create bilbao self-tests (currently to run manually)

Author: briantoby

GSASII/GSASIIpwdGUI.py

@@ -4840,11 +4840,11 @@ def OnLatSym(event):
         else:
             dlg.Destroy()
             return
-        wx.BeginBusyCursor()
         wx.MessageBox(' For use of PSEUDOLATTICE, please cite:\n\n'+
                           G2G.GetCite('Bilbao: PSEUDOLATTICE'),
                           caption='Bilbao PSEUDOLATTICE',
                           style=wx.ICON_INFORMATION)
+        wx.BeginBusyCursor()
         page = kSUB.subBilbaoCheckLattice(sgNum,cell,tolerance)
         wx.EndBusyCursor()
         if not page: return

GSASII/SUBGROUPS.py

@@ -1,4 +1,14 @@
 # -*- coding: utf-8 -*-
+'''
+Module SUBGROUPS
+========================
+
+Routines that access the Bilbao Crystallographic Server. 
+
+Note that there is a test for some of these routines in 
+file ``tests/run_bilbao.py``.
+'''
+
 from __future__ import division, print_function
 import re
 import copy
@@ -22,6 +32,7 @@
 def postpostURL(page):
     '''warn on Bilbao down
     '''
+    if page is None: return
     if "currently down" in page:
         # Bilbao is down. Tell user
         import re
@@ -263,7 +274,6 @@ def subBilbaoCheckLattice(spgNum,cell,tol=5):
     cellstr = '+'.join(['{:.5f}'.format(i) for i in cell])
     datastr = "sgr={:}&cell={:}&tol={:}&submit=Show".format(
         str(int(spgNum)),cellstr,str(int(tol)))
-    # self-tested?
     page = GSASIIpath.postURL(psSite,datastr,timeout=timeout)
     if postpostURL(page): return None
     if not page:
@@ -368,7 +378,6 @@ def GetSupergroup(SGnum,dlg=None):
     import re
     Site = bilbaoSite + 'nph-minsup'
     if dlg: dlg.Update(0,newmsg='Waiting for initial web response')
-    # self-tested?
     out = GSASIIpath.postURL(Site,{'gnum':f'{SGnum:}'},timeout=timeout)
     if postpostURL(out): return None
     if not out: return None
@@ -396,7 +405,6 @@ def GetSupergroup(SGnum,dlg=None):
     for i,line in enumerate(xforms):
         click = line[-1]
         print(SGnum,click)
-        # self-tested?
         out1 = GSASIIpath.postURL(Site,{'gnum':SGnum,'show':'show','click':click}
                                 ,timeout=timeout)
         if postpostURL(out1): return None
@@ -572,7 +580,6 @@ def BilbaoSymSearch1(sgnum, phase, maxdelta=2, angtol=None,
         postdict["stru"] += f"{el:4s} {i} - {atom[cx]:.5f} {atom[cx+1]:.5f} {atom[cx+2]:.5f}\n"
 #    if GSASIIpath.GetConfigValue('debug'): print(postdict["stru"])
     savedcookies = {}
-    # self-tested?
     page0 = GSASIIpath.postURL(bilbaoSite+pseudosym,postdict,
                              getcookie=savedcookies,timeout=timeout)
     if postpostURL(page0): return None
@@ -666,7 +673,6 @@ def BilbaoLowSymSea1(valsdict,row,savedcookies,pagelist=None):
     num = row[0]
     if GSASIIpath.GetConfigValue('debug'): print(f"processing cell #{num}")
     postdict['lattice'] = num
-    # self-tested?
     page1 = GSASIIpath.postURL(bilbaoSite+pseudosym,postdict,
                                      usecookie=savedcookies,timeout=timeout)
     if postpostURL(page1) or not page1: return None,None,None,None
@@ -703,7 +709,6 @@ def BilbaoLowSymSea2(num,valsdict,row,savedcookies,pagelist=None):
     postdict.update(valsdict)
     postdict['super_numind'] = row[1]
     if GSASIIpath.GetConfigValue('debug'): print(f"processing cell #{num} supergroup {row[1]}")
-    # self-tested?
     page1 = GSASIIpath.postURL(bilbaoSite+pseudosym,postdict,
                                      usecookie=savedcookies,timeout=timeout)
     if postpostURL(page1) or page1 is None: return '',None
@@ -734,7 +739,6 @@ def BilbaoSymSearch2(valsdict,csdict,rowdict,savedcookies,
             postdict = {}
             postdict.update(valsdict)
             postdict['cs'] = num
-            # self-tested?
             page1 = GSASIIpath.postURL(bilbaoSite+pseudosym,postdict,
                                      usecookie=savedcookies,timeout=timeout)
             if postpostURL(page1) or pagelist is not None:
@@ -797,7 +801,6 @@ def BilbaoReSymSearch(key,postdict,pagelist=None):
 
