bump xrayutilities to 1.1.2

remove old deprecated patches

4 files changed, 2 insertions, 908 deletions

diff --git a/sci-physics/xrayutilities/Manifest b/sci-physics/xrayutilities/Manifest
index 5d01eaa..e0eec10 100644
--- a/sci-physics/xrayutilities/Manifest
+++ b/sci-physics/xrayutilities/Manifest
@@ -1,6 +1,4 @@
-AUX xrayutilities-1.0.3-python3.patch 17984 SHA256 fd3fde5d21669cd4d56b0b451fddc750f1eea5e409300450f75079d4594b6c91 SHA512 3a5055d14e4c69a2a867bf6a23daddfca0d3c5fb0934d67b84d442d6ea53852b700cf9e57e71b5d3a31b2353777e822d735d53aa1fe05ae5abc95cefce8a861b WHIRLPOOL 87cf4ae234e54dc9f37f46e2bc25ca570af377b25dc729eae1eaa9ab708fe440f0ee351936ca9675ed3228beee9e928207961a1c5e84f7c7eae27b57d343eb19
-AUX xrayutilities-9999-python3.patch 17984 SHA256 fd3fde5d21669cd4d56b0b451fddc750f1eea5e409300450f75079d4594b6c91 SHA512 3a5055d14e4c69a2a867bf6a23daddfca0d3c5fb0934d67b84d442d6ea53852b700cf9e57e71b5d3a31b2353777e822d735d53aa1fe05ae5abc95cefce8a861b WHIRLPOOL 87cf4ae234e54dc9f37f46e2bc25ca570af377b25dc729eae1eaa9ab708fe440f0ee351936ca9675ed3228beee9e928207961a1c5e84f7c7eae27b57d343eb19
-DIST xrayutilities-1.1.1.tar.gz 11556155 SHA256 b4150e94c5644647be979b2526d085fb5b4c27377bc0be7c84a15634375bc1db SHA512 827e8ca73b6c3183b5ae8dd801a21cc7e48e1918ccf47f69728eb2b44eda978c2f3f9aaaadc6e7e061cbd91eb821f1d1122e399b2a89a0ee724a95dba305dcf2 WHIRLPOOL 95ed892939da7a4c4570c1ddd0cde36216a649c7e9ef4064b82f5523ce67c85d05cc51a11812d480c4662c0a070545808f554cf1aeefaa4e4b71234fd737b9eb
-EBUILD xrayutilities-1.1.1.ebuild 795 SHA256 f0362aa677f8e022462b6c0011b9489b17be37fdfea61fd96cda27a80558614f SHA512 ac37539766b5c635f4e6703dc4718b33e7ab13cfcaacbce998ece91acad48c27054c72df19e74078dee489de9b41c2fa0d70bb8fbfd71e4982a4bf17e8ba59c7 WHIRLPOOL 837432839bb6b915d3f9fca09d6b60c8a000446f5d34fc13f4b82c0352bff38064f3763c544d5a536991a2c87f03dc9d20f111603af40daf812c792d4776f215
+DIST xrayutilities-1.1.2.tar.gz 11481448 SHA256 2cb739949938206d0d08fb2aeaa8dd790cd4c36f1f2524e3ff324c43e5c4c515 SHA512 bfe0dfe2efdc681e5564aa5fc86e4dec662c30446dc16b2b94c94bf2621af34930affd45662e054a685bee6ea01024f7e7cc65b6d8684fe758e664e24534caa7 WHIRLPOOL 00042e48b482ca480830adf9fa8918e1ad7bfba4196ec2328d6f1d0c83f4109a36cac8cfef711c0d4ed5dd35db4b8cf3c252a426729879ac2eeafe093a4b45fd
+EBUILD xrayutilities-1.1.2.ebuild 795 SHA256 f0362aa677f8e022462b6c0011b9489b17be37fdfea61fd96cda27a80558614f SHA512 ac37539766b5c635f4e6703dc4718b33e7ab13cfcaacbce998ece91acad48c27054c72df19e74078dee489de9b41c2fa0d70bb8fbfd71e4982a4bf17e8ba59c7 WHIRLPOOL 837432839bb6b915d3f9fca09d6b60c8a000446f5d34fc13f4b82c0352bff38064f3763c544d5a536991a2c87f03dc9d20f111603af40daf812c792d4776f215
 EBUILD xrayutilities-9999.ebuild 874 SHA256 8c633ad27bf57f4fcf973794395c75449e5034dad68c9e89bcef963d18f0aa60 SHA512 12a808ddf6a7351d4ff743f2c537335195b7b16b3610ec702a3ecfacd88aa30c610f43e692305800948a14d24570bccacea8dac30229cbe784f6e2c8c05576c9 WHIRLPOOL 5981ae8add4b7aaaec1033c64b1ba924d1388f7f8386226cac48cd23793e296b0daa684620c9807a9ded5a1c0bb78a0d4ed29710243c1bb1fca56985e4d86b89
 MISC metadata.xml 482 SHA256 f940902fa0beaac5c87eff05802c4b480ac6c854a8c8d15372e05695218b3afb SHA512 fed1eb362030ba39e5ec9b8bc0cfc8a4d4de1b3a92817a8de311e9de0db20fe5e7f53adb8860a7e82e06a6676134327849a75f318bb9e5f5640f28dd623190da WHIRLPOOL bee4fd34d8179e705ffbf87319b57feb8005756835b78684d3c7aaad448c82120e913a43ddb5237e8d5d209fde484c82d330a193b1d9f5378cc40abf013d8a8f
diff --git a/sci-physics/xrayutilities/files/xrayutilities-1.0.3-python3.patch b/sci-physics/xrayutilities/files/xrayutilities-1.0.3-python3.patch
deleted file mode 100644
index f0e3326..0000000
--- a/sci-physics/xrayutilities/files/xrayutilities-1.0.3-python3.patch
+++ /dev/null
@@ -1,452 +0,0 @@
---- xrayutilities/config.py	(original)
-+++ xrayutilities/config.py	(refactored)
-@@ -29,7 +29,7 @@
- try:
-     import configparser
- except ImportError:
--    import ConfigParser as configparser
-+    import configparser as configparser
- 
- from . import __path__
- from . import utilities_noconf
---- xrayutilities/experiment.py	(original)
-+++ xrayutilities/experiment.py	(refactored)
-@@ -88,7 +88,7 @@
-                         (default: identity matrix)
-         """
- 
--        for k in kwargs.keys():
-+        for k in list(kwargs.keys()):
-             if k not in ['wl','en','UB']:
-                 raise Exception("unknown keyword argument given: allowed are 'en': for x-ray energy, 'wl': x-ray wavelength, 'UB': orientation/orthonormalization matrix")
-         
-@@ -153,13 +153,13 @@
-          sampleAxis:     list or tuple of sample circles, e.g. ['x+','z+']
-         """
- 
--        if isinstance(sampleAxis,(basestring,list,tuple)):
--            if isinstance(sampleAxis,basestring):
-+        if isinstance(sampleAxis,(str,list,tuple)):
-+            if isinstance(sampleAxis,str):
-                 sAxis = list([sampleAxis])
-             else:
