Packaging for conda in a container

How to build BrainVisa packages and publish them for end users in a container

Creating an Apptainer/Singularity container with a pixi installation inside

A developer environment is needed for this containerization: it is barely used but relies on the infrastructure of Casa-distro and Brainvisa-cmake. Packages are actually the ones already published thus this is clearly overkill, we could simplify this in the future.

• Install a developer environment, as described in https://github.com/brainvisa/soma-env

• Install apptainer

Make sure that the apptainer distribution works with the "fakeroot" features

• Install casa-dstro

• pull an Unbintu-24.04 image for apptainer:

apptainer pull ubuntu-24.04.sif docker://ubuntu:24.04

• Create a casa-distro "base image" for pixi:

export CASA_BASE_DIRECTORY=$(pwd)
casa_distro_admin create_base_image type=pixi image_version=5.4 base=ubuntu-24.04.sif

• Option 1: lightweight modular container: the brainvisa installation will be done at setup time by the user:

casa_distro_admin create_user_image container_type=apptainer_pixi image_version=5.4 base_image=casa-pixi-5.4.sif version=6.0 distro=brainvisa install=0

• Option 2: monolithic self-contained container:

casa_distro_admin create_user_image container_type=apptainer_pixi image_version=5.4 base_image=casa-pixi-5.4.sif version=6.0 distro=brainvisa

Installing an apptainer/pixi environment (user side):

(note: this doc section should end up in a user installation doc)

• download the .sif image (let's call it brainvisa-6.0.sif

• run the image setup, as in casa-distro. However, as pixi uses a cache directory, the cache directory has to be mounted in the image read-write. This amounts to mounting (using the -B option) either $XDG_CACHE_HOME, $RATTLER_CACHE_DIR, or $HOME.

mkdir brainvisa-6.0
apptainer run -c -B $HOME -B brainvisa-6.0:/casa/setup brainvisa-6.0.sif

Creating a self-contained container from the modular one

• download a lightweight image (you don't need to run its setup)

• save the following recipe file. Let's call it here brainvisa-monolithic.recipe:

Bootstrap: localimage

From: brainvisa-6.0.sif

%post
cd /casa/install
pixi add brainvisa=6.0
pixi run bv_update_bin_links

• build the container image from this directory. The current dir is important as files will be copied from the local installation into the image from the relative current directory.

apptainer build brainvisa_monolithic-6.0.sif brainvisa-monolithic.recipe

• OK you can try installing an environment from it:

mkdir brainvisa-monomithic-6.0
apptainer run -c -B brainvisa-monlithic-6.0:/casa/setup brainvisa-monolithic-6.0.sif