Doctweaks

Author: marcelzwiers

bidscoin/cli/_bidscoiner.py

@@ -34,6 +34,6 @@ def get_parser():
     parser.add_argument('-b','--bidsmap',     help='The study bidsmap file with the mapping heuristics. If the bidsmap filename is just the base name (i.e. no "/" in the name) then it is assumed to be located in the current directory or in bidsfolder/code/bidscoin. Default: bidsmap.yaml', metavar='NAME', default='bidsmap.yaml')
     parser.add_argument('-f','--force',       help='Process all subjects, regardless of existing subject folders in the bidsfolder. Otherwise these subject folders will be skipped', action='store_true')
     parser.add_argument('-c','--cluster',     help='Use the DRMAA library to submit the bidscoiner jobs to a high-performance compute (HPC) cluster. You can add an opaque DRMAA argument with native specifications for your HPC resource manager (NB: Use quotes and include at least one space character to prevent premature parsing -- see examples)', metavar='SPECS', nargs='?', const='-l walltime=00:30:00,mem=4gb', type=str)
-    parser.add_argument('-w','--workdir',     help='Optional working directory for temporary unpacking of zipped or DICOMDIR data. Defaults to the system temporary folder if not specified', default='')
+    parser.add_argument('-w','--workdir',     help='Optional working directory for temporary unpacking of zipped or DICOMDIR data. Defaults to the system temporary folder if not specified', metavar='PATH', default='')
 
     return parser

bidscoin/cli/_bidsmapper.py

@@ -44,7 +44,7 @@ def get_parser() -> argparse.ArgumentParser:
     parser.add_argument('-s','--store',       help='Store newly discovered data samples in the bidsfolder/code/provenance folder (useful for editing e.g. zipped or DICOMDIR datasets)', action='store_true')
     parser.add_argument('-a','--automated',   help='Save the automatically generated bidsmap to disk and without interactively tweaking it with the bidseditor', action='store_true')
     parser.add_argument('-f','--force',       help='Discard the previously saved bidsmap and log file, instead of reusing them (use this option for a fresh start)', action='store_true')
-    parser.add_argument('-w','--workdir',     help='Optional working directory for temporary unpacking of zipped or DICOMDIR data. Defaults to the system temporary folder if not specified', default='')
+    parser.add_argument('-w','--workdir',     help='Optional working directory for temporary unpacking of zipped or DICOMDIR data. Defaults to the system temporary folder if not specified', metavar='PATH', default='')
     parser.add_argument('--no-update',        help="Do not update any sub-/ses-prefixes in or prepend the sourcefolder name to the <<filepath:regex>> expression that extracts the subject/session labels. This is normally done to make the extraction more robust, but could cause problems for certain use cases", action='store_true')
 
     return parser

docs/workflow.rst

@@ -82,6 +82,8 @@ Here is how to run the bidsmapper command:
                             tweaking it with the bidseditor
       -f, --force           Discard the previously saved bidsmap and log file, instead of reusing them
                             (use this option for a fresh start)
+      -w, --workdir PATH    Optional working directory for temporary unpacking of zipped or DICOMDIR data.
+                            Defaults to the system temporary folder if not specified
       --no-update           Do not update any sub-/ses-prefixes in or prepend the sourcefolder name to the
                             <<filepath:regex>> expression that extracts the subject/session labels. This
                             is normally done to make the extraction more robust, but could cause problems
@@ -263,6 +265,8 @@ Here is how to run the bidscoiner command:
                             compute (HPC) cluster. You can add an opaque DRMAA argument with native
                             specifications for your HPC resource manager (NB: Use quotes and include at
                             least one space character to prevent premature parsing -- see examples)
+      -w, --workdir PATH    Optional working directory for temporary unpacking of zipped or DICOMDIR data.
+                            Defaults to the system temporary folder if not specified
 
     ::