Prepare the 4.2.0 release

Dockerfile

@@ -16,8 +16,8 @@ FROM python:3.10-slim
 COPY --from=builder /usr/local/bin/dcm2niix /usr/local/bin/dcm2niix
 
 # First install pyqt5 as Debian package to solve dependencies issues occurring when installed with pip
-# Then install the latest stable BIDScoin release from Python repository
+# Then install the latest stable BIDScoin Qt5 release from Github (install the normal Qt6 branch from PyPi when using recent base images such as Ubuntu:22.04)
 ENV PIP_NO_CACHE_DIR=off
 RUN apt update && apt -y --no-install-recommends install pigz curl python3-pyqt5 python3-pyqt5.qtx11extras git && apt clean; \
     pip install --upgrade pip; \
-    pip install bidscoin[spec2nii2bids,deface,pet2bids]@git+https://github.com/Donders-Institute/bidscoin@v4.1.1+qt5
+    pip install bidscoin[spec2nii2bids,deface,pet2bids]@git+https://github.com/Donders-Institute/bidscoin@v4.2.0+qt5

apptainer.def

@@ -22,8 +22,8 @@ Stage: final
     This BIDScoin Apptainer image includes:
 
     * Debian stable,
-    * the latest version of dcm2niix (https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage)
-    * the latest stable release (v4.1.1+qt5) of BIDScoin and its plugins. The general form to run BIDScoin commands is:
+    * The latest version of dcm2niix (https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage)
+    * The latest stable release (v4.2.0+qt5) of BIDScoin and its plugins. The general form to run BIDScoin commands is:
 
         apptainer exec bidscoin.sif <bidscoin_tool> <bidscoin_tool_args>
 
@@ -50,11 +50,11 @@ Stage: final
     # Install curl (sometimes needed by dcm2niix) and pigz (to speed up dcm2niix)
     apt update && apt -y --no-install-recommends install pigz curl
 
-    # Install the latest stable BIDScoin release from Python repository
+    # Install the latest stable BIDScoin Qt5 release from Github (install the normal Qt6 branch from PyPi when using recent base images such as Ubuntu:22.04)
     # NOTE: PyQt5 is installed as Debian package to solve dependencies issues occurring when installed with pip
     apt -y --no-install-recommends install python3-pyqt5 python3-pyqt5.qtx11extras git && apt clean
     pip install --upgrade pip
-    pip install bidscoin[spec2nii2bids,deface,pet2bids]@git+https://github.com/Donders-Institute/bidscoin@v4.1.1+qt5
+    pip install bidscoin[spec2nii2bids,deface,pet2bids]@git+https://github.com/Donders-Institute/bidscoin@v4.2.0+qt5
 
     # Uncomment the line below if you get errors like: ImportError: libQt5Core.so.5: cannot open shared object file: No such file or directory
     # strip --remove-section=.note.ABI-tag /usr/lib/x86_64-linux-gnu/libQt5Core.so.5

bidscoin/heuristics/bidsmap_dccn.yaml

@@ -22,7 +22,7 @@ Options:
 # General options and plugins
 # --------------------------------------------------------------------------------
   bidscoin:
-    version: 4.1.1                  # BIDScoin version (should correspond with the version in pyproject.toml)
+    version: 4.2.0                  # BIDScoin version (should correspond with the version in pyproject.toml)
     bidsignore: mrs/;extra_data/;sub-*_ct.*    # 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

bidscoin/heuristics/bidsmap_sst.yaml

@@ -21,7 +21,7 @@ Options:
 # General options and plugins
 # --------------------------------------------------------------------------------
   bidscoin:
-    version: 4.1.1                  # BIDScoin version (should correspond with the version in pyproject.toml)
+    version: 4.2.0                  # 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

docs/CHANGELOG.md

@@ -4,6 +4,8 @@
 
 ## [dev]
 
+## [4.2.0] - 2023-10-16
+
 ### Added
 - The option to pip-install dcm2niix as `extras`
 - A user config file (github issue #197)
@@ -251,14 +253,14 @@ A significant rewrite and evolution of BIDScoin!
 ## [3.0.4] - 2020-05-14
 
 ### Added
-* `Export` function in the bidseditor to allow for adding run items to existing (template) bidsmaps
-* Support for Unix-shell style wildcards for matching run items in the bidsmap
+- `Export` function in the bidseditor to allow for adding run items to existing (template) bidsmaps
+- Support for Unix-shell style wildcards for matching run items in the bidsmap
 
 ### Changed
-* Improved DCCN example template bidsmap
+- Improved DCCN example template bidsmap
 
 ### Fixed
-* Various minor bugs
+- Various minor bugs
 
 ## [3.0.3] - 2020-04-14
 
@@ -281,118 +283,119 @@ A significant rewrite and evolution of BIDScoin!
 A Significant rewrite to make BIDScoin more robust, user-friendly and feature-rich :-)
 
 ### Added
-* First support for Philips PAR / REC data format
-* A BIDS compliant defacing tool
-* A BIDS compliant multi-echo combination tool
-* Much improved documentation (https://bidscoin.readthedocs.io)
+- First support for Philips PAR / REC data format
+- A BIDS compliant defacing tool
+- A BIDS compliant multi-echo combination tool
+- Much improved documentation (https://bidscoin.readthedocs.io)
 
 ## [2.3.1] - 2019-09-12
 
 ### Fixed
-* a small but important bug that caused datasets without field maps to crash (my test datasets all had field maps :-))
+- a small but important bug that caused datasets without field maps to crash (my test datasets all had field maps :-))
 
 ## [2.3] - 2019-08-29
 
 A lot of improvements have landed in 2.3, making it the best release of the 2-series by far!
 
