deal sensibly if PyCifRW (CifFile) not installed; minor cleanup for importer package install

Author: briantoby

GSASII/GSASIIctrlGUI.py

@@ -9646,9 +9646,9 @@ def ImportMsg(parent,msgs):
     could not be installed (due to uninstalled Python packages). Then
     offer the chance to install GSAS-II packages using :func:`SelectPkgInstall`
     '''
-    text = ('Message(s) from load of importers\n\n  '+
-                '\n\n'.join(msgs)+
-                '\n\nNote: These errors only need to be addressed if you want to use the importers listed above')
+    text = ('Warnings message(s) from load of importers:\n\n * '+
+                '\n\n * '.join(msgs)+
+                '\n\n\tTo use any of these importers, press the "Install packages" button\n\tbelow. It is fine to ignore these warnings if you will not need to read\n\tthat file type.')
     ShowScrolledInfo(parent,text,
                     header='Importer load problems',
                     width=650,
@@ -9678,17 +9678,22 @@ def SelectPkgInstall(event):
     dlg = event.GetEventObject().GetParent()
     dlg.EndModal(wx.ID_OK)
     G2frame = wx.App.GetMainTopWindow()
-    choices = []
+
+    choices = {}
     for key in G2fil.condaRequestList:
         for item in G2fil.condaRequestList[key]:
-            choices.append((item,key))
-    msg = 'Select packages to install'
+            if item in choices:
+                choices[item] += f', {key}'
+            else:
+                choices[item] = key
+    msg = 'Select package(s) to install'
     if GSASIIpath.condaTest():
         msg += ' using conda'
     else:
         msg += ' using pip'
     sel = MultiColMultiSelDlg(G2frame, 'Install packages?', msg,
-                             [('package',120,0),('needed by',300,0)], choices)
+                             [('package',120,0),('needed by',300,0)],
+                             [i for i in choices.items()])
     if sel is None: return
     if not any(sel): return
     pkgs = [choices[i][0] for i,f in enumerate(sel) if f]

GSASII/GSASIIobj.py

@@ -229,14 +229,22 @@ def ReadCIF(URLorFile):
     (from James Hester).
     The open routine gets confused with DOS names that begin with a letter and colon
     "C:\\dir\" so this routine will try to open the passed name as a file and if that
-    fails, try it as a URL
+    fails, try it as a URL.
+
+    Used for CIF imports and for reading CIF templates for project CIF exports
 
     :param str URLorFile: string containing a URL or a file name. Code will try first
       to open it as a file and then as a URL.
 
-    :returns: a PyCifRW CIF object.
+    :returns: a PyCifRW CIF object or an empty string if PyCifRW is not accessible
     '''
-    import CifFile as cif # PyCifRW from James Hester
+    try:
+        import CifFile as cif # PyCifRW from James Hester as a package
+    except ImportError:
+        try:
+            from .. import CifFile as cif # PyCifRW, as distributed w/G2 (old)
+        except ImportError:
+            return ''
 
     # alternate approach:
     #import urllib

GSASII/exports/G2export_CIF.py

@@ -18,8 +18,9 @@
     import wx.lib.scrolledpanel as wxscroll
     import wx.lib.resizewidget as rw
     interactive = True
-    from . import GSASIIctrlGUI as G2G
+    from .. import GSASIIctrlGUI as G2G
 except ImportError:
+    G2G = None
     # Avoid wx dependency for Scriptable
     class Placeholder(object):
         def __init__(self):
@@ -1679,6 +1680,7 @@ def writeCIFtemplate(G2dict,tmplate,defaultname='',
             In all cases the initial data_ header is stripped (there should only be one!)
             '''
             CIFobj = G2dict.get(cifKey)
+            if CIFobj is None: return
             if defaultname:
                 defaultname = G2obj.StripUnicode(defaultname)
                 defaultname = re.sub(r'[^a-zA-Z0-9_-]','',defaultname)
@@ -4668,6 +4670,17 @@ def Exporter(self,event=None,seqData=None,Controls=None):
         #print('reloaded GSASIImapvars')
         #### end debug stuff ##############################
 
