Merge remote-tracking branch 'origin/main' into MAXIV-HDF5

to bring up to date for additional work

Author: briantoby

.github/workflows/update_help.yml

@@ -0,0 +1,71 @@
+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.
+
+on:
+  repository_dispatch: # run from Web API
+  workflow_dispatch:
+
+permissions:
+  contents: write
+  id-token: write
+  pages: write
+
+jobs:
+  build:       # Build web pages
+    runs-on: ubuntu-latest
+    steps:
+
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Checkout
+        # get the help pages from GSAS-II docs repo
+        uses: actions/checkout@v4
+        with:
+            repository: AdvancedPhotonSource/GSAS-II-tutorials.git
+            path: _docs
+            ref: main
+
+      - name: Python setup
+        uses: actions/setup-python@v3
+
+      - name: mkdocs setup
+        run: |
+          pip install mkdocs mkdocs-material python-markdown-math mkdocs-static-i18n
+          pip install mkdocs-to-pdf pymdown-extensions
+
+      # MD help conversion
+      - name: convert MDhelp
+        run: |
+          pwd
+          cd _docs/MDhelp
+          mkdocs build
+          python findMDanchors.py  # create an anchor index
+          rm -rf ../../GSASII/help/assets/javascripts/
+          rm -rf ../../GSASII/help/assets/stylesheets/
+          cp -vr site/* ../../GSASII/help
+          cd ../../GSASII/help
+          pwd
+          ls -lt
+
+      - name: git diagnostics
+        run: |
+          pwd 
+          git status
+          git diff
+          git add GSASII/help
+          echo "After add"
+          git status
+
+      - name: commit changes
+        run: |
+          git add GSASII/help
+          git config user.name "github-actions[bot]"
+          git config user.email "github-actions[bot]@users.noreply.github.com"
+          git commit -m"update help files"
+
+      - name: push help into repo
+        run: |
+          git push

GSASII/GSASIIElem.py

@@ -89,7 +89,6 @@ def GetFFtable(atomTypes):
 
 def GetEFFtable(atomTypes):
     ''' returns a dictionary of electron form factor data for atom types found in atomTypes
-    might not be needed?
 
     :param list atomTypes: list of atom types
     :return: FFtable, dictionary of form factor data; key is atom type
@@ -242,6 +241,14 @@ def CheckElement(El):
         return True
     else:
         return False
+def StripValence(El):
+    'Returns element symbol without valence'
+    if '+' in El:
+        return El.split('+')[0]
+    elif '-' in El:
+        return El.split('-')[0]
+    else:
+        return El
 
 def FixValence(El):
     'Returns the element symbol, even when a valence is present'
@@ -906,12 +913,17 @@ def SetupGeneral(data, dirname):
 
     F000X = 0.
     F000N = 0.
+    F000E = 0.
+    ElTypes = [StripValence(elem) for elem in generalData['AtomTypes']]
+    EFFtables = GetEFFtable(ElTypes) # broken for charged species
     for i,elem in enumerate(generalData['AtomTypes']):
         F000X += generalData['NoAtoms'][elem]*generalData['Z']
         isotope = generalData['Isotope'][elem]
         F000N += generalData['NoAtoms'][elem]*generalData['Isotopes'][elem][isotope]['SL'][0]
+        F000E += generalData['NoAtoms'][elem]*ScatFac(EFFtables[StripValence(elem)],0.)[0]
     generalData['F000X'] = F000X
     generalData['F000N'] = F000N
+    generalData['F000E'] = F000E
     generalData['Mass'] = G2mth.getMass(generalData)
 
     if badList:

