Merge pull request #2 from CNS-OIST/py2py3

[py2py3-patch] cannot open unbuffered io stream in py3

Author: FrancescoCasalegno

publication_models/Anwar_J Neurosci_2013/StochasticCaburst_cluster.py

@@ -698,19 +698,19 @@
             if cap_m0_count<round(CaP_ro*surfarea*CaP_m0_p):
                 sim.setTriCount(i, 'CaP_m0', sim.getTriCount(i, 'CaP_m0') + 1)
                 cap_m0_count = cap_m0_count + 1
-		count = count +1
+                count = count +1
             elif cap_m1_count<round(CaP_ro*surfarea*CaP_m1_p):
                 sim.setTriCount(i, 'CaP_m1', sim.getTriCount(i, 'CaP_m1') + 1)
                 cap_m1_count = cap_m1_count + 1
-		count = count +1
+                count = count +1
             elif cap_m2_count<round(CaP_ro*surfarea*CaP_m2_p):
                 sim.setTriCount(i, 'CaP_m2', sim.getTriCount(i, 'CaP_m2') + 1)
                 cap_m2_count = cap_m2_count + 1
-		count = count +1
+                count = count +1
             elif cap_m3_count<round(CaP_ro*surfarea*CaP_m3_p):
                 sim.setTriCount(i, 'CaP_m3', sim.getTriCount(i, 'CaP_m3') + 1)
                 cap_m3_count = cap_m3_count + 1
-		count = count +1
+                count = count +1
             else:
                 print('Cluster size is larger than the number of CaP channels available')
 

publication_models/Chen_FNeuroinf__2017/purkinje_model/parallel_branch_background.py

@@ -89,7 +89,7 @@
 sim.run(SIM_TIME)
 time_cost = (time.time()  - start_time)
 
-proc_file = open(RESULT_DIR + '/proc_%i.csv' % (steps.mpi.rank), 'w', 0)
+proc_file = open(RESULT_DIR + '/proc_%i.csv' % (steps.mpi.rank), 'w', 1)
 proc_file.write("SimTime,CompTime,SyncTime,IdleTime,nIteration\n")
 proc_file.write("%f,%f,%f,%f,%i\n" % (time_cost, sim.getCompTime(), sim.getSyncTime(), sim.getIdleTime(), sim.getNIteration()))
 proc_file.close()

publication_models/Chen_FNeuroinf__2017/purkinje_model/parallel_branch_influx.py

@@ -78,7 +78,7 @@
 ca_conc_preset_file.close()
 
 if steps.mpi.rank == 0:
-    conc_result = open(RESULT_DIR + '/calcium_conc_%iprocs.dat' % (steps.mpi.nhosts), 'w', 0)
+    conc_result = open(RESULT_DIR + '/calcium_conc_%iprocs.dat' % (steps.mpi.nhosts), 'w', 1)
     conc_result.write('#Entries: Time ')
     for roi in rois:
         conc_result.write('%s ' % (roi))
@@ -150,7 +150,7 @@
 time_cost = (time.time()  - start_time)
 conc_result.close()
 
-proc_file = open(RESULT_DIR + '/proc_%i.csv' % (steps.mpi.rank), 'w', 0)
+proc_file = open(RESULT_DIR + '/proc_%i.csv' % (steps.mpi.rank), 'w', 1)
 proc_file.write("SimTime,CompTime,SyncTime,IdleTime,nIteration\n")
 proc_file.write("%f,%f,%f,%f,%i\n" % (time_cost, sim.getCompTime(), sim.getSyncTime(), sim.getIdleTime(), sim.getNIteration()))
 proc_file.close()

publication_models/Chen_FNeuroinf__2017/purkinje_model/parallel_fullcell_background.py

@@ -89,7 +89,7 @@
 sim.run(SIM_TIME)
 time_cost = (time.time()  - start_time)
 
-proc_file = open(RESULT_DIR + '/proc_%i.csv' % (steps.mpi.rank), 'w', 0)
+proc_file = open(RESULT_DIR + '/proc_%i.csv' % (steps.mpi.rank), 'w', 1)
 proc_file.write("SimTime,CompTime,SyncTime,IdleTime,nIteration\n")
 proc_file.write("%f,%f,%f,%f,%i\n" % (time_cost, sim.getCompTime(), sim.getSyncTime(), sim.getIdleTime(), sim.getNIteration()))
 proc_file.close()

publication_models/Chen_FNeuroinf__2017/purkinje_model/ssa_branch_influx.py

@@ -49,7 +49,7 @@
 try: os.mkdir(RESULT_DIR)
 except: pass
 
-conc_result = open(RESULT_DIR + '/ssa_calcium_conc.dat', 'w', 0)
+conc_result = open(RESULT_DIR + '/ssa_calcium_conc.dat', 'w', 1)
 conc_result.write('#Entries: Time ')
 for roi in rois:
     conc_result.write('%s ' % (roi))

publication_models/Chen_FNeuroinf__2017/simple_model/parallel_simulation.py

@@ -125,7 +125,7 @@ def gen_geom():
     sim_result_dir = RESULT_DIR + "/%e_%s_%ihosts" % (MOLECULE_RATIO, MESHFILE, steps.mpi.nhosts)
     try: os.mkdir(sim_result_dir)
     except: pass
-    summary_file = open(sim_result_dir + "/result.csv", 'w', 0)
+    summary_file = open(sim_result_dir + "/result.csv", 'w', 1)
     summary_file.write("Simulation Time,")
 
 ########################################################################
@@ -144,7 +144,7 @@ def gen_geom():
 start_time = time.time()
 sim.run(ENDTIME)
 end_time = (time.time()  - start_time)
-proc_file = open(sim_result_dir + "/proc_%i.csv" % (steps.mpi.rank), 'w', 0)
+proc_file = open(sim_result_dir + "/proc_%i.csv" % (steps.mpi.rank), 'w', 1)
 proc_file.write("SimTime,CompTime,SyncTime,IdleTime,nIteration\n")
 proc_file.write("%f,%f,%f,%f,%i\n" % (end_time, sim.getCompTime(), sim.getSyncTime(), sim.getIdleTime(), sim.getNIteration()))
 proc_file.close()

publication_models/Chen_FNeuroinf__2017/simple_model/ssa_simulation.py

@@ -117,7 +117,7 @@ def gen_geom():
 except: pass
 try: os.mkdir(sim_result_dir)
 except: pass
-summary_file = open(sim_result_dir + "/result.csv", 'w', 0)
+summary_file = open(sim_result_dir + "/result.csv", 'w', 1)
 summary_file.write("Simulation Time,")
 
 ########################################################################