===== Migration from Newton =====

==== Consequences of the HPC renovation to be aware of ====
  * Home directories have moved from "/home" to "/trinity/home" --- old hard-coded absolute paths will no longer work
  * Operating system changed from Ubuntu 18.04 to Rocky Linux 9.7 --- binaries built on Newton may not run reliably
  * Workflow for running sbatch scripts has changed --- jobs are now recommended to be submitted from the web portal rather than from JupyterLab

==== Steps to migrate ====
  * Update hard-coded absolute paths to start with "/trinity/home". Where possible, avoid fixed paths and use portable alternatives (e.g., "~" in Bash or path utilities such as "os.path.abspath()" in Python)
  * Fix user-space Conda/pip environments (contact an administrator if shared environments need recreating), for that you can either:
    * Use VS Code. It enables a flexible way of finding kernels, so **ipykernel** reinstallation is not needed
    * Fix kernel path inside **/trinity/home/<USER>/.conda/envs/<ENV>/share/jupyter/kernels/python3/kernel.json**: \\ "/home/<USER>/.conda/envs/<ENV>/bin/python" ---> "**/trinity**/home/<USER>/.conda/envs/<ENV>/bin/python"
    * Reinstall **ipykernel** in your environment: \\ <code>conda install -n <ENV> ipykernel -c conda-forge --force-reinstall -y</code>for all envs: <code>for name in $(ls ~/.conda/envs);
do 
  conda install -n $name ipykernel -c conda-forge --force-reinstall -y; 
done</code>
    *  Recreate environment (if above does not work):
      * Export Conda environment to a file: \\ <code>conda env export -n <OLD_ENV> --no-builds -f environment.yml</code>
      * Create a new Conda environment from the file: \\ <code>conda env create -n <NEW_ENV> -f environment.yml</code>
      * In case the new environment does not work (e.g., cannot solve the environment/conflicts), repeat the first step, using: <code>conda env export -n <OLD_ENV> --from-history -f environment.yml</code>
  * Rebuild manually compiled software and contact an administrator if centrally installed software needs to be rebuilt

==== Tips & Bonuses ====
  * JupyterLab now has a Python LSP server (jump to definitions and references, make use of dynamic tips)
  * JupyterLab now supports showing hidden files (can be enabled in JupyterLab settings)
  * JupyterLab now has a bunch of color themes
  * It is recommended to try VS Code (codeserver) instead of JupyterLabs. Advantages: a lot of features to be overwhelmed by. Disadvantages: a lot of features to be overwhelmed by