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jmrohwerjmrohwer
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replace file(path) with open(path) - Py3 compatibility
1 parent b5eee20 commit 835c626

16 files changed

+51
-51
lines changed

‎pysces/PyscesLink.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -159,7 +159,7 @@ def loadSBMLFileFromDisk(self, File, Dir=None):
159159
self.svg = None
160160
self.DRAWNETWORKLOADED = False
161161
self.LAYOUTMODULELOADED = False
162-
sbmlF = file(path, 'r')
162+
sbmlF = open(path, 'r')
163163
self.sbml = sbmlF.read()
164164
sbmlF.close()
165165
return True

‎pysces/PyscesPlot.py

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -264,11 +264,11 @@ def save_html(self,imagename,File=None,path=None,name=None,close_file=1):
264264
if path != None:
265265
imagenameout = os.path.join(path,imagename)
266266
if File == None:
267-
File = file(os.path.join(path,imagename[:-3]+'html'),'w')
267+
File = open(os.path.join(path,imagename[:-3]+'html'),'w')
268268
else:
269269
imagenameout = os.path.join(os.getcwd(),imagename)
270270
if File == None:
271-
File = file(os.path.join(os.getcwd(),imagename[:-3]+'html'),'w')
271+
File = open(os.path.join(os.getcwd(),imagename[:-3]+'html'),'w')
272272
self.__save_command__(imagename)
273273

274274
fname = 'PySCeS generated image - '+imagename+'" generated from model file: ' + strftime("%H:%M:%S")
@@ -888,11 +888,11 @@ def save_html(self,imagename,File=None,path=None,name=None,close_file=1):
888888
if path != None:
889889
imagenameout = os.path.join(path,imagename)
890890
if File == None:
891-
File = file(os.path.join(path,imagename[:-3]+'html'),'w')
891+
File = open(os.path.join(path,imagename[:-3]+'html'),'w')
892892
else:
893893
imagenameout = os.path.join(os.getcwd(),imagename)
894894
if File == None:
895-
File = file(os.path.join(os.getcwd(),imagename[:-3]+'html'),'w')
895+
File = open(os.path.join(os.getcwd(),imagename[:-3]+'html'),'w')
896896
self.P.savefig(imagenameout,dpi=80)
897897

898898
fname = 'PySCeS generated image - '+imagename+'" generated from model file: ' + strftime("%H:%M:%S")

‎pysces/PyscesPlot2.py

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -337,7 +337,7 @@ def g_file_write_array3D(self, arr, yaxis=1, dfmt=None):
337337
if len(outlist) <= 1:
338338
self.g_file_write_array(arr, dfmt=dfmt)
339339
else:
340-
F = file(self.__DATA_FILE_PATH__, 'w+')
340+
F = open(self.__DATA_FILE_PATH__, 'w+')
341341
for d in range(len(outlist)):
342342
numpy.savetxt(F, outlist.pop(0), fmt=dfmt)
343343
F.write(' \n')
@@ -497,12 +497,12 @@ def save(self, name, directory=None, dfmt=None):
497497
out_n = os.path.join(self.__WORK_DIR__, name)
498498
self.g_write('save "%s.plt"' % out_n)
499499
shutil.copy(os.path.join(self.__WORK_DIR__, self.__DATA_FILE_NAME__), "%s.dat" % out_n)
500-
F = file('%s.plt'% out_n, 'r')
500+
F = open('%s.plt'% out_n, 'r')
501501
fnew = F.read().replace('_gnuplot.dat','%s.dat' % name)
502502
fnew = fnew.replace('noequal_axes','') # fixes the "noequal_axes" bug in gnuplot save
503503
fnew = fnew.replace('#!/gnuplot','#!/gnuplot\n#\n# Plot created using PySCeS %s (http://pysces.sourceforge.net)' % __version__) # fixes the "noequal_axes" bug in gnuplot save
504504
F.close()
505-
F = file('%s.plt'% out_n, 'w')
505+
F = open('%s.plt'% out_n, 'w')
506506
F.write(fnew)
507507
F.flush()
508508
F.close()

