to somewhere non-GUI
+    like :mod:`~GSASII.GSASIIstrIO` to create a single routine that can be used
     in both places, but this means returning some
-    of the code that has been removed from there
+    of the code that has been removed from there.
     '''
 
     newAtomDict = seqData[seqHistList[0]].get('newAtomDict',{}) # dict with atom positions; relative & absolute
@@ -4657,7 +4657,9 @@ def SelectDisAglFlags(event):
 class ExportProjectCIF(ExportCIF):
     '''Used to create a CIF of an entire project
 
-    also called directly in :func:`GSASIImiscGUI.ExportSequentialFullCIF`
+    also called directly in 
+    :func:`~GSASII.GSASIImiscGUI.ExportSequentialFullCIF`
+    in :mod:`~GSASII.GSASIImiscGUI`
 
     :param wx.Frame G2frame: reference to main GSAS-II frame
     '''
diff --git a/GSASII/exports/G2export_FIT2D.py b/GSASII/exports/G2export_FIT2D.py
@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-'''Classes in :mod:`G2export_FIT2D` follow:
+'''Classes in :mod:`~GSASII.exports.G2export_FIT2D` follow:
 '''
 from __future__ import division, print_function
 import os.path
diff --git a/GSASII/exports/G2export_JSON.py b/GSASII/exports/G2export_JSON.py
@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-'''Classes in :mod:`G2export_JSON` follow:
+'''Classes in :mod:`~GSASII.exports.G2export_JSON` follow:
 
 This code is to honor my friend Robert Papoular, who wants to see what is 
 inside a .gpx file.
diff --git a/GSASII/exports/G2export_PDB.py b/GSASII/exports/G2export_PDB.py
@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-'''Classes in :mod:`G2export_PDB` follow:
+'''Classes in :mod:`~GSASII.exports.G2export_PDB` follow:
 '''
 from __future__ import division, print_function
 import numpy as np
diff --git a/GSASII/exports/G2export_csv.py b/GSASII/exports/G2export_csv.py
@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-'''Classes in :mod:`G2export_csv` follow:
+'''Classes in :mod:`~GSASII.exports.G2export_csv` follow:
 '''
 # note documentation in docs/source/exports.rst
 #
diff --git a/GSASII/exports/G2export_examples.py b/GSASII/exports/G2export_examples.py
@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-'''Classes in :mod:`G2export_examples` follow:
+'''Classes in :mod:`~GSASII.exports.G2export_examples` follow:
 '''
 # note documentation in docs/source/exports.rst
 #
diff --git a/GSASII/exports/G2export_image.py b/GSASII/exports/G2export_image.py
@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-'''Classes in :mod:`G2export_image` follow:
+'''Classes in :mod:`~GSASII.exports.G2export_image` follow:
 '''
 from __future__ import division, print_function
 import os.path
diff --git a/GSASII/exports/G2export_map.py b/GSASII/exports/G2export_map.py
@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-'''Classes in :mod:`G2export_map` follow:
+'''Classes in :mod:`~GSASII.exports.G2export_map` follow:
 '''
 from __future__ import division, print_function
 import platform
diff --git a/GSASII/exports/G2export_pwdr.py b/GSASII/exports/G2export_pwdr.py
@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-'''Classes in :mod:`G2export_pwdr` follow:
+'''Classes in :mod:`~GSASII.exports.G2export_pwdr` follow:
 '''
 from __future__ import division, print_function
 import os.path
diff --git a/GSASII/exports/G2export_shelx.py b/GSASII/exports/G2export_shelx.py
@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-'''Classes in :mod:`G2export_shelx` follow:
+'''Classes in :mod:`~GSASII.exports.G2export_shelx` follow:
 '''
 from __future__ import division, print_function
 import os.path
diff --git a/GSASII/git_verinfo.py b/GSASII/git_verinfo.py
@@ -1,10 +1,10 @@
 # -*- coding: utf-8 -*-
 # git_verinfo.py - GSAS-II version info from git
-# Do not edit, generated by 'GSASII/install/tag-version.py' script
-# Created 2025-04-22 20:32:33.394287-05:00
+# Do not edit, generated by 'install/incr-mini-version.py' script
+# Created 2025-04-24 15:28:29.910598-05:00
 
