Installation¶

ISF is available for Linux and macOS.

For installation and environment management, ISF uses pixi. You can install pixi by running:

curl -fsSL https://pixi.sh/latest | sh

To install ISF with pixi, simply:

git clone https://github.com/mpinb/in_silico_framework_hot_zone.git --depth 1 &&
cd in_silico_framework_hot_zone &&
pixi install

Usage¶

ISF works best with a dask server for parallel computing:

pixi run launch_dask_server

pixi run launch_dask_workers

We recommend to use ISF within a JupyterLab server for interactive use:

pixi run launch_jupyter_lab_server

To get started with ISF, feel free to consult the Tutorials.

Test ISF¶

To test if all components of ISF are working as intended, you can run the test suite locally. To do so, you will need three shells in total: one for launching a dask server, one for launching dask workers, and one for running the test suite itself.

pixi run launch_dask_server

pixi run launch_dask_workers

pixi run test

Configuration¶

The scripts above have been configured for local use. For High Performance Computing (HPC) environments, you may want to adapt these to you own needs. The underlying commands for these shortcuts are configured in the pyproject.toml file.

pixi also supports a conda-style shell activation:

pixi shell

This can be useful for executing shell scripts within the ISF environment, configuring HPC job submissions, or simply interactive IPython sessions.