-                 sAxis = list(sampleAxis)
-             for circ in sAxis:
--                if not isinstance(circ,basestring) or len(circ)!=2:
-+                if not isinstance(circ,str) or len(circ)!=2:
-                     raise InputError("QConversion: incorrect sample circle type or syntax (%s)" %repr(circ))
-                 if not circleSyntaxSample.search(circ):
-                     raise InputError("QConversion: incorrect sample circle syntax (%s)" %circ)
-@@ -232,13 +232,13 @@
-          detrot:           flag to tell that the detector rotation is going to be added
-                            (used internally to avoid double adding of detector rotation axis)
-         """
--        if isinstance(detectorAxis,(basestring,list,tuple)):
--            if isinstance(detectorAxis,basestring):
-+        if isinstance(detectorAxis,(str,list,tuple)):
-+            if isinstance(detectorAxis,str):
-                 dAxis = list([detectorAxis])
-             else:
-                 dAxis = list(detectorAxis)
-             for circ in dAxis:
--                if not isinstance(circ,basestring) or len(circ)!=2:
-+                if not isinstance(circ,str) or len(circ)!=2:
-                     raise InputError("QConversion: incorrect detector circle type or syntax (%s)" %repr(circ))
-                 if not circleSyntax.search(circ):
-                     raise InputError("QConversion: incorrect detector circle syntax (%s)" %circ)
-@@ -352,7 +352,7 @@
-         where * corresponds to the number of points given in the input
-         """
- 
--        for k in kwargs.keys():
-+        for k in list(kwargs.keys()):
-             if k not in ['wl','deg','UB','delta']:
-                 raise Exception("unknown keyword argument given: allowed are 'delta': angle offsets, 'wl': x-ray wavelength, 'UB': orientation/orthonormalization matrix, 'deg': flag to tell if angles are in degrees")
-         
-@@ -478,12 +478,12 @@
-           roi:           region of interest for the detector pixels; e.g. [100,900]
-         """
- 
--        for k in kwargs.keys():
-+        for k in list(kwargs.keys()):
-             if k not in ['Nav','roi']:
-                 raise Exception("unknown keyword argument given: allowed are 'Nav': number of channels for block-average, 'roi': region of interest")
-         
-         # detectorDir
--        if not isinstance(detectorDir,basestring) or len(detectorDir)!=2:
-+        if not isinstance(detectorDir,str) or len(detectorDir)!=2:
-             raise InputError("QConversion: incorrect detector direction type or syntax (%s)" %repr(detectorDir))
-         if not circleSyntax.search(detectorDir):
-             raise InputError("QConversion: incorrect detector direction syntax (%s)" %detectorDir)
-@@ -557,7 +557,7 @@
-         if not self._linear_init:
-             raise Exception("QConversion: linear detector not initialized -> call Ang2Q.init_linear(...)")
-         
--        for k in kwargs.keys():
-+        for k in list(kwargs.keys()):
-             if k not in ['wl','deg','UB','delta','Nav','roi']:
-                 raise Exception("unknown keyword argument given: allowed are 'delta': angle offsets, 'wl': x-ray wavelength, 'UB': orientation/orthonormalization matrix, 'deg': flag to tell if angles are in degrees, 'Nav': number of channels for block-averaging, 'roi': region of interest")
- 
-@@ -702,17 +702,17 @@
-           roi:            region of interest for the detector pixels; e.g. [100,900,200,800]
-         """
- 
--        for k in kwargs.keys():
-+        for k in list(kwargs.keys()):
-             if k not in ['Nav','roi']:
-                 raise Exception("unknown keyword argument given: allowed are 'Nav': number of channels for block-average, 'roi': region of interest")
-         
-         # detectorDir
--        if not isinstance(detectorDir1,basestring) or len(detectorDir1)!=2:
-+        if not isinstance(detectorDir1,str) or len(detectorDir1)!=2:
-             raise InputError("QConversion: incorrect detector direction1 type or syntax (%s)" %repr(detectorDir1))
-         if not circleSyntax.search(detectorDir1):
-             raise InputError("QConversion: incorrect detector direction1 syntax (%s)" %detectorDir1)
-         self._area_detdir1 = detectorDir1
--        if not isinstance(detectorDir2,basestring) or len(detectorDir2)!=2:
-+        if not isinstance(detectorDir2,str) or len(detectorDir2)!=2:
-             raise InputError("QConversion: incorrect detector direction2 type or syntax (%s)" %repr(detectorDir2))
-         if not circleSyntax.search(detectorDir2):
-             raise InputError("QConversion: incorrect detector direction2 syntax (%s)" %detectorDir2)
-@@ -804,7 +804,7 @@
-         if not self._area_init:
-             raise Exception("QConversion: area detector not initialized -> call Ang2Q.init_area(...)")
