Changeset 3506

Timestamp:

Jul 25, 2018 12:12:20 AM (3 years ago)

Author:

svnjenkins

Message:

fix scriptable problem due to change in Restraints; update Tutorials; misc. fixes for Sphinx docs

Location:

trunk

Files:

• GSASIIIO.py (modified) (1 diff)
• GSASIIctrlGUI.py (modified) (2 diffs)
• GSASIIobj.py (modified) (1 diff)
• GSASIIplot.py (modified) (4 diffs)
• GSASIIscriptable.py (modified) (5 diffs)
• help/Tutorials.html (modified) (3 diffs)

trunk/GSASIIIO.py

@@ -566 +566 @@
     return
 
-objectScanIgnore = [int,bool,float,str,np.float64,np.int32,np.int64,np.ndarray,G2obj.G2VarObj,ma.MaskedArray]
+objectScanIgnore = [int,bool,float,str,np.float64,np.int32,np.int64,np.ndarray,G2obj.G2VarObj]
+try:
+    objectScanIgnore += [ma.MaskedArray] # fails in doc builds
+except AttributeError:
+    pass
+    
 if '2' in platform.python_version_tuple()[0]:
     objectScanIgnore += [unicode,long,]

trunk/GSASIIctrlGUI.py

@@ -434 +434 @@
        is either 'f' (default) or 'g'. Alternately, None can be specified which 
        causes numbers to be displayed with approximately 5 significant figures
-       for floats. If this is specified, then :obj:`typeHint`=float becomes the
+       for floats. If this is specified, then :obj:`typeHint` = float becomes the
        default. 
        (Default=None).
@@ -2838 +2838 @@
     :param int height: an optional height (pixels) for the table (defaults to 400)
     
-    Example use:: 
+    Example use::
+    
         lbls = ('col 1','col 2','col 3')
         choices=(['test1','explanation of test 1'],

trunk/GSASIIobj.py

@@ -1899 +1899 @@
     def ExtensionValidator(self, filename):
         '''This methods checks if the file has the correct extension
-        Return False if this filename will not be supported by this reader (only
-          when strictExtension is True)
-        Return True if the extension matches the list supplied by the reader
-        Return None if the reader allows un-registered extensions
+        
+        :returns:
+        
+          * False if this filename will not be supported by this reader (only
+            when strictExtension is True)
+          * True if the extension matches the list supplied by the reader
+          * None if the reader allows un-registered extensions
+          
         '''
         if filename:

trunk/GSASIIplot.py

@@ -157 +157 @@
 except ImportError:
     from matplotlib.backends.backend_agg import FigureCanvas as hcCanvas # standard name
+except RuntimeError:  # happens during doc builds
+    pass
 
 # useful degree trig functions
@@ -256 +258 @@
         Add a set of subplots to this figure.
         
-        Parameters
-        ----------
-        nrows, ncols : int, default: 1
+        :param nrows, ncols : int, default: 1
             Number of rows/cols of the subplot grid.
-        sharex, sharey : bool or {'none', 'all', 'row', 'col'}, default: False
+        :param sharex, sharey : bool or {'none', 'all', 'row', 'col'}, default: False
             Controls sharing of properties among x (`sharex`) or y (`sharey`)
             axes:
+            
                 - True or 'all': x- or y-axis will be shared among all
                   subplots.
@@ -269 +270 @@
                 - 'row': each subplot row will share an x- or y-axis.
                 - 'col': each subplot column will share an x- or y-axis.
+                
             When subplots have a shared x-axis along a column, only the x tick
             labels of the bottom subplot are visible.  Similarly, when
             subplots have a shared y-axis along a row, only the y tick labels
             of the first column subplot are visible.
-        squeeze : bool, default: True
+        :param squeeze : bool, default: True
             - If True, extra dimensions are squeezed out from the returned
               axis object:
+              
                 - if only one subplot is constructed (nrows=ncols=1), the
                   resulting single Axes object is returned as a scalar.
@@ -283 +286 @@
                 - for NxM, subplots with N>1 and M>1 are returned as a 2D
                   arrays.
+                  
             - If False, no squeezing at all is done: the returned Axes object
               is always a 2D array containing Axes instances, even if it ends
               up being 1x1.
-        subplot_kw : dict, default: {}
+              
+        :param subplot_kw : dict, default: {}
             Dict with keywords passed to the
             :meth:`~matplotlib.figure.Figure.add_subplot` call used to create
             each subplots.
-        gridspec_kw : dict, default: {}
+        :param gridspec_kw : dict, default: {}
             Dict with keywords passed to the
             :class:`~matplotlib.gridspec.GridSpec` constructor used to create
             the grid the subplots are placed on.
-        Returns
-        -------
-        ax : single Axes object or array of Axes objects
+            
+        :return: ax : single Axes object or array of Axes objects
             The added axes.  The dimensions of the resulting array can be
             controlled with the squeeze keyword, see above.
-        See Also
-        --------
-        pyplot.subplots : pyplot API; docstring includes examples.
+            
+        See Also pyplot.subplots : pyplot API; docstring includes examples.
+        
         """
 

trunk/GSASIIscriptable.py

@@ -1201 +1201 @@
     Represents an entire GSAS-II project.
 