GSASII/GSASIIGUI.py

@@ -66,10 +66,15 @@ def MacOpenFiles(self, filenames):
         application = wx.App(0) # create the GUI framework
     try:
         GSASIIpath.SetBinaryPath(True)
-    except:
-        print('Unable to run with current installation, please reset or reinstall')
+    except Exception as msg:
+        print(
+'''Unable to run with current installation due to lack of binary (compiled) 
+files, please reset or reinstall''')
+        print('\nError:')
+        print(msg)
         # if GSASIIpath.HowIsG2Installed().startswith('git'):
         #     print('use this command w/gitstrap')
+        
         sys.exit()
         # print('Unable to run with current setup, do you want to update to the')
         # try:

GSASII/GSASIIconstrGUI.py

@@ -266,56 +266,65 @@ class ConstraintDialog(wx.Dialog):
     '''
     def __init__(self,parent,title,text,data,separator='*',varname="",varyflag=False):
         wx.Dialog.__init__(self,parent,-1,'Edit '+title, 
-            pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
+            pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE | wx.RESIZE_BORDER)
         self.data = data[:]
         self.newvar = [varname,varyflag]
-        panel = wx.Panel(self)
         mainSizer = wx.BoxSizer(wx.VERTICAL)
-        topLabl = wx.StaticText(panel,-1,text)
-        mainSizer.Add((10,10),1)
-        mainSizer.Add(topLabl,0,wx.LEFT,10)
-        mainSizer.Add((10,10),1)
+        self.SetSizer(mainSizer)
+        topLabl = wx.StaticText(self,-1,text) # top label
+        # bottom buttons
+        self.OkBtn = wx.Button(self,wx.ID_OK)
+        self.OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
+        self.OkBtn.SetDefault()
+        cancelBtn = wx.Button(self,wx.ID_CANCEL)
+        cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel)
+        btnSizer = wx.BoxSizer(wx.HORIZONTAL)
+        btnSizer.Add((20,20),1)
+        btnSizer.Add(self.OkBtn)
+        btnSizer.Add((20,20),1)
+        btnSizer.Add(cancelBtn)
+        btnSizer.Add((20,20),1)
+
+        # create scrolled edit contents        
+        size=(600,350) # initial scrolled region size
+        subpanel = wxscroll.ScrolledPanel(self, wx.ID_ANY,size=size,
+            style = wx.TAB_TRAVERSAL|wx.SUNKEN_BORDER)
         dataGridSizer = wx.FlexGridSizer(cols=3,hgap=2,vgap=2)
-        self.OkBtn = wx.Button(panel,wx.ID_OK)
+        subpanel.SetSizer(dataGridSizer)
         for id in range(len(self.data)):
             lbl1 = lbl = str(self.data[id][1])
             if lbl[-1] != '=': lbl1 = lbl + ' ' + separator + ' '
-            name = wx.StaticText(panel,wx.ID_ANY,lbl1,style=wx.ALIGN_RIGHT)
-            scale = G2G.ValidatedTxtCtrl(panel,self.data[id],0,OKcontrol=self.DisableOK)
+            name = wx.StaticText(subpanel,wx.ID_ANY,lbl1,style=wx.ALIGN_RIGHT)
+            scale = G2G.ValidatedTxtCtrl(subpanel,self.data[id],0,OKcontrol=self.DisableOK)
             dataGridSizer.Add(name,0,wx.LEFT|wx.RIGHT|WACV,5)
             dataGridSizer.Add(scale,0,wx.RIGHT,3)
             if ':' in lbl:
                 dataGridSizer.Add(
-                    wx.StaticText(panel,-1,G2obj.fmtVarDescr(lbl)),
+                    wx.StaticText(subpanel,-1,G2obj.fmtVarDescr(lbl)),
                     0,wx.RIGHT|WACV,3)
             else:
                 dataGridSizer.Add((-1,-1))
         if title == 'New Variable':
-            name = wx.StaticText(panel,wx.ID_ANY,"New variable's\nname (optional)",
+            name = wx.StaticText(subpanel,wx.ID_ANY,"New variable's\nname (optional)",
                 style=wx.ALIGN_CENTER)
-            scale = G2G.ValidatedTxtCtrl(panel,self.newvar,0,notBlank=False)
+            scale = G2G.ValidatedTxtCtrl(subpanel,self.newvar,0,notBlank=False)
             dataGridSizer.Add(name,0,wx.LEFT|wx.RIGHT|WACV,5)
             dataGridSizer.Add(scale,0,wx.RIGHT|WACV,3)
-            self.refine = wx.CheckBox(panel,label='Refine?')
+            self.refine = wx.CheckBox(subpanel,label='Refine?')
             self.refine.SetValue(self.newvar[1]==True)
             self.refine.Bind(wx.EVT_CHECKBOX, self.OnCheckBox)
             dataGridSizer.Add(self.refine,0,wx.RIGHT|WACV,3)
-            
-        mainSizer.Add(dataGridSizer,0,wx.EXPAND)
-        self.OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
-        self.OkBtn.SetDefault()
-        cancelBtn = wx.Button(panel,wx.ID_CANCEL)
-        cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel)
-        btnSizer = wx.BoxSizer(wx.HORIZONTAL)
-        btnSizer.Add((20,20),1)
-        btnSizer.Add(self.OkBtn)
-        btnSizer.Add((20,20),1)
-        btnSizer.Add(cancelBtn)
-        btnSizer.Add((20,20),1)
-
+        # layout window
+        mainSizer.Add((-1,10),0)
+        mainSizer.Add(topLabl,0,wx.LEFT,10)
+        mainSizer.Add((-1,10),0)
+        mainSizer.Add(subpanel,1,wx.EXPAND)
+        mainSizer.Add((-1,3),0)
         mainSizer.Add(btnSizer,0,wx.EXPAND, 10)
-        panel.SetSizer(mainSizer)
-        panel.Fit()
+        mainSizer.Add((-1,3),0)
+        # finish up ScrolledPanel & then window
+        subpanel.SetAutoLayout(1)
+        subpanel.SetupScrolling()
         self.Fit()
         self.CenterOnParent()
 

