cli: Prettify CL help messages, relates to tomazc#86

iCount/__init__.py

@@ -14,8 +14,7 @@
 A number of analyses are included in iCount that provide insights into the properties of
 protein-RNA interaction.
 
-.. _iCLIP:
-    http://www.ulelab.info
+.. _iCLIP: http://www.ulelab.info
 
 """
 

iCount/cli.py

@@ -65,14 +65,18 @@ def _list_str(string, separator=','):
 PARAMETERS = {}
 
 
-def remove_comments(description):
+def _remove_comments(description_in):
     """Remove reStructuredText comment lines."""
-    description = description.splitlines()
-    if len(description) > 0:
-        if description[0].startswith('..'):
-            description = description[1:]
-    while description and description[0].strip() == '':
-        description.pop(0)
+    description = []
+    for line in description_in.splitlines():
+        if not line.startswith('..'):
+            description.append(line)
+
+    # Remove first/last line if it is empty:
+    while description[0] == '':
+        description = description[1:]
+    while description[-1] == '':
+        description = description[:-1]
 
     return '\n'.join(description)
 
@@ -248,7 +252,7 @@ def make_parser_from_function(function, subparsers, module=None, only_func=False
         name = module.__name__.split('.')[-1]
         # Description is determined from module docstring:
         description = inspect.getdoc(module)
-        description = remove_comments(description)
+        description = _remove_comments(description)
         description = '\n'.join(description.split('\n')[3:])
     elif only_func:
         # If only_func=True than name of the command equals function name
@@ -257,13 +261,13 @@ def make_parser_from_function(function, subparsers, module=None, only_func=False
         desc = inspect.getdoc(function).split('\n')
         idx = [i for i, d in enumerate(desc) if d == 'Parameters' or d == 'Returns'][0]
         description = '\n'.join(desc[:idx])
-        description = remove_comments(description)
+        description = _remove_comments(description)
     else:
         # Command name is determined from module name:
         name = inspect.getmodule(function).__name__.split('.')[-1]
         # Description is determined from module docstring:
         description = inspect.getdoc(inspect.getmodule(function))
-        description = remove_comments(description)
+        description = _remove_comments(description)
         description = '\n'.join(description.split('\n')[3:])
 
     if not description:
@@ -275,7 +279,7 @@ def make_parser_from_function(function, subparsers, module=None, only_func=False
         name,
         description=description,
         help=short_description,
-        formatter_class=argparse.RawTextHelpFormatter  # ArgumentDefaultsHelpFormatter
+        formatter_class=argparse.RawDescriptionHelpFormatter  # ArgumentDefaultsHelpFormatter
     )
 
     # Add each of the function parameter as CLI argument:
@@ -293,14 +297,14 @@ def make_parser_from_function(function, subparsers, module=None, only_func=False
 
     parser.add_argument('-S', '--stdout_log', default=logging.INFO, type=int, metavar='',
                         help='Threshold value (0-50) for logging to stdout. If 0,'
-                        ' logging to stdout if turned OFF.')
+                        ' logging to stdout if turned OFF. (default: {})'.format(logging.INFO))
     parser.add_argument('-F', '--file_log', default=0, type=int, metavar='',
                         help='Threshold value (0-50) for logging to file. If 0,'
-                        ' logging to file if turned OFF.')
+                        ' logging to file if turned OFF. (default: {})'.format(0))
     parser.add_argument('-P', '--file_logpath', default=None, type=str, metavar='',
-                        help="Path to log file.")
+                        help="Path to log file. (default: {})".format(None))
     parser.add_argument('-M', '--results_file', default=None, type=argparse.FileType('wt'),
-                        metavar='', help="File into which to store Metrics.")
+                        metavar='', help="File to store Metrics. (default: {})".format(None))
 
     # Connect parser with function to execute:
     parser.set_defaults(func=function)
@@ -320,8 +324,8 @@ def main():
     #####################
 
     root_parser = argparse.ArgumentParser(
-        description=remove_comments(inspect.getdoc(iCount)).split('\n..')[0],
-        formatter_class=argparse.RawTextHelpFormatter  # ArgumentDefaultsHelpFormatter,
+        description=_remove_comments(inspect.getdoc(iCount)),
+        formatter_class=argparse.RawDescriptionHelpFormatter,
     )
     # Parser (general) arguments
     root_parser.add_argument('-v', '--version', action='version',