feat: add hip, ankle/foot, and wrist anatomy prompt templates (#10, #11, #12)

[Liohtml]

Closes

• Closes Add hip anatomy prompt template #10 — hip anatomy prompt template
• Closes Add ankle/foot anatomy prompt template #11 — ankle/foot anatomy prompt template
• Closes Add wrist anatomy prompt template #12 — wrist anatomy prompt template

Changes

Adds three detailed MRI analysis templates, modelled on the existing knee.txt, which the prompt loader (load_anatomy_instructions(), added in #43) picks up automatically:

• prompts/anatomy/hip.txt — labrum, cartilage, FAI (cam/pincer), AVN, gluteal/iliopsoas tendons, bursae
• prompts/anatomy/ankle.txt — Achilles, peroneal & tib-post tendons, ATFL/CFL/deltoid ligaments, talar OCD, plantar fascia
• prompts/anatomy/wrist.txt — TFCC, SL/LT ligaments, scaphoid/lunate (AVN), tendons, carpal tunnel, DRUJ

Extends detect_anatomy() with hip/ankle/wrist keyword patterns (including German terms: Hüfte, Sprunggelenk, Handgelenk).

Note: removed the over-broad gelenk keyword from the knee pattern — it previously would have mis-matched Handgelenk (wrist) and Sprunggelenk (ankle). Knie/knee still match knee, and the existing "Gelenke^Knie" test case still passes.

Validation

• ruff ✅ · mypy ✅ · 115 tests pass (+5: detect_anatomy for hip/ankle/wrist + template-loading assertions)

Note: development is constrained to the claude/repo-issues-features-3ZLdb branch.

https://claude.ai/code/session_01KYcUxCGAHaTPrRHTzJCWQz

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Generated by Claude Code

Summary by CodeRabbit

Release Notes

• New Features

  • Added comprehensive MRI analysis prompt templates for hip, ankle, and wrist regions with detailed structural assessment criteria.
  • Enabled keyword detection support for these newly added anatomy regions.

• Tests

  • Added unit tests for anatomy detection and prompt template loading for hip, ankle, and wrist regions.

[coderabbitai]

📝 Walkthrough

Walkthrough

This PR extends the MedCheck anatomy analysis system to recognize and analyze hip, ankle/foot, and wrist MRI scans. It adds keyword patterns to enable detection, introduces three detailed anatomical analysis prompt templates, and includes comprehensive test coverage validating both keyword detection and template loading.

Changes

Anatomy Templates and Detection

Layer / File(s)	Summary
Anatomy keyword pattern infrastructure src/medcheck/pipeline/preprocess.py	_ANATOMY_PATTERNS regex entries are updated to recognize hip, ankle, and wrist keywords in addition to existing anatomy types, enabling detect_anatomy() to classify these new anatomy categories.
Anatomy prompt templates for hip, ankle, and wrist src/medcheck/prompts/anatomy/hip.txt, src/medcheck/prompts/anatomy/ankle.txt, src/medcheck/prompts/anatomy/wrist.txt	Three new medical analysis prompt templates provide structured assessment checklists: hip (labrum, cartilage, FAI morphology, bone, effusions, tendons, soft tissues); ankle (tendons, ligaments, talar dome cartilage, bone, plantar fascia, soft tissues); wrist (TFCC, intrinsic ligaments, carpal bones, tendons, carpal tunnel, joints/cartilage).
Test coverage for anatomy detection and templates tests/unit/test_pipeline/test_preprocess.py, tests/unit/test_pipeline/test_vision_analysis.py	Unit tests verify detect_anatomy() correctly maps English and German keywords for hip, ankle, and wrist, and integration tests confirm load_anatomy_instructions() returns expected detailed template content for all three new anatomies.
Changelog documentation CHANGELOG.md	New entry documents the addition of detailed anatomy prompt templates for hip, ankle/foot, and wrist with corresponding keyword detection support.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~10 minutes

Possibly related PRs

• Liohtml/MedCheck#45: Adds the load_anatomy_instructions() template-loader function that is directly used by this PR's tests to verify template loading for the new hip, ankle, and wrist anatomies.

Poem

A rabbit hops through hip and wrist,
Ankle structures none are missed,
With keywords matched and templates bright,
MRI analysis takes flight! 🐰✨
Three anatomies, now complete and right.

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title accurately and specifically describes the main change: adding three anatomy prompt templates (hip, ankle/foot, wrist) with linked issue references.
Description check	✅ Passed	The description covers all key aspects: linked issues