Merge remote-tracking branch 'origin/main' into TOFgroup

Author: briantoby

GSASII/GSASIIctrlGUI.py

@@ -429,6 +429,7 @@ def __init__(self,parent,loc,key,nDig=None,notBlank=True,xmin=None,xmax=None,
             else:
                 self.invalid = True
                 self._IndicateValidity()
+            wx.CallAfter(self._TestValidity)    # test/show validity
         else:
             if self.CIFinput:
                 wx.TextCtrl.__init__(
@@ -468,7 +469,7 @@ def SetValue(self,val,warn=True):
         # for debugging flag calls. Set warn to False for calls that are not in callbacks
         # and thus are OK
         if GSASIIpath.GetConfigValue('debug') and warn:
-            print('ValidatedTxtCtrl.SetValue() used in callback. Batter as ChangeValue()?')
+            print('ValidatedTxtCtrl.SetValue() used in callback. Better as ChangeValue()?')
             G2obj.HowDidIgetHere(True)
         if self.result is not None:
             self.result[self.key] = val
@@ -567,9 +568,12 @@ def _onStringKey(self,event):
 
     def _TestValidity(self):
         'Check validity and change colors accordingly'
-        if self.Validator:
-            self.Validator.TestValid(self)
-            self._IndicateValidity()
+        try:
+            if self.Validator:
+                self.Validator.TestValid(self)
+                self._IndicateValidity()
+        except RuntimeError:    #bandaid to avoid C++ error; deleted self.Validator?
+            pass
 
     def _IndicateValidity(self):
         'Set the control colors to show invalid input'

GSASII/GSASIIdataGUI.py

@@ -8126,9 +8126,9 @@ def ClearGroups(event):
     G2frame.dataWindow.SetDataSize()
 #    G2frame.SendSizeEvent()
 
-####  Main PWDR panel ########################################################
+####  Main PWDR & HKLF panel ########################################################
 def UpdatePWHKPlot(G2frame,kind,item):
-    '''Called when the histogram main tree entry is called. Displays the
+    '''Called when the PWDR & HKLF histogram main tree entry is called. Displays the
     histogram weight factor, refinement statistics for the histogram
     and the range of data for a simulation.
 

GSASII/GSASIIimgGUI.py

@@ -3036,12 +3036,8 @@ def OnSetCol(event):
         StrainGrid.SetTable(StrainTable,True)
         StrainGrid.AutoSizeColumns(True)
         for r in range(len(data['d-zero'])):
-            StrainGrid.SetCellStyle(r,2,VERY_LIGHT_GREY,True)
-            StrainGrid.SetCellStyle(r,5,VERY_LIGHT_GREY,True)
-            StrainGrid.SetCellStyle(r,6,VERY_LIGHT_GREY,True)
-            StrainGrid.SetCellStyle(r,7,VERY_LIGHT_GREY,True)
-            StrainGrid.SetCellStyle(r,9,VERY_LIGHT_GREY,True)
-            StrainGrid.SetCellStyle(r,10,VERY_LIGHT_GREY,True)
+            for c in [2,5,6,7,9,10]:
+                StrainGrid.SetCellStyle(r,c,VERY_LIGHT_GREY,True)
         if 'phoenix' in wx.version():
             StrainGrid.Bind(wg.EVT_GRID_CELL_CHANGED, OnStrainChange)
         else:

GSASII/GSASIIlattice.py

@@ -2989,8 +2989,8 @@ def SetUVvec(Neigh):
     return UVvec,UVchoice
 
 def SHarmcal(SytSym,SHFln,psi,gam):
-    '''Perform a surface spherical harmonics computation.
-    Presently only used for plotting
+    '''Perform a surface spherical harmonics computation & return sum of squares.
+    Only used for plotting
     Note that the the number of gam values must either be 1 or must match psi
 
     :param str SytSym: site symmetry - only looking for cubics
@@ -3008,9 +3008,8 @@ def SHarmcal(SytSym,SHFln,psi,gam):
             if SytSym in ['m3m','m3','43m','432','23'] or 'c' in trm:
                 Ksl = CubicSHarm(l,m,psi,gam)
             else:
-                # p = SHFln[term][2]
                 Ksl = SphHarmAng(l,m,1.0,psi,gam)
-            SHVal += SHFln[term][0]*Ksl
+            SHVal += (SHFln[term][0]*Ksl)**2
     return SHVal
 
 def KslCalc(trm,psi,gam):

