Argument linking fails when setting model and data via command line instead of passing it to the CLI.

[tobemo]

Bug description

Argument linking when passing model and datamodule to the cli constructor works; like so: MyLightningCLI(MyModel, MyData).

Argument linking when setting model and datamodule via the command line interface using flags like --model, --data and/or --config raises a ValueError saying Target key "model.foo" must be for an individual argument.
See code below.

How to reproduce the bug

from pytorch_lightning.cli import LightningCLI
from pytorch_lightning import LightningModule, LightningDataModule


activations = {
    'MaxAbsScaler': 'Sigmoid',
    'Normalizer': 'Sigmoid',
    'QuantileTransformer': 'Sigmoid',
    'RobustScaler': 'PReLU',
    'StandardScaler': 'PReLU',
    'PowerTransformer': 'TanhShrink',
}


class MyLightningCLI(LightningCLI):
    def add_arguments_to_parser(self, parser):
        parser.link_arguments(
            "data.scaler", "model.scaler",
            compute_fn=lambda scaler: activations.get(scaler, 'linear'),
            apply_on='instantiate'
        )


class MyModel(LightningModule):
    def __init__(self, activation: str) -> None:
        super().__init__()
        self.save_hyperparameters()
        print(activation)


class MyData(LightningDataModule):
    def __init__(self, scaler: str) -> None:
        super().__init__()
        self.save_hyperparameters()
        print(scaler)


def main():
    # this works :)
    # cli = MyLightningCLI(MyModel, MyData)
    # > python fit .\debug.py --data.scaler MaxAbsScaler
    # > prints Sigmoid
    
    # this does not work :(
    cli = MyLightningCLI()
    # > python .\debug.py fit --data MyData --data.scaler MaxAbsScaler --model MyModel
    # > ValueError: Target key "model.activation" must be for an individual argument.

if __name__ == '__main__':
    main()

Error messages and logs

Traceback (most recent call last):
  File "D:\Users\MC\Documents\ALGO_TRADING\0 BIAS\VAE\debug.py", line 50, in <module>
    main()
  File "D:\Users\MC\Documents\ALGO_TRADING\0 BIAS\VAE\debug.py", line 45, in main
    cli = MyLightningCLI()
  File "D:\Users\MC\Documents\ALGO_TRADING\0 BIAS\VAE\.venv\lib\site-packages\pytorch_lightning\cli.py", line 343, in __init__
    self.setup_parser(run, main_kwargs, subparser_kwargs)
  File "D:\Users\MC\Documents\ALGO_TRADING\0 BIAS\VAE\.venv\lib\site-packages\pytorch_lightning\cli.py", line 403, in setup_parser
    self._add_subcommands(self.parser, **subparser_kwargs)
  File "D:\Users\MC\Documents\ALGO_TRADING\0 BIAS\VAE\.venv\lib\site-packages\pytorch_lightning\cli.py", line 480, in _add_subcommands
    subcommand_parser = self._prepare_subcommand_parser(trainer_class, subcommand, **subparser_kwargs)
  File "D:\Users\MC\Documents\ALGO_TRADING\0 BIAS\VAE\.venv\lib\site-packages\pytorch_lightning\cli.py", line 486, in _prepare_subcommand_parser
    self._add_arguments(parser)
  File "D:\Users\MC\Documents\ALGO_TRADING\0 BIAS\VAE\.venv\lib\site-packages\pytorch_lightning\cli.py", line 439, in _add_arguments
    self.add_arguments_to_parser(parser)
  File "D:\Users\MC\Documents\ALGO_TRADING\0 BIAS\VAE\debug.py", line 17, in add_arguments_to_parser
    parser.link_arguments(
  File "D:\Users\MC\Documents\ALGO_TRADING\0 BIAS\VAE\.venv\lib\site-packages\jsonargparse\link_arguments.py", line 379, in link_arguments
    ActionLink(self, source, target, compute_fn, apply_on)
  File "D:\Users\MC\Documents\ALGO_TRADING\0 BIAS\VAE\.venv\lib\site-packages\jsonargparse\link_arguments.py", line 141, in __init__
    raise ValueError(f'Target key "{target}" must be for an individual argument.')
ValueError: Target key "model.scaler" must be for an individual argument.