-         
--        for k in kwargs.keys():
-+        for k in list(kwargs.keys()):
-             if k not in ['wl','deg','UB','delta','Nav','roi']:
-                 raise Exception("unknown keyword argument given: allowed are 'delta': angle offsets, 'wl': x-ray wavelength, 'UB': orientation/orthonormalization matrix, 'deg': flag to tell if angles are in degrees, 'Nav': number of channels for block-averaging, 'roi': region of interest")
- 
-@@ -956,7 +956,7 @@
-                      the en keyword overrulls the wl keyword
-         """
- 
--        for k in keyargs.keys():
-+        for k in list(keyargs.keys()):
-             if k not in ['qconv','wl','en']:
-                 raise Exception("unknown keyword argument given: allowed are 'en': for x-ray energy, 'wl': x-ray wavelength, 'qconv': reciprocal space conversion.")
- 
-@@ -1121,7 +1121,7 @@
- 
-         """
- 
--        for k in kwargs.keys():
-+        for k in list(kwargs.keys()):
-             if k not in ['U','B','mat','dettype']:
-                 raise Exception("unknown keyword argument given: allowed are 'B': orthonormalization matrix, 'U': orientation matrix, 'mat': material object, 'dettype': string with detector type")
-         
-@@ -1328,7 +1328,7 @@
-          pdi_d: offset ot the diffracted beam from the scattering plane due to refraction
-         """
- 
--        for k in keyargs.keys():
-+        for k in list(keyargs.keys()):
-             if k not in ['trans','deg','geometry','refrac','mat','fi','fd','full_output']:
-                 raise Exception("unknown keyword argument given: see documentation for details")
-         
-@@ -1589,7 +1589,7 @@
-          twotheta:   scattering angle (detector)
-         """
- 
--        for k in keyargs.keys():
-+        for k in list(keyargs.keys()):
-             if k not in ['trans','deg']:
-                 raise Exception("unknown keyword argument given: allowed are 'trans': coordinate transformation flag, 'deg': degree-flag")
-         
-@@ -1733,7 +1733,7 @@
-          beta:       exit angle from surface (at the moment always 0)
-         """
- 
--        for k in kwargs.keys():
-+        for k in list(kwargs.keys()):
-             if k not in ['trans','deg']:
-                 raise Exception("unknown keyword argument given: allowed are 'trans': coordinate transformation flag, 'deg': degree-flag")
-         
-@@ -1894,7 +1894,7 @@
-          gamma:    scattering angle
-         """
- 
--        for k in kwargs.keys():
-+        for k in list(kwargs.keys()):
-             if k not in ['trans','deg']:
-                 raise Exception("unknown keyword argument given: allowed are 'trans': coordinate transformation flag, 'deg': degree-flag")
-         
---- xrayutilities/normalize.py	(original)
-+++ xrayutilities/normalize.py	(refactored)
-@@ -178,7 +178,7 @@
-         >>> detcorr = IntensityNormalizer(det="MCA",time="Seconds",absfun=lambda d: d["PSDCORR"]/d["PSD"].astype(numpy.float))
-         """
- 
--        for k in keyargs.keys():
-+        for k in list(keyargs.keys()):
-             if k not in ['mon','time','smoothmon','av_mon','absfun','flatfield','darkfield']:
-                 raise Exception("unknown keyword argument given: allowed are 'mon', 'smoothmon', 'av_mon', 'absfun', 'flatfield' and 'darkfield'")
-         
-@@ -232,7 +232,7 @@
-         det  property handler
-         sets the detector field name
-         """
--        if isinstance(det,basestring):
-+        if isinstance(det,str):
-             self._det = det
-         else:
-             self._det = None
-@@ -251,7 +251,7 @@
-         time property handler
-         sets the count time field or value
-         """
--        if isinstance(time,basestring):
-+        if isinstance(time,str):
-             self._time = time
-         elif isinstance(time,(float,int)):
-             self._time = float(time)
-@@ -272,7 +272,7 @@
-         mon property handler
-         sets the monitor field name
-         """
--        if isinstance(mon,basestring):
-+        if isinstance(mon,str):
-             self._mon = mon
-         elif isinstance(mon,type(None)):
-             self._mon = None
-@@ -395,7 +395,7 @@
-         else:
-             mon = 1.
