Drop support for Qt5

Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.10-slim AS builder
+FROM python:3-slim AS builder
 
 # Install the latest dcm2niix from sources
 # Or install the latest dcm2niix release from the base repository (= typically outdated)
@@ -26,27 +26,20 @@ RUN mkdir -p /opt/miniconda3; \
     conda install -c conda-forge conda-pack; \
     conda pack -n fsl; \
     mkdir /opt/fsl && tar -xzf fsl.tar.gz -C /opt/fsl; \
-    /opt/fsl/bin/conda-unpack; \
-    \
-# Clone bidscoin and switch to the qt5 branch \
-    git clone https://github.com/Donders-Institute/bidscoin.git /opt/bidscoin; \
-    cd /opt/bidscoin; \
-    git checkout v4.3.3+qt5; \
-    rm -rf docs tests .git
+    /opt/fsl/bin/conda-unpack
 
 
-FROM python:3.10-slim
+FROM python:3-slim
 
 # Install the dcm2niix build. NB: Obsolete with the new `pip install bidscoin[dcm2niix2bids]` extras option
-COPY --from=builder /opt/bidscoin /opt/bidscoin
 COPY --from=builder /usr/local/bin/dcm2niix /usr/local/bin/dcm2niix
 COPY --from=builder /opt/fsl /opt/fsl
 
 ENV FSLDIR=/opt/fsl FSLOUTPUTTYPE=NIFTI_GZ \
     PATH=$PATH:/opt/fsl/bin \
     PIP_NO_CACHE_DIR=off
 
-# First install pyqt5 as Debian package to solve dependencies issues occurring when installed with pip
-# Then install the latest stable BIDScoin release from the local qt5 branch (install the normal Qt6 branch from PyPi when using recent base images such as Ubuntu)
-RUN apt update && apt -y --no-install-recommends install pigz curl python3-pyqt5 && apt clean; \
-    pip install /opt/bidscoin[spec2nii2bids,deface]
+# First install pyqt as Debian package to solve dependencies issues occurring when installed with pip
+# Then install the latest stable BIDScoin release (add build-essential for newer python:3-slim base images (pip needs gcc))
+RUN apt update && apt -y --no-install-recommends install pigz curl python3-pyqt6 build-essential libgl1 libxcb-cursor-dev && apt clean; \
+    pip install bidscoin[spec2nii2bids,deface]

apptainer.def

@@ -1,5 +1,5 @@
 Bootstrap: docker
-From: python:3.10-slim
+From: python:3-slim
 Stage: builder
 
 %post
@@ -33,22 +33,16 @@ Stage: builder
     mkdir /opt/fsl && tar -xzf fsl.tar.gz -C /opt/fsl
     /opt/fsl/bin/conda-unpack
 
-    # Clone bidscoin and switch to the qt5 branch
-    git clone https://github.com/Donders-Institute/bidscoin.git /opt/bidscoin
-    cd /opt/bidscoin
-    git checkout v4.3.3+qt5
-    rm -rf docs tests .git
-
 
 Bootstrap: docker
-From: python:3.10-slim
+From: python:3-slim
 Stage: final
 
 %help
     This BIDScoin Apptainer image includes:
 
     * Debian stable,
-    * The latest stable release of BIDScoin (v4.3.3+qt5)
+    * The latest stable release of BIDScoin (v4.4.0)
     * The latest versions of dcm2niix, pydeface, spec2nii and some FSL tools
 
     The general form to run BIDScoin commands is:
@@ -64,7 +58,6 @@ Stage: final
         3) The current image does not include the Freesurfer/synthstrip software (needed for `skullstrip`)
 
 %files from builder
-    /opt/bidscoin /opt/bidscoin
     /usr/local/bin/dcm2niix /usr/local/bin/dcm2niix
     /opt/fsl /opt/fsl
 