‎pysces/PyscesSBML.py

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
1-
"""
21
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
2+
"""
33
44
Copyright (C) 2004-2020 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
55
@@ -586,7 +586,7 @@ def getName(i):
586586
#print init_fixed
587587

588588
# sometimes things just work lekker (replaced all the old showS^&t) - brett 20050913
589-
outFile = file(self.model_filename+'.psc','w')
589+
outFile = open(self.model_filename+'.psc','w')
590590
self.PSC_writeHeader(outFile)
591591
self.PSC_writeFixedSpeciesList(outFile,init_fixed)
592592
self.PSC_writeRateEquations(outFile,NetworkDict,number_format='%2.3f')

‎pysces/PyscesSED.py

Lines changed: 9 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -263,7 +263,7 @@ def writeSedScript(self, sedx=False):
263263
sf = os.path.join(self.sedpath, '%s.txt' % (self.id))
264264
else:
265265
sf = os.path.join(self.sedpath, 'sedxtmp', '%s.txt' % (self.id))
266-
F = file(sf, 'w')
266+
F = open(sf, 'w')
267267
F.write(sedscr.read())
268268
F.flush()
269269
F.close()
@@ -295,7 +295,7 @@ def writeSedXML(self, sedx=False):
295295
except Exception as ex:
296296
print('\nOops no SED: %s' % ex)
297297
self.__sedxml__ = sf
298-
F = file(sf, 'r')
298+
F = open(sf, 'r')
299299
self._SED_XML_ = F.read()
300300
F.close()
301301
del F
@@ -311,11 +311,11 @@ def writeSedXML(self, sedx=False):
311311
#else:
312312
#sf = os.path.join(self.sedpath, 'sedxtmp', sedname)
313313

314-
F = file(self.__sedscript__, 'r')
314+
F = open(self.__sedscript__, 'r')
315315
sedscr = F.read()
316316
F.close()
317317
self._SED_XML_ = self.sbwsedclient.ConvertScriptToSedML(sedscr)
318-
F = file(sf, 'w')
318+
F = open(sf, 'w')
319319
F.write(self._SED_XML_)
320320
F.flush()
321321
F.close()
@@ -326,7 +326,7 @@ def writeSedXML(self, sedx=False):
326326
else:
327327
raise RuntimeError('\n')
328328
if self._SED_CURRENT_:
329-
F = file(self.__sedxml__, 'w')
329+
F = open(self.__sedxml__, 'w')
330330
F.write(self._SED_XML_)
331331
F.flush()
332332
F.close()
@@ -386,11 +386,11 @@ def writeCOMBINEArchive(self, vc_given='PySCeS', vc_family='Software', vc_email=
386386
MFstr += ' <content location="./%s" format="http://identifiers.org/combine.specifications/sbml"/>\n' % modname
387387
MFstr += ' <content location="./metadata.rdf" format="http://identifiers.org/combine.specifications/omex-metadata"/>'
388388

389-
MF = file(os.path.join(ptmp, 'manifest.xml'), 'w')
389+
MF = open(os.path.join(ptmp, 'manifest.xml'), 'w')
390390
MF.write('<?xml version="1.0" encoding="utf-8"?>\n%s\n</omexManifest>\n' % MFstr)
391391
MF.close()
392392

393-
MD = file(os.path.join(ptmp, 'metadata.rdf'), 'w')
393+
MD = open(os.path.join(ptmp, 'metadata.rdf'), 'w')
394394
MD.write('<?xml version="1.0" encoding="UTF-8"?>\n')
395395
MD.write('<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"\n')
396396
MD.write(' xmlns:dcterms="http://purl.org/dc/terms/"\n')
@@ -441,7 +441,7 @@ def storeObj(obj, filename):
441441
442442
"""
443443
filename = filename+'.dat'
444-
F = file(filename, 'wb')
444+
F = open(filename, 'wb')
445445
pickle.dump(obj, F, protocol=2)
446446
print('Object serialised as %s' % filename)
447447
F.close()
@@ -452,7 +452,7 @@ def loadObj(filename):
452452
453453
"""
454454
assert os.path.exists(filename), '\nTry again mate!'
455-
F = file(filename, 'rb')
455+
F = open(filename, 'rb')
456456
obj = pickle.load(F)
457457
F.close()
458458
return obj