GSASII/GSASIIpath.py

@@ -1095,69 +1095,145 @@ def runScript(cmds=[], wait=False, G2frame=None):
         sys.exit()
 
 def IPyBreak_base(userMsg=None):
-    '''A routine that invokes an IPython session at the calling location
+    '''A routine that invokes an IPython session at the calling location.
+    Called by a call to :func:`IPyBreak` or command ``breakpoint()``.
     This routine is only used when debug=True is set in the configuration
-    settings
+    settings.
     '''
     savehook = sys.excepthook # save the exception hook
     try:
-        from IPython.terminal.embed import InteractiveShellEmbed
+        import IPython.core
+        # get the Ipython shell routine
+        if IPython.core.getipython.get_ipython() is None:
+            ipshell = IPython.terminal.embed.InteractiveShellEmbed.instance(banner1='')
+        else: # older IPython (still needed?)
+            ipshell = IPython.terminal.embed.InteractiveShellEmbed()
+        import inspect
     except ImportError:
-        try:
-            # try the IPython 0.12 approach
-            from IPython.frontend.terminal.embed import InteractiveShellEmbed
-        except ImportError:
-            print ('IPython InteractiveShellEmbed not found')
-            return
-    import inspect
-    #from IPython import __version__
-    #if __version__.startswith('8.12.'): # see https://github.com/ipython/ipython/issues/13966
-    from IPython.core import getipython
-    if getipython.get_ipython() is None:
-        ipshell = InteractiveShellEmbed.instance()
-    else:
-        ipshell = InteractiveShellEmbed()
+        return
+
+    stack = inspect.stack()     # Get the full stack
+    current_level = [1]  # mutable so inner function can modify it
+    
+    def up(levels=1):
+        '''Move the IPython shell environment up the call stack.
+        Initially coded by Claude Sonnet 4.5
+        '''
+        new_level = current_level[0] + levels
+        if new_level < len(stack):
+            current_level[0] = new_level
+            frame = stack[current_level[0]].frame
+            print(f"Moving to: {stack[current_level[0]].filename}:{stack[current_level[0]].lineno} in {stack[current_level[0]].function}")
+            # Replace the IPython namespace (not update), but preserve IPython internals
+            # Save IPython internal variables and built-in commands
+            ipython_preserve = {k: v for k, v in ipshell.user_ns.items() 
+                              if k.startswith('_') or k in ('exit', 'quit', 'get_ipython')}
+            ipshell.user_ns.clear()
+            ipshell.user_ns.update(ipython_preserve)  # Restore IPython internals
+            ipshell.user_ns.update(frame.f_globals)
+            ipshell.user_ns.update(frame.f_locals)
+            ipshell.user_ns['TB'] = TB
+            ipshell.user_ns['up'] = up
+            ipshell.user_ns['down'] = down
+            ipshell.user_ns['where'] = where
+        else:
+            print(f"Already at top of stack (level {current_level[0]} of {len(stack)-1})")
+    
+    def down(levels=1):
+        '''Move the IPython shell environment down the call stack.
+        Initially coded by Claude Sonnet 4.5
+        '''
+        new_level = current_level[0] - levels
+        if new_level >= 0:
+            current_level[0] = new_level
+            frame = stack[current_level[0]].frame
+            print(f"Moving to: {stack[current_level[0]].filename}:{stack[current_level[0]].lineno} in {stack[current_level[0]].function}")
+            # Replace the IPython namespace (not update), but preserve IPython internals
+            # Save IPython internal variables and built-in commands
+            ipython_preserve = {k: v for k, v in ipshell.user_ns.items() 
+                              if k.startswith('_') or k in ('exit', 'quit', 'get_ipython')}
+            ipshell.user_ns.clear()
+            ipshell.user_ns.update(ipython_preserve)  # Restore IPython internals
+            ipshell.user_ns.update(frame.f_globals)
+            ipshell.user_ns.update(frame.f_locals)
+            ipshell.user_ns['TB'] = TB
+            ipshell.user_ns['up'] = up
+            ipshell.user_ns['down'] = down
+            ipshell.user_ns['where'] = where
+        else:
+            print(f"Already at bottom of stack (level 0)")
+    
+    def where():
+        '''Show current position in stack related to up/down commands.
+        Initially coded by Claude Sonnet 4.5 & revised to reverse display order.
+        '''
+        i = len(stack)
+        for frame_info in reversed(stack):
+            i -= 1
+            marker = ">>>" if i == current_level[0] else "   "
+            print(f"{marker} [{i}] {frame_info.filename}:{frame_info.lineno} in {frame_info.function}")
+
+    def TB(depth=None):
+        '''Show a traceback (to the optional specified depth) to how we got to
+        the breakpoint. Omit the current level as the calling level to here 
+        and above is likely all that we would be interested in.
+        '''
+        if depth is not None: depth += 1
+        for frame_info in reversed(stack[1:depth]):
+            print(f'  File "{frame_info.filename}", line {frame_info.lineno}, in {frame_info.function}')
+            if frame_info.code_context:
+                print(f'    {frame_info.code_context[0].strip()}')
 