     '''
     savedcookies = {}
-    # self-tested?
     page1 = GSASIIpath.postURL(bilbaoSite+pseudosym,postdict
                              ,getcookie=savedcookies,timeout=timeout)
     if postpostURL(page1) or pagelist is not None:
@@ -810,7 +813,10 @@ def BilbaoReSymSearch(key,postdict,pagelist=None):
 def createStdSetting(cifFile,rd):
     '''Use the Bilbao "CIF to Standard Setting" web service to obtain a 
     structure in a standard setting. Then update the reader object with
-    the space group, cell and atom positions from this.
+    the space group, cell and atom positions from this. This is called
+    from the CIF importer in :mod:`G2phase_CIF` when a structure is 
+    encountered that has different symmetry operators from what GSAS-II 
+    generates.
     '''
     try:
         import requests # delay this until now, since rarely needed
@@ -854,61 +860,5 @@ def createStdSetting(cifFile,rd):
         if i == int(natom)-1: break
     del rd.SymOps['xyz'] # as-read sym ops now obsolete
 
-def test():
-    '''This tests that routines in Bilbao Crystallographic Server 
-    are accessible and produce output that we can parse. The output 
-    is displayed but not checked to see that it agrees with what 
-    has been provided previously.
-
-
-    The list of routines that access the Bilbao site and are tested here are:
-    * GetNonStdSubgroupsmag (uses subgrmag1_general_GSAS.pl)
-    * GetNonStdSubgroups (subgrmag1_general_GSAS.pl)
-    * GetStdSGset (checkgr.pl)
-
-    The other routines are not yet tested that access the Bilbao site are:
-
-    * subBilbaoCheckLattice
-    * GetSupergroup
-    * BilbaoSymSearch1
-    * BilbaoSymSearch2
-    * BilbaoReSymSearch
-    * createStdSetting
-
-    '''    
-    SGData = G2spc.SpcGroup('f d -3 m')[1]
-    
-    print('test SUBGROUPSMAG')
-    results,baseList = GetNonStdSubgroupsmag(SGData,('0','0','0',' ',' ',' ',' ',' ',' ',' '))
-    print(results)
-    if results:
-        for [spgp,bns,mv,gid,altList,supList] in results:
-            if gid in baseList:
-                print('Space group: %d %s BNS: %s'%(gid,spgp,bns))
-                print('MV',mv)
-                print('altList:',altList)
-                print('superList: ',supList)
-                
-    print('\n\ntest SUBGROUPS')
-    results,baseList = GetNonStdSubgroups(SGData,('1/3','1/3','1/2',' ',' ',' ',' ',' ',' ',' '))
-    print(results)
-    if results:
-        for [spgp,mv,gid,altList,supList] in results:
-            if gid in baseList:
-                print('Space group: %d %s'%(gid,spgp))
-                print('MV',mv)
-                print('altList:',altList)
-                print('superList: ',supList)
-                
-    print('\n\ntest Bilbao IDENTIFY GROUP')
-    sgnum,sgsym,xmat,xoff = GetStdSGset(G2spc.SpcGroup('R 3 C r')[1])
-    if sgnum:
-        print(f'Space group R3c (rhomb) transforms to std setting: {sgsym} (#{sgnum})')
-        print('  xform matrix',xmat)
-        print('  coord offset:',xoff)
-
-if __name__ == '__main__':
-    # run self-tests
-    selftestquiet = False
-    test()
-    print ("OK")
+#if __name__ == '__main__':
+    # Note that self-tests have been moved to file ``tests/run_bilbao.py``.

