Merge pull request #47 from SystemsBioinformatics/dev

Dev

Author: bgoli

cbmpy/CBCPLEX.py

@@ -2165,7 +2165,7 @@ def cplx_MultiFluxVariabilityAnalysis(
     iter_cnt = 0
 
     # raw_input('\n*****\nMultiFVA ready, press <enter> to continue:')
-    Rdump = file(os.path.join(work_dir, TFname + '_resTemp.txt'), 'w')
+    Rdump = open(os.path.join(work_dir, TFname + '_resTemp.txt'), 'w')
     NEW_RUN = True
     ADD_MILP_CONSTR = False
     for Ridx in range(NUM_FLX):

cbmpy/CBConfig.py

@@ -39,7 +39,7 @@
 
 __VERSION_MAJOR__ = 0
 __VERSION_MINOR__ = 8
-__VERSION_MICRO__ = 2
+__VERSION_MICRO__ = 3
 
 __CBCONFIG__ = {
     'VERSION_MAJOR': __VERSION_MAJOR__,

cbmpy/CBMultiEnv.py

@@ -265,7 +265,7 @@ def runMultiStateFBA(
             biomass_name, options['target_biomass']
         )
     )
-    F = file(
+    F = open(
         os.path.join(
             work_dir,
             'find_input(%s)_(%s).csv' % (ModelPrefixStrIO, options['target_biomass']),
@@ -681,7 +681,7 @@ def runMultiStateFBA(
         RESULT_DATA.append(DD)
         RESULT_LPS.append(mGlp)
 
-        FR = file(os.path.join(work_dir, '%s_rpt.txt' % MultiFNbase), 'w')
+        FR = open(os.path.join(work_dir, '%s_rpt.txt' % MultiFNbase), 'w')
         FR.write('MultipleInput(%s states) Result:\n' % len(multisolve))
         # FR.write(' Flux diff: %s\n' % all_flux_diff.sum())
         FR.write(' optimum: %s = %s\n' % (mGobid, mGobjval))
@@ -704,7 +704,7 @@ def runMultiStateFBA(
 
         FR.close()
 
-        FD = file(os.path.join(work_dir, '%s_dat.test.csv' % MultiFNbase), 'w')
+        FD = open(os.path.join(work_dir, '%s_dat.test.csv' % MultiFNbase), 'w')
         head = 'Flux, '
         for p in ModelPrefixes:
             head += '%s,' % p
@@ -722,7 +722,7 @@ def runMultiStateFBA(
             FD.write('%s,%s\n' % (FluxScaling[F], FlxAO_scaled[F, -1]))
         FD.flush()
         FD.close()
-        FD = file(os.path.join(work_dir, '%s_dat.csv' % MultiFNbase), 'w')
+        FD = open(os.path.join(work_dir, '%s_dat.csv' % MultiFNbase), 'w')
         head = 'Flux, '
         for p in ModelPrefixes:
             head += '%s,' % p
@@ -755,9 +755,9 @@ def runMultiStateFBA(
 
     # multi file
     # if options['algorithm'] == "ABS_L1_METHOD":
-    # FD = file(os.path.join(work_dir, '%s_ABSL1_multi.csv' % OFname), 'w')
+    # FD = open(os.path.join(work_dir, '%s_ABSL1_multi.csv' % OFname), 'w')
     # elif options['algorithm'] == "L1_METHOD":
-    # FD = file(os.path.join(work_dir, '%s_L1_multi.csv' % OFname), 'w')
+    # FD = open(os.path.join(work_dir, '%s_L1_multi.csv' % OFname), 'w')
 
     # dat_arr = [a['solution'] for a in RESULT_DATA]
     # dat_arr = numpy.hstack(dat_arr)
@@ -807,9 +807,9 @@ def runMultiStateFBA(
 
     opt_out = [(a['dev_factor'], a['obj_val'], a['flux_diff']) for a in RESULT_DATA]
     if options['algorithm'] == "ABS_L1_METHOD":
-        FR2 = file(os.path.join(work_dir, '%s_ABSL1_opt.csv' % OFname), 'w')
+        FR2 = open(os.path.join(work_dir, '%s_ABSL1_opt.csv' % OFname), 'w')
     elif options['algorithm'] == "L1_METHOD":
-        FR2 = file(os.path.join(work_dir, '%s_L1_opt.csv' % OFname), 'w')
+        FR2 = open(os.path.join(work_dir, '%s_L1_opt.csv' % OFname), 'w')
     head = 'ObjDist(%s),optimum (%s),raw diff (%s)' % (
         ModelPrefixStr,
         ModelPrefixStr,
@@ -1005,7 +1005,7 @@ def runMultiStateFBA(
                 (fva_time_end - fva_time_start) / 60.0,
             )
         )
-        F = file(os.path.join(work_dir, '%s_fva_stats.txt' % OFname), 'a')
+        F = open(os.path.join(work_dir, '%s_fva_stats.txt' % OFname), 'a')
         F.write(
             '*****\nTotal (%s LP\'s) time for FVA (%s threads) min: %s\n*****\n'
             % (