‎pysces/PyscesTest.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -100,7 +100,7 @@ def __init__(self,lvl=2,std2file=0):
100100
class NullWriter:
101101
def __init__(self,dres=0):
102102
if dres:
103-
self.Fout = file(os.path.join(os.getcwd(),'pysces_test_results.txt'),'w')
103+
self.Fout = open(os.path.join(os.getcwd(),'pysces_test_results.txt'),'w')
104104
self.fof = 1
105105
else:
106106
self.fof = 0

‎pysces/PyscesUtils.py

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -194,7 +194,7 @@ def exportLabelledArray(self, arr, names, fname, sep=',', format='%f'):
194194
"""
195195
if names != None:
196196
assert arr.shape[0] == len(names), '\n ... rows must equal number of names!'
197-
F = file(fname, 'w')
197+
F = open(fname, 'w')
198198
cntr = 0
199199
for r in range(arr.shape[0]):
200200
if names != None:
@@ -230,7 +230,7 @@ def exportLabelledArrayWithHeader(self, arr, names, header, fname, sep=',', form
230230
assert arr.shape[0] == len(names), '\n ... rows must equal number of names!'
231231
if header != None:
232232
assert arr.shape[1] == len(header), '\n ... cols must equal number of header names!'
233-
F = file(fname, 'w')
233+
F = open(fname, 'w')
234234
cntr = 0
235235
if header != None:
236236
if names != None:
@@ -275,9 +275,9 @@ def exportLabelledLinkedList(self, arr, fname, names=None, sep=',', format='%s',
275275
if names != None:
276276
assert len(arr) == len(names), '\n ... rows must equal number of names!'
277277
if not appendlist:
278-
F = file(fname, 'w')
278+
F = open(fname, 'w')
279279
else:
280-
F = file(fname, 'a')
280+
F = open(fname, 'a')
281281
cntr = 0
282282
for r in range(len(arr)):
283283
if names != None:

‎pysces/RateChar.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -91,7 +91,7 @@ def pscFile2str(self, name):
9191
"""
9292
if name[-4:] != '.psc':
9393
name += '.psc'
94-
F = file(os.path.join(pysces.PyscesModel.MODEL_DIR, name),'r')
94+
F = open(os.path.join(pysces.PyscesModel.MODEL_DIR, name),'r')
9595
fstr = F.read()
9696
F.close()
9797
return fstr

‎pysces/contrib/sbw/sbw_func.py

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -57,7 +57,7 @@ def loadSBMLfromFile(self,filename,dir=None):
5757
if dir != None:
5858
filename = os.path.join(dir,filename)
5959
self.sbml_file = filename
60-
sbml_file = file(filename,'r')
60+
sbml_file = open(filename,'r')
6161
self.sbml_string = ''
6262
for line in sbml_file: self.sbml_string += line
6363
sbml_file.close()
@@ -79,7 +79,7 @@ def SBW_Methods(self):
7979
def WriteOutputToFile(self,filename,dir=None):
8080
if dir != None:
8181
filename = os.path.join(dir,filename)
82-
Fout = file(filename,'w')
82+
Fout = open(filename,'w')
8383
Fout.write(self.output)
8484
Fout.flush()
8585
Fout.close()

‎pysces/kraken/Kraken.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -276,7 +276,7 @@ def buildCycler(self, lst):
276276

277277
def Dump(self, thing, fname):
278278
try:
279-
F = file(os.path.join(self.working_dir, fname.replace('.bin','')+'.bin'), 'wb')
279+
F = open(os.path.join(self.working_dir, fname.replace('.bin','')+'.bin'), 'wb')
280280
cPickle.dump(thing, F, 2)
281281
F.flush()
282282
F.close()

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