@@ -77,13 +70,14 @@ 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 the local qt5 branch (install the normal Qt6 branch from PyPi when using recent base images such as Ubuntu)
-    # NOTE: PyQt5 is installed as Debian package to solve dependencies issues occurring when installed with pip
-    apt -y --no-install-recommends install python3-pyqt5 && apt clean     # Add build-essential for newer python:3-slim base images (pip needs gcc)
-    pip install /opt/bidscoin[spec2nii2bids,deface]
+    # Install the latest stable BIDScoin release
+    # NOTE: PyQt is installed as Debian package to solve dependencies issues occurring when installed with pip
+    apt -y --no-install-recommends install python3-pyqt6 build-essential libgl1 libxcb-cursor-dev && apt clean     # Add build-essential for newer python:3-slim base images (pip needs gcc)
+    pip install bidscoin[spec2nii2bids,deface]
 
     # 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
+    # strip --remove-section=.note.ABI-tag libQt6Core.so.6
 
     # Finally, create the necessary links and cache to the most recent shared libraries (= best practise)
     ldconfig

docs/CHANGELOG.md

@@ -11,6 +11,7 @@
 
 ### Changed
 - BIDScoin's main API, which now includes new classes to separate the logic from the data and make the code cleaner, better organized and maintainable
+- Dropped support for Qt5
 
 ## [4.3.3] - 2024-07-12
 

docs/installation.rst

@@ -42,7 +42,7 @@ 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 4.3.3:
+If you are installing BIDScoin on an older system and you are getting Qt6 errors, you can try to install an older ``+qt5`` build, e.g. for version 4.3.3 (the last Qt5 build):
 
 .. code-block:: console
 
@@ -94,7 +94,7 @@ An alternative for installing Python, BIDScoin and it's dependencies yourself is
 The current Apptainer image includes:
 
 * Debian stable,
-* The latest stable release (v4.3.3+qt5) of BIDScoin
+* The latest stable release of BIDScoin
 * The latest versions of dcm2niix, pydeface, spec2nii
 
 This image does not include FreeSurfer/synthstrip (needed for ``skullstrip``)
@@ -150,7 +150,7 @@ 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 (v4.3.3+qt5)
+* The latest stable release of BIDScoin
 * The latest versions of dcm2niix, pydeface, spec2nii and some FSL tools
 
 Likewise, the current image does not include FreeSurfer/synthstrip (needed for ``skullstrip``)

release_procedure.rst

@@ -9,8 +9,7 @@ This document describes how to prepare a new BIDScoin release from within the DC
 3. Inspect the git history and update the CHANGELOG (including the links)
 4. Update the version string everywhere (i.e. search without word matching), COPYRIGHT and cli help texts
 5. Add a git version tag
-6. Backport to PyQt5 in a v4.#.#+qt5 branch
-7. Build & test the containers in a Linux VM::
+6. Build & test the containers in a Linux VM::
 
     VERSION="4.4.0"
     rm -rf ~/.bidscoin/$VERSION
@@ -21,13 +20,11 @@ This document describes how to prepare a new BIDScoin release from within the DC
     apptainer exec --cleanenv --env DISPLAY=:0 bidscoin.sif pngappend
     apptainer cache clean
 
-8. Run tox@DCCN::
+7. Run tox@DCCN::
 
     VERSION="4.4.0"
     cd ~/python/bidscoin
     git pull
-    git checkout v${VERSION}+qt5
-    git pull
     module load bidscoin/dev
     source activate tox
     rm -rf ~/.bidscoin/$VERSION
@@ -36,16 +33,13 @@ This document describes how to prepare a new BIDScoin release from within the DC
     source activate /opt/bidscoin
     ~/python/bidscoin/bidscoin/bcoin.py -t
 
-9. Push the qt5-branch
-
 DCCN deployment
 ---------------
 
-1. Copy the dev folder, checkout the Qt5 branch, update the bidsmaps and module::
+1. Copy the dev folder, update the bidsmaps and module::
 
     cp -r /opt/bidscoin/dev /opt/bidscoin/$VERSION
     cd /opt/bidscoin/$VERSION
-    git checkout v${VERSION}+qt5 -f
     for TEMPLATE in bidscoin/heuristics/*.yaml; do
         sed -i 's/command: dcm2niix/command: module add dcm2niix; dcm2niix/' $TEMPLATE
     done