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author | 2015-04-28 23:32:16 +0200 | |
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committer | 2015-04-28 23:32:16 +0200 | |
commit | 86ae3535fe363ecc99657394c0f11db1c728a692 (patch) | |
tree | 6150c1dd82f5644bb8d8d432975e8da2696f54b9 | |
parent | add metadata.xml files (diff) | |
download | anaximander-86ae3535fe363ecc99657394c0f11db1c728a692.tar.gz anaximander-86ae3535fe363ecc99657394c0f11db1c728a692.tar.bz2 anaximander-86ae3535fe363ecc99657394c0f11db1c728a692.zip |
bump xrayutilities to 1.1.2
remove old deprecated patches
-rw-r--r-- | sci-physics/xrayutilities/Manifest | 6 | ||||
-rw-r--r-- | sci-physics/xrayutilities/files/xrayutilities-1.0.3-python3.patch | 452 | ||||
-rw-r--r-- | sci-physics/xrayutilities/files/xrayutilities-9999-python3.patch | 452 | ||||
-rw-r--r-- | sci-physics/xrayutilities/xrayutilities-1.1.2.ebuild (renamed from sci-physics/xrayutilities/xrayutilities-1.1.1.ebuild) | 0 |
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 |