Installation¶
Before installing ISF, make sure you have the following requirements installed:
Requirement |
Download |
|
|---|---|---|
Likely already installed |
Check requirements
You can check if the requirements are installed correctly by running the following commands in your terminal:
which pixi
which git
Each command should return a path to the program. If it doesn’t, you may need to restart your shell, or something went wrong during the installation of the requirements.
You can then install ISF:
git clone https://github.com/mpinb/in_silico_framework.git --depth 1
cd in_silico_framework
pixi run install
Before installing ISF, make sure you have the following requirements installed:
Requirement |
Download |
|---|---|
Check requirements
You can check if the requirements are installed correctly by running the following commands in your terminal:
which pixi
which git
Each command should return a path to the program. If it doesn’t, you may need to restart your shell, or something went wrong during the installation of the requirements.
You can then install ISF:
git clone https://github.com/mpinb/in_silico_framework.git --depth 1
cd in_silico_framework
pixi run install
Important
Windows support is still experimental. If you are using ISF with Dask parallellization on Windows, please monitor your dask dashboard closely. In case you encounter any issues, feel free to open an issue and include relevant logs. Note that many of the core ISF workflows (network mapping, neuron model generation etc.) require extensive resources, which often implies a (Linux-based) High Performance Computing environment.
Before installing ISF, make sure you have the following requirements installed:
Requirement |
Download |
|
|---|---|---|
7.8 ≤ version ≤ 8.2 |
Check requirements
You can check if the requirements are installed correctly by running the following commands in your terminal:
which pixi
which git
which neuron
Each command should return a path to the program. If it doesn’t, you may need to restart your shell, or something went wrong during the installation of the requirements.
You can then install ISF:
git clone https://github.com/mpinb/in_silico_framework.git --depth 1
cd in_silico_framework
pixi run install
Developer installation¶
If you are planning to contribute to ISF and you have read the contributor guidelines,
you should also clone the develop branch of the repository:
git remote set-branches origin 'develop'
git fetch --depth 1 origin develop
Configuration¶
ISF works best with a dask server for parallel computing. We provide default scripts to launch a dask server and workers that should work on most systems.
pixi run launch_dask_server
pixi run launch_dask_workers
For High-Performance Computing (HPC), you may want to launch the dask server with custom configuration instead of these default scripts.
The underlying commands for these shortcuts are configured in the pyproject.toml file.
Usage¶
We recommend to use ISF within a JupyterLab server for interactive use:
pixi run launch_jupyter_lab_server
pixi also supports a conda-style shell activation:
pixi shell
This can be useful for executing shell scripts within the ISF environment, or configuring HPC job submissions. 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.
pixi run test