     frame = inspect.currentframe().f_back
     msg   = 'Entering IPython console inside {0.f_code.co_filename} at line {0.f_lineno}\n'.format(frame)
+    msg += '\n[up()/down()/where() to navigate stack; TB()/TB(n) for n level tracebacks]'
     if userMsg: msg += userMsg
+    
+    # Add commands to shell namespace
+    locals = frame.f_locals
+    locals['TB'] = TB
+    locals['up'] = up
+    locals['down'] = down
+    locals['where'] = where
+    
     # globals().update(locals()) # This might help with vars inside list comprehensions, etc.
-    ipshell(msg,stack_depth=2) # Go up one level, to see the calling routine
+    ipshell(msg,stack_depth=2,local_ns=locals,global_ns=frame.f_globals)
     sys.excepthook = savehook # reset IPython's change to the exception hook
 
 def exceptHook(*args):
     '''A routine to be called when an exception occurs. It prints the traceback
     with fancy formatting and then calls an IPython shell with the environment
     of the exception location.
 
-    This routine is only used when debug=True is set in the configuration settings
+    This routine is only used when debug=True is set in the configuration 
+    settings.
     '''
     import IPython.core
     savehook = sys.excepthook # save the exception hook
     # show the error location
-    tb_formatter = IPython.core.ultratb.FormattedTB()
-    #tb_formatter = IPython.core.ultratb.ListTB() # better for windows?
-    print() # blank line
+    if sys.platform == "win32":
+        tb_formatter = IPython.core.ultratb.ListTB() # better for windows?
+    else:
+        tb_formatter = IPython.core.ultratb.FormattedTB()
     print(tb_formatter.text(*args,-1),end='') # show only last routine
     # get the Ipython shell routine
     if IPython.core.getipython.get_ipython() is None:
         ipshell = IPython.terminal.embed.InteractiveShellEmbed.instance(banner1='')
     else: # older IPython (still needed?)
         ipshell = IPython.terminal.embed.InteractiveShellEmbed()
     # traceback display routines
-    def TB(): print(IPython.core.ultratb.FormattedTB().text(*args))
-    def vTB(): print(IPython.core.ultratb.VerboseTB().text(*args))
-    def bwTB(): print(IPython.core.ultratb.ListTB().text(*args)) # uncolored
+    def TB(depth=None): print(IPython.core.ultratb.FormattedTB().text(*args,depth))
+    def vTB(depth=-1): print(IPython.core.ultratb.VerboseTB().text(*args,depth))
+    def bwTB(depth=None): print(IPython.core.ultratb.ListTB().text(*args,depth)) # uncolored
     try:     # get to the right frame
         import inspect
         frame = inspect.getinnerframes(args[2])[-1][0]
-        import copy
         locals = frame.f_locals  # add traceback commands to shell namespace
         locals['TB'] = TB
         locals['vTB'] = vTB
         locals['bwTB'] = bwTB
         msg = f'IPython console: {frame.f_code.co_filename}, line {frame.f_lineno}'
-        msg += '\n[TB(), vTB() & bwTB() for tracebacks]'
+        msg += '\n[TB()/TB(-n), vTB()/vTB(-n)/vTB(0) & bwTB() for tracebacks to n levels back]'
         ipshell(msg,local_ns=locals,global_ns=frame.f_globals)
     except:
         msg = 'Entering IPython console (not in error contex)'
@@ -1854,16 +1930,6 @@ def postURL(URL,postdict,getcookie=None,usecookie=None,
             if r.status_code == 200:
                 if GetConfigValue('debug'): print('request OK')
                 page = r.text
-                if 'cryst.ehu.es' in URL and "currently down" in page:
-                    # Bilbao is down. Tell user
-                    import re
-                    print(f"Website down? See message below:\n\n{re.sub('<.+>','',page)}")
-                    try:
-                        import wx
-                        import GSASII.GSASIIctrlGUI as G2G
-                        dlg = G2G.viewWebPage(wx.GetApp().GetMainTopWindow(),URL,HTML=page)
-                    except:
-                        pass
                 if getcookie is not None:
                     getcookie.update(r.cookies)
                 return page # success

