[BUG] Argdump mutually exclusive options with a flag creates weird Boutiques descriptor

[michellewang]

I get this Boutiques descriptor from the argdump below:

{
  "schema-version": "0.5+styx",
  "name": "petprep",
  "description": "PETPrep: PET PREProcessing workflows v0.1.dev1+g2f5176c",
  "command-line": "petprep [FS_SUBJECTS_DIR_OR_RUN_RECONALL]",
  "inputs": [
    {
      "id": "fs_subjects_dir_or_run_reconall",
      "type": [
        {
          "command-line": "--fs-subjects-dir [FS_SUBJECTS_DIR]",
          "inputs": [
            {
              "id": "fs_subjects_dir",
              "type": "File",
              "value-key": "[FS_SUBJECTS_DIR]",
              "name": "fs_subjects_dir"
            }
          ],
          "name": "fs-subjects-dir",
          "id": "fs_subjects_dir"
        },
        {
          "name": "run_reconall",
          "id": "run_reconall",
          "command-line": "[RUN_RECONALL]",
          "inputs": [
            {
              "id": "run_reconall",
              "type": "String",
              "value-key": "[RUN_RECONALL]",
              "value-choices": [
                "--fs-no-reconall"
              ],
              "name": "run_reconall"
            }
          ]
        }
      ],
      "value-key": "[FS_SUBJECTS_DIR_OR_RUN_RECONALL]",
      "optional": true,
      "name": "fs_subjects_dir_or_run_reconall"
    }
  ]

It is not intuitive since the invocation would have to be something like this:

{
  "fs_subjects_dir_or_run_reconall": {
    "run_reconall": "--fs-no-reconall"
  }
}

There are two problems:

• run_reconall should be fs_no_reconall to match the flag
• run_reconall should have type Flag

A better descriptor would accept an invocation like this:

{
  "fs_subjects_dir_or_fs_no_reconall": {
    "fs_no_reconall": true
  }
}

Argdump input:

  {
    "$schema": "https://niwrap.dev/argdump/schema-v1.json",
    "$env": {
      "python_version": "3.13.15",
      "python_implementation": "CPython",
      "platform_system": "Linux",
      "platform_release": "6.17.0-1022-azure",
      "platform_machine": "x86_64",
      "argdump_version": "0.1.3"
    },
    "prog": "petprep",
    "description": "PETPrep: PET PREProcessing workflows v0.1.dev1+g2f5176c",
    "formatter_class": "ArgumentDefaultsHelpFormatter",
    "actions": [
      {
        "option_strings": [
          "--fs-subjects-dir"
        ],
        "dest": "fs_subjects_dir",
        "action_type": "store",
        "type_info": {
          "name": "Path",
          "module": "pathlib._local"
        },
        "help": "Path to existing FreeSurfer subjects directory to reuse. (default: OUTPUT_DIR/freesurfer)",
        "metavar": "PATH"
      },
      {
        "option_strings": [
          "--fs-no-reconall"
        ],
        "dest": "run_reconall",
        "action_type": "store_false",
        "nargs": 0,
        "const": false,
        "default": true,
        "help": "Disable FreeSurfer surface preprocessing."
      }
   ],
    "mutually_exclusive_groups": [
      {
        "actions": [
          "fs_subjects_dir",
          "run_reconall"
        ]
      }
    ]
  }

[nx10]

Naming is fixed in #90, both halves. The arm is now fs_no_reconall rather than run_reconall, and the group is fs_subjects_dir_or_fs_no_reconall rather than ..._or_run_reconall.

Note this renames generated ids for any argdump mutex group, so it's breaking for anything pinned to the old ones.

The Flag-vs-String half is the same question as #89