From 290321cefd0bc377a25022d3b681fc1079bea4d8 Mon Sep 17 00:00:00 2001 From: Marcel Zwiers Date: Fri, 29 Mar 2024 16:11:13 +0100 Subject: [PATCH] Prepare a 4.3.2 release Revert commit df7032f6e3a43fafa727a5a9d1e2142c6f50ad34 (see Github issue #229 for explanation) --- Dockerfile | 2 +- apptainer.def | 4 ++-- bidscoin/heuristics/bidsmap_bids2bids.yaml | 2 +- bidscoin/heuristics/bidsmap_dccn.yaml | 2 +- bidscoin/heuristics/bidsmap_sst.yaml | 2 +- docs/CHANGELOG.md | 8 +++++++- docs/installation.rst | 8 ++++---- pyproject.toml | 2 +- release_procedure.rst | 3 ++- tests/test_data/bidsmap.yaml | 2 +- 10 files changed, 21 insertions(+), 14 deletions(-) diff --git a/Dockerfile b/Dockerfile index ac104bba..7e3c6d1d 100644 --- a/Dockerfile +++ b/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 v4.3.1+qt5; \ + git checkout v4.3.2+qt5; \ rm -rf docs tests .git diff --git a/apptainer.def b/apptainer.def index 77820e91..d16b734c 100644 --- a/apptainer.def +++ b/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 v4.3.1+qt5 + git checkout v4.3.2+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 (v4.3.1+qt5) + * The latest stable release of BIDScoin (v4.3.2+qt5) * The latest versions of dcm2niix, pydeface, spec2nii and some FSL tools The general form to run BIDScoin commands is: diff --git a/bidscoin/heuristics/bidsmap_bids2bids.yaml b/bidscoin/heuristics/bidsmap_bids2bids.yaml index 6e42e80b..a87fe92c 100644 --- a/bidscoin/heuristics/bidsmap_bids2bids.yaml +++ b/bidscoin/heuristics/bidsmap_bids2bids.yaml @@ -22,7 +22,7 @@ Options: # General BIDScoin and plugin options # -------------------------------------------------------------------------------- bidscoin: - version: 4.3.1+qt5 # BIDScoin version (should correspond with the version in pyproject.toml) + version: 4.3.2+qt5 # 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] diff --git a/bidscoin/heuristics/bidsmap_dccn.yaml b/bidscoin/heuristics/bidsmap_dccn.yaml index d219a83a..7dde7009 100644 --- a/bidscoin/heuristics/bidsmap_dccn.yaml +++ b/bidscoin/heuristics/bidsmap_dccn.yaml @@ -23,7 +23,7 @@ Options: # General BIDScoin and plugin options # -------------------------------------------------------------------------------- bidscoin: - version: 4.3.1+qt5 # BIDScoin version (should correspond with the version in pyproject.toml) + version: 4.3.2+qt5 # 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] diff --git a/bidscoin/heuristics/bidsmap_sst.yaml b/bidscoin/heuristics/bidsmap_sst.yaml index 0915bec2..178120ad 100644 --- a/bidscoin/heuristics/bidsmap_sst.yaml +++ b/bidscoin/heuristics/bidsmap_sst.yaml @@ -22,7 +22,7 @@ Options: # General BIDScoin and plugin options # -------------------------------------------------------------------------------- bidscoin: - version: 4.3.1+qt5 # BIDScoin version (should correspond with the version in pyproject.toml) + version: 4.3.2+qt5 # 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] diff --git a/docs/CHANGELOG.md b/docs/CHANGELOG.md index 3815a824..8606b98d 100644 --- a/docs/CHANGELOG.md +++ b/docs/CHANGELOG.md @@ -4,6 +4,11 @@ ## [dev] +## [4.3.2] - 2024-03-29 + +### Fixed +- A regression was introduced when fixing Github issue #229 (now reverted) + ## [4.3.1] - 2024-03-27 ### Added @@ -438,7 +443,8 @@ A first stable release of BIDScoin :-) ### To do - Add support for non-imaging data -[dev]: https://github.com/Donders-Institute/bidscoin/compare/4.3.1...HEAD +[dev]: https://github.com/Donders-Institute/bidscoin/compare/4.3.2...HEAD +[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 [4.2.1]: https://github.com/Donders-Institute/bidscoin/compare/4.2.0...4.2.1 diff --git a/docs/installation.rst b/docs/installation.rst index 3bad93db..673b4040 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -35,11 +35,11 @@ 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 4.3.1: +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 4.3.2: .. code-block:: console - $ pip install bidscoin[dcm2niix2bids]@git+https://github.com/Donders-Institute/bidscoin@v4.3.1+qt5 + $ pip install bidscoin[dcm2niix2bids]@git+https://github.com/Donders-Institute/bidscoin@v4.3.2+qt5 Updating BIDScoin ^^^^^^^^^^^^^^^^^ @@ -92,7 +92,7 @@ An alternative for installing Python, BIDScoin and it's dependencies yourself is The current Apptainer image includes: * Debian stable, -* The latest stable release (v4.3.1+qt5) of BIDScoin +* The latest stable release (v4.3.2+qt5) of BIDScoin * The latest versions of dcm2niix, pydeface, spec2nii This image does not include FreeSurfer/synthstrip (needed for ``skullstrip``) @@ -148,7 +148,7 @@ If the Apptainer container is not working for you, it is also possible to use a The current Docker image includes the same as the Apptainer image: * Debian stable, -* The latest stable release of BIDScoin (v4.3.1+qt5) +* The latest stable release of BIDScoin (v4.3.2+qt5) * The latest versions of dcm2niix, pydeface, spec2nii and some FSL tools Likewise, the current image does not include FreeSurfer/synthstrip (needed for ``skullstrip``) diff --git a/pyproject.toml b/pyproject.toml index 875997a0..c9300df4 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 = '4.3.1+qt5' +version = '4.3.2+qt5' readme = 'README.rst' requires-python = '>= 3.8' license = {file = 'LICENSE.txt'} diff --git a/release_procedure.rst b/release_procedure.rst index 4b2c546a..b3a332c1 100644 --- a/release_procedure.rst +++ b/release_procedure.rst @@ -12,7 +12,7 @@ This document describes how to prepare a new BIDScoin release from within the DC 6. Manually run the bidscoin, bidsmapper, bidscoiner, bids-validator and other integration tests 7. Run tox@DCCN:: - VERSION="4.3.1" + VERSION="4.3.2" cd ~/python/bidscoin git checkout v${VERSION}+qt5 module load bidscoin/dev @@ -62,6 +62,7 @@ Dockerhub 1. In the VM, build, test and push a Docker image:: + VERSION="4.3.2" sudo docker build -t marcelzwiers/bidscoin:$VERSION . sudo docker run --rm marcelzwiers/bidscoin:$VERSION bidscoin -v sudo docker run --rm marcelzwiers/bidscoin:$VERSION pngappend diff --git a/tests/test_data/bidsmap.yaml b/tests/test_data/bidsmap.yaml index 5d27d725..517dc526 100644 --- a/tests/test_data/bidsmap.yaml +++ b/tests/test_data/bidsmap.yaml @@ -22,7 +22,7 @@ Options: # General options and plugins # -------------------------------------------------------------------------------- bidscoin: - version: 4.3.1+qt5 # BIDScoin version (should correspond with the version in pyproject.toml) + version: 4.3.2+qt5 # 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