#345 things are starting to work up to Qt configuration

conda/apptainer.def

@@ -2,14 +2,25 @@ Bootstrap: docker
 From: ubuntu:22.04
 
 %environment
-    export HOME=/casa/home
+    export CASA=/casa
+    export CASA_CONF=$CASA/conf
+    export HOME=$CASA/home
+    export CASA_SRC=$CASA/src
+    export CASA_BUILD=$CASA/build
+    export CASA_INSTALL=$CASA/install
+    export CASA_TESTS=$CASA/tests
+    export BRAINVISA_BVMAKER_CFG=$CASA_SRC/bv_maker.cfg
+    for f in "$CASA_SRC/environment.sh" "$CASA_CONF/environment.sh" "$CASA/environment.sh"; do
+        if [ -e "$f" ]; then
+            source "$f"
+        fi
+    done
 
 %post
     mkdir /casa
     apt update
 
 %runscript
-    echo "Start casa container"
     export PATH=/casa/conda/bin:$PATH
     export LD_LIBRARY_PATH=/casa/conda/lib:$LD_LIBRARY_PATH
 

conda/setup_conda

@@ -25,33 +25,48 @@ if [ ! -e "$casaconda/home" ]; then
 fi
 
 system_image="$casaconda/system"
+apptainer="apptainer -s run --containall -B $casaconda:/casa -B /tmp $system_image"
+root_apptainer="apptainer run --writable --fakeroot --containall -B $casaconda:/casa -B /tmp $system_image"
+
 if [ ! -e "$system_image" ]; then
     apptainer build --sandbox "$casaconda/system" "$script_dir/apptainer.def"
+    cp -a "$script_dir/setup_run_apt" "$casaconda"
+    $root_apptainer /casa/setup_run_apt
 fi
 
 if [ ! -e "$casaconda/Miniforge3-Linux-x86_64.sh" ]; then
     wget -O "$casaconda/Miniforge3-Linux-x86_64.sh" https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh
 fi
 
-apptainer="apptainer run --containall $mounts-B $casaconda:/casa -B /tmp $system_image"
-root_apptainer="apptainer run --writable --fakeroot --containall -B $casaconda:/casa -B /tmp $system_image"
 
 conda="$apptainer /casa/conda/bin/conda"
 if [ ! -e "$casaconda/conda" ]; then
     mkdir "$casaconda/conda"
     $apptainer sh "/casa/Miniforge3-Linux-x86_64.sh" -u -b -p "/casa/conda"
     $conda update conda -y
+    cp -a "$script_dir/setup_run_conda" "$casaconda"
+    $apptainer /casa/setup_run_conda
+    cp -a "$script_dir/setup_dev_conda" "$casaconda"
+    $apptainer /casa/setup_dev_conda
 fi
 
-for script in setup_run_apt setup_run_conda setup_run_compiled; do
-    cp -a "$script_dir/$script" "$casaconda"
-    $root_apptainer /casa/$script
-done
+cp -a "$script_dir/setup_run_compiled" "$casaconda"
+$root_apptainer /casa/setup_run_compiled
 
 if [ ! -e "$casaconda/src" ]; then
     $apptainer git clone https://github.com/sapetnioc/brainvisa-submodules /casa/src
     $apptainer git -C /casa/src submodule update --init --recursive
+    cd $casaconda/src
+    for d in *; do
+        if [ -d "$d" ]; then
+            main_branch=$( $apptainer git -C /casa/src/$d branch -r --contains HEAD --format '%(refname)' | grep --invert-match HEAD | python -c 'import sys; print(sys.stdin.read().split("/")[-1])' )
+            $apptainer git -C "/casa/src/$d" checkout $main_branch
+        fi
+    done
 fi
 
+
 # Update all sources
-$apptainer git -C /casa/src submodule foreach ls
+# $apptainer git -C /casa/src submodule foreach git pull
+
+$apptainer /casa/src/brainvisa-cmake/bin/bv_env bash

conda/setup_dev_conda

@@ -9,8 +9,8 @@ set -e
 
 conda=/casa/conda/bin/conda
 
-if [ -e /casa/conda/bin/nano ]; then
-    # if nano is installed, we assume that this script has already been
+if [ -e /casa/conda/bin/gdb ]; then
+    # if gdb is installed, we assume that this script has already been
     # executed.
     echo "setup_dev_conda already executed => execution canceled"
     exit 0
@@ -44,34 +44,32 @@ toolchain_packages=(
 
 # Development tools and convenience utilities
 development_tools=(
-    ack-grep
+    #! ack-grep
     bash-completion
-    emacs-nox
+    nox #? was emacs-nox
     flake8
     gdb
-    gdbserver
+    #! gdbserver
     valgrind
-    gedit
-    git-man
-    gitg
-    gitk
-    kate
-    kdiff3
-    kompare
-    kwrite
-    locate
+    #! gedit
+    #! git-man
+    #! gitg
+    #! gitk
+    #! kate
+    #! kdiff3
+    #! kompare
+    #! kwrite
+    #! locate
     meld
-    nano
-    python2  # only for flake8 tests of casa-distro
-    python3-autopep8
-    python3-objgraph
-    python3-venv
+    autopep8
+    objgraph
+    #! venv
     spyder
-    strace
+    #! strace
     tox
     vim
-    xterm
-    xdot
+    #! xterm
+    #! xdot
 )
 
 # Documentation building
@@ -108,13 +106,14 @@ brainvisa_standard_dev_dependencies=(
     libpng #? was libpng-dev
     #! libqt5x11extras5-dev
     #! libqwt-qt5-dev
-    libsigcpp #? was libsigc++-2.0-dev
+    libsigcpp<3 #? was libsigc++-2.0-dev
     #! libspnav-dev
     libsvm #? was libsvm-dev
     libtiff #? was libtiff-dev
     #! libvtk9-dev
     #! libvtk9-qt-dev
     libxml2 #? was libxml2-dev
+    mesalib # necessary to have GL/gl.h found by Qt CMake files
     #! qttools5-dev
     #! qtmultimedia5-dev
     #! qttools5-dev-tools