Environment

Current environment

* CUDA:
        - GPU:
                - NVIDIA GeForce GTX 970
        - available:         True
        - version:           11.7
* Lightning:
        - lightning-utilities: 0.3.0
        - pytorch-lightning: 1.8.3.post1
        - torch:             1.13.0+cu117
        - torchaudio:        0.13.0+cu117
        - torchmetrics:      0.11.0
        - torchvision:       0.14.0+cu117
* Packages:
        - absl-py:           1.3.0
        - aiohttp:           3.8.3
        - aiosignal:         1.3.1
        - alembic:           1.8.1
        - antlr4-python3-runtime: 4.9.3
        - asttokens:         2.1.0
        - async-timeout:     4.0.2
        - attrs:             22.1.0
        - autopage:          0.5.1
        - backcall:          0.2.0
        - cachetools:        5.2.0
        - certifi:           2022.9.24
        - charset-normalizer: 2.1.1
        - cliff:             4.1.0
        - cmaes:             0.9.0
        - cmd2:              2.4.2
        - colorama:          0.4.6
        - colorlog:          6.7.0
        - commonmark:        0.9.1
        - contourpy:         1.0.6
        - cycler:            0.11.0
        - debugpy:           1.6.3
        - decorator:         5.1.1
        - docstring-parser:  0.15
        - entrypoints:       0.4
        - executing:         1.2.0
        - fire:              0.4.0
        - fonttools:         4.38.0
        - frozenlist:        1.3.3
        - fsspec:            2022.11.0
        - google-auth:       2.15.0
        - google-auth-oauthlib: 0.4.6
        - greenlet:          2.0.1
        - grpcio:            1.51.1
        - hydra-core:        1.2.0
        - idna:              3.4
        - imageio:           2.22.4
        - importlib-metadata: 4.13.0
        - ipykernel:         6.17.1
        - ipython:           8.6.0
        - jedi:              0.18.1
        - joblib:            1.2.0
        - jsonargparse:      4.18.0
        - jupyter-client:    7.4.6
        - jupyter-core:      5.0.0
        - kiwisolver:        1.4.4
        - lightning-utilities: 0.3.0
        - mako:              1.2.4
        - markdown:          3.4.1
        - markupsafe:        2.1.1
        - matplotlib:        3.6.2
        - matplotlib-inline: 0.1.6
        - multidict:         6.0.2
        - nest-asyncio:      1.5.6
        - networkx:          2.8.8
        - numpy:             1.23.4
        - oauthlib:          3.2.2
        - omegaconf:         2.2.3
        - optuna:            3.0.4
        - packaging:         21.3
        - pandas:            1.5.1
        - parso:             0.8.3
        - pbr:               5.11.0
        - pickleshare:       0.7.5
        - pillow:            9.3.0
        - pip:               22.3.1
        - platformdirs:      2.5.4
        - prettytable:       3.5.0
        - prompt-toolkit:    3.0.32
        - protobuf:          3.20.1
        - psutil:            5.9.4
        - pure-eval:         0.2.2
        - pyarrow:           10.0.0
        - pyasn1:            0.4.8
        - pyasn1-modules:    0.2.8
        - pygments:          2.13.0
        - pyparsing:         3.0.9
        - pyperclip:         1.8.2
        - pyreadline3:       3.4.1
        - python-dateutil:   2.8.2
        - pytorch-lightning: 1.8.3.post1
        - pytz:              2022.6
        - pywavelets:        1.4.1
        - pywin32:           305
        - pyyaml:            6.0
        - pyzmq:             24.0.1
        - requests:          2.28.1
        - requests-oauthlib: 1.3.1
        - rich:              12.6.0
        - rsa:               4.9
        - scikit-image:      0.19.3
        - scikit-learn:      1.1.3
        - scipy:             1.8.1
        - setuptools:        58.1.0
        - six:               1.16.0
        - sqlalchemy:        1.4.44
        - stack-data:        0.6.1
        - stevedore:         4.1.1
        - tensorboard:       2.11.0
        - tensorboard-data-server: 0.6.1
        - tensorboard-plugin-wit: 1.8.1
        - tensorboardx:      2.5.1
        - termcolor:         2.1.1
        - threadpoolctl:     3.1.0
        - tifffile:          2022.10.10
        - torch:             1.13.0+cu117
        - torchaudio:        0.13.0+cu117
        - torchmetrics:      0.11.0
        - torchvision:       0.14.0+cu117
        - tornado:           6.2
        - tqdm:              4.64.1
        - traitlets:         5.5.0
        - typing-extensions: 4.4.0
        - ujson:             5.5.0
        - urllib3:           1.26.12
        - wcwidth:           0.2.5
        - werkzeug:          2.2.2
        - wheel:             0.38.4
        - yarl:              1.8.1
        - zipp:              3.11.0
* System:
        - OS:                Windows
        - architecture:
                - 64bit
                - WindowsPE
        - processor:         AMD64 Family 23 Model 8 Stepping 2, AuthenticAMD
        - python:            3.10.4
        - version:           10.0.19045

More info

No response

cc @carmocca @mauvilsa

[samvanstroud]

See also omni-us/jsonargparse#208

[mauvilsa]

In pull request omni-us/jsonargparse#218 this error message has been changed to make it more clear what the problem is. Note that the link_arguments in the code above is a mistake and should give an error. The correct link would be:

        parser.link_arguments(
            "data.scaler", "model.init_args.activation",
            compute_fn=lambda scaler: activations.get(scaler, 'linear'),
            apply_on='instantiate'
        )

[tobemo]

Great, this works!
For completeness sake I would like to mention that since data.scaler will already be instantiated by the time it goes through the linking process it is no longer a string but an object.

This works:

parser.link_arguments(
    "data.scaler", "model.init_args.activation",
    compute_fn=lambda scaler: activations.get(type(scaler).__name__, 'linear'),
    apply_on='instantiate'
)