Prepare a v4.3.3 release

Author: marcelzwiers

Dockerfile

@@ -31,7 +31,7 @@ RUN mkdir -p /opt/miniconda3; \
 # Clone bidscoin and switch to the qt5 branch \
     git clone https://github.com/Donders-Institute/bidscoin.git /opt/bidscoin; \
     cd /opt/bidscoin; \
-    git checkout v4.3.2+qt5; \
+    git checkout v4.3.3+qt5; \
     rm -rf docs tests .git
 
 

README.rst

@@ -43,10 +43,10 @@ Features
 
 .. note::
 
-   * All **source code** is hosted at `Github <https://github.com/Donders-Institute/bidscoin>`__ and **freely available** under the GPL-3.0-or-later `license <https://spdx.org/licenses/GPL-3.0-or-later.html>`__.
+   * All **source code** is hosted at `GitHub <https://github.com/Donders-Institute/bidscoin>`__ and **freely available** under the GPL-3.0-or-later `license <https://spdx.org/licenses/GPL-3.0-or-later.html>`__.
    * The full BIDScoin **documentation** is hosted at `Read the Docs <https://bidscoin.readthedocs.io>`__
    * For citation and more information, see our `BIDScoin publication <https://www.frontiersin.org/articles/10.3389/fninf.2021.770608>`__ in **Frontiers in Neuroinformatics** (`DOI: 10.3389/fninf.2021.770608 <https://doi.org/10.3389/fninf.2021.770608>`__). See `here <./plugins.html>`__ for citations of the plugins. A custom-made citation report can be generated with the help of `duecredit <https://github.com/duecredit/duecredit>`__
-   * You are encouraged to **post issues or questions at** `Github <https://github.com/Donders-Institute/bidscoin/issues>`__ or `NeuroStars <https://neurostars.org/tag/bidscoin>`__ (tag: #bidscoin)
+   * You are encouraged to **post issues or questions at** `GitHub <https://github.com/Donders-Institute/bidscoin/issues>`__ or `NeuroStars <https://neurostars.org/tag/bidscoin>`__ (tag: #bidscoin)
 
 How to contribute
 -----------------

apptainer.def

@@ -36,7 +36,7 @@ Stage: builder
     # Clone bidscoin and switch to the qt5 branch
     git clone https://github.com/Donders-Institute/bidscoin.git /opt/bidscoin
     cd /opt/bidscoin
-    git checkout v4.3.2+qt5
+    git checkout v4.3.3+qt5
     rm -rf docs tests .git
 
 
@@ -48,7 +48,7 @@ Stage: final
     This BIDScoin Apptainer image includes:
 
     * Debian stable,
-    * The latest stable release of BIDScoin (v4.3.2+qt5)
+    * The latest stable release of BIDScoin (v4.3.3+qt5)
     * The latest versions of dcm2niix, pydeface, spec2nii and some FSL tools
 
     The general form to run BIDScoin commands is:

bidscoin/cli/_rawmapper.py

@@ -30,7 +30,7 @@ class CustomFormatter(argparse.ArgumentDefaultsHelpFormatter, argparse.RawDescri
     parser.add_argument('-s','--sessions',  help='Space separated list of selected sub-#/ses-# names/folders to be processed. Otherwise all sessions in the bidsfolder will be processed', nargs='+', metavar='SESSION')
     parser.add_argument('-f','--field',     help='The fieldname(s) of the DICOM attribute(s) used to rename or map the subid/sesid foldernames', default=['PatientComments', 'ImageComments'], nargs='+', metavar='NAME')
     parser.add_argument('-w','--wildcard',  help='The Unix style pathname pattern expansion that is used to select the series from which the dicomfield is being mapped (can contain wildcards)', default='*', metavar='PATTERN')
-    parser.add_argument('-o','--outfolder', help='The mapper-file is normally saved in sourcefolder or, when using this option, in outfolder', metavar='DESTINATION')
+    parser.add_argument('-o','--outfolder', help='The mapper-file is normally saved in sourcefolder or, when using this option, in outfolder', metavar='FOLDER')
     parser.add_argument('-r','--rename',    help='Rename sub-subid/ses-sesid directories in the sourcefolder to sub-dcmval/ses-dcmval', action='store_true')
     parser.add_argument('-c','--clobber',   help='Rename the sub/ses directories, even if the target-directory already exists', action='store_true')
     parser.add_argument('-n','--subprefix', help="The prefix common for all the source subject-folders. Use a '*' wildcard if there is no prefix", default='sub-', metavar='PREFIX')