+        if G2G is None:
+            print('Unable to export without GUI access')
+            return
+        try:
+            import CifFile as cif # PyCifRW from James Hester as a package
+        except ImportError:
+            try:
+                from .. import CifFile as cif # PyCifRW, as distributed w/G2 (old)
+            except ImportError:
+                msg = 'The PyCifRW package is not installed. CIF templates cannot be accessed. Created CIFs will be incomplete'
+                G2G.G2MessageBox(self.G2frame,msg,'no PyCifRW')
         self.CIFname = ''
         self.seqData = seqData
         self.Controls = Controls
@@ -5038,7 +5051,11 @@ def PickleCIFdict(fil):
     try:
         import CifFile as cif # PyCifRW from James Hester as a package
     except ImportError:
-        from .. import CifFile as cif # PyCifRW, as distributed w/G2 (old)
+        try:
+            from .. import CifFile as cif # PyCifRW, as distributed w/G2 (old)
+        except ImportError:
+            print('Warning: Unable to import PyCifRW')
+            return {}
     cifdic = {}
     try:
         fp = open(fil,'r')             # patch: open file to avoid windows bug
@@ -5178,7 +5195,11 @@ def dict2CIF(dblk,loopstructure,blockname='Template'):
     try:
         import CifFile as cif # PyCifRW from James Hester as a package
     except ImportError:
-        from .. import CifFile as cif # PyCifRW, as distributed w/G2 (old)
+        try:
+            from .. import CifFile as cif # PyCifRW, as distributed w/G2 (old)
+        except ImportError:
+            print('Warning: Unable to import PyCifRW')
+            return {}
     # compile a 'list' of items in loops
     loopnames = set()
     for i in loopstructure:
@@ -5654,6 +5675,8 @@ def _onEditTemplateContents(self,event):
             dblk,loopstructure = copy.deepcopy(self.CIF_template) # don't modify original
         else:
             cf = G2obj.ReadCIF(self.CIF_template)
+            if len(cf) == 0:
+                raise Exception("No CIF data_ blocks found")
             dblk,loopstructure = CIF2dict(cf)
         dlg = EditCIFtemplate(self.cifdefs,dblk,loopstructure,self.defaultname)
         val = dlg.Post()

GSASII/imports/G2phase_CIF.py

@@ -9,22 +9,29 @@
 import re
 import copy
 import os.path
+from .. import GSASIIpath
 from .. import GSASIIobj as G2obj
 from .. import GSASIIspc as G2spc
 from .. import GSASIIElem as G2elem
 from .. import GSASIIlattice as G2lat
-from .. import GSASIIpath
 from .. import GSASIIfiles as G2fil
 try:
     import CifFile as cif # PyCifRW from James Hester as a package
 except ImportError:
-    from .. import CifFile as cif # PyCifRW, as distributed w/G2 (old)
+    try:
+        from .. import CifFile as cif # PyCifRW, as distributed w/G2 (old)
+    except ImportError:
+        cif = None
 debug = GSASIIpath.GetConfigValue('debug')
 #debug = False
 
 class CIFPhaseReader(G2obj.ImportPhase):
     'Implements a phase importer from a possibly multi-block CIF file'
     def __init__(self):
+        if cif is None:
+            self.UseReader = False
+            msg = 'CIFPhase Reader skipped because PyCifRW (CifFile) module is not installed.'
+            G2fil.ImportErrorMsg(msg,{'CIF Phase importer':['pycifrw']})
         super(self.__class__,self).__init__( # fancy way to say ImportPhase.__init__
             extensionlist=('.CIF','.cif','.mcif'),
             strictExtension=False,

GSASII/imports/G2pwd_BrukerBRML.py

@@ -24,8 +24,6 @@ def __init__(self):
         if xml is None:
             self.UseReader = False
             msg = 'Bruker .brml Reader skipped because xmltodict module is not installed.'
-            if GSASIIpath.condaTest():
-                msg += ' To fix this press "Install packages" button below'
             from .. import GSASIIfiles as G2fil
             G2fil.ImportErrorMsg(msg,{'Bruker .brml Importer':['xmltodict']})
         self.scriptable = True

GSASII/imports/G2pwd_CIF.py

@@ -4,17 +4,25 @@
 from __future__ import division, print_function
 import numpy as np
 import os.path
-from .. import GSASIIobj as G2obj
 from .. import GSASIIpath
+from .. import GSASIIobj as G2obj
+from .. import GSASIIfiles as G2fil
 try:
     import CifFile as cif # PyCifRW from James Hester as a package
 except ImportError:
-    from .. import CifFile as cif # PyCifRW, as distributed w/G2 (old)
+    try:
+        from .. import CifFile as cif # PyCifRW, as distributed w/G2 (old)
+    except ImportError:
+        cif = None
 asind = lambda x: 180.*np.arcsin(x)/np.pi
 
 class CIFpwdReader(G2obj.ImportPowderData):
     'Routines to import powder data from a CIF file'
     def __init__(self):
+        if cif is None:
+            self.UseReader = False
+            msg = 'CIF PWDR Reader skipped because PyCifRW (CifFile) module is not installed.'
+            G2fil.ImportErrorMsg(msg,{'CIF powder importer':['pycifrw']})
         super(self.__class__,self).__init__( # fancy way to self-reference
             extensionlist=('.CIF','.cif'),
             strictExtension=False,

