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.
Most action with neuro-forge requires to install Pixi. It is a binary without dependency to put somewhere in the PATH. If you want to avoid the use of the script proposed by Pixi team (that install in ~/.pixi/bin and changes ~/.bashrc), you can download the latest release of pixiexecutable for Linux x86_64 achitecture with the following command:
curl -fsSL https://github.com/prefix-dev/pixi/releases/latest/download/pixi-x86_64-unknown-linux-musl.tar.gz | tar zx
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:
- Standard packages that are standard rattler-build recipes that can be built independently using only dependencies from standard channels such as conda-forge and bioconda.
- soma-forge packages that are packages from the BrainVISA project and requires a soma-forge development environement to be build.
In order to build standard packages, the neuro-forge build command can be used. To setup an environment for this command, one can use git and pixi with the following script:
git clone https://github.com/neurospin/neuro-forge
cd neuro-forge
pixi shell
pip install -e . # necessary to have the neuro-forge command in the PATH
Then, one or more packages can be built by using the following command.
neuro-forge build {output directory} {package} [{package}...]
For instance, to build a package for the latest ldscore release:
neuro-forge build /tmp/channel ldscore
First install soma-forge command that is located in neuro-forge project.
git clone https://github.com/neurospin/neuro-forge
cd neuro-forge
git checkout rolling-release
pixi run python -m pip install -e recipes/soma-forge
Then create the BrainVISA development directory by giving its location and the target packages. Target packages are the name of soma-forge packages. It will select all corresponding brainvisa-cmake components (taking into account pakages dependencies) and put them in bv_maker.cfg file. By default, all known packages are included including ones that had not been tested at all and will make compilation fail. Options can be given to select some build options : python version, Qt major version and Capsul major version.
pixi run soma-forge init /somewhere/brainvisa-py3.11-cap2-qt5 brainvisa cortical-surface morphologist-baby constellation
Finally, the development directory can be used independently of neuroforge:
cd /somewhere/brainvisa-py3.11-cap2-qt5
pixi shell
bv_maker
The packages currently built have the following dependencies:
- green: package containing brainvisa-cmake components ;
- olive: empty package with dependencies ;
- bisque: neuro-forge base package ;
- light blue: package from conda-forge.
