Minor tweaks

bidscoin/__init__.py

@@ -207,10 +207,12 @@ def trackusage(event: str, dryrun: bool=False) -> dict:
 
     except Exception as shelveerror:
         warnings.warn(f"Please report the following error to the developers:\n{shelveerror}: {trackfile}", RuntimeWarning)
-        for corruptfile in trackfile.parent.glob(trackfile.name + '.*'):
+        for corruptfile in shelvefiles := list(trackfile.parent.glob(trackfile.name + '.*')):
             print(f"Deleting corrupt file: {corruptfile}")
             corruptfile.unlink()
         data['event'] = 'trackusage_exception'
+        if not shelvefiles:         # Return without uploading (no shelve files means no sleep)
+            return data
 
     # Upload the usage data
     try:

bidscoin/cli/_bidsmapper.py

@@ -42,7 +42,7 @@ def get_parser() -> argparse.ArgumentParser:
     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 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('-f','--force',       help='Discard the previously saved bidsmap and log file, instead of re-using them (use this option for a fresh start)', 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')
 
     return parser

docs/CHANGELOG.md

@@ -255,7 +255,7 @@ The bidscoiner no longer sometimes crashes when dcm2niix produces custom suffixe
 - Separate tabs for DICOM and PAR to edit all the mappings of mixed datasets in a single bidseditor session
 - Run-item matching on filesystem properties, i.e. on the pathname, filename and filesize and nr of files in the folder. This can be used in conjunction with the (DICOM/PAR) attributes
 - A metadata dictionary that can be edited with the bidseditor and that will be added to the json sidecar files by the bidscoiner
-- More user feedback in the GUI for new BIDS-compliancy checks on missing or invalid bids data
+- More user feedback in the GUI for new BIDS-compliance checks on missing or invalid BIDS data
 - A right-click menu option to remove a run-item from the bidsmap (advanced usage)
 - The option to load a new bidsmap in the bidseditor
 - Enable the user to edit json, yaml, tsv and other non-DICOM/non-PAR files with double-clicks in the data browser

docs/_static/dictionary-custom.txt

@@ -163,7 +163,6 @@ bugfixes
 bval
 bvec
 cli
-compliancy
 conda
 config
 copymetadata

docs/workflow.rst

@@ -80,7 +80,8 @@ Here is how to run the bidsmapper command:
                             (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
+      -f, --force           Discard the previously saved bidsmap and log file, instead of re-using them
+                            (use this option for a fresh start)
       --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

pyproject.toml

@@ -130,4 +130,4 @@ commands         = make -C docs html
 skip = '.git,*.pdf,*.svg,go.sum'
 check-hidden = true
 ignore-regex = '\b(PULS|TE|ALS)\b'
-ignore-words-list = 'compliancy,uptodate,mis'
+ignore-words-list = 'uptodate,mis'

release_procedure.rst

@@ -53,7 +53,7 @@ DCCN deployment
     source activate /opt/bidscoin
     bidscoin -v
     bidscoin -t
-    conda deactivate bidscoin
+    conda deactivate
 
 4. Post a release message on the MM data management channel
 
@@ -92,20 +92,20 @@ Dockerhub
     sudo docker run --rm marcelzwiers/bidscoin:$VERSION pngappend
     sudo docker run --rm -e DISPLAY=$DISPLAY -v /tmp/.X11-unix:/tmp/.X11-unix marcelzwiers/bidscoin:$VERSION bidscoin -t
     sudo docker push marcelzwiers/bidscoin:$VERSION
-    sudo docker system prune -a
 
 Neurodesk
 ---------
 
 1. Pull and edit the bidscoin neurocontainer in a separate release branch
-2. Build and test a neurodocker image::
+2. In the VM, build and test a neurodocker image::
 
     VERSION="4.5.0"
     cd ~/PycharmProjects/neurocontainers/recipes/bidscoin
     conda activate neurodocker
     ./build.sh -ds
     sudo docker image list         # Checkout the TAG
     sudo docker run --rm -e DISPLAY=$DISPLAY -v /tmp/.X11-unix:/tmp/.X11-unix bidscoin_${VERSION}:TAG bidscoin -t
+    sudo docker system prune -a
 
 3. Create a neurocontainers PR from the release branch