Merge remote-tracking branch 'origin/master'

bidscoin/cli/_slicereport.py

@@ -56,7 +56,7 @@ def get_parser():
     parser.add_argument('-r','--reportfolder',      help="The folder where the report is saved (default: bidsfolder/derivatives/slicereport)")
     parser.add_argument('-x','--xlinkfolder',       help="A (list of) QC report folder(s) with cross-linkable sub-reports, e.g. bidsfolder/derivatives/mriqc", nargs='+')
     parser.add_argument('-q','--qcscores',          help="Column names for creating an accompanying tsv-file to store QC-rating scores (default: rating_overall)", default=['rating_overall'], nargs='+')
-    parser.add_argument('-c','--cluster',           help='Use `torque` or `slurm` to submit the skullstrip jobs to a high-performance compute (HPC) cluster', choices=['torque','slurm'])
+    parser.add_argument('-c','--cluster',           help='Use `torque` or `slurm` to submit the slicereport jobs to a high-performance compute (HPC) cluster', choices=['torque','slurm'])
     parser.add_argument('--options',                help='Main options of slicer (see below). (default: "s 1")', default=['s','1'], nargs='+')
     parser.add_argument('--outputs',                help='Output options of slicer (see below). (default: "x 0.4 x 0.5 x 0.6 y 0.4 y 0.5 y 0.6 z 0.4 z 0.5 z 0.6")', default=['x','0.4','x','0.5','x','0.6','y','0.4','y','0.5','y','0.6','z','0.4','z','0.5','z','0.6'], nargs='+')
     parser.add_argument('--suboptions',             help='Main options of slicer for creating the sub-reports (same as OPTIONS, see below). (default: OPTIONS)', nargs='+')

bidscoin/heuristics/bidsmap_dccn.yaml

@@ -23,7 +23,7 @@ Options:
 # General BIDScoin and plugin options
 # --------------------------------------------------------------------------------
   bidscoin:
-    version: 4.2.0                  # BIDScoin version (should correspond with the version in pyproject.toml)
+    version: 4.2.1                  # BIDScoin version (should correspond with the version in pyproject.toml)
     bidsignore: [mrs/, extra_data/, sub-*_ct.*]    # List of entries that are added to the .bidsignore file (for more info, see BIDS specifications), e.g. [extra_data/, pet/, myfile.txt, yourfile.csv]
     subprefix: sub-                 # The subject prefix of the source data
     sesprefix: ses-                 # The session prefix of the source data

bidscoin/heuristics/bidsmap_sst.yaml

@@ -22,7 +22,7 @@ Options:
 # General BIDScoin and plugin options
 # --------------------------------------------------------------------------------
   bidscoin:
-    version: 4.2.0                  # BIDScoin version (should correspond with the version in pyproject.toml)
+    version: 4.2.1                  # BIDScoin version (should correspond with the version in pyproject.toml)
     bidsignore: [mrs/, extra_data/, sub-*_ct.*]    # List of entries that are added to the .bidsignore file (for more info, see BIDS specifications), e.g. [extra_data/, pet/, myfile.txt, yourfile.csv]
     subprefix: sub-                 # The subject prefix of the source data
     sesprefix: ses-                 # The session prefix of the source data

docs/CHANGELOG.md

@@ -4,6 +4,17 @@
 
 ## [dev]
 
+## [4.2.1] - 2023-10-28
+
+### Added
+- A bidsmap schema file
+- Enhanced DICOM (XA-30) support for physiological data (backported from the CMRR repository)
+- Slurm support for some bidsapps
+
+### Changed
+- Use a true list (instead of a semi-colon separated string) for the bidsmap's `bidsignore` field
+- The telemetry url
+
 ## [4.2.0] - 2023-10-16
 
