SCHWED-5907 Fixes for updated OST Singularity image

The following issues were observed:
- warning about non-writable directory which was set as IPYTHONDIR env var
  Not very surprising, it's a directory that lives in container space...
- stale kernels
  I didn't investigate that one properly. It had something to do with bending
  around all Jupyter/IPython relevant directories to custom set directories
  in the image. Reason for doing that is potential Python modules that reside
  in user home of the host that get imported in the container. I removed the
  bending around with the full knowledge that the described problem may occur.
- version updates
  Some changes related to different Python versions between old base image
  (Ubuntu 20.04) and the new one (Ubuntu 22.04).

singularity/Singularity

@@ -5,18 +5,15 @@ From: registry.scicore.unibas.ch/schwede/openstructure:2.4.0-jammy
 # POST
 ##############################################################################
 
-
 # CHANGE DASH TO BASH
 rm /bin/sh
 ln -sf /bin/bash /bin/sh
 
-
 # INSTALL SYSTEM DEPS
 #####################
-apt-get update -y && apt-get install -y python3-pip
+apt-get update -y && apt-get install -y ipython3 jupyter python3-pip
+pip3 install ipywidgets==7.6.0
 pip3 install nglview \
-             ipython \
-             jupyter \
              six
 
 # SET LOCALE
@@ -28,23 +25,9 @@ locale-gen en_US.UTF-8
 
 # SETUP IPYTHON / JUPYTER
 #########################
-# As the Singularity mounts $HOME by default Jupyter and Ipython config files
-# are moved to separate directories. Proper environmental variables are also 
-# set
-export IPYTHONDIR="/usr/local/share/ipython"
-export JUPYTER_CONFIG_DIR="/usr/local/etc/jupyter"
 export JUPYTER_PATH="/usr/local/share/jupyter"
-export JUPYTER_RUNTIME_DIR="/tmp/jupyter_runtime"
-
-mkdir -p /usr/local/share/ipython
 mkdir -p $JUPYTER_PATH
-mkdir -p $JUPYTER_RUNTIME_DIR
-mkdir -p $JUPYTER_CONFIG_DIR
 mkdir -p $JUPYTER_PATH/kernels/ost-kernel
-chmod a+rw -R /usr/local/share/ipython
-chmod a+rw -R $JUPYTER_PATH
-chmod a+rw -R $JUPYTER_CONFIG_DIR
-chmod a+rw -R $JUPYTER_RUNTIME_DIR
 cat > $JUPYTER_PATH/kernels/ost-kernel/kernel.json <<EOF
 {
   "display_name": "OST",
@@ -54,7 +37,7 @@ cat > $JUPYTER_PATH/kernels/ost-kernel/kernel.json <<EOF
     "-m", "ipykernel",
         "-f", "{connection_file}",
     "--InteractiveShellApp.exec_PYTHONSTARTUP=False",
-    "--InteractiveShellApp.exec_files=['/usr/local/lib64/python3.8/site-packages/ost/ost_startup.py']"
+    "--InteractiveShellApp.exec_files=/usr/local/lib64/python3.10/site-packages/ost/ost_startup.py"
   ],
   "env": {
   }
@@ -71,10 +54,7 @@ export TEMP="/tmp"
 export TEMPDIR="/tmp"
 export TMPDIR="/tmp"
 export TMP="/tmp"
-export IPYTHONDIR="/usr/local/share/ipython"
-export JUPYTER_CONFIG_DIR="/usr/local/etc/jupyter"
 export JUPYTER_PATH="/usr/local/share/jupyter"
-export JUPYTER_RUNTIME_DIR="$TMPDIR/jupyter_runtime"
 
 %apprun ChemdictTool
 ##############################################################################
@@ -173,15 +153,15 @@ goes to CWD. Thus this sould work as expected out of the box.
 
 %appenv IPython
 ##############################################################################
-# NOTEBOOK ENV
+# IPYTHON ENV
 ##############################################################################
 export DNG_ROOT=$OST_ROOT
-export DNG_INITDIR=${DNG_ROOT}/lib64/python3.8/site-packages/ost
+export DNG_INITDIR=${DNG_ROOT}/lib64/python3.10/site-packages/ost
 
 
 %apprun IPython
 ##############################################################################
-# OST IPYTON APP
+# OST IPYTHON APP
 ##############################################################################
 ipython3 -i $DNG_INITDIR/ost_startup.py "$@"
 
@@ -235,9 +215,6 @@ load all necessary OST components just like in the OST shell. We also enabled
 the nglview widget to interactively view molecular structures and trajectories.
 For more details on how to use nglview see http://nglviewer.org/nglview/latest/.
 
-As the Singularity mounts $HOME by default Jupyter and Ipython config files
-are moved to separate directories. Proper environmental variables are also set.
-
 To list of all available options:
 
     singularity run --app Notebook <IMAGE> --help