GSASII/GSASIIctrlGUI.py

@@ -4961,7 +4961,7 @@ def AddSpinner(varSizer,label,SelCtrl,binding):
         parmSizer.Add(selectionsSizer,0)
         refChoices = ['All','Refined']
         txt = ('"R" indicates a refined variable\n'+
-               '"C" indicates generated from a user entered constraint')
+               '"C" value generated from a constraint')
         if fcount:
             refChoices += ['Frozen']
             txt += '\n"F" indicates a variable that is Frozen due to exceeding min/max'
@@ -5900,13 +5900,13 @@ def __init__(self,frame,includeTree=False,morehelpitems=[]):
             helpobj = self.Append(wx.ID_ANY,lbl,'')
             frame.Bind(wx.EVT_MENU, self.OnHelpById, helpobj)
             self.HelpById[helpobj.GetId()] = indx
-        # add help lookup(s) in gsasii.html
+        # add help lookup(s) in GSAS-II Help
         self.AppendSeparator()
         if includeTree:
             helpobj = self.Append(wx.ID_ANY,'Help on GSAS-II',
-                'Access web page with information on GSAS-II')
+                'Access web pages with information on GSAS-II')
             frame.Bind(wx.EVT_MENU, self.OnHelpById, id=helpobj.GetId())
-            self.HelpById[helpobj.GetId()] = 'Data tree'
+            self.HelpById[helpobj.GetId()] = 'HelpIntro'
         helpobj = self.Append(wx.ID_ANY,'Help on current data tree item\tF1',
                 'Access web page on selected item in tree')
         frame.Bind(wx.EVT_MENU, self.OnHelpById, id=helpobj.GetId())
@@ -5916,21 +5916,18 @@ def __init__(self,frame,includeTree=False,morehelpitems=[]):
 