-    There are two ways to initialize it:
+    :param str gpxfile: Existing .gpx file to be loaded. If nonexistent,
+            creates an empty project.
+    :param str author: Author's name (not yet implemented)
+    :param str newgpx: The filename the project should be saved to in
+            the future. If both newgpx and gpxfile are present, the project is
+            loaded from the gpxfile, then when saved will be written to newgpx.
+    :param str filename: Name to be used to save the project. Has same function as
+            parameter newgpx (do not use both gpxfile and filename). Use of newgpx
+            is preferred over filename.
+
+    There are two ways to initialize this object:
 
     >>> # Load an existing project file
@@ -1237 +1247 @@
     """
     def __init__(self, gpxfile=None, author=None, filename=None, newgpx=None):
-        """Loads a GSAS-II project from a specified filename.
-
-        :param str gpxfile: Existing .gpx file to be loaded. If nonexistent,
-            creates an empty project.
-        :param str author: Author's name (not yet implemented)
-        :param str newgpx: The filename the project should be saved to in
-            the future. If both newgpx and gpxfile are present, the project is
-            loaded from the gpxfile, then when saved will be written to newgpx.
-        :param str filename: Name to be used to save the project. Has same function as
-            parameter newgpx (do not use both gpxfile and filename). Use of newgpx
-            is preferred over filename.
-        """
         if filename is not None and newgpx is not None:
             raise G2ScriptException('Do not use filename and newgpx together')
@@ -1592 +1590 @@
             """
         output = []
+        # loop through each tree entry. If it is more than one level (more than one item in the
+        # list of names) then it must be a histogram, unless labeled Phases or Restraints
         for obj in self.names:
-            if len(obj) > 1 and obj[0] != u'Phases':
+            if len(obj) > 1 and obj[0] != u'Phases' and obj[0] != u'Restraints':
                 output.append(self.histogram(obj[0]))
         return output
@@ -2346 +2346 @@
     def set_peakFlags(self,peaklist=None,area=None,pos=None,sig=None,gam=None):
         '''Set refinement flags for peaks
+        
         :param list peaklist: a list of peaks to change flags. If None (default), changes
           are made to all peaks.
@@ -3311 +3312 @@
 
 if __name__ == '__main__':
+    #fname='/tmp/corundum-template.gpx'
+    #prj = G2Project(fname)
     main()

trunk/help/Tutorials.html

@@ -15 +15 @@
  [No exercise files].
 <blockquote><I>An introduction to GSAS-II with starting instructions and a brief description of the displays.</I></blockquote>
-<LI><A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/BkgFit/FitBkgTut.htm">Fitting the Starting Background using Fixed Points</A>
- [link: <A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/BkgFit/data">Exercise files</A>].
-<blockquote><I>This shows how to get an initial estimate of background parameters from a suite of fixed points 
-     before beginning Rietveld refinement.</I></blockquote>
 </UL><h4>Rietveld refinement</H4><UL>
 <LI><A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/CWNeutron/Neutron CW Powder Data.htm">CW Neutron Powder fit for Yttrium-Iron Garnet</A>
@@ -33 +29 @@
  [link: <A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/TOF-CW Joint Refinement/data">Exercise files</A>].
 <blockquote><I>This shows Rietveld refinement with high resolution synchrotron powder data and neutron TOF data</I></blockquote>
+<LI><A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/SimpleMagnetic/Simple Magnetic.htm">Simple Magnetic Structure Analysis</A>
+ [link: <A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/SimpleMagnetic/data">Exercise files</A>].
+<blockquote><I>Analysis of a simple antiferromagnet and a simple ferromagnet from CW neutron powder data</I></blockquote>
 <LI><A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/Simulation/SimTutorial.htm">Simulating Powder Diffraction with GSAS-II</A>
  [link: <A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/Simulation/data">Exercise files</A>].
 <blockquote><I>This show how to create a simulated powder pattern from a lab diffractometer.</I></blockquote>
+<LI><A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/BkgFit/FitBkgTut.htm">Fitting the Starting Background using Fixed Points</A>
+ [link: <A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/BkgFit/data">Exercise files</A>].
+<blockquote><I>This shows how to get an initial estimate of background parameters from a suite of fixed points 
+     before beginning Rietveld refinement.</I></blockquote>
 </UL><h4>Parametric sequential fitting</H4><UL>
 <LI><A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/SeqRefine/SequentialTutorial.htm">Sequential refinement of multiple datasets</A>
@@ -45 +48 @@
 <blockquote><I>This explores the results of the sequential refinement obtained in the previous tutorial; includes 
      plotting of variables and fitting the changes with simple equations.</I></blockquote>
+</UL>
+<UL><LI><A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/TOF Sequential Single Peak Fit/TOF Sequential Single Peak Fit.htm">Sequential fitting of single peaks and strain analysis of reult</A> <A href="#prereq">*</A>
+ [link: <A href="https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/TOF Sequential Single Peak Fit/data">Exercise files</A>].
+<blockquote><I>This shows the fitting of single peaks in a sequence of TOF powder patterns from a sample under load; includes
+      fitting of the result to get Hookes Law coefficients for elastic deformations.</I></blockquote>
 </UL>
 </UL><h4>Structure solution</H4><UL>