[wli51]

To mitigate training artifact

Summary by CodeRabbit

• New Features
  • Added configurable zero or reflect padding for convolution blocks and ConvNeXt U-Net encoder and decoder layers. Zero padding remains the default, and encoder or decoder settings can inherit the shared padding choice.
  • Padding settings are included in model configuration and restored when loading a configuration.
• Bug Fixes
  • Loading older configurations now uses appropriate defaults for missing options while preserving historical pixel-shuffle behavior. Configuration inputs are left unchanged during loading.

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📥 Commits

Reviewing files that changed from the base of the PR and between 3acb304 and 56bbff4.

📒 Files selected for processing: 5

• src/virtual_stain_flow/models/blocks/blocks.py
• src/virtual_stain_flow/models/unext.py
• tests/conftest.py
• tests/datasets/conftest.py
• tests/datasets/ds_engine/test_crop_manifest.py

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

• src/virtual_stain_flow/models/blocks/blocks.py

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📝 Walkthrough

Convolution blocks and ConvNeXtUNet now support zero or reflection padding. ConvNeXtUNet accepts shared and branch-specific settings and includes them in configuration serialization. Tests also update TIFF image creation to omit explicit PIL mode arguments.

Changes: Padding mode configuration

Layer / File(s)	Summary
Add padding modes to convolution blocks src/virtual_stain_flow/models/blocks/blocks.py, tests/models/test_compute_blocks.py	Both block constructors accept padding_mode, defaulting to "zeros", and reject unsupported values. Padded convolutions use the selected mode. Tests check reflection mode propagation.
Configure padding in ConvNeXtUNet src/virtual_stain_flow/models/unext.py, tests/models/test_unext.py, tests/vsf_logging/test_mlflow_logger_model_config_unext.py	ConvNeXtUNet accepts shared and branch-specific padding modes and applies them to padded encoder and decoder convolutions. Configuration serialization and restoration include these settings. Tests cover mode selection, validation, round-tripping, and a forward pass; the logging test checks the default values.
Update TIFF test image creation tests/conftest.py, tests/datasets/conftest.py, tests/datasets/ds_engine/test_crop_manifest.py	Fixtures and crop-manifest tests create PIL images without explicit mode arguments.

Priority: ➖ Normal

Estimated code review effort: 3 (Moderate) | ~20 minutes

Change: Feature

Merge Risk: ⚪ Minimal · up to 56bbf

The models gain configurable padding while retaining zero padding by default, and the TIFF test-image edits retain their generated arrays and paths. No actionable merge-blocking risk is established by the supplied evidence.

Pre-merge checks: 4 · 1

Failed checks: 1 warning

Check name	Status	Explanation	Resolution
Docstring Coverage		Docstring coverage is 56.76% which is insufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff. Analyzed 37 functions across 8 files.	Write docstrings for the functions missing them to satisfy the coverage threshold.

Passed checks: 4 passed

Check name	Status	Explanation
Description Check		Check skipped - CodeRabbit’s high-level summary is enabled.
Title check		The title clearly and concisely describes the primary change: configurable convolutional padding in ConvNeXtUNet/UNeXt.
Linked Issues check		Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check		Check skipped because no linked issues were found for this pull request.

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Actionable comments posted: 1

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• 🪄 Fix comments: Fix CodeRabbit comments on this PR

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Inline comments:
Review comments at @src/virtual_stain_flow/models/unext.py:
- Line 52: Move the `padding_mode` parameter in the relevant constructor after
the existing parameters so positional arguments such as `_num_units` keep their
original meaning. Preserve the default padding behavior and the existing
constructor validation.

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ℹ️ Review info

⚙️ Run configuration

• Configuration used: defaults
• Review profile: CHILL
• Plan: Advanced
• Run ID: cd26d2be-6aef-425e-a022-d50d417212a1

📥 Commits

Reviewing files that changed from the base of the PR and between 8c8eaab and 3acb304.

📒 Files selected for processing: 5

• src/virtual_stain_flow/models/blocks/blocks.py
• src/virtual_stain_flow/models/unext.py
• tests/models/test_compute_blocks.py
• tests/models/test_unext.py
• tests/vsf_logging/test_mlflow_logger_model_config_unext.py

Included review availability: This review used your included allowance. Your plan provides up to 1 included review per hour; 0 remain after this review.