Running T1-linear raises an error related to CAPS

[AliceJoubert]

While running the T1-linear pipeline with the latest dev version of Clinica, I encountered an error seemingly related to #1158.

I ran the following cmd line :
clinica run t1-linear .../BIDS20_OASIS3 .../CAPS20_OASIS3
to process a BIDS folder which normally contains all the expected files (dataset_description.json, participants.tsv...).

The environnement used to run clinica contains the following dependencies (sample) :

attrs==23.2.0
cattrs==1.10.0
isodate==0.6.1
isoduration==20.11.0
requests==2.32.3
requests-oauthlib==2.0.0

The output was the following error log :

/Users/alice.joubert/miniconda/envs/clinicaEnv/lib/python3.11/site-packages/requests/__init__.py:86: RequestsDependencyWarning: Unable to find acceptable character detection dependency (chardet or charset_normalizer).
  warnings.warn(
Traceback (most recent call last):
  File "/Users/alice.joubert/miniconda/envs/clinicaEnv/bin/clinica", line 6, in <module>
    sys.exit(main())
             ^^^^^^
  File "/Users/alice.joubert/clinica/clinica/cmdline.py", line 113, in main
    cli()
  File "/Users/alice.joubert/miniconda/envs/clinicaEnv/lib/python3.11/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/alice.joubert/miniconda/envs/clinicaEnv/lib/python3.11/site-packages/click/core.py", line 1078, in main
    rv = self.invoke(ctx)
         ^^^^^^^^^^^^^^^^
  File "/Users/alice.joubert/miniconda/envs/clinicaEnv/lib/python3.11/site-packages/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/alice.joubert/miniconda/envs/clinicaEnv/lib/python3.11/site-packages/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/alice.joubert/miniconda/envs/clinicaEnv/lib/python3.11/site-packages/click/core.py", line 1434, in invoke
    return ctx.invoke(self.callback, **ctx.params)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/alice.joubert/miniconda/envs/clinicaEnv/lib/python3.11/site-packages/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/alice.joubert/clinica/clinica/pipelines/t1_linear/t1_linear_cli.py", line 63, in cli
    pipeline = AnatLinear(
               ^^^^^^^^^^^
  File "/Users/alice.joubert/clinica/clinica/pipelines/t1_linear/anat_linear_pipeline.py", line 42, in __init__
    super().__init__(
  File "/Users/alice.joubert/clinica/clinica/pipelines/engine.py", line 427, in __init__
    from clinica.utils.caps import (
  File "/Users/alice.joubert/clinica/clinica/utils/caps.py", line 351, in <module>
    converter.register_unstructure_hook(IsoDate, lambda dt: dt.isoformat())
  File "/Users/alice.joubert/miniconda/envs/clinicaEnv/lib/python3.11/site-packages/cattr/converters.py", line 225, in register_unstructure_hook
    self._unstructure_func.register_cls_list([(cls, func)])
  File "/Users/alice.joubert/miniconda/envs/clinicaEnv/lib/python3.11/site-packages/cattr/dispatch.py", line 57, in register_cls_list
    self._single_dispatch.register(cls, handler)
  File "/Users/alice.joubert/miniconda/envs/clinicaEnv/lib/python3.11/functools.py", line 864, in register
    raise TypeError(
TypeError: Invalid first argument to `register()`. clinica.utils.caps.IsoDate is not a class or union type.

[NicolasGensollen]

Hi @AliceJoubert

Thanks for reporting. It looks like your version of cattrs is pretty old (1.10.0) while the current one is 23.2.3 (they changed from semantic to calendar versioning a couple years ago).
Could you delete your environment and re-install clinica ? I think that should fix this issue.

[AliceJoubert]

Indeed, it works now ! Thanks @NicolasGensollen :)