fix(pipeline): survive heterogeneous or empty DICOM series in preprocessing

[Liohtml]

Summary

_build_volume stacked all slice arrays with np.stack, which raises ValueError when a series mixes matrix sizes (embedded localizers, mixed acquisitions — common in real MRI studies) or is empty, aborting the entire study with a raw numpy traceback.

Fixes #138

Changes

• src/medcheck/pipeline/preprocess.py:
  • _build_volume: slices whose shape deviates from the series' dominant shape are dropped with a console warning; empty series raise a descriptive ValueError
  • PreprocessStep.run: per-series try/except — one malformed series no longer kills the run; skipped series are recorded in context.limitations, which flows into the generated report
• tests/unit/test_pipeline/test_preprocess.py: 3 new tests — mixed slice shapes keep the dominant group, empty series skipped with a limitation note, a completely broken series doesn't abort the study

Testing

• Existing tests pass (uv run pytest) — 178 passed
• New tests added for new functionality — 3 new preprocess tests
• Coverage does not decrease (uv run pytest --cov-fail-under=85) — 87.51%
• Linting passes (uv run ruff check .)
• Type checking passes (uv run mypy src/medcheck --strict)
• Pre-commit hooks pass — ruff hooks pass locally; full pre-commit not run

Additional Notes

Dropped/skipped series are deliberately surfaced in the report's limitations section rather than only logged — for a medical-imaging pipeline, silent data loss is the failure mode to avoid (see also #135, which addresses the series-keying collision separately).

🤖 Generated with Claude Code

https://claude.ai/code/session_01W4svt5QTs4WUMSy4HwiVt9

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Review details

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro Plus

Run ID: c1a7eee8-b7c8-41bb-ba24-6549d9f04a6d

📥 Commits

Reviewing files that changed from the base of the PR and between 9592f2e and 38e8437.

📒 Files selected for processing (2)

• src/medcheck/pipeline/preprocess.py
• tests/unit/test_pipeline/test_preprocess.py

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch claude/dependabot-prs-q6u94z

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.

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