-         # count time
--        if isinstance(self._time,basestring):
-+        if isinstance(self._time,str):
-             time = data[self._time]
-         elif isinstance(self._time,float):
-             time = self._time
---- xrayutilities/utilities_noconf.py	(original)
-+++ xrayutilities/utilities_noconf.py	(refactored)
-@@ -78,7 +78,7 @@
- 
-     if numpy.isreal(en):
-         return numpy.double(en)
--    elif isinstance(en,basestring):
-+    elif isinstance(en,str):
-         return energies[en]
-     else:
-         raise InputError("wrong type for argument en")
-@@ -104,7 +104,7 @@
- 
-     if numpy.isreal(wl):
-         return numpy.double(wl)
--    elif isinstance(wl,basestring):
-+    elif isinstance(wl,str):
-         return lam2en(energies[wl])
-     else:
-         raise InputError("wrong type for argument wavelength")
---- xrayutilities/io/edf.py	(original)
-+++ xrayutilities/io/edf.py	(refactored)
-@@ -153,19 +153,19 @@
-                         self.header[key] = value
- 
-         # try to parse motor positions and counters from header into separate dictionary
--        if 'motor_mne' in self.header.keys():
-+        if 'motor_mne' in list(self.header.keys()):
-             tkeys = self.header['motor_mne'].split()
-             try: 
-                 tval = numpy.array(self.header['motor_pos'].split(),dtype=numpy.double)
--                self.motors = dict(zip(tkeys,tval))
-+                self.motors = dict(list(zip(tkeys,tval)))
-             except:
-                 print("XU.io.EDFFile.ReadData: Warning: header conversion of motor positions failed")
- 
--        if 'counter_mne' in self.header.keys():
-+        if 'counter_mne' in list(self.header.keys()):
-             tkeys = self.header['counter_mne'].split()
-             try: 
-                 tval = numpy.array(self.header['counter_pos'].split(),dtype=numpy.double)
--                self.counters = dict(zip(tkeys,tval))
-+                self.counters = dict(list(zip(tkeys,tval)))
-             except:
-                 print("XU.io.EDFFile.ReadData: Warning: header conversion of counter values failed")
- 
-@@ -299,7 +299,7 @@
-         ca[...] = self.data[...]
- 
-         #finally we have to append the attributes
--        for k in self.header.keys():
-+        for k in list(self.header.keys()):
-             aname = k.replace(".","_")
-             aname = aname.replace(" ","_")
-             ca.attrs.__setattr__(aname,self.header[k])
---- xrayutilities/io/panalytical_xml.py	(original)
-+++ xrayutilities/io/panalytical_xml.py	(refactored)
-@@ -114,12 +114,12 @@
-                         is_scalar = 0
- 
-         #finally all scan data needs to be converted to numpy arrays
--        for k in self.ddict.keys():
-+        for k in list(self.ddict.keys()):
-             self.ddict[k] = numpy.array(self.ddict[k])
- 
-         #flatten output if only one scan was present
-         if len(slist) == 1:
--            for k in self.ddict.keys():
-+            for k in list(self.ddict.keys()):
-                 self.ddict[k] = numpy.ravel(self.ddict[k])
- 
-     def __getitem__(self,key):
-@@ -127,7 +127,7 @@
- 
-     def __str__(self):
-         ostr = "XRDML Measurement\n"
--        for k in self.ddict.keys():
-+        for k in list(self.ddict.keys()):
-             ostr += "%s with %s points\n" %(k,str(self.ddict[k].shape))
- 
-         return ostr
---- xrayutilities/io/rotanode_alignment.py	(original)
-+++ xrayutilities/io/rotanode_alignment.py	(refactored)
-@@ -206,7 +206,7 @@
- 
-         # get number aligned axis for the current peak
-         axnames = []
--        for k in self.keys():
-+        for k in list(self.keys()):
-             if k.find(pname)>=0:
-                 axnames.append(k)
- 
---- xrayutilities/io/seifert.py	(original)
-+++ xrayutilities/io/seifert.py	(refactored)
-@@ -80,7 +80,7 @@
- 
-     def __str__(self):
-         ostr = ""
--        for k in self.__dict__.keys():
-+        for k in list(self.__dict__.keys()):
-             value = self.__getattribute__(k)
-             if isinstance(value,float):
-                 ostr += k + " = %f\n" %value
-@@ -90,7 +90,7 @@
-         return ostr
- 
-     def save_h5_attribs(self,obj):
--        for a in self.__dict__.keys():
-+        for a in list(self.__dict__.keys()):
-             value = self.__getattribute__(a)
-             obj._v_attrs.__setattr__(a,value)
- 
---- xrayutilities/io/spec.py	(original)
-+++ xrayutilities/io/spec.py	(refactored)
-@@ -511,7 +511,7 @@
-         g._v_attrs.Time = self.time
- 
-         #write the initial motor positions as attributes
--        for k in self.init_motor_pos.keys():
-+        for k in list(self.init_motor_pos.keys()):
-             g._v_attrs.__setattr__(k,numpy.float(self.init_motor_pos[k]))
- 
-         #if scan contains MCA data write also MCA parameters
-@@ -519,7 +519,7 @@
-         g._v_attrs.mca_stop_channel = numpy.uint(self.mca_stop_channel)
-         g._v_attrs.mca_nof_channels = numpy.uint(self.mca_channels)
- 
--        for k in optattrs.keys():
-+        for k in list(optattrs.keys()):
-             g._v_attrs.__setattr__(k,opattrs[k])
- 
-         h5.flush()
-@@ -973,7 +973,7 @@
-         scanlist = list([scans])
- 
-     angles = dict.fromkeys(args)
--    for key in angles.keys():
-+    for key in list(angles.keys()):
-         if not isinstance(key,str):
-             raise InputError("*arg values need to be strings with motornames")
-         angles[key] = numpy.zeros(0)
---- xrayutilities/io/spectra.py	(original)
-+++ xrayutilities/io/spectra.py	(refactored)
-@@ -79,13 +79,13 @@
- 
-     def __str__(self):
-         ostr = ""
--        n = len(self.keys())
-+        n = len(list(self.keys()))
-         lmax_key = 0
-         lmax_item = 0
-         strlist = []
- 
-         #find the length of the longest key
--        for k in self.keys():
-+        for k in list(self.keys()):
-             if len(k)>lmax_key: lmax_key = len(k)
- 
-             i = self[k]
-@@ -99,14 +99,14 @@
-         kvfmt = "|%%-%is = %%-%is" %(lmax_key,lmax_item)
- 
-         nc = 3
--        nres = len(self.keys())%nc
--        nrow = (len(self.keys())-nres)/nc
-+        nres = len(list(self.keys()))%nc
-+        nrow = (len(list(self.keys()))-nres)/nc
- 
-         cnt = 0