     def OnHelpById(self,event):
         '''Called when Help on... is pressed in a menu. Brings up a web page
-        for documentation. Uses the helpKey value from the dataWindow window
-        unless a special help key value has been defined for this menu id in
-        self.HelpById
-
-        Note that self should now (2frame) be child of the main window (G2frame)
+        for documentation. Uses the G2frame.dataWindow.helpKey value to select
+        what help is shown, unless a special help key value has been defined 
+        for the calling menu id (via a lookup in self.HelpById[], which is used
+        for Tutorials & Overall help). 
+        Note that G2frame.dataWindow.helpKey SelectDataTreeItem and reflects 
+        the data tree item that has been selected.
+
+        Note that self here should be a child of the main window (G2frame)
+        where self.frame is G2frame
         '''
-        if hasattr(self.frame,'dataWindow'):  # Debug code: check this is called from menu in G2frame
-            # should always be true in 2 Frame version
-            dW = self.frame.dataWindow
-        else:
-            print('help error: not called from standard menu?')
-            print (self)
-            return
         try:
-            helpKey = dW.helpKey # look up help from helpKey in data window
+            helpKey = self.frame.dataWindow.helpKey # look up help from helpKey in data window
             #if GSASIIpath.GetConfigValue('debug'): print 'DBG_dataWindow help: key=',helpKey
         except AttributeError:
             helpKey = ''
@@ -6035,7 +6032,7 @@ def copy2clip(event):
 class HelpButton(wx.Button):
     '''Create a help button that displays help information.
     The text can be displayed in a modal message window or it can be
-    a reference to a location in the gsasII.html (etc.) help web page, in which
+    a reference to a location in the gsasII help web pages, in which
     case that page is opened in a web browser.
 
     TODO: it might be nice if it were non-modal: e.g. it stays around until
@@ -6046,9 +6043,12 @@ class HelpButton(wx.Button):
     :param str msg: the help text to be displayed. Indentation on
        multiline help text is stripped (see :func:`StripIndents`). If wrap
        is set as non-zero, all new lines are
-    :param str helpIndex: location of the help information in the gsasII.html
-      help file in the form of an anchor string. The URL will be
-      constructed from: location + gsasII.html + "#" + helpIndex
+    :param str helpIndex: selection for the help information in the GSAS-II
+      help files, in the form of an anchor string. That anchor is looked 
+      up to find the file name and the URL is constructed from: 
+
+         <location> + <filename> + "#" + helpIndex
+
     :param int wrap: if specified, the text displayed is reformatted by
       wrapping it to fit in wrap pixels. Default is None which prevents
       wrapping.
@@ -7626,22 +7626,31 @@ class G2LstCtrl(wx.ListCtrl):
 htmlPanel = None
 htmlFrame = None
 htmlFirstUse = True
-#helpLocDict = {}  # to be implemented if we ever split gsasii.html over multiple files
+helpLocDict = {}
+'This is an index to the HTML anchors defined in the GSAS-II help files'
 path2GSAS2 = os.path.dirname(os.path.realpath(__file__)) # save location of this file
 def ShowHelp(helpType,frame,helpMode=None):
     '''Called to bring up a web page for documentation.'''
     global htmlFirstUse,htmlPanel,htmlFrame
+    if not helpLocDict: # load the anchor index
+        indx = os.path.abspath(os.path.join(path2GSAS2,'help','anchorIndex.txt'))
+        print('reading file',indx)
+        with open(indx,'r') as indexfile:
+            for line in indexfile.readlines():
+                fil,anchors = line.split(':')
+                for a in anchors.split(','):
+                    #if a in helpLocDict: print(a,'repeated!')
+                    helpLocDict[a.strip()] = fil
     # no defined link to use, create a default based on key
-    if helpType.lower().startswith('pwdr'):
-        helplink = 'gsasII-pwdr.html#'+helpType.replace(')','').replace('(','_').replace(' ','_')
-    elif helpType.lower().startswith('phase'):
-        helplink = 'gsasII-phase.html#'+helpType.replace(')','').replace('(','_').replace(' ','_')
-    elif helpType.lower().startswith('hist/phase'):
-        helplink = 'gsasII-phase.html#Phase-Data'
-    elif helpType:
-        helplink = 'gsasII.html#'+helpType.replace(')','').replace('(','_').replace(' ','_')
-    else:
-        helplink = 'gsasII.html'
+    helplink = 'index.html'
+    if helpType:
+        anchor = helpType.replace(')','').replace('(','_').replace(' ','_')
+        if anchor not in helpLocDict:
+            print(f'Help lookup problem, anchor {anchor} not found'
+                      '\nPlease report this to [email protected] along with a'
+                      '\nscreen image showing where you tried to get help')
+        else:
+            helplink = f'{helpLocDict[anchor]}#{anchor}'
     # determine if a web browser or the internal viewer should be used for help info
     if helpMode:
         pass