GSASII/imports/G2pwd_MIDAS.py

@@ -14,8 +14,8 @@
 from .. import GSASIIfiles as G2fil
 from .. import GSASIIpath
 
-instprmList = [('Bank',1.0), ('Lam',0.413263), ('Polariz.',0.99), 
-            ('SH/L',0.002), ('Type','PXC'), ('U',1.163), ('V',-0.126), 
+instprmList = [('Bank',1.0), ('Lam',0.413263), ('Polariz.',0.99),
+            ('SH/L',0.002), ('Type','PXC'), ('U',1.163), ('V',-0.126),
             ('W',0.063), ('X',0.0), ('Y',0.0), ('Z',0.0), ('Zero',0.0)]
 #   comments
 #   sample parameters
@@ -28,12 +28,12 @@
 # 'Thick': 1.0, 'Contrast': [0.0, 0.0], 'Trans': 1.0, 'SlitLen': 0.0}
 
 class MIDAS_Zarr_Reader(G2obj.ImportPowderData):
-    '''Routine to read multiple powder patterns from a Zarr file 
-    created by MIDAS. Perhaps in the future, other software might also 
-    use this file type as well. 
+    '''Routine to read multiple powder patterns from a Zarr file
+    created by MIDAS. Perhaps in the future, other software might also
+    use this file type as well.
 
-    For Midas, the main file is <file>.zip, but optionally sample and 
-    instrument parameters can be placed in <file>.samprm and <file>.instprm. 
+    For Midas, the main file is <file>.zip, but optionally sample and
+    instrument parameters can be placed in <file>.samprm and <file>.instprm.
     Any parameters placed in those files will override values set in the .zip
     file.
     '''
@@ -43,8 +43,6 @@ def __init__(self):
         if zarr is None:
             self.UseReader = False
             msg = 'MIDAS_Zarr Reader skipped because zarr module is not installed.'
-            if GSASIIpath.condaTest():
-                msg += ' To fix this press "Install packages" button below'
             G2fil.ImportErrorMsg(msg,{'MIDAS Zarr importer':['zarr']})
         super(self.__class__,self).__init__( # fancy way to self-reference
             extensionlist=('.zarr.zip',),strictExtension=True,
@@ -68,18 +66,18 @@ def ContentsValidator(self, filename):
         return False
 
     def Reader(self, filename, ParentFrame=None, **kwarg):
-        '''Scan file for sections needed by defined file types (currently 
+        '''Scan file for sections needed by defined file types (currently
         only Midas) and then use appropriate routine to read the file.
-        Most of the time the results are placed in the buffer arg (if supplied) 
-        so the file is not read on most calls. 
+        Most of the time the results are placed in the buffer arg (if supplied)
+        so the file is not read on most calls.
 
-        For MIDAS, masking can eliminate some or all points in an azimuthal 
-        region. This will only return "lineouts" (aka diffractograms) that 
-        have 20 or more points in them. 
+        For MIDAS, masking can eliminate some or all points in an azimuthal
+        region. This will only return "lineouts" (aka diffractograms) that
+        have 20 or more points in them.
 
-        Note that if Reader.selections is used to select individual 
-        "lineouts", the selections are numbered against all possible 
-        "lineouts" not the ones that have 20 or more points. 
+        Note that if Reader.selections is used to select individual
+        "lineouts", the selections are numbered against all possible
+        "lineouts" not the ones that have 20 or more points.
         '''
         fpbuffer = kwarg.get('buffer',{})
         if not hasattr(self,'blknum'):
@@ -99,7 +97,7 @@ def Reader(self, filename, ParentFrame=None, **kwarg):
                 return False
             finally:
                 del fp
-                    
+
         if self.mode == 'midas':
             return self.readMidas(filename, fpbuffer)
 
