Minor tweaks + fix

.github/workflows/tests.yaml

@@ -28,7 +28,7 @@ jobs:
         if: runner.os != 'Windows'
         run: |
           if [ "$RUNNER_OS" == "Linux" ]; then
-            sudo apt update && sudo apt install qt6-base
+            sudo apt update && sudo apt install qt6-base-dev
             mkdir dcm2niix_install/ && cd dcm2niix_install/
             curl -fLO https://github.com/rordenlab/dcm2niix/releases/latest/download/dcm2niix_lnx.zip
             unzip dcm2niix*.zip

Dockerfile

@@ -1,14 +1,14 @@
 FROM python:3.10-slim AS builder
 
 # Make a dcm2niix build from the latest stable source code
-RUN apt-get update && apt-get -y install git build-essential cmake; \
+RUN apt update && apt -y install git build-essential cmake; \
     git clone https://github.com/rordenlab/dcm2niix.git; \
     cd dcm2niix; mkdir build && cd build; \
     cmake -DZLIB_IMPLEMENTATION=Cloudflare -DUSE_JPEGLS=ON -DUSE_OPENJPEG=ON ..; \
     make install
 
 # Or install the latest dcm2niix release from the base repository (= typically outdated)
-# RUN apt-get update && apt-get -y install dcm2niix
+# RUN apt update && apt -y install dcm2niix
 
 FROM python:3.10-slim
 
@@ -18,6 +18,6 @@ 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
 ENV PIP_NO_CACHE_DIR=off
-RUN apt-get update && apt-get -y --no-install-recommends install pigz curl python3-pyqt5 python3-pyqt5.qtx11extras git && apt-get clean; \
+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[all]@git+https://github.com/Donders-Institute/[email protected]+qt5

apptainer.def

@@ -4,10 +4,10 @@ Stage: builder
 
 %post
     # Install the latest dcm2niix release from the base repository (= typically outdated)
-    # apt-get update && apt-get -y install dcm2niix
+    # apt update && apt -y install dcm2niix
 
     # Install the latest dcm2niix from sources
-    apt-get update && apt-get -y install git build-essential cmake
+    apt update && apt -y install git build-essential cmake
     git clone https://github.com/rordenlab/dcm2niix.git
     cd dcm2niix; mkdir build && cd build
     cmake -DZLIB_IMPLEMENTATION=Cloudflare -DUSE_JPEGLS=ON -DUSE_OPENJPEG=ON ..
@@ -23,7 +23,7 @@ Stage: final
 
     * Debian stable,
     * the latest version of dcm2niix (https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage)
-    * the latest stable release of BIDScoin and its plugins. The general form to run BIDScoin commands is:
+    * the latest stable release (4.1.0+qt5) of BIDScoin and its plugins. The general form to run BIDScoin commands is:
 
         apptainer exec bidscoin.sif <bidscoin_tool> <bidscoin_tool_args>
 
@@ -48,11 +48,11 @@ Stage: final
 
 %post
     # Install curl (sometimes needed by dcm2niix) and pigz (to speed up dcm2niix)
-    apt-get update && apt-get -y --no-install-recommends install pigz curl
+    apt update && apt -y --no-install-recommends install pigz curl
 
     # Install the latest stable BIDScoin release from Python repository
     # NOTE: PyQt5 is installed as Debian package to solve dependencies issues occurring when installed with pip
-    apt-get -y --no-install-recommends install python3-pyqt5 python3-pyqt5.qtx11extras git && apt-get clean
+    apt -y --no-install-recommends install python3-pyqt5 python3-pyqt5.qtx11extras git && apt clean
     pip install --upgrade pip
     pip install bidscoin[all]@git+https://github.com/Donders-Institute/[email protected]+qt5
 

docs/troubleshooting.rst

@@ -11,15 +11,19 @@ This is an `installation <installation.html#dcm2niix-installation>`__ problem an
 
 Could not load the Qt platform plugin "xcb"
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-This error message may occur on certain Linux platforms when opening the bidseditor. This is an `installation <installation.html#bidscoin-installation>`__ issue that may occur if you have installed a ``+qt5`` build of BIDScoin (e.g. because your system does not support Qt6). Sometimes this error can be solved by downgrading your PyQt5 library, e.g. by running ``pip install --upgrade pyqt5==5.14`` in your terminal environment. Another solution might be to use your Linux package manager to install PyQt5, e.g. like this: ``apt-get install python3-pyqt5 python3-pyqt5.qtx11extras``
+This error message may occur on certain Linux platforms when opening the bidseditor. This is an `installation <installation.html#bidscoin-installation>`__ issue that may occur if you have installed the ``+qt5`` build of BIDScoin (e.g. because your system does not support Qt6). Sometimes this error can be solved by downgrading your PyQt5 library, e.g. by running ``pip install --upgrade pyqt5==5.14`` in your terminal environment. Another solution might be to use your Linux package manager to install PyQt5, e.g. like this: ``apt install python3-pyqt5 python3-pyqt5.qtx11extras``
 
 ImportError: libEGL.so.1: cannot open shared object file: No such file or directory
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 This may error message may be reported on Linux systems that do not support Qt6 out of the box. On Debian/Ubuntu systems this may be solved by running:
 
 .. code-block::
 
-   sudo apt install qt6-base-dev
+   sudo apt install qt6-base
+   sudo apt install qt6-base-dev     # If the above package cannot be located
+   sudo apt install python3-pyqt6    # If the above commands do not solve the issue
+
+An alternative solution may be to install the ``+qt5`` build of BIDScoin (see `installation <installation.html#bidscoin-installation>`__)
 
 My Apptainer/Singularity container fails
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^