-         ostr += (3*(lmax_key+lmax_item+4)+1)*"-"+"\n"
-         ostr += "|Parameters:" +(3*(lmax_key+lmax_item))*" "+"|\n"
-         ostr += (3*(lmax_key+lmax_item+4)+1)*"-"+"\n"
--        for key in self.keys():
-+        for key in list(self.keys()):
-             value = self[key]
-             if not isinstance(value,str): value = "%f" %value
- 
-@@ -275,14 +275,14 @@
- 
- 
-         #start with saving scan comments
--        for k in self.comments.keys():
-+        for k in list(self.comments.keys()):
-             try:
-                 h5.setNodeAttr(g,k,self.comments[k])
-             except:
-                 print("XU.io.spectra.Save2HDF5: cannot save file comment %s = %s to group %s!" %(k,self.comments[k],name))
- 
-         #save scan parameters
--        for k in self.params.keys():
-+        for k in list(self.params.keys()):
-             try:
-                 h5.setNodeAttr(g,k,self.params[k])
-             except:
-@@ -639,7 +639,7 @@
-         self.recarray2hdf5(sg,data,"data","SPECTRA tabular data")
- 
-         #write attribute data
--        for k in hdr.keys():
-+        for k in list(hdr.keys()):
-             self.h5_file.setNodeAttr(sg,"MOPOS_"+k,hdr[k])
- 
-         if has_mca:
-@@ -783,7 +783,7 @@
-     generic
-     """
- 
--    fnums = range(cntstart,cntstop+1)
-+    fnums = list(range(cntstart,cntstop+1))
-     mcalist = []
- 
-     for i in fnums:
-@@ -938,7 +938,7 @@
-         scanlist = list([scans])
- 
-     angles = dict.fromkeys(args)
--    for key in angles.keys():
-+    for key in list(angles.keys()):
-         angles[key] = numpy.zeros(0)
-     buf=numpy.zeros(0)
-     MAP = numpy.zeros(0)
---- xrayutilities/math/fit.py	(original)
-+++ xrayutilities/math/fit.py	(refactored)
-@@ -20,7 +20,7 @@
- the odr package
- """
- 
--from __future__ import print_function
-+
- import numpy
- import scipy.optimize as optimize
- import time
diff --git a/sci-physics/xrayutilities/files/xrayutilities-9999-python3.patch b/sci-physics/xrayutilities/files/xrayutilities-9999-python3.patch
deleted file mode 100644
index f0e3326..0000000
--- a/sci-physics/xrayutilities/files/xrayutilities-9999-python3.patch
+++ /dev/null
@@ -1,452 +0,0 @@
---- xrayutilities/config.py	(original)
-+++ xrayutilities/config.py	(refactored)
-@@ -29,7 +29,7 @@
- try:
-     import configparser
- except ImportError:
--    import ConfigParser as configparser
-+    import configparser as configparser
- 
- from . import __path__
- from . import utilities_noconf
---- xrayutilities/experiment.py	(original)
-+++ xrayutilities/experiment.py	(refactored)
-@@ -88,7 +88,7 @@
-                         (default: identity matrix)
-         """
- 
--        for k in kwargs.keys():
-+        for k in list(kwargs.keys()):
-             if k not in ['wl','en','UB']:
-                 raise Exception("unknown keyword argument given: allowed are 'en': for x-ray energy, 'wl': x-ray wavelength, 'UB': orientation/orthonormalization matrix")
-         
-@@ -153,13 +153,13 @@
-          sampleAxis:     list or tuple of sample circles, e.g. ['x+','z+']
-         """
- 
--        if isinstance(sampleAxis,(basestring,list,tuple)):
--            if isinstance(sampleAxis,basestring):
-+        if isinstance(sampleAxis,(str,list,tuple)):
-+            if isinstance(sampleAxis,str):
-                 sAxis = list([sampleAxis])
-             else:
-                 sAxis = list(sampleAxis)
-             for circ in sAxis:
--                if not isinstance(circ,basestring) or len(circ)!=2:
-+                if not isinstance(circ,str) or len(circ)!=2:
-                     raise InputError("QConversion: incorrect sample circle type or syntax (%s)" %repr(circ))
-                 if not circleSyntaxSample.search(circ):
-                     raise InputError("QConversion: incorrect sample circle syntax (%s)" %circ)
-@@ -232,13 +232,13 @@
-          detrot:           flag to tell that the detector rotation is going to be added
-                            (used internally to avoid double adding of detector rotation axis)
-         """
--        if isinstance(detectorAxis,(basestring,list,tuple)):
--            if isinstance(detectorAxis,basestring):
-+        if isinstance(detectorAxis,(str,list,tuple)):
-+            if isinstance(detectorAxis,str):
-                 dAxis = list([detectorAxis])
-             else:
-                 dAxis = list(detectorAxis)
-             for circ in dAxis:
--                if not isinstance(circ,basestring) or len(circ)!=2:
-+                if not isinstance(circ,str) or len(circ)!=2:
-                     raise InputError("QConversion: incorrect detector circle type or syntax (%s)" %repr(circ))
-                 if not circleSyntax.search(circ):
-                     raise InputError("QConversion: incorrect detector circle syntax (%s)" %circ)
-@@ -352,7 +352,7 @@
-         where * corresponds to the number of points given in the input
-         """
- 
--        for k in kwargs.keys():
-+        for k in list(kwargs.keys()):
-             if k not in ['wl','deg','UB','delta']:
-                 raise Exception("unknown keyword argument given: allowed are 'delta': angle offsets, 'wl': x-ray wavelength, 'UB': orientation/orthonormalization matrix, 'deg': flag to tell if angles are in degrees")
-         
-@@ -478,12 +478,12 @@
-           roi:           region of interest for the detector pixels; e.g. [100,900]
-         """
- 
--        for k in kwargs.keys():
-+        for k in list(kwargs.keys()):
-             if k not in ['Nav','roi']:
-                 raise Exception("unknown keyword argument given: allowed are 'Nav': number of channels for block-average, 'roi': region of interest")
-         
-         # detectorDir
--        if not isinstance(detectorDir,basestring) or len(detectorDir)!=2:
-+        if not isinstance(detectorDir,str) or len(detectorDir)!=2:
-             raise InputError("QConversion: incorrect detector direction type or syntax (%s)" %repr(detectorDir))
-         if not circleSyntax.search(detectorDir):
-             raise InputError("QConversion: incorrect detector direction syntax (%s)" %detectorDir)
-@@ -557,7 +557,7 @@
-         if not self._linear_init:
-             raise Exception("QConversion: linear detector not initialized -> call Ang2Q.init_linear(...)")
