LORIS BIDS importer package (PR 2)

[MaximeBICMTL]

Builds on #1424 (diff)

Description

This PR isolates the LORIS BIDS importer out of the core lib module into its own loris-bids-importer package.

List of changes

Architecture

• Moved the BIDS importer code from the scripts and lib.import_bids_dataset modules to a new loris-bids-importer package, which is installed by default with LORIS Python.
• Also moved the Eeg and Physiological classes to this new package.
• Renamed check_or_create_subject/session(params, create=False) functions to validate_subject/session(params, create=False) to be more concise and better emphasize the validation step of the pipeline.
• Added some modality-specific submodules to the loris-bids-importer to better organize the files.

Old file structure:

python
├── lib
│   ├── eeg.py
│   ├── import_bids_dataset
│   │   ├── acquisitions.py
│   │   ├── archive.py
│   │   ├── args.py
│   │   ├── channels.py
│   │   ├── check_sessions.py
│   │   ├── check_subjects.py
│   │   ├── copy_files.py
│   │   ├── env.py
│   │   ├── events.py
│   │   ├── file_type.py
│   │   ├── main.py
│   │   ├── mri.py
│   │   ├── mri_sidecar.py
│   │   ├── physio.py
│   │   ├── print.py
│   │   └── scans.py
│   └── physiological.py
└── scripts
    └── import_bids_dataset.py

New file structure:

python
└── loris_bids_importer
    ├── pyproject.toml
    ├── README.md
    └── src
        └── loris_bids_importer
            ├── acquisitions.py
            ├── archive.py
            ├── args.py
            ├── channels.py
            ├── copy_files.py
            ├── eeg
            │   ├── main.py
            │   └── physiological.py
            ├── env.py
            ├── events.py
            ├── file_type.py
            ├── main.py
            ├── mri
            │   ├── main.py
            │   └── sidecar.py
            ├── physio.py
            ├── print.py
            ├── scans.py
            ├── scripts
            │   └── import_bids_dataset.py
            └── validation
                ├── sessions.py
                └── subjects.py

Documentation

Added a README file to the new package. Included MEG because I don't want to change the README soon. Did not talk about default_bids_vl because it is a horrible design (it should be a CLI parameter, not a global config value).

CLI parameters (breaking changes)

Renamed the BIDS importer command from import_bids_dataset.py (bids_import.py in LORIS 27) to import-bids-dataset.

Renamed CLI options to use kebab-case:

• --createcandidate → --create-candidate
• --createsession → --create-session
• --nobidsvalidation → --no-bids-validation
• --nocopy → --no-copy