-git_version = 'dfc4cc57bfa3a65d8b086eac2dfcc470d4c95187'
-git_tags = ['5806']
-git_prevtaggedversion = '56a08a464b5470a65b3ff5c5e162b88146f7be5b'
-git_prevtags = ['5805']
-git_versiontag = 'v5.3.0'
+git_version = '13b43cde12bb04aa4928c7884f0699d14111889b'
+git_tags = []
+git_prevtaggedversion = 'dfc4cc57bfa3a65d8b086eac2dfcc470d4c95187'
+git_prevtags = ['5806']
+git_versiontag = 'v5.3.1'
diff --git a/GSASII/imports/G2phase.py b/GSASII/imports/G2phase.py
@@ -1,6 +1,7 @@
 # -*- coding: utf-8 -*-
 #
-'''
+'''There are several classes in :mod:`~GSASII.imports.G2phase`. 
+The documentation for them follows.
 '''
 
 from __future__ import division, print_function
@@ -51,7 +52,7 @@ def ContentsValidator(self, filename):
         return False
 
     def Reader(self,filename, ParentFrame=None, **unused):
-        'Read a PDF file using :meth:`ReadPDBPhase`'
+        'Read a PDB file using :meth:`ReadPDBPhase`'
         self.Phase = self.ReadPDBPhase(filename, ParentFrame)
         return True
         
@@ -192,7 +193,9 @@ def ContentsValidator(self, filename):
         return False
 
     def Reader(self,filename,ParentFrame=None,usedRanIdList=[],**unused):
-        'Read a phase from a GSAS .EXP file using :meth:`ReadEXPPhase`'
+        '''Read a phase from a GSAS .EXP file using 
+        :meth:`~EXP_ReaderClass.ReadEXPPhase`
+        '''
         self.Phase = G2obj.SetNewPhase(Name='new phase') # create a new empty phase dict
         while self.Phase['ranId'] in usedRanIdList:
             self.Phase['ranId'] = ran.randint(0,sys.maxsize)
@@ -612,7 +615,8 @@ def ReadJANAPhase(self,filename,parent=None):
         return Phase
     
 class PDF_ReaderClass(G2obj.ImportPhase):
-    'Routine to import Phase information from ICDD PDF Card files'
+    '''Routine to import Phase information from ICDD Powder Diffraction 
+    File(r) Card, exported by their software.'''
     def __init__(self):
         super(self.__class__,self).__init__( # fancy way to say ImportPhase.__init__
             extensionlist=('.str',),
diff --git a/GSASII/imports/G2phase_rmc6f.py b/GSASII/imports/G2phase_rmc6f.py
@@ -30,7 +30,9 @@ def ContentsValidator(self, filename):
         return True
 
     def Reader(self,filename,filepointer, ParentFrame=None, **unused):
-        'Read a rmc6f file using :meth:`ReadINSPhase`'
+        '''Read a rmc6f file using 
+        :meth:`~GSASII.imports.G2phase_rmc6f.PhaseReaderClass.Readrmc6fPhase`
+        '''
         self.Phase = self.Readrmc6fPhase(filename, ParentFrame)
         return True
 
diff --git a/GSASII/imports/G2phase_xyz.py b/GSASII/imports/G2phase_xyz.py
@@ -32,7 +32,7 @@ def ContentsValidator(self, filename):
         return True
 
     def Reader(self,filename, ParentFrame=None, **unused):
-        'Read a PDF file using :meth:`ReadPDBPhase`'
+        'Read a phase from an XYZ file.'
         self.errors = 'Error opening file'
         fp = open(filename, 'r')
         self.Phase = {}
diff --git a/docs/environment.yml b/docs/environment.yml
@@ -15,3 +15,4 @@ dependencies:
   - matplotlib
   - wxpython
   - gitpython
+  - pytest
diff --git a/docs/source/GSASIIGUIr.rst b/docs/source/GSASIIGUIr.rst
@@ -4,18 +4,11 @@
 The modules documented here provide GUI or graphics capabilities that
 are used in multiple sections of the GSAS-II GUI or graphics. 
 
