Prepare repository for MICCAI camera-ready release - #8
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| # Medical imaging data, model outputs, and experiment artifacts | ||
| data/ |
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Because this ignore pattern is unanchored, Git treats data/ as any directory named data under the repo, so new files beneath the existing src/data/ package are ignored as well (e.g. git check-ignore -v src/data/new_dataset/prepare.py reports this line). That makes future dataset preparation code or docs easy to miss from commits; use a rooted pattern like /data/ if only the repository-level artifact directory should be excluded.
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Pull request overview
Prepares the repository for a MICCAI 2026 camera-ready companion release by removing the previously referenced values submodule integration, tightening CI behavior, and updating documentation/dependencies to better reflect expected local artifact handling and dataset prep.
Changes:
- Removed the
valuessubmodule wiring and its Python bridge module. - Updated documentation for installation, dataset preparation, and clarified that data/model artifacts are local-only.
- Updated dependency requirements and made CI tests run strictly (no placeholder-pass behavior).
Reviewed changes
Copilot reviewed 6 out of 8 changed files in this pull request and generated 1 comment.
Show a summary per file
| File | Description |
|---|---|
src/ensemble_metrics/values_bridge.py |
Removed the bridge module that attempted to import metrics from the former values submodule. |
src/data/README.md |
Documented nnU-Net environment variables and clarified dataset placement/preprocessing instructions. |
requirements.txt |
Adjusted NumPy requirement and added missing image I/O dependencies (Pillow, opencv-python-headless). |
README.md |
Expanded project description, added install/test instructions, and documented local artifact expectations. |
.gitmodules |
Removed the values submodule configuration. |
.gitignore |
Added ignores for medical imaging datasets, nnU-Net folders, checkpoints, and common artifact file types. |
.github/workflows/tests.yml |
Added the camera-ready branch trigger and made test execution strict (pytest -q). |
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| If you use this work, please cite: | ||
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| ``` | ||
| [Citation placeholder — add BibTeX or reference when published.] | ||
| TODO(author): Add BibTeX or proceedings reference when published. | ||
| ``` |
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