Following installation steps, but casa_distro setup_dev does not work

[maciej-jedynak]

Hello, my intention is to start an environment in which I could import soma and anatomist. I follow steps from this page, so I first clone: git clone https://github.com/brainvisa/casa-distro.git /tmp/casa-distro then I issue two commands not covered in the documentation page, but I understand they are needed: cd /tmp/casa-distro/ python3 setup.py install and then I do:

casa_distro setup_dev system=ubuntu-18.04 distro=brainvisa branch=master
usage: casa_distro [-v] [--version] [-h] [{help,distro,list,run,pull_image,shell,mrun,bv_maker}] ...
casa_distro: error: argument command: invalid choice: 'setup_dev' (choose from 'help', 'distro', 'list', 'run', 'pull_image', 'shell', 'mrun', 'bv_maker')

so, seems like the setup_dev option of the casa_distro command does not work.

[JoelChavas]

It will not solve the bug, but there is a way to make a virtualenv environment inside casa-distro. 1) install a brainvisa developer following the instructions in https://brainvisa.info/web/download.html#developer-environment-installation 2) Then enter into brainvisa bash and install and activate the virtual env:

bv bash
virtualenv --python=python3 --system-site-packages venv
. venv/bin/activate 

[sapetnioc]

We have several outdated docs, sorry. We now only use casa_distro from within a container (or virtual machine when container is not possible). If it is compatible with your use case, I would recommend to follow the instruction from this page to setup a development environment. These instruction mus be updated too ; you should use apptainer instead of singularity, this is the new name of this project since a fork a few years ago. Using a container is the best option to have all the required dependencies to build BrainVISA projects.

[maciej-jedynak]

Thank you. Short version: imports of soma and anatomist work now when using casa_distro from the container.

Long version: I did the following: according to your instruction I install appteiner, however: trying to overwrite '/usr/bin/run-singularity', which is also in package singularity-ce 3.8.3~ubuntu-20.04 it might be just a matter of names then. I try with singularity, easily installable from the Ubuntu packages repo: singularity run -c -B $HOME/casa_distro/brainvisa-opensource-master:/casa/setup /media/maciek/Data_Partition/BrainVISA/casa-dev-5.0.sif branch=master distro=opensource export PATH="$HOME/casa_distro/brainvisa-opensource-master/bin:$PATH" bv_maker The last command finishes with the following error:

bv_maker summary:
OK          step sources: /casa/host/src, started: 2024/01/31 13:36, stopped: 2024/01/31 13:36
OK          step configure: /casa/host/build, started: 2024/01/31 13:36, stopped: 2024/01/31 13:37
OK          step build: /casa/host/build, started: 2024/01/31 13:37, stopped: 2024/01/31 13:56
FAILED      step doc: /casa/host/build, started: 2024/01/31 13:56, stopped: 2024/01/31 13:59
There were errors.

It seems to me it only concerns documentation, so the environment should work. I therefore do: bv bash A conda-like environment name "opensource-master-5.3" appears before the command prompt. python3 my_code_with_brainvisa_imports.py executes the import section of my code without errors! Sadly, it crashes later, but that is probably a different story. Not sure if you want to leave this bug open, so it reminds of the original problem (in the title).

[denisri]

Yes there is a problem with the docs. There is a crash in sphinx somewhere in the version we are using, but if we upgrade it, it doesn't crash there, but hangs at another place, which is worse. Maybe a later version will fix all these (I hope so) but for now it's broken. Anyway you're right, it's not important for you.

Sadly, it crashes later,

it it a problem with brainvisa code ?

Not sure if you want to leave this bug open, so it reminds of the original problem (in the title).

I think we should consider this issue closed (thus close it), and reopen another ticket on a different topic if needed.

[maciej-jedynak]

it it a problem with brainvisa code ?

I think rather my use of it. Thank you.