-.. TODO: The tables below need work. The references such as :class:`EnumSelector`
-.. and :func:`G2RadioButtons` don't work. What is needed is 
-.. :class:`~GSASII.GSASIIctrlGUI.EnumSelector` and 
-.. :func:`~GSASII.GSASIIctrlGUI.G2RadioButtons`. That will require 
-.. realigning the tables big-time. 
-
-
 ---------------------------------------------
 *GSASIIctrlGUI: Custom GUI controls*
 ---------------------------------------------
 
- .. py:currentmodule:: GSASIIctrlGUI
+ .. py:currentmodule:: GSASII.GSASIIctrlGUI
 
 A library of specialized widgets (GUI controls) for use in the GSAS-II
 data window or dialogs:
@@ -145,13 +138,14 @@ Miscellaneous GUI support routines:
 ================================  =================================================================
 Function name                      Description
 ================================  =================================================================
-:func:`Define_wxId`                Create a unique wx.Id symbol in _initMenus in :mod:`GSASIIdataGUI`.
+:func:`Define_wxId`                Create a unique wx.Id symbol in _initMenus in 
+                                   :mod:`GSASII.GSASIIdataGUI`.
                                    Such symbols are needed when the menu item is defined in a 
                                    different location from the wx.Bind that links the menu item 
                                    to a function. This function allows all the menu Ids to be
                                    defined as the menus are created in one place and then can be 
                                    used in Bind elsewhere in the code.
-:func:`openInNewTerm`              opens a Python routine (usually G2.py) in a
+:func:`openInNewTerm`              opens a Python routine (usually ``G2.py``) in a
                                    new terminal window (works on all platforms)				   
 ================================  =================================================================
 
@@ -167,12 +161,12 @@ Function name                      Description
                                    of each line.
 :func:`StripUnicode`               Removes unicode characters from strings 
 :func:`GetImportPath`              Determines the default location to use for importing files.
-                                   Tries sequentially :attr:`G2frame.TutorialImportDir`,
+                                   Tries sequentially ``G2frame.TutorialImportDir``,
                                    config var ``Import_directory`` and
-                                   :attr:`G2frame.LastImportDir`.
+                                   ``G2frame.LastImportDir``.
 :func:`GetExportPath`              Determines the default location to use for writing files.
-                                   Tries sequentially :attr:`G2frame.LastExportDir` and
-                                   :attr:`G2frame.LastGPXdir`
+                                   Tries sequentially ``G2frame.LastExportDir`` and
+                                   ``G2frame.LastGPXdir``
 ================================  =================================================================
 
 
diff --git a/docs/source/GSASIImapvars.rst b/docs/source/GSASIImapvars.rst
diff --git a/docs/source/exports.rst b/docs/source/exports.rst
diff --git a/docs/source/imports.rst b/docs/source/imports.rst
diff --git a/docs/source/packages.rst b/docs/source/packages.rst
diff --git a/docs/source/versioning.rst b/docs/source/versioning.rst

Original file line number	Diff line number	Diff line change
`@@ -1,5 +1,5 @@`
`1`	`1`	`# -- coding: utf-8 --`
`2`		-'''Classes in :mod:`G2export_csv` follow:
	`2`	+'''Classes in :mod:`~GSASII.exports.G2export_csv` follow:
`3`	`3`	`'''`
`4`	`4`	`# note documentation in docs/source/exports.rst`
`5`	`5`	`#`
Original file line number	Diff line number	Diff line change
`@@ -1,5 +1,5 @@`
`1`	`1`	`# -- coding: utf-8 --`
`2`		-'''Classes in :mod:`G2export_examples` follow:
	`2`	+'''Classes in :mod:`~GSASII.exports.G2export_examples` follow:
`3`	`3`	`'''`
`4`	`4`	`# note documentation in docs/source/exports.rst`
`5`	`5`	`#`