 ### Added
@@ -394,7 +405,8 @@ A first stable release of BIDScoin :-)
 ### To do
 - Add support for non-imaging data
 
-[dev]: https://github.com/Donders-Institute/bidscoin/compare/4.2.0...HEAD
+[dev]: https://github.com/Donders-Institute/bidscoin/compare/4.2.1...HEAD
+[4.2.1]: https://github.com/Donders-Institute/bidscoin/compare/4.2.0...4.2.1
 [4.2.0]: https://github.com/Donders-Institute/bidscoin/compare/4.1.1...4.2.0
 [4.1.1]: https://github.com/Donders-Institute/bidscoin/compare/4.1.0...4.1.1
 [4.1.0]: https://github.com/Donders-Institute/bidscoin/compare/4.0.0...4.1.0

docs/bidsapps.rst

@@ -210,8 +210,10 @@ The ``skullstrip``-tool is a wrapper around the synthstrip tool that writes BIDS
                             (i.e. if {'SkullStripped': True} in the json sidecar file) (default: False)
       -a ARGS, --args ARGS  Additional arguments that are passed to synthstrip (NB: Use quotes and a
                             leading space to prevent unintended argument parsing) (default: )
-      -c, --cluster         Use `qsub` to submit the skullstrip jobs to a high-performance compute (HPC)
-                            cluster. Can only be used if `--masked` is left empty (default: False)
+      -c {torque,slurm}, --cluster {torque,slurm}
+                            Use `torque` or `slurm` to submit the skullstrip jobs to a high-performance
+                            compute (HPC) cluster. Can only be used if `--masked` is left empty (default:
+                            None)
 
     examples:
       skullstrip myproject/bids anat/*_T1w*
@@ -270,6 +272,9 @@ Quality control
       -q QCSCORES [QCSCORES ...], --qcscores QCSCORES [QCSCORES ...]
                             Column names for creating an accompanying tsv-file to store QC-rating scores
                             (default: rating_overall)
+      -c {torque,slurm}, --cluster {torque,slurm}
+                            Use `torque` or `slurm` to submit the slicereport jobs to a high-performance
+                            compute (HPC) cluster
       -c, --cluster         Use `qsub` to submit the slicer jobs to a high-performance compute (HPC) cluster
       --options OPTIONS [OPTIONS ...]
                             Main options of slicer (see below). (default: "s 1")

docs/installation.rst

@@ -35,7 +35,7 @@ If you do not have git (or any other version control system) installed you can `
 
    $ pip install ./bidscoin[dcm2niix2bids]
 
-If you are installing BIDScoin on an older system and you are getting Qt6 errors, you can try to install a ``+qt5`` build, e.g. for version 4.2.0:
+If you are installing BIDScoin on an older system and you are getting Qt6 errors, you can try to install a ``+qt5`` build, e.g. for version 4.2.1:
 
 .. code-block:: console
 

pyproject.toml

@@ -7,7 +7,7 @@ build-backend    = 'setuptools.build_meta'
 [project]
 name             = 'bidscoin'
 description      = 'Converts and organises raw MRI data-sets according to the Brain Imaging Data Structure (BIDS)'
-version          = '4.2.0'
+version          = '4.2.1'
 readme           = 'README.rst'
 requires-python  = '>= 3.8'
 license          = {file = 'LICENSE.txt'}

tests/test_data/bidsmap.yaml

@@ -20,7 +20,7 @@ Options:
 # General options and plugins
 # --------------------------------------------------------------------------------
   bidscoin:
-    version: 4.2.0                  # BIDScoin version (should correspond with the version in pyproject.toml)
+    version: 4.2.1                  # BIDScoin version (should correspond with the version in pyproject.toml)
     bidsignore: mrs/;extra_data/    # Semicolon-separated list of entries that are added to the .bidsignore file (for more info, see BIDS specifications), e.g. extra_data/;pet/;myfile.txt;yourfile.csv
     subprefix: sub-                 # The subject prefix of the source data
     sesprefix: ses-                 # The session prefix of the source data