GSASII/GSASIIdataGUI.py

@@ -680,6 +680,7 @@ def OnwxInspect(event):
     def _Add_DataMenuItems(self,parent):
         '''Add items to Data menu
         '''
+        #(7/2025) next duplicated in Import menu; patch: remove this someday
         item = parent.Append(wx.ID_ANY,'Read Powder Pattern Peaks...','')
         self.Bind(wx.EVT_MENU, self.OnReadPowderPeaks, id=item.GetId())
         item = parent.Append(wx.ID_ANY,'Sum or Average powder data','')
@@ -2759,6 +2760,8 @@ def FillMainMenu(self,menubar,addhelp=True):
         self._Add_ImportMenu_smallangle(Import)
         self._Add_ImportMenu_reflectometry(Import)
         self._Add_ImportMenu_PDF(Import)
+        item = Import.Append(wx.ID_ANY,'Read Powder Pattern Peaks...','')
+        self.Bind(wx.EVT_MENU, self.OnReadPowderPeaks, id=item.GetId())
 
         item = Import.Append(wx.ID_ANY,'Column metadata test','Test Column (.par) metadata import')
         self.Bind(wx.EVT_MENU, self.OnColMetaTest, id=item.GetId())
@@ -2860,9 +2863,9 @@ def _init_ctrls(self, parent):
         self.dataWindow = G2DataWindow(self.mainPanel)
         dataSizer = wx.BoxSizer(wx.VERTICAL)
         self.dataWindow.SetSizer(dataSizer)
-        self.mainPanel.SplitVertically(self.treePanel,
-                                           self.dataWindow.outer, 400)
-        self.Status.SetStatusWidths([200,-1])   # make these match?
+        sash = min(max(100,GSASIIpath.GetConfigValue('Split_Loc',250)),500)
+        self.mainPanel.SplitVertically(self.treePanel, self.dataWindow.outer, sash)
+        self.Status.SetStatusWidths([sash,-1])   # make these match?
 
         G2G.wxID_GPXTREE = wx.NewId()
         treeSizer = wx.BoxSizer(wx.VERTICAL)
@@ -4534,7 +4537,8 @@ def ExitMain(self, event):
                      'Main_Size':tuple(self.GetSize()),
                      'Plot_Pos':tuple(self.plotFrame.GetPosition()),
                      'Plot_Size':tuple(self.plotFrame.GetSize())}
-            GSASIIpath.SetConfigValue(FrameInfo)
+            GSASIIpath.AddConfigValue(FrameInfo)
+            GSASIIpath.AddConfigValue({'Split_Loc':self.mainPanel.GetSashPosition()})
             config = G2G.GetConfigValsDocs()
             G2G.SaveConfigVars(config)
         except:
@@ -8560,7 +8564,7 @@ def OnShowShift(event):
     parentID = G2frame.root
     if item == G2frame.root:
         G2frame.dataWindow.ClearData()
-        G2frame.helpKey = "Data tree"
+        G2frame.dataWindow.helpKey = "Data tree"
         mainSizer =  wx.BoxSizer(wx.VERTICAL)
         G2frame.dataWindow.SetSizer(mainSizer)
         mainSizer.Add(wx.StaticText(G2frame.dataWindow, wx.ID_ANY,