Made printing all the timestamping optional

Author: dhdegroot

ecmtool/helpers.py

@@ -342,8 +342,6 @@ def process_mplrs_output(width_matrix, verbose=True):
  remove(mplrs_input_path)
  remove(mplrs_redund_path)
  remove(mplrs_output_path)
- if verbose:
- print("Done removing files. This took " + str(time() - start) + " seconds.")
 
  return rays
 

main.py

@@ -335,7 +335,7 @@ def save_data(data, filename):
  parser.add_argument('--path2mplrs', type=str, default=None,
  help='if mplrs binary is not accessable via PATH variable "mplrs", the absolute path to the binary can be provided with "--path2mplrs" e.g. "--path2mplrs /home/user/mplrs/lrslib-071b/mplrs" ')
 
- parser.add_argument('--timestamp', type=str2bool, default=False,
+ parser.add_argument('--timestamp', type=str2bool, default=True,
  help='Determines whether we print timestamps for several steps in the program.')
  args = parser.parse_args()
 
@@ -526,9 +526,9 @@ def save_data(data, filename):
  mp_print("Saving C_rays to file.")
  startSaving = time()
  save_data(C_rays, 'C_rays.dat')
- if args.verbose:
+ if args.timestamp:
  mp_print("Saving C_rays took " + str(time() - startSaving) + " seconds.")
- if args.verbose:
+ if args.timestamp:
  mp_print("Procesing C_rays took %f seconds." % (time() - startProcessingC))
 
  if args.command in ['postprocess', 'all_from_mplrs', 'all']:
@@ -566,7 +566,8 @@ def save_data(data, filename):
 
  if args.command not in ['all_from_mplrs', 'all']:
  save_data(cone, 'cone.dat')
- mp_print("Postprocessing took %f seconds." % (time()-startPostprocess))
+ if args.timestamp:
+ mp_print("Postprocessing took %f seconds." % (time()-startPostprocess))
 
  if args.command in ['save_ecms', 'all_from_mplrs', 'all'] and mpi_wrapper.is_first_process():
  startUnsplitting = time()
@@ -578,7 +579,7 @@ def save_data(data, filename):
 
  cone_transpose, ids = unsplit_metabolites(np.transpose(cone), network)
  cone = np.transpose(cone_transpose)
- if args.verbose:
+ if args.timestamp:
  mp_print("Unsplitting metabolites took %f seconds." % (time() - startUnsplitting))
 
  # internal_ids = []
@@ -603,13 +604,13 @@ def save_data(data, filename):
  if args.print_conversions is True:
  print_ecms_direct(np.transpose(cone), ids)
 
- if args.verbose:
+ if args.timestamp:
  mp_print("Saving ecms took %f seconds." % (time()-startSaveEcms))
 
  if args.make_unique is True:
  startMakeUnique = time()
  uniqueReadWrite(args.out_path)
- if args.verbose:
+ if args.timestamp:
  mp_print("Making unique took %f seconds." % (time() - startMakeUnique))
 
  end = time()