Fix nnUNet runner store_true flag command construction (#8941)#8944
Fix nnUNet runner store_true flag command construction (#8941)#8944aymuos15 wants to merge 5 commits into
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The kwargs loop in train_single_model always appended str(_value), so documented boolean flags (c, val, use_compressed, disable_checkpointing) were emitted as '--c True' / '--val True' instead of bare flags, and a falsy pretrained_weights was passed as '-pretrained_weights False'. Emit store_true flags only when truthy, and only include pretrained_weights when a real path is given. Signed-off-by: Soumya Snigdha Kundu <soumya_snigdha.kundu@kcl.ac.uk>
Cover that c/val/use_compressed/disable_checkpointing emit as bare flags when True and are omitted when False, and that pretrained_weights is only included for a real path. These fail against the pre-fix argv builder. Signed-off-by: Soumya Snigdha Kundu <soumya_snigdha.kundu@kcl.ac.uk>
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🧹 Nitpick comments (1)
tests/apps/nnunet/test_nnunetv2_runner_command.py (1)
19-24: 📐 Maintainability & Code Quality | 🔵 Trivial | 💤 Low valueConsider adding a docstring to the helper function.
Path instructions require docstrings for all definitions. While the function name is clear, a brief docstring would improve maintainability.
📝 Suggested docstring
def _make_runner(export_validation_probabilities=False): + """Create a minimal nnUNetV2Runner instance for testing without full initialization.""" runner = nnUNetV2Runner.__new__(nnUNetV2Runner)As per path instructions: "Docstrings should be present for all definition which describe each variable, return value, and raised exception in the appropriate section of the Google-style of docstrings."
🤖 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 `@tests/apps/nnunet/test_nnunetv2_runner_command.py` around lines 19 - 24, The _make_runner helper function is missing a docstring, which violates the project's path instructions requiring Google-style docstrings for all definitions. Add a docstring to the _make_runner function that describes what it does (creates and returns a partially initialized nnUNetV2Runner instance), documents the export_validation_probabilities parameter and its purpose, and describes the return value as a nnUNetV2Runner instance with pre-configured attributes.Source: Path instructions
🤖 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.
Nitpick comments:
In `@tests/apps/nnunet/test_nnunetv2_runner_command.py`:
- Around line 19-24: The _make_runner helper function is missing a docstring,
which violates the project's path instructions requiring Google-style docstrings
for all definitions. Add a docstring to the _make_runner function that describes
what it does (creates and returns a partially initialized nnUNetV2Runner
instance), documents the export_validation_probabilities parameter and its
purpose, and describes the return value as a nnUNetV2Runner instance with
pre-configured attributes.
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Plan: Pro
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📒 Files selected for processing (3)
monai/apps/nnunet/nnunetv2_runner.pytests/apps/nnunet/__init__.pytests/apps/nnunet/test_nnunetv2_runner_command.py
validate_single_model passed only_run_validation=True, which the command builder emitted as --only_run_validation True. nnUNetv2_train has no such flag; the validation-only flag is the store_true --val. Pass val=True so it routes through the store_true handling and emits a bare --val. Signed-off-by: Soumya Snigdha Kundu <soumya_snigdha.kundu@kcl.ac.uk>
Signed-off-by: Soumya Snigdha Kundu <soumya_snigdha.kundu@kcl.ac.uk>
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Also fixed the same bug in the |
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Description
nnUNetV2Runner.train_single_model_commandbuilds thennUNetv2_trainargv by iteratingkwargsand always appendingstr(_value), so documentedstore_trueflags were emitted with a value instead of bare. Passingc=Trueproduced--c True,val=Trueproduced--val True, and likewise foruse_compressedanddisable_checkpointing.nnUNetv2_traindeclares these asstore_true, so the trailingTrueis parsed as a positional argument and the command fails. A falsypretrained_weightswas similarly emitted as-pretrained_weights Falseinstead of being omitted.The builder now appends
store_trueflags only when their value is truthy and skips them otherwise, and includespretrained_weights/-ponly when given a real path. Regular value kwargs and the existing--npzhandling are unchanged.Fixes #8941, originally flagged in a review thread on #8887.
Types of changes
./runtests.sh -f -u --net --coverage../runtests.sh --quick --unittests --disttests.