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

• Install apptainer

On Debian/Ubuntu systems for instance:

sudo apt install apptainer apptainer-suid

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

sudo apptainer config fakeroot --add $USER

• Install casa-dstro

git clone https://github.com/brainvisa/casa-distro
export PATH=$(pwd)/casa-distro/bin:"$PATH"

• pull a "casa-pixi" apptainer image from the BrainVISA server:

export CASA_BASE_DIRECTORY=$(pwd)
casa_distro pull_image image=casa-pixi-5.4.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

(note that the only difference is the install option)

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.

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

• if the image is a lightweight one, then the actuall installation of brainvisa packages will take place at the first run of the container:

brainvisa-6.0/bin/bv bash

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

Rebuilding the base casa-pixi image

Users should not need to do that, this doc is mainly for casa-distro developers (us), unless you need to ship additional packages in the image.

• 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

• Optionally, if you have the acces authorization to the server, publish the image:

casa_distro_admin publish_base_image type=casa-pixi image=casa-pixi-5.4.sif