Minor doctweaks

Author: marcelzwiers

bidscoin/bidseditor.py

@@ -341,7 +341,7 @@ def samples_menu(self, pos):
                     datatype   = table.item(index, 2).text()
                     provenance = table.item(index, 5).text()
                     if not Path(provenance).is_file():
-                        QMessageBox.warning(self, 'Edit BIDS mapping', f"Cannot reliably change the data type and/or suffix because the source file '{provenance}' can no longer be found.\n\nPlease restore the source data or use the `bidsmapper -s` option to solve this issue")
+                        QMessageBox.warning(self, 'Edit BIDS mapping', f"Cannot reliably change the data type and/or suffix because the source file '{provenance}' can no longer be found.\n\nPlease restore the source data or use the `bidsmapper -s -f` options to solve this issue")
                         continue
 
                     # Get the new run from the template

bidscoin/cli/_bidsmapper.py

@@ -40,7 +40,7 @@ def get_parser() -> argparse.ArgumentParser:
     parser.add_argument('-n','--subprefix',   help="The prefix common for all the source subject-folders (e.g. 'Pt' is the subprefix if subject folders are named 'Pt018', 'Pt019', ...). Use '*' when your subject folders do not have a prefix. Default: the value of the study/template bidsmap, e.g. 'sub-'", metavar='PREFIX')
     parser.add_argument('-m','--sesprefix',   help="The prefix common for all the source session-folders (e.g. 'M_' is the subprefix if session folders are named 'M_pre', 'M_post', ..). Use '*' when your session folders do not have a prefix. Default: the value of the study/template bidsmap, e.g. 'ses-'", metavar='PREFIX')
     parser.add_argument('-u','--unzip',       help='Wildcard pattern to unpack tarball/zip-files in the sub/ses sourcefolder that need to be unzipped (in a tempdir) to make the data readable. Default: the value of the study/template bidsmap', metavar='PATTERN')
-    parser.add_argument('-s','--store',       help='Store provenance data samples in the bidsfolder/code/provenance folder (useful for inspecting e.g. zipped or transferred datasets)', action='store_true')
+    parser.add_argument('-s','--store',       help='Store newly discovered data samples in the bidsfolder/code/provenance folder (useful for editing e.g. zipped or transferred 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 logfile', action='store_true')
     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')

docs/workflow.rst

@@ -76,8 +76,8 @@ Here is how to run the bidsmapper command:
                             Wildcard pattern to unpack tarball/zip-files in the sub/ses sourcefolder that
                             need to be unzipped (in a tempdir) to make the data readable. Default: the
                             value of the study/template bidsmap
-      -s, --store           Store provenance data samples in the bidsfolder/code/provenance folder
-                            (useful for inspecting e.g. zipped or transferred datasets)
+      -s, --store           Store newly discovered data samples in the bidsfolder/code/provenance folder
+                            (useful for editing e.g. zipped or transferred datasets)
       -a, --automated       Save the automatically generated bidsmap to disk and without interactively
                             tweaking it with the bidseditor
       -f, --force           Discard the previously saved bidsmap and log file