bidscoin/heuristics/bidsmap_bids2bids.yaml

@@ -22,7 +22,7 @@ Options:
 # General BIDScoin and plugin options
 # --------------------------------------------------------------------------------
   bidscoin:
-    version: 4.3.2                  # BIDScoin version (should correspond with the version in pyproject.toml)
+    version: 4.3.3                  # BIDScoin version (should correspond with the version in pyproject.toml)
     subprefix: sub-                 # The subject prefix of the source data
     sesprefix: ses-                 # The session prefix of the source data
     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]

bidscoin/heuristics/bidsmap_dccn.yaml

@@ -23,7 +23,7 @@ Options:
 # General BIDScoin and plugin options
 # --------------------------------------------------------------------------------
   bidscoin:
-    version: 4.3.2                  # BIDScoin version (should correspond with the version in pyproject.toml)
+    version: 4.3.3                  # BIDScoin version (should correspond with the version in pyproject.toml)
     subprefix: sub-                 # The subject prefix of the source data
     sesprefix: ses-                 # The session prefix of the source data
     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]

bidscoin/heuristics/bidsmap_sst.yaml

@@ -22,7 +22,7 @@ Options:
 # General BIDScoin and plugin options
 # --------------------------------------------------------------------------------
   bidscoin:
-    version: 4.3.2                  # BIDScoin version (should correspond with the version in pyproject.toml)
+    version: 4.3.3                  # BIDScoin version (should correspond with the version in pyproject.toml)
     subprefix: sub-                 # The subject prefix of the source data
     sesprefix: ses-                 # The session prefix of the source data
     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]

docs/CHANGELOG.md

@@ -4,22 +4,25 @@
 
 ## [dev]
 
+## [4.3.3] - 2024-07-12
+
 ### Added
-- A bidseditor context menu for comparing selected run-items
-- A bidseditor context menu for changing the data type of selected run-items
+- A bidseditor context menu for comparing, editing or adding multiple run-items (GitHub issue #239)
+- A ``fixmeta`` bidsapp for retrospective metadata editing
 
 ### Changed
 - Merged the DRMAA `cluster` and `nativespec` input arguments
+- DRMAA support for slicereport (instead of calling qsub or sbatch)
 
 ## [4.3.2] - 2024-03-29
 
 ### Fixed
-- A regression was introduced when fixing Github issue #229 (now reverted)
+- A regression was introduced when fixing GitHub issue #229 (now reverted)
 
 ## [4.3.1] - 2024-03-27
 
 ### Added
-- Update B0FieldIdentifier/Source when having multiple fieldmap runs (Github issue [#198](https://github.com/Donders-Institute/bidscoin/issues/198))
+- Update B0FieldIdentifier/Source when having multiple fieldmap runs (`GitHub` issue [#198](https://github.com/Donders-Institute/bidscoin/issues/198))
 - Slicereport support for all nibabel file-formats
 - The `BIDSCOIN_TRACKUSAGE` environment variable for setting trackusage on the fly (see `bidscoin --trackusage show`)
 
@@ -450,7 +453,8 @@ A first stable release of BIDScoin :-)
 ### To do
 - Add support for non-imaging data
 
-[dev]: https://github.com/Donders-Institute/bidscoin/compare/4.3.2...HEAD
+[dev]: https://github.com/Donders-Institute/bidscoin/compare/4.3.3...HEAD
+[4.3.3]: https://github.com/Donders-Institute/bidscoin/compare/4.3.2...4.3.3
 [4.3.2]: https://github.com/Donders-Institute/bidscoin/compare/4.3.1...4.3.2
 [4.3.1]: https://github.com/Donders-Institute/bidscoin/compare/4.3.0...4.3.1
 [4.3.0]: https://github.com/Donders-Institute/bidscoin/compare/4.2.1...4.3.0