 ### Added
-* The possibility to edit Participant labels
-* Various tests and checks in Options to ensure creating good working bidsmaps / BIDS output data
-* Upgraded compliance with bids v1.2.1
-* The possibility to leave-out certain data types / runs
+- The possibility to edit Participant labels
+- Various tests and checks in Options to ensure creating good working bidsmaps / BIDS output data
+- Upgraded compliance with bids v1.2.1
+- The possibility to leave-out certain data types / runs
 
 ### Changed
-* A new workflow that is easier and more consistent
-* Greatly improved graphical user interface and error/warning reporting
-* Improved bidsmap_dccn template
+- A new workflow that is easier and more consistent
+- Greatly improved graphical user interface and error/warning reporting
+- Improved bidsmap_dccn template
 
 ### Fixed
-* Significant code refactoring to squash a number of important bugs and make the code more robust and maintainable
+- Significant code refactoring to squash a number of important bugs and make the code more robust and maintainable
 
 ## [2.2] - 2019-07-11
 
 ### Added
-* Options tab to edit and test the bidscoin Options
-* A leave-out option (to ignore runs / prevent them from showing up in the BIDS directory)
-* A graphical interface to the bidsmapper
-* Improved logging
-* Improved the DICOM attribute *wildcard* feature
+- Options tab to edit and test the bidscoin Options
+- A leave-out option (to ignore runs / prevent them from showing up in the BIDS directory)
+- A graphical interface to the bidsmapper
+- Improved logging
+- Improved the DICOM attribute *wildcard* feature
 
 ### Changed
-* New layout of the main and edit windows
+- New layout of the main and edit windows
 
 ### Fixed
-* Various bugfixes
+- Various bugfixes
 
 ## [2.1] - 2019-06-23
 
 ### Added
-* Editing of bidsmap Options
+- Editing of bidsmap Options
 
 ### Fixed
-* `IntendedFor` in field map json sidecar files
-* Code redundancy
+- `IntendedFor` in field map json sidecar files
+- Code redundancy
 
 ## [2.0] - 2019-06-18
 
 A major release and rewrite with important user-facing improvements
 
 ### Added
-* A shiny GUI :-)
-* A new and much easier workflow
+- A shiny GUI :-)
+- A new and much easier workflow
 
 ### Fixed
-* Various bugfixes
+- Various bugfixes
 
 ## [1.5] - 2019-03-06
 
 ### Added
-* Support for PET scans
-* Support for DICOMDIR data
-* Saving of template sidecar files in the bids output directory
+- Support for PET scans
+- Support for DICOMDIR data
+- Saving of template sidecar files in the bids output directory
 
 ### Changed
-* increased flexibility for renaming / reorganising the raw (input) data structure
-* Added provenance data to the bidsmap/yaml files
+- increased flexibility for renaming / reorganising the raw (input) data structure
+- Added provenance data to the bidsmap/yaml files
 
 ### Fixed
-* various bugfixes
+- various bugfixes
 
 ## [1.4] - 2018-10-22
 
 ### Added
-* Cross-platform support
-* Installation as a Python module
-* Improved version control
-* Improved BIDS compliance
+- Cross-platform support
+- Installation as a Python module
+- Improved version control
+- Improved BIDS compliance
 
 ## [1.3] - 2018-09-28
 
 ### Changed
-* Refactored bidsmap naming
+- Refactored bidsmap naming
 
 ### Fixed
-* Various bugs
+- Various bugs
 
 ## [1.2] - 2018-09-14
 
 ### Added
-* Improved field map support
+- Improved field map support
 
 ### Changed
-* Yaml-syntax
+- Yaml-syntax
 
 ## 1.0 - 2018-07-04
 
 A first stable release of BIDScoin :-)
 
 ### Added
-* Support the conversion of organised sub/ses DICOM folders to BIDS
+- Support the conversion of organised sub/ses DICOM folders to BIDS
 
 ### To do
-* Add support for non-imaging data
+- Add support for non-imaging data
 
-[dev]: https://github.com/Donders-Institute/bidscoin/compare/4.1.1...HEAD
+[dev]: https://github.com/Donders-Institute/bidscoin/compare/4.2.0...HEAD
+[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
 [4.0.0]: https://github.com/Donders-Institute/bidscoin/compare/3.7.4...4.0.0

docs/installation.rst

@@ -33,11 +33,11 @@ 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 4.1.1:
+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:
 
 .. code-block:: console
 
-   $ pip install bidscoin[dcm2niix2bids]@git+https://github.com/Donders-Institute/bidscoin@v4.1.1+qt5
+   $ pip install bidscoin[dcm2niix2bids]@git+https://github.com/Donders-Institute/bidscoin@v4.2.0+qt5
 
 Updating BIDScoin
 ^^^^^^^^^^^^^^^^^

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          = '4.1.1'
+version          = '4.2.0'
 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: 4.1.1                  # BIDScoin version (should correspond with the version in pyproject.toml)
+    version: 4.2.0                  # 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