-         
--        for k in kwargs.keys():
-+        for k in list(kwargs.keys()):
-             if k not in ['wl','deg','UB','delta','Nav','roi']:
-                 raise Exception("unknown keyword argument given: allowed are 'delta': angle offsets, 'wl': x-ray wavelength, 'UB': orientation/orthonormalization matrix, 'deg': flag to tell if angles are in degrees, 'Nav': number of channels for block-averaging, 'roi': region of interest")
- 
-@@ -702,17 +702,17 @@
-           roi:            region of interest for the detector pixels; e.g. [100,900,200,800]
-         """
- 
--        for k in kwargs.keys():
-+        for k in list(kwargs.keys()):
-             if k not in ['Nav','roi']:
-                 raise Exception("unknown keyword argument given: allowed are 'Nav': number of channels for block-average, 'roi': region of interest")
-         
-         # detectorDir
--        if not isinstance(detectorDir1,basestring) or len(detectorDir1)!=2:
-+        if not isinstance(detectorDir1,str) or len(detectorDir1)!=2:
-             raise InputError("QConversion: incorrect detector direction1 type or syntax (%s)" %repr(detectorDir1))
-         if not circleSyntax.search(detectorDir1):
-             raise InputError("QConversion: incorrect detector direction1 syntax (%s)" %detectorDir1)
-         self._area_detdir1 = detectorDir1
--        if not isinstance(detectorDir2,basestring) or len(detectorDir2)!=2:
-+        if not isinstance(detectorDir2,str) or len(detectorDir2)!=2:
-             raise InputError("QConversion: incorrect detector direction2 type or syntax (%s)" %repr(detectorDir2))
-         if not circleSyntax.search(detectorDir2):
-             raise InputError("QConversion: incorrect detector direction2 syntax (%s)" %detectorDir2)
-@@ -804,7 +804,7 @@
-         if not self._area_init:
-             raise Exception("QConversion: area detector not initialized -> call Ang2Q.init_area(...)")
-         
--        for k in kwargs.keys():
-+        for k in list(kwargs.keys()):
-             if k not in ['wl','deg','UB','delta','Nav','roi']:
-                 raise Exception("unknown keyword argument given: allowed are 'delta': angle offsets, 'wl': x-ray wavelength, 'UB': orientation/orthonormalization matrix, 'deg': flag to tell if angles are in degrees, 'Nav': number of channels for block-averaging, 'roi': region of interest")
- 
-@@ -956,7 +956,7 @@
-                      the en keyword overrulls the wl keyword
-         """
- 
--        for k in keyargs.keys():
-+        for k in list(keyargs.keys()):
-             if k not in ['qconv','wl','en']:
-                 raise Exception("unknown keyword argument given: allowed are 'en': for x-ray energy, 'wl': x-ray wavelength, 'qconv': reciprocal space conversion.")