GSASII/GSASIIphsGUI.py

@@ -3252,7 +3252,7 @@ def _showWebPage(event):
             with open(tmp.name,'w') as fp:
                 fp.write(pagelist[num].replace(
                 '<head>',
-                '<head><base href="https://www.cryst.ehu.es/">',
+               f'<head><base href="{SUBGROUPS.bilbaoURL}/">',
                 ))
             fileList.append(tmp.name)
             G2G.ShowWebPage('file://'+tmp.name,G2frame)
@@ -3439,7 +3439,7 @@ def _showWebPage(event):
                 with open(tmp.name,'w') as fp:
                     fp.write(f.replace(
                         '<head>',
-                        '<head><base href="https://www.cryst.ehu.es/">',
+                        f'<head><base href="{SUBGROUPS.bilbaoURL}/">',
                         ))
                 fileList.append(tmp.name)
                 G2G.ShowWebPage('file://'+tmp.name,G2frame)
@@ -3919,6 +3919,9 @@ def OnTransform2Std(event):
         generalData = data['General']
         cx,ct,cs,cia = generalData['AtomPtrs']
         sgnum,sgsym,xmat,xoff = SUBGROUPS.GetStdSGset(generalData['SGData'])
+        if xmat is None:
+            G2G.G2MessageBox(G2frame,"Unable to reach web site.",'No connection')
+            return
         if np.allclose(np.eye(3),xmat) and np.allclose(xoff,np.zeros_like(xoff)):
             msg = "Nothing to do. Structure is already set in the standard setting."
             G2G.G2MessageBox(G2frame,msg,'No change needed')

GSASII/GSASIIphsGUI2.py

@@ -207,20 +207,20 @@ def OnRadFxn(event):
         wx.CallAfter(UpdateDeformation,G2frame,data,dId)
 
     def MakeUVmat(defData,U,V):
-        MX = U
+        MX = U/nl.norm(U)
         if 'A' in defData['MUV']:
-            MY = V
+            MY = V/nl.norm(V)
             MZ = np.cross(MX,MY)
             MZ /= nl.norm(MZ)
             MY = np.cross(MZ,MX)
             MY /= nl.norm(MY)
         else:
-            MZ = V
+            MZ = V/nl.norm(V)
             MY = np.cross(MZ,MX)
             MY /= nl.norm(MY)
             MZ = np.cross(MX,MY)
             MZ /= nl.norm(MZ)
-        return np.array([MX,MY,MZ])
+        return np.array([MX,MY,MZ]).T
 
     def OnDeformRef(event):
         Obj = event.GetEventObject()
@@ -507,10 +507,10 @@ def OnAtCol(event):
             oriSizer.Add(delHarm,0,WACV)
         mainSizer.Add(oriSizer)
         G2G.HorizontalLine(mainSizer,deformation)
-        Names = {'D(1,-1)':'px','D(1,0)':'pz','D(1,1)':'py',
-                 'D(2,-2)':'dxy','D(2,-1)':'dxz','D(2,0)':'dz2','D(2,1)':'dyz','D(2,2)':'dx2-y2',
-                 'D(3,-3)':'fy(3x2-y2)','D(3,-2)':'fz(x2-y2)','D(3,-1':'fyz2','D(3,0)':'fz3',
-                 'D(3,1)':'fxz2','D(3,2)':'fxyz','D(3,3)':'fy(3x2-y2)',}
+        Names = {'D(1,-1)':'py','D(1,0)':'pz','D(1,1)':'px',
+                 'D(2,-2)':'dxy','D(2,-1)':'dyz','D(2,0)':'dz2','D(2,1)':'dxz','D(2,2)':'dx2-y2',
+                 'D(3,-3)':'fy(3x2-y2)','D(3,-2)':'fxyz','D(3,-1)':'fyz2','D(3,0)':'fz3',
+                 'D(3,1)':'fxz2','D(3,2)':'fz(x2-y2)','D(3,3)':'fx(x2-3y2)',}
         mainSizer.Add(wx.StaticText(deformation,label=' Deformation parameters:'))
         orbSizer = wx.FlexGridSizer(0,9,2,2)
         for iorb,orb in enumerate(deformationData[dId]):