From d03fd2083984fabf7b90853a9f5970cde954b775 Mon Sep 17 00:00:00 2001 From: Marcel Zwiers Date: Mon, 16 Oct 2023 13:10:33 +0200 Subject: [PATCH] Prepare the 4.2.0 release --- Dockerfile | 4 +- apptainer.def | 8 +-- bidscoin/heuristics/bidsmap_dccn.yaml | 2 +- bidscoin/heuristics/bidsmap_sst.yaml | 2 +- docs/CHANGELOG.md | 97 ++++++++++++++------------- docs/installation.rst | 4 +- pyproject.toml | 2 +- tests/test_data/bidsmap.yaml | 2 +- 8 files changed, 62 insertions(+), 59 deletions(-) diff --git a/Dockerfile b/Dockerfile index c3dfac55..693acba8 100644 --- a/Dockerfile +++ b/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 diff --git a/apptainer.def b/apptainer.def index 5346c577..38364c44 100644 --- a/apptainer.def +++ b/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 @@ -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 diff --git a/bidscoin/heuristics/bidsmap_dccn.yaml b/bidscoin/heuristics/bidsmap_dccn.yaml index 4d7ed3d9..895c5e71 100644 --- a/bidscoin/heuristics/bidsmap_dccn.yaml +++ b/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 diff --git a/bidscoin/heuristics/bidsmap_sst.yaml b/bidscoin/heuristics/bidsmap_sst.yaml index 9244bc5b..15ca8f7d 100644 --- a/bidscoin/heuristics/bidsmap_sst.yaml +++ b/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 diff --git a/docs/CHANGELOG.md b/docs/CHANGELOG.md index 36947f69..0c0ed52e 100644 --- a/docs/CHANGELOG.md +++ b/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 diff --git a/docs/installation.rst b/docs/installation.rst index e99d020a..304705be 100644 --- a/docs/installation.rst +++ b/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 ^^^^^^^^^^^^^^^^^ diff --git a/pyproject.toml b/pyproject.toml index b72b38b5..eee64b05 100644 --- a/pyproject.toml +++ b/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'} diff --git a/tests/test_data/bidsmap.yaml b/tests/test_data/bidsmap.yaml index bace80d4..12af964f 100644 --- a/tests/test_data/bidsmap.yaml +++ b/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