cbmpy/CBRead.py

@@ -255,7 +255,7 @@ def readLPtoList(fname, work_dir):
     Object = []
     Constr = []
     Bounds = []
-    F = file(os.path.join(work_dir, fname), 'r')
+    F = open(os.path.join(work_dir, fname), 'r')
     for l in F:
         if l == '' or l[:2] == '\\\\' or l == '\n' or l.strip() == 'END':
             print('skipping')
@@ -301,7 +301,7 @@ def readSK_FVA(filename):
     assert os.path.exists(filename), '\nGive me a break!\n'
     ##  name = []
     vari = []
-    F = file(filename, 'r')
+    F = open(filename, 'r')
     for l in F:
         L = l.split(':')
         Jn = L[0].strip()
@@ -333,7 +333,7 @@ def readSK_FVA(filename):
 ##  assert _HAVE_SYMPY_, 'Install Sympy for rational IO support'
 
 ##  assert os.path.exists(fname), 'Uhm exqueeze me ...'
-##  SK_vert_file = file(fname, 'r')
+##  SK_vert_file = open(fname, 'r')
 ##  VertOut = []
 ##  LinOut = []
 ##  RayOut = []
@@ -471,7 +471,7 @@ def readSK_vertexOld(
     print('nformat: {}'.format(nformat % 0.12345678901234567890))
     print('**********\n')
 
-    SK_vert_file = file(fname, 'r')
+    SK_vert_file = open(fname, 'r')
     VertOut = []
     LinOut = []
     RayOut = []
@@ -646,7 +646,7 @@ def readSK_vertex(
     print('nformat: {}'.format(nformat % 0.12345678901234567890))
     print('**********\n')
 
-    SK_vert_file = file(fname, 'r')
+    SK_vert_file = open(fname, 'r')
     VCNTR = 0
     LCNTR = 0
     RCNTR = 0
@@ -1239,7 +1239,7 @@ def logMsg(msg):
 
     # write log to file
     """
-    F = file(os.path.join(cDir,'{}.log'.format(xlname)),'w')
+    F = open(os.path.join(cDir,'{}.log'.format(xlname)),'w')
     MSGLog.seek(0)
     F.write(MSGLog.read())
     F.close()

cbmpy/CBReadtxt.py

@@ -53,7 +53,7 @@
 
 
 def getBounds(fname, reaction_prefix='R_', has_header=False):
-    bndsF = file(fname, 'r')
+    bndsF = open(fname, 'r')
     bndsLst = []
     bndsOut = {}
     for L in bndsF:
@@ -89,7 +89,7 @@ def getReactions(
     ignore_duplicates=False,
 ):
     assert os.path.exists(fname), '\n%s is not a valid file!'
-    rF = file(fname, 'r')
+    rF = open(fname, 'r')
     rxnLst = []
     Reac = {}
     dupcntr = {}
@@ -180,7 +180,7 @@ def getReactions_old_format(
     ignore_duplicates=False,
 ):
     assert os.path.exists(fname), '\n%s is not a valid file!'
-    rF = file(fname, 'r')
+    rF = open(fname, 'r')
     rxnLst = []
     Reac = {}
     dupcntr = {}
@@ -361,7 +361,7 @@ def addBoundsToReactions(Reactions, Bounds, default=1111.0):
 
 
 def dumpReactionsToTxt(Reactions, fname):
-    dF = file(fname, 'w')
+    dF = open(fname, 'w')
     for rx in Reactions:
         dF.write('\n%s\n' % Reactions[rx]['id'])
         dF.write('Name: %s\n' % Reactions[rx]['name'])
@@ -399,7 +399,7 @@ def getSpecies(reactions):
 
 
 def dumpSpeciesToTxt(species, fname):
-    dF = file(fname, 'w')
+    dF = open(fname, 'w')
     for s in species:
         dF.write('\n%s\n' % s)
         dF.write('Compartment: %s\n' % species[s]['compartment'])

cbmpy/CBTools.py

@@ -89,7 +89,7 @@ def storeObj(obj, filename, compress=False):
     """
     if filename[-4:] != '.dat':
         filename = filename + '.dat'
-    F = file(filename, 'wb')
+    F = open(filename, 'wb')
     pickle.dump(obj, F, protocol=2)
     print('Object serialised as {}'.format(filename))
     F.close()
@@ -103,7 +103,7 @@ def loadObj(filename):
     if filename[-4:] != '.dat':
         filename = filename + '.dat'
     assert os.path.exists(filename), '\nFile \"{}\" does not exist'.format(filename)
-    F = file(filename, 'rb')
+    F = open(filename, 'rb')
     obj = pickle.load(F)
     F.close()
     return obj
@@ -123,7 +123,7 @@ def deSerializeFromDisk(filename):
 
     """
     assert os.path.exists(filename), '\nFile \"{}\" does not exist'.format(filename)
-    F = file(filename, 'rb')
+    F = open(filename, 'rb')
     obj = pickle.load(F)
     F.close()
     return obj
@@ -460,7 +460,7 @@ def exportLabelledArray(arr, fname, names=None, sep=',', fmt='%f'):
     """
     if names != None:
         assert arr.shape[0] == len(names), '\n ...  rows must equal number of names!'
-    F = file(fname, 'w')
+    F = open(fname, 'w')
     cntr = 0
     for r in range(arr.shape[0]):
         if names != None:
@@ -502,7 +502,7 @@ def exportLabelledArrayWithHeader(
             header
         ), '\n ...  cols must equal number of header names!'
 