- 
-@@ -1121,7 +1121,7 @@
- 
-         """
- 
--        for k in kwargs.keys():
-+        for k in list(kwargs.keys()):
-             if k not in ['U','B','mat','dettype']:
-                 raise Exception("unknown keyword argument given: allowed are 'B': orthonormalization matrix, 'U': orientation matrix, 'mat': material object, 'dettype': string with detector type")
-         
-@@ -1328,7 +1328,7 @@
-          pdi_d: offset ot the diffracted beam from the scattering plane due to refraction
-         """
- 
--        for k in keyargs.keys():
-+        for k in list(keyargs.keys()):
-             if k not in ['trans','deg','geometry','refrac','mat','fi','fd','full_output']:
-                 raise Exception("unknown keyword argument given: see documentation for details")
-         
-@@ -1589,7 +1589,7 @@
-          twotheta:   scattering angle (detector)
-         """
- 
--        for k in keyargs.keys():
-+        for k in list(keyargs.keys()):
-             if k not in ['trans','deg']:
-                 raise Exception("unknown keyword argument given: allowed are 'trans': coordinate transformation flag, 'deg': degree-flag")
-         
-@@ -1733,7 +1733,7 @@
-          beta:       exit angle from surface (at the moment always 0)
-         """
- 
--        for k in kwargs.keys():
-+        for k in list(kwargs.keys()):
-             if k not in ['trans','deg']:
-                 raise Exception("unknown keyword argument given: allowed are 'trans': coordinate transformation flag, 'deg': degree-flag")
-         
-@@ -1894,7 +1894,7 @@
-          gamma:    scattering angle
-         """
- 
--        for k in kwargs.keys():
-+        for k in list(kwargs.keys()):
-             if k not in ['trans','deg']:
-                 raise Exception("unknown keyword argument given: allowed are 'trans': coordinate transformation flag, 'deg': degree-flag")
-         
---- xrayutilities/normalize.py	(original)
-+++ xrayutilities/normalize.py	(refactored)
-@@ -178,7 +178,7 @@
-         >>> detcorr = IntensityNormalizer(det="MCA",time="Seconds",absfun=lambda d: d["PSDCORR"]/d["PSD"].astype(numpy.float))
-         """
- 
--        for k in keyargs.keys():
-+        for k in list(keyargs.keys()):
-             if k not in ['mon','time','smoothmon','av_mon','absfun','flatfield','darkfield']:
-                 raise Exception("unknown keyword argument given: allowed are 'mon', 'smoothmon', 'av_mon', 'absfun', 'flatfield' and 'darkfield'")
-         
-@@ -232,7 +232,7 @@
-         det  property handler
-         sets the detector field name
-         """
--        if isinstance(det,basestring):
-+        if isinstance(det,str):
-             self._det = det
-         else:
-             self._det = None
-@@ -251,7 +251,7 @@
-         time property handler
-         sets the count time field or value
-         """
--        if isinstance(time,basestring):
-+        if isinstance(time,str):
-             self._time = time
-         elif isinstance(time,(float,int)):
-             self._time = float(time)
-@@ -272,7 +272,7 @@
-         mon property handler
-         sets the monitor field name
-         """
--        if isinstance(mon,basestring):
-+        if isinstance(mon,str):
-             self._mon = mon
-         elif isinstance(mon,type(None)):
-             self._mon = None
-@@ -395,7 +395,7 @@
-         else:
-             mon = 1.
-         # count time
--        if isinstance(self._time,basestring):
-+        if isinstance(self._time,str):
-             time = data[self._time]
-         elif isinstance(self._time,float):
-             time = self._time
---- xrayutilities/utilities_noconf.py	(original)
-+++ xrayutilities/utilities_noconf.py	(refactored)
-@@ -78,7 +78,7 @@
- 
-     if numpy.isreal(en):
-         return numpy.double(en)
--    elif isinstance(en,basestring):
-+    elif isinstance(en,str):
-         return energies[en]
-     else:
-         raise InputError("wrong type for argument en")
-@@ -104,7 +104,7 @@
- 
-     if numpy.isreal(wl):
-         return numpy.double(wl)
--    elif isinstance(wl,basestring):
-+    elif isinstance(wl,str):
-         return lam2en(energies[wl])
-     else:
-         raise InputError("wrong type for argument wavelength")
---- xrayutilities/io/edf.py	(original)
-+++ xrayutilities/io/edf.py	(refactored)
-@@ -153,19 +153,19 @@
-                         self.header[key] = value
- 
-         # try to parse motor positions and counters from header into separate dictionary
--        if 'motor_mne' in self.header.keys():
-+        if 'motor_mne' in list(self.header.keys()):
-             tkeys = self.header['motor_mne'].split()
-             try: 
-                 tval = numpy.array(self.header['motor_pos'].split(),dtype=numpy.double)
--                self.motors = dict(zip(tkeys,tval))
-+                self.motors = dict(list(zip(tkeys,tval)))
-             except:
-                 print("XU.io.EDFFile.ReadData: Warning: header conversion of motor positions failed")
- 
--        if 'counter_mne' in self.header.keys():
-+        if 'counter_mne' in list(self.header.keys()):
-             tkeys = self.header['counter_mne'].split()
-             try: 
-                 tval = numpy.array(self.header['counter_pos'].split(),dtype=numpy.double)
--                self.counters = dict(zip(tkeys,tval))
-+                self.counters = dict(list(zip(tkeys,tval)))
-             except:
-                 print("XU.io.EDFFile.ReadData: Warning: header conversion of counter values failed")
- 
-@@ -299,7 +299,7 @@
-         ca[...] = self.data[...]