@@ -125,7 +123,7 @@ def readMidas(self, filename, fpbuffer={}):
             try:
                 fp = zarr.open(filename, 'r')
                 fpbuffer['REtaMap'] = np.array(fp['REtaMap']) # 4 x Nbins x Nazimuth
-                # [0]: radius; [1] 2theta; [2] eta; [3] bin area 
+                # [0]: radius; [1] 2theta; [2] eta; [3] bin area
                 # tabulate integrated intensities image & eta
                 fpbuffer['intenArr'] = []
                 fpbuffer['attributes'] = []
@@ -143,20 +141,20 @@ def readMidas(self, filename, fpbuffer={}):
                 fpbuffer['unmasked'] = [(fpbuffer['REtaMap'][3][:,i] != 0) for i in range(Nazim)] # will be True if area is >0
                 # find the azimuths with more than 20 points
                 mAzm = [i for i in range(Nazim) if sum(fpbuffer['unmasked'][i]) > 20]
-                
+
                 # generate a list of lineouts to be read from selections
                 if self.selections:
                     sel = self.selections
                 else:
                     sel = range(Nimg*Nazim) # nothing selected, use all
                 # fpbuffer['2Read'] is the list of lineouts to be read, where each entry
                 # contains two values, the azumuth and the image number (iAzm,iImg)
-                # defined points for each lineout are then 
+                # defined points for each lineout are then
                 #   intensities : fpbuffer['intenArr'][iImg][:,iAzm][unmasked[iAzm]]
                 #   2thetas: fpbuffer['REtaMap'][1][:,iAzm][unmasked[iAzm]]
                 fpbuffer['2Read'] = [(i%Nazim,i//Nazim) for i in sel if i%Nazim in mAzm]
                 # xfrom Zarr dict into a native dict
-                self.MIDASinstprm = {i:j[0] for i,j in fp['InstrumentParameters'].items()} 
+                self.MIDASinstprm = {i:j[0] for i,j in fp['InstrumentParameters'].items()}
                 # change a few keys
                 for key,newkey in [('Polariz','Polariz.'),('SH_L','SH/L')]:
                     if key in self.MIDASinstprm:
@@ -167,7 +165,7 @@ def readMidas(self, filename, fpbuffer={}):
                 return False
             finally:
                 del fp
-            # get overriding sample & instrument parameters 
+            # get overriding sample & instrument parameters
             self.MIDASsampleprm = {}
             samplefile = os.path.splitext(filename)[0] + '.samprm'
             if os.path.exists(samplefile):
@@ -189,7 +187,7 @@ def readMidas(self, filename, fpbuffer={}):
                 fp.close()
                 nbank,self.instvals = G2fil.ReadInstprm(instLines, None, self.Sample)
         #======================================================================
-        # start reading 
+        # start reading
         #======================================================================
         # look for the next non-empty scan (lineout)
         iAzm,iImg = fpbuffer['2Read'][self.blknum]
@@ -211,16 +209,16 @@ def readMidas(self, filename, fpbuffer={}):
         omega = 999.  # indicates an error
         try:
             omega = 0.5 * (
-                fpbuffer['attributes'][iImg]['FirstOme'] + 
+                fpbuffer['attributes'][iImg]['FirstOme'] +
                 fpbuffer['attributes'][iImg]['LastOme'])
         except:
             pass
         eta = sum(fpbuffer['REtaMap'][2][:,iAzm][unmasked])/sum(unmasked) # compute an averaged Phi value
         radius = 1000   # sample to detector distance (mm)
         if 'Distance' in self.MIDASinstprm:
             radius = self.MIDASinstprm['Distance']/1000   # convert from microns
-        
-        # now transfer instprm & sample prms into current histogram 
+
+        # now transfer instprm & sample prms into current histogram
         self.pwdparms['Instrument Parameters'] = [{}, {}]
         inst = {}
         inst.update(instprmList)

GSASII/imports/G2sfact_CIF.py

@@ -6,15 +6,24 @@
 from __future__ import division, print_function
 import numpy as np
 import os.path
+from .. import GSASIIpath
 from .. import GSASIIobj as G2obj
+from .. import GSASIIfiles as G2fil
 try:
     import CifFile as cif # PyCifRW from James Hester as a package
 except ImportError:
-    from .. import CifFile as cif # PyCifRW, as distributed w/G2 (old)
+    try:
+        from .. import CifFile as cif # PyCifRW, as distributed w/G2 (old)
+    except ImportError:
+        cif = None
 
 class CIFhklReader(G2obj.ImportStructFactor):
     'Routines to import Phase information from a CIF file'
     def __init__(self):
+        if cif is None:
+            self.UseReader = False
+            msg = 'CIF Xtal Reader skipped because PyCifRW (CifFile) module is not installed.'
+            G2fil.ImportErrorMsg(msg,{'CIF HKLF importer':['pycifrw']})
         super(self.__class__,self).__init__( # fancy way to self-reference
             extensionlist = ('.CIF','.cif','.FCF','.fcf','.HKL','.hkl'),
             strictExtension = False,