-    F = file(fname, 'w')
+    F = open(fname, 'w')
     cntr = 0
     if header != None:
         if names != None:
@@ -549,9 +549,9 @@ def exportLabelledLinkedList(
     if names != None:
         assert len(arr) == len(names), '\n ...  rows must equal number of names!'
     if not appendlist:
-        F = file(fname, 'w')
+        F = open(fname, 'w')
     else:
-        F = file(fname, 'a')
+        F = open(fname, 'a')
     cntr = 0
     for r in range(len(arr)):
         if names != None:
@@ -1014,23 +1014,23 @@ def generateInputScanReports(
     modName += tag
     rnames = fba.getReactionNames()
     rid = fba.getReactionIds()
-    F = file(os.path.join(wDir, '%s.medium.csv' % modName), 'w')
+    F = open(os.path.join(wDir, '%s.medium.csv' % modName), 'w')
     F.write('J, lb, ub\n')
     for r in mediumDict:
         RN = rnames[rid.index(r)]
         F.write('%s, %s, %s, %s\n' % (r, mediumDict[r]['lb'], mediumDict[r]['ub'], RN))
     F.write('\n')
     F.close()
 
-    F = file(os.path.join(wDir, '%s.exchange.csv' % modName), 'w')
+    F = open(os.path.join(wDir, '%s.exchange.csv' % modName), 'w')
     F.write('J, lb, ub\n')
     for r in exDict:
         RN = rnames[rid.index(r)]
         F.write('%s, %s, %s, %s\n' % (r, exDict[r]['lb'], exDict[r]['ub'], RN))
     F.write('\n')
     F.close()
 
-    F = file(os.path.join(wDir, '%s.optima.csv' % modName), 'w')
+    F = open(os.path.join(wDir, '%s.optima.csv' % modName), 'w')
     F.write('J, lb, ub, optimum, "name"\n')
     if __DEBUG__:
         print(rnames)

cbmpy/CBWx.py

@@ -1219,7 +1219,7 @@ def MENUExport(self, e):
                 self.OUT_dir = dlg.GetDirectory()
                 if OUT_file[-3:] != '.py':
                     OUT_file += '.py'
-                F = file(os.path.join(self.OUT_dir, OUT_file), 'w')
+                F = open(os.path.join(self.OUT_dir, OUT_file), 'w')
                 F.write(self.PyBox.GetValue())
                 F.flush()
                 F.close()

cbmpy/_multicoreenvfva.py

@@ -113,14 +113,14 @@ def multiCoreEnvFVA(MEargs, procs=2, timeout=None):
     print(os.sys.argv)
 
     cores = int(os.sys.argv[1])
-    F = file(os.sys.argv[2], 'rb')
+    F = open(os.sys.argv[2], 'rb')
     MEargs = pickle.load(F)
     print('\t', MEargs)
     F.close()
 
     res = multiCoreEnvFVA(MEargs, procs=cores)
 
-    F = file(os.sys.argv[2], 'wb')
+    F = open(os.sys.argv[2], 'wb')
     pickle.dump(res, F, protocol=-1)
     F.flush()
     F.close()

setup.py

@@ -76,16 +76,13 @@
 needs PySCeS CBMPy supports user interaction via:
 """
 
-description=""" CBMPy 
-=====
-CBMPy https://github.com/SystemsBioinformatics/cbmpy is a platform for constraint based modelling and analysis. CBMPy implements popular analyses such as FBA, FVA, element/charge balancing, network analysis and model editing as well as advanced methods.
-"""
+description="""CBMPy: https://github.com/SystemsBioinformatics/cbmpy is a platform for constraint based modelling and analysis. CBMPy implements popular analyses such as FBA, FVA, element/charge balancing, network analysis and model editing as well as advanced methods."""
 
 setup(
     package_dir={'cbmpy': 'cbmpy'},
     packages=mypackages,
     data_files=mydata_files,
-    long_description=readme,
+    long_description=description,
     name="cbmpy",
     summary="CBMPy: Constraint Based Modelling in Python",
     version='{}.{}.{}'.format(vmaj, vmin, vmic),
@@ -114,7 +111,7 @@
         'Topic :: Scientific/Engineering :: Bio-Informatics',
         'Topic :: Scientific/Engineering :: Chemistry',
     ],
-    description=readme,
+    description=description,
 )
 try:
     os.chdir(os.path.join(local_path, 'cbmpy', 'fluxmodules'))