- 
-         #finally we have to append the attributes
--        for k in self.header.keys():
-+        for k in list(self.header.keys()):
-             aname = k.replace(".","_")
-             aname = aname.replace(" ","_")
-             ca.attrs.__setattr__(aname,self.header[k])
---- xrayutilities/io/panalytical_xml.py	(original)
-+++ xrayutilities/io/panalytical_xml.py	(refactored)
-@@ -114,12 +114,12 @@
-                         is_scalar = 0
- 
-         #finally all scan data needs to be converted to numpy arrays
--        for k in self.ddict.keys():
-+        for k in list(self.ddict.keys()):
-             self.ddict[k] = numpy.array(self.ddict[k])
- 
-         #flatten output if only one scan was present
-         if len(slist) == 1:
--            for k in self.ddict.keys():
-+            for k in list(self.ddict.keys()):
-                 self.ddict[k] = numpy.ravel(self.ddict[k])
- 
-     def __getitem__(self,key):
-@@ -127,7 +127,7 @@
- 
-     def __str__(self):
-         ostr = "XRDML Measurement\n"
--        for k in self.ddict.keys():
-+        for k in list(self.ddict.keys()):
-             ostr += "%s with %s points\n" %(k,str(self.ddict[k].shape))
- 
-         return ostr
---- xrayutilities/io/rotanode_alignment.py	(original)
-+++ xrayutilities/io/rotanode_alignment.py	(refactored)
-@@ -206,7 +206,7 @@
- 
-         # get number aligned axis for the current peak
-         axnames = []
--        for k in self.keys():
-+        for k in list(self.keys()):
-             if k.find(pname)>=0:
-                 axnames.append(k)
- 
---- xrayutilities/io/seifert.py	(original)
-+++ xrayutilities/io/seifert.py	(refactored)
-@@ -80,7 +80,7 @@
- 
-     def __str__(self):
-         ostr = ""
--        for k in self.__dict__.keys():
-+        for k in list(self.__dict__.keys()):
-             value = self.__getattribute__(k)
-             if isinstance(value,float):
-                 ostr += k + " = %f\n" %value
-@@ -90,7 +90,7 @@
-         return ostr
- 
-     def save_h5_attribs(self,obj):
--        for a in self.__dict__.keys():
-+        for a in list(self.__dict__.keys()):
-             value = self.__getattribute__(a)
-             obj._v_attrs.__setattr__(a,value)
- 
---- xrayutilities/io/spec.py	(original)
-+++ xrayutilities/io/spec.py	(refactored)
-@@ -511,7 +511,7 @@
-         g._v_attrs.Time = self.time
- 
-         #write the initial motor positions as attributes
--        for k in self.init_motor_pos.keys():
-+        for k in list(self.init_motor_pos.keys()):
-             g._v_attrs.__setattr__(k,numpy.float(self.init_motor_pos[k]))
- 
-         #if scan contains MCA data write also MCA parameters
-@@ -519,7 +519,7 @@
-         g._v_attrs.mca_stop_channel = numpy.uint(self.mca_stop_channel)
-         g._v_attrs.mca_nof_channels = numpy.uint(self.mca_channels)
- 
--        for k in optattrs.keys():
-+        for k in list(optattrs.keys()):
-             g._v_attrs.__setattr__(k,opattrs[k])
- 
-         h5.flush()
-@@ -973,7 +973,7 @@
-         scanlist = list([scans])
- 
-     angles = dict.fromkeys(args)
--    for key in angles.keys():
-+    for key in list(angles.keys()):
-         if not isinstance(key,str):
-             raise InputError("*arg values need to be strings with motornames")
-         angles[key] = numpy.zeros(0)
---- xrayutilities/io/spectra.py	(original)
-+++ xrayutilities/io/spectra.py	(refactored)
-@@ -79,13 +79,13 @@
- 
-     def __str__(self):
-         ostr = ""
--        n = len(self.keys())
-+        n = len(list(self.keys()))
-         lmax_key = 0
-         lmax_item = 0
-         strlist = []
- 
-         #find the length of the longest key
--        for k in self.keys():
-+        for k in list(self.keys()):
-             if len(k)>lmax_key: lmax_key = len(k)
- 
-             i = self[k]
-@@ -99,14 +99,14 @@
-         kvfmt = "|%%-%is = %%-%is" %(lmax_key,lmax_item)
- 
-         nc = 3
--        nres = len(self.keys())%nc
--        nrow = (len(self.keys())-nres)/nc
-+        nres = len(list(self.keys()))%nc
-+        nrow = (len(list(self.keys()))-nres)/nc
- 
-         cnt = 0
-         ostr += (3*(lmax_key+lmax_item+4)+1)*"-"+"\n"
-         ostr += "|Parameters:" +(3*(lmax_key+lmax_item))*" "+"|\n"
-         ostr += (3*(lmax_key+lmax_item+4)+1)*"-"+"\n"
--        for key in self.keys():
-+        for key in list(self.keys()):
-             value = self[key]
-             if not isinstance(value,str): value = "%f" %value
- 
-@@ -275,14 +275,14 @@
- 
- 
-         #start with saving scan comments
--        for k in self.comments.keys():
-+        for k in list(self.comments.keys()):
-             try:
-                 h5.setNodeAttr(g,k,self.comments[k])
-             except:
-                 print("XU.io.spectra.Save2HDF5: cannot save file comment %s = %s to group %s!" %(k,self.comments[k],name))
- 
-         #save scan parameters
--        for k in self.params.keys():
-+        for k in list(self.params.keys()):
-             try:
-                 h5.setNodeAttr(g,k,self.params[k])
-             except:
-@@ -639,7 +639,7 @@
-         self.recarray2hdf5(sg,data,"data","SPECTRA tabular data")
- 
-         #write attribute data
--        for k in hdr.keys():
-+        for k in list(hdr.keys()):
-             self.h5_file.setNodeAttr(sg,"MOPOS_"+k,hdr[k])
- 
-         if has_mca:
-@@ -783,7 +783,7 @@
-     generic
-     """
- 
--    fnums = range(cntstart,cntstop+1)
-+    fnums = list(range(cntstart,cntstop+1))
-     mcalist = []
- 
-     for i in fnums:
-@@ -938,7 +938,7 @@
-         scanlist = list([scans])
- 
-     angles = dict.fromkeys(args)
--    for key in angles.keys():
-+    for key in list(angles.keys()):
-         angles[key] = numpy.zeros(0)
-     buf=numpy.zeros(0)
-     MAP = numpy.zeros(0)
---- xrayutilities/math/fit.py	(original)
-+++ xrayutilities/math/fit.py	(refactored)
-@@ -20,7 +20,7 @@
- the odr package
- """
- 
--from __future__ import print_function
-+
- import numpy
- import scipy.optimize as optimize
- import time
diff --git a/sci-physics/xrayutilities/xrayutilities-1.1.1.ebuild b/sci-physics/xrayutilities/xrayutilities-1.1.2.ebuild
index c44dbd3..c44dbd3 100644
--- a/sci-physics/xrayutilities/xrayutilities-1.1.1.ebuild
+++ b/sci-physics/xrayutilities/xrayutilities-1.1.2.ebuild