updated documentation and cleaned up for release

estimate.py

@@ -114,17 +114,23 @@ def parse_arguments(defined_tasks, defined_estimation_methods):
 
  Estimate the history dependence and temporal depth of a single
  neuron, based on information-theoretical measures for spike time
- data, as presented in (Rudelt et al, in prep.). Parameters can be
- passed via the command line or through files, where command line
- options are prioritised over those passed by file. (If none are
- supplied, settings are read from the 'default.yaml' file.) A user
- new to this tool is encouraged to run
+ data, as presented in (Rudelt et al, in prep.) [1]. Parameters
+ can be passed via the command line or through files, where command
+ line options are prioritised over those passed by file. (If none
+ are supplied, settings are read from the 'default.yaml' file.) A
+ user new to this tool is encouraged to run
 
  python3 {} sample_data/spike_times.dat -o sample_output.pdf \\
  -s settings/test.yaml
 
  to test the functionality of this tool. A more detailed
- description can be found in the guide provided with the tool.
+ description can be found in the guide provided with the tool [2].
+
+ [1]: L. Rudelt, D. G. Marx, M. Wibral, V. Priesemann: Embedding
+ optimization reveals long-lasting history dependence in
+ neural spiking activity (in prep.)
+
+ [2]: https://github.com/Priesemann-Group/hdestimator
  """.format(__version__, argv[0]), formatter_class=argparse.RawDescriptionHelpFormatter)
  optional_arguments = parser._action_groups.pop()
 
@@ -142,6 +148,7 @@ def parse_arguments(defined_tasks, defined_estimation_methods):
  optional_arguments.add_argument("-s", "--settings-file", metavar="SETTINGS_FILE", action="store", help="Specify yaml file from which to load custom settings.")
  optional_arguments.add_argument("-l", "--label", metavar="LABEL", action="store", help="Include a label in the output to classify the analysis.")
  # optional_arguments.add_argument("-v", "--verbose", action="store_true", help="Print more info at run time.")
+ optional_arguments.add_argument('--version', action='version', version='hdestimator v. {}'.format(__version__), help="Show version of the tool and exit.")
  parser._action_groups.append(optional_arguments)
  args = parser.parse_args()