tests/run_bilbao.py

@@ -0,0 +1,116 @@
+'''
+run_bilbao.py
+=====================
+
+Run self-tests using the Bilbao Crystallographic Server 
+checking that the server is accessible and that the GSAS-II 
+routines that access the server work.
+No attempt is made for any comprehensive testing of the server. 
+
+Routines tested:
+
+* createStdSetting (uses nph-cif2std)
+* subBilbaoCheckLattice (uses nph-pseudolattice)
+* GetNonStdSubgroupsmag (uses subgrmag1_general_GSAS.pl)
+* GetNonStdSubgroups (uses subgrmag1_general_GSAS.pl)
+* GetStdSGset (uses checkgr.pl)
+
+The other major routines are:
+
+* BilbaoSymSearch1 (pseudosym)
+* BilbaoSymSearch2 (pseudosym)
+* BilbaoReSymSearch (pseudosym)
+
+These are not tested as they use the GUI extensively, but there is 
+a test that:
+
+* directly calls pseudosym & checks output with scanBilbaoSymSearch1
+'''
+
+import os
+import sys
+import importlib.util
+home = os.path.dirname(__file__)
+if importlib.util.find_spec('GSASII') is None: # hack path if GSASII not installed into Python
+    sys.path.append(os.path.dirname(home))
+from GSASII import GSASIIobj
+from GSASII import SUBGROUPS
+from GSASII import GSASIIpath
+from GSASII import GSASIIspc as G2spc
+
+def test_createStdSetting():
+    rd = GSASIIobj.ImportPhase('Null')
+    rd.Phase = {}
+    rd.Phase['General'] = {}
+    rd.SymOps['xyz'] = None
+    cifFile = os.path.join(home,'testinp','diamond.cif')
+    SUBGROUPS.createStdSetting(cifFile,rd)
+    assert len(rd.Phase['Atoms']) == 1
+    assert rd.Phase['General']['Cell'][1] == 3.5668
+    assert len(rd.Phase['General']['SGData']['SGOps']) == 24
+
+def test_CheckLattice():
+    print('test PSEUDOLATTICE')
+    cell = [14.259, 22.539, 8.741, 90.0, 114.1, 90.0]
+    page = SUBGROUPS.subBilbaoCheckLattice(12,cell,5)
+    found = SUBGROUPS.parseBilbaoCheckLattice(page)
+    assert found[0][0][0] == found[0][0][1] == 22.5418
+    assert found[0][0][5] == 120.
+
+def test_pseudosym():
+    postdict = {'formulae': '', 'cifile': '', 'filename': '', 'what': 'minsup',
+                    'maxik': '1', 'onlythisik': '1', 'mysuper2': '211',
+                    'x1': '1', 'x2': '0', 'x3': '0',
+                    'y1': '0', 'y2': '1', 'y3': '0',
+                    'z1': '0', 'z2': '0', 'z3': '1', 'x4': '0',
+                    'y4': '0', 'z4': '0',
+                    'angtol': '5', 'submit': 'Show', 'maxdelta': '2.0',
+                    'stru': '# Space Group ITA number\n227\n# Lattice parameters\n5.43123 5.43123 5.43123 90.0 90.0 90.0\n# number of atoms & atoms\n1\nSi   1 - 0.12500 0.12500 0.12500\n'}
+    savedcookies = {}
+    URL = SUBGROUPS.bilbaoSite+ SUBGROUPS.pseudosym
+    print('test PSEUDOSYM')
+    page0 = GSASIIpath.postURL(URL,postdict,
+                             getcookie=savedcookies,timeout=SUBGROUPS.timeout)
+    res = SUBGROUPS.scanBilbaoSymSearch1(page0,postdict)+[savedcookies]
+    assert res[2]['1'][0] == 'Pn-3m'
+    assert abs(float(res[2]['1'][5].split()[0]) -  5.43123/2) < 2e-5
+
+def test_SUBGROUPSMAG():
+    SGData = G2spc.SpcGroup('f d -3 m')[1]
+    
+    print('test SUBGROUPSMAG')
+    results,baseList = SUBGROUPS.GetNonStdSubgroupsmag(
+        SGData,('0','0','0',' ',' ',' ',' ',' ',' ',' '))
+    assert len(results) == 322
+    assert results[0][0] == "Fd'-3'm'"
+    assert results[1][0] == "Fd-3m'"
+    #print(results)
+
+def test_SUBGROUPS():
+    SGData = G2spc.SpcGroup('f d -3 m')[1]
+    print('\n\ntest SUBGROUPS')
+    results,baseList = SUBGROUPS.GetNonStdSubgroups(
+        SGData,('1/3','1/3','1/2',' ',' ',' ',' ',' ',' ',' '))
+    assert len(results) == 51
+    assert results[0][0] == "P21/c"
+    assert results[-1][0] == "P1"
+    
+def test_GetStdSGset():
+    print('\n\ntest Bilbao IDENTIFY GROUP')
+    sgnum,sgsym,xmat,xoff = SUBGROUPS.GetStdSGset(G2spc.SpcGroup('R 3 C r')[1])
+    assert sgnum == 161
+    assert sgsym == 'R 3 c'
+    assert xoff == [0,0,0]
+
+#GSASIIpath.IPyBreak_base()
+
+    
+if __name__ == '__main__':
+    # run self-tests
+    test_GetStdSGset()
+    test_SUBGROUPSMAG()
+    test_SUBGROUPS()
+    test_pseudosym()
+    test_CheckLattice()
+    test_createStdSetting()
+    print ("OK")