Fix: Override hparams via CLI

[Berezin-Leonid]

Allow CLI arguments to override checkpoint hyperparameters in LightningCLI

What does this PR do?

Currently, when LightningCLI loads a configuration from a checkpoint (using --ckpt_path), the hyperparameters stored in the checkpoint overwrite any arguments passed via the command line. This behavior prevents users from overriding specific parameters (e.g., changing the learning rate) when resuming training or fine-tuning.

This PR adjusts the configuration merging logic. Now, arguments provided explicitly via the CLI (including parameters defined in config files via --config) take precedence over the hyperparameters loaded from the checkpoint.

Example:
With this change, the following command will correctly use lr=0.001 instead of the value stored in epoch=1.ckpt:

python main.py fit --ckpt_path=epoch=1.ckpt --model.learning_rate=0.001

Implementation Details

To achieve this, I modified the loading logic so that hyperparameters from the checkpoint are applied as parser defaults rather than being merged directly into the configuration object.

This leverages the standard jsonargparse priority order:

1. Command Line Arguments (Highest priority)
2. Config Files (e.g., --config)
3. Defaults (now includes Checkpoint Hyperparameters)

This ensures that any value explicitly provided by the user will correctly override the value stored in the checkpoint.

Addressing the conversation in #21255 about CLI override priority.

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📚 Documentation preview 📚: https://pytorch-lightning--21455.org.readthedocs.build/en/21455/

[mauvilsa]

I like the idea of setting the hparams as defaults. So it seems this wasn't as difficult as I thought. There are a few details I think should change as I comment below.

Please change the pull request description avoiding Fixes #21255. I mean, merging this pull request should not close #21255, since it isn't an actual fix for it. It would be a fix for your specific comment, but not the entire issue. As a side note, the fix for #21255 would be #21408.

[Berezin-Leonid]

I've addressed all the feedback
Ready for review!

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 79%. Comparing base (9df1910) to head (fb86acf).
⚠️ Report is 1 commits behind head on master.
✅ All tests successful. No failed tests found.

❗ There is a different number of reports uploaded between BASE (9df1910) and HEAD (fb86acf). Click for more details.

HEAD has 717 uploads less than BASE

Flag	BASE (9df1910)	HEAD (fb86acf)
cpu	196	33
python	18	3
lightning_fabric	53	0
pytest	98	0
python3.12	53	9
python3.10	18	3
lightning	90	15
python3.12.7	54	9
python3.11	36	6
python3.13	17	3
pytorch2.2.2	9	3
pytest-full	98	33
pytorch2.8	18	6
pytorch_lightning	53	18
pytorch2.4.1	9	3
pytorch2.1	18	6
pytorch2.7	9	3
pytorch2.6	9	3
pytorch2.3	9	3
pytorch2.9	8	3
pytorch2.5.1	9	3

Additional details and impacted files

@@            Coverage Diff            @@
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- Coverage      87%      79%     -8%     
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  Files         270      267      -3     
  Lines       24059    24008     -51     
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- Hits        20855    18959   -1896     
- Misses       3204     5049   +1845