cleaned up argparse

bin/xnat-get

@@ -34,15 +34,17 @@ credentials.
 """
 import os.path
 import argparse
-from xnatutils import get, XnatUtilsUsageError, data_format_exts
+from xnatutils import get, XnatUtilsUsageError, data_format_exts, __version__
 
 
 conv_choices = [f.lower() for f in data_format_exts if f != 'DICOM']
 converter_choices = ('dcm2niix', 'mrconvert')
 
-parser = argparse.ArgumentParser(__doc__)
-parser.add_argument('session', type=str, nargs='+',
-                    help="Name of the session(s) to download the dataset from")
+parser = argparse.ArgumentParser(description=__doc__,
+                                 formatter_class=argparse.RawTextHelpFormatter)
+parser.add_argument('session_or_regex', type=str, nargs='+',
+                    help=("Name or regular expression of the session(s) to "
+                          "download the dataset from"))
 parser.add_argument('--target', '-t', type=str, default=None,
                     help=("Path to download the scans to. If not provided the "
                           "current working directory will be used"))
@@ -83,6 +85,8 @@ parser.add_argument('--strip_name', '-n', action='store_true', default=False,
                     help=("Whether to strip the default name of each dicom"
                           " file to have just a number. Ex. 0001.dcm. It will"
                           " work just on DICOM files, not NIFTI."))
+parser.add_argument('--version', '-V', action='version',
+                    version='%(prog)s ' + __version__)
 args = parser.parse_args()
 
 
@@ -92,7 +96,7 @@ else:
     download_dir = os.path.expanduser(args.target)
 
 try:
-    get(args.session, download_dir, scans=args.scans,
+    get(args.session_or_regex, download_dir, scans=args.scans,
         data_format=args.format, with_scans=args.with_scans,
         without_scans=args.without_scans, convert_to=args.convert_to,
         converter=args.converter, subject_dirs=args.subject_dirs,

bin/xnat-ls

@@ -25,14 +25,16 @@ exist the tool will ask whether to create a ~/.netrc file with the given
 credentials.
 """
 import argparse
-from xnatutils import ls, XnatUtilsUsageError
+from xnatutils import ls, XnatUtilsUsageError, __version__
 
 
 DATATYPES = ('project', 'subject', 'session', 'scan')
 
-parser = argparse.ArgumentParser(__doc__)
-parser.add_argument('id', type=str, nargs='*',
-                    help="The ID of the project/subject/session to list from")
+parser = argparse.ArgumentParser(description=__doc__,
+                                 formatter_class=argparse.RawTextHelpFormatter)
+parser.add_argument('id_or_regex', type=str, nargs='*',
+                    help=("The ID or regular expression of the "
+                          "project/subject/session to list from."))
 parser.add_argument('--datatype', '-d', type=str, choices=DATATYPES,
                     default=None, help=(
                         "The data type to list, can be one of '{}'"
@@ -45,11 +47,13 @@ parser.add_argument('--without_scans', '-o', type=str, default=None, nargs='+',
                           "specified scans"))
 parser.add_argument('--user', '-u', type=str, default=None,
                     help=("The user to connect to MBI-XNAT with"))
+parser.add_argument('--version', '-V', action='version',
+                    version='%(prog)s ' + __version__)
 args = parser.parse_args()
 
 try:
-    print '\n'.join(ls(args.id, datatype=args.datatype, user=args.user,
-                       with_scans=args.with_scans,
+    print '\n'.join(ls(args.id_or_regex, datatype=args.datatype,
+                       user=args.user, with_scans=args.with_scans,
                        without_scans=args.without_scans))
 except XnatUtilsUsageError as e:
     print e

bin/xnat-put

@@ -20,9 +20,10 @@ credentials.
 """
 import argparse
 import re
-from xnatutils import put, XnatUtilsUsageError
+from xnatutils import put, XnatUtilsUsageError, __version__
 
-parser = argparse.ArgumentParser(__doc__)
+parser = argparse.ArgumentParser(description=__doc__,
+                                 formatter_class=argparse.RawTextHelpFormatter)
 parser.add_argument('filename', type=str,
                     help="Filename of the dataset to upload to XNAT")
 parser.add_argument('session', type=str,
@@ -42,6 +43,8 @@ parser.add_argument('--format', '-f', type=str, default=None,
                           "in most cases it won't be necessary to specify"))
 parser.add_argument('--user', '-u', type=str, default=None,
                     help=("The user to connect to MBI-XNAT with"))
+parser.add_argument('--version', '-V', action='version',
+                    version='%(prog)s ' + __version__)
 args = parser.parse_args()
 
 try:

bin/xnat-varget

@@ -10,9 +10,10 @@ credentials.
 """
 from __future__ import print_function
 import argparse
-from xnatutils import varget, XnatUtilsUsageError
+from xnatutils import varget, XnatUtilsUsageError, __version__
 
-parser = argparse.ArgumentParser(__doc__)
+parser = argparse.ArgumentParser(description=__doc__,
+                                 formatter_class=argparse.RawTextHelpFormatter)
 parser.add_argument('subject_or_session_id', type=str,
                     help="Name of subject or session to get the variable from")
 parser.add_argument('variable', type=str,
@@ -21,6 +22,8 @@ parser.add_argument('--default', type=str, default='',
                     help="Default value if object does not have a value")
 parser.add_argument('--user', '-u', type=str, default=None,
                     help=("The user to connect to MBI-XNAT with"))
+parser.add_argument('--version', '-V', action='version',
+                    version='%(prog)s ' + __version__)
 args = parser.parse_args()
 
 try:

bin/xnat-varput

@@ -10,9 +10,10 @@ credentials.
 """
 import argparse
 import re
-from xnatutils import varput, XnatUtilsUsageError
+from xnatutils import varput, XnatUtilsUsageError, __version__
 
-parser = argparse.ArgumentParser(__doc__)
+parser = argparse.ArgumentParser(description=__doc__,
+                                 formatter_class=argparse.RawTextHelpFormatter)
 parser.add_argument('subject_or_session_id', type=str,
                     help="Name of subject or session to set the variable of")
 parser.add_argument('variable', type=str,
@@ -20,6 +21,8 @@ parser.add_argument('variable', type=str,
 parser.add_argument('value', help="Value of the variable")
 parser.add_argument('--user', '-u', type=str, default=None,
                     help=("The user to connect to MBI-XNAT with"))
+parser.add_argument('--version', '-V', action='version',
+                    version='%(prog)s ' + __version__)
 args = parser.parse_args()
 
 

xnatutils.py

@@ -9,6 +9,8 @@ import xnat
 from xnat.exceptions import XNATResponseError
 import warnings
 
+__version__ = '0.1'
+
 MBI_XNAT_SERVER = 'https://mbi-xnat.erc.monash.edu.au'
 
 data_format_exts = {