neuro-forge: reproducible provisioning of neuroimaging workspaces for image processing and data analysis
This project contains everything needed to build and update the neuro-forge packages. neuro-forge is a set of packages for the Conda ecosystem dedicated to image analysis and data analysis in neuroimaging.
neuro-forge is still in early alpha stage and should only be used for testing.
neuro-forge packages are contained in a Conda channel located in https://brainvisa.info/neuro-forge (this is a temporary URL, it may change at any moment). They can be installed using Pixi, Mamba or Conda. We recommand the use of pixi. For instance, once pixi is installed, one can use the following script to setup a workspace containing anatomist:
# Create a workspace directory
mkdir ~/workspace
# Setup workspace
cd ~/workspace
pixi init -c https://brainvisa.info/neuro-forge -c conda-forge
# Enter workspace
pixi shell
# Install anatomist
pixi add anatomist
# Run anatomist
anatomist
The creation of packages for neuro-forge is based on the use of rattler-build. The neuro-forge channel is composed of two kinds of packages:
- Base packages that are standard rattler-build recipes that can be built independently using only dependencies from conda-forge.
- soma-forge packages that are packages from the BrainVISA project and requires a soma-forge development environement to be build.
In order to build a neuro-forge channel from scratch, one must use pixi. The following script will create a channel directory containing the base packages that are necessary to complement conda-forge in order to build other packages.
git clone https://github.com/neurospin/neuro-forge
cd neuro-forge
pixi run neuro-forge init channel