fix: emit nnUNet store_true flags as bare CLI args in nnUNetV2Runner

[aymuos15]

Fixes #8237 .

Description

The runner passed boolean flags like --c through as --c True, but nnU-Net treats these as store_true flags that take no value, so it errored out with unrecognized arguments: True. Now we emit just the bare flag when it's set, drop it when it isn't, and leave the other args alone.

Types of changes

• Non-breaking change (fix or new feature that would not break existing functionality).

Summary by CodeRabbit

• Bug Fixes
  • Improved how command-line options are passed for training and validation, so boolean settings now behave as expected.
  • Validation now runs through the standard training workflow with validation enabled, helping ensure more consistent results.

[coderabbitai]

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: 8889d8a5-fba7-4667-8f09-002ae4658796

📥 Commits

Reviewing files that changed from the base of the PR and between ea63acf and d3c93d3.

📒 Files selected for processing (1)

• monai/apps/nnunet/nnunetv2_runner.py

🚧 Files skipped from review as they are similar to previous changes (1)

• monai/apps/nnunet/nnunetv2_runner.py

---

Walkthrough

The pull request updates nnUNetV2Runner so boolean kwargs become CLI flags only when True, are omitted when False, and validation now uses val=True when invoking training.

Changes

nnUNet runner argument handling

Layer / File(s)	Summary
Flag emission and validation call monai/apps/nnunet/nnunetv2_runner.py	Boolean kwargs now render as bare flags only when True, are skipped when False, and validation uses val=True.

Estimated code review effort: 1 (Trivial) | ~3 minutes

Possibly related issues

• --c Flag for Continuing Training Not Implemented in MONAI nnUNet Runner #8237: The boolean flag handling change matches the reported --c continuation flag issue in the nnUNet runner.

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title clearly describes the main fix: emitting nnUNet store_true flags as bare CLI args in nnUNetV2Runner.
Description check	✅ Passed	The PR description matches the template's description and types-of-changes sections; only optional checklist items are left blank.
Linked Issues check	✅ Passed	The code change addresses #8237 by emitting boolean flags as bare args, matching nnU-Net's store_true behavior.
Out of Scope Changes check	✅ Passed	The validation-call adjustment stays within the same runner flag-handling fix and does not introduce unrelated scope.
Docstring Coverage	✅ Passed	Docstring coverage is 100.00% which is sufficient. The required threshold is 80.00%.

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests

---

Thanks for using CodeRabbit! It's free for OSS, and your support helps us grow. If you like it, consider giving us a shout-out.

❤️ Share

• X
• Mastodon
• Reddit
• LinkedIn

_{Comment @coderabbitai help to get the list of available commands.}

[ericspod]

Is this an alternative to #8944 or should we merge that one first?

[coderabbitai]

Caution

Some comments are outside the diff and can’t be posted inline due to platform limitations.

⚠️ Outside diff range comments (1)

monai/apps/nnunet/nnunetv2_runner.py (1)

765-765: 🎯 Functional Correctness | 🟠 Major | ⚡ Quick win

Use val=True here
validate_single_model() forwards only_run_validation=True, which becomes --only_run_validation on the nnUNetv2_train CLI. That command uses --val for validation-only mode, so this path still passes an unrecognized flag.

🐛 Proposed fix

-        self.train_single_model(config=config, fold=fold, only_run_validation=True, **kwargs)
+        self.train_single_model(config=config, fold=fold, val=True, **kwargs)

🤖 Prompt for AI Agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@monai/apps/nnunet/nnunetv2_runner.py` at line 765, The validation-only path
in validate_single_model is forwarding the wrong flag through
train_single_model, causing nnUNetv2_train to receive --only_run_validation
instead of the expected validation mode flag. Update the call in
validate_single_model to pass val=True rather than only_run_validation=True, and
ensure the train_single_model / CLI argument mapping uses the val parameter so
validation-only runs invoke the correct nnUNetv2_train option.

🤖 Prompt for all review comments with AI agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

Outside diff comments:
In `@monai/apps/nnunet/nnunetv2_runner.py`:
- Line 765: The validation-only path in validate_single_model is forwarding the
wrong flag through train_single_model, causing nnUNetv2_train to receive
--only_run_validation instead of the expected validation mode flag. Update the
call in validate_single_model to pass val=True rather than
only_run_validation=True, and ensure the train_single_model / CLI argument
mapping uses the val parameter so validation-only runs invoke the correct
nnUNetv2_train option.

---

ℹ️ Review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: 02927779-bfeb-4b26-b032-67292bec7c9f

📥 Commits

Reviewing files that changed from the base of the PR and between 482d1d9 and 559864f.

📒 Files selected for processing (1)

• monai/apps/nnunet/nnunetv2_runner.py

[aymuos15]

Is this an alternative to #8944 or should we merge that one first?

May you please merge that first? also happy to jsut add this commit onto that.