add mrtrix in capsul

[manuegrx]

Hi,

I would like to add mrtrix (mrtrix3) in Capsul in order to use it in populse mia.

As I am not sure about which is the new method and which is the old one, I modified study_config, in_context and engine methods.

It seems to work fine on my side when I used mrtrix in populse (see https://github.com/populse/populse_mia/pull/313) and when I used the script the following script (with a config file: python -m capsul --config=/tmp/config_mrtrix.json /tmp/mrtrix_capsul.py /tpm/out_config.json):

from capsul.api import Process
from traits.api import File
from capsul.in_context import mrtrix
import json

class mrinfo_help(Process):
    output_config = File(output=True, desc='output file to write config',
                         allowed_extensions=['.json'])

    def requirements(self):
        return {'mrtrix': 'any'}

    def _run_process(self):
        import capsul.engine
        fconf = capsul.engine.configurations.get(
            'capsul.engine.module.mrtrix')
        if not fconf:
            raise RuntimeError('mrtrix config is not present')
        with open(self.output_config, 'w') as f:
            json.dump(fconf, f)
        mrtrix.mrtrix_check_call(['mrinfo', '-h'])

Are there any other tests I need to perform?

Moreover, regarding the test done in Capsul I have few questions:

• in test_capsul_engine I do not understand what I should use for cif for mrtrix ?

• in study config should we add some test as for AFNI or ANTs ?

As it is my first steps in Capsul I think it could be a greta idea if someone can check what I have done :)

[manuegrx]

Thanks for your feedback !

I will wait for Denis's advice about the cif value before to merge this branch (there's no hurry about this subject)

[manuegrx]

Moreover some of the GitHub automatic test are failing, is it normal ?

[denisri]

Thanks for your feedback !

I will wait for Denis's advice about the cif value before to merge this branch (there's no hurry about this subject)

I haven't read the code thoroughly but it seems OK for me.

[denisri]

Moreover some of the GitHub automatic test are failing, is it normal ?

codespell has many false positive that I don't know how to disable. I'm not sure if we should use it at all, it's sometimes useful but makes checks systematically fail in many projects. For Macos tests, I have no idea...