CODE

This is the ITPcp plasma group meta-repository that collects scripts to setup development and use of internal and external codes. Our development environment is Visual Studio Code, and we strongly recommend GitHub Copilot there and in the CLI.

CODE is based around our standard Debian bookworm system at ITPcp and provides

• Setup scripts scripts/setup/...
• Quality-of-life shell commands via scripts/util.sh
• A standardized activation together with a Python virtual environment from requirements.txt
• CI/CD for integration between codes and data
• Container definitions
• VSCode settings

Getting Started

If you haven't done so earlier, set up your SSH keys in ~/.ssh via ssh-keygen with a blank passphrase and add the content of id_rsa.pub to Gitlab and GitHub for authentication.

Perparing your machine

On Linux: At ITPcp computers all packages should be installed to get going. On your own Debian system, run scripts/setup/debian.sh.

On Mac: The recommended way via orbstack and devpod as described in scripts/setup/mac.sh.

On Windows: Prepare your machine with scripts/setup/windows.bat first to install Debian Linux via WSL2. Then follow the Linux instructions.

Initial setup

Clone the repository to your working copy, at the institute this is

git clone [email protected]:itpplasma/code /proj/plasma/CODE/<username>

Then open the directory in VS Code with

code code

When asked to initialize the devcontainer, remove the message. Run the setup script manually with

scripts/setup.sh

The setup will install external dependencies and create a Python virtual environment in the hidden .venv directory.

Finally, activate the environment with

source activate.sh

To use this environment as a standard, put the activation script into bashrc with

echo "source $PWD/activate.sh" >> ~/.bashrc

External codes

Intel compiler for codes GPEC and MARS

GPEC and MARS require the Intel toolchain with classic ifort to be installed. Run

scripts/setup/compiler_intel.sh

to install the compiler and libraries HDF5 and NetCDFwith modules. Then the commands

scripts/setup/gpec.sh
scripts/setup/mars.sh

will install GPEC and MARS into $CODE/external/intel. They can then be loaded with

module load gpec
module load mars

to make dependencies and binaries available in the shell. Be careful not to work on codes based on GNU Fortran in the same shell.

OMFIT

OMFIT requires its own Python environment provided via conda. Both will be installed to $CODE/external by running

deactivate
scripts/setup/omfit.sh

OMFIT can then be loaded with

deactivate
source $CODE/external/mambaforge/bin/activate omfit
module load omfit

and then started with omfit in the shell. Be careful not to work on codes based on the standard Python venv in the same shell.

Testing

Integration tests are run by

pytest tests/

This will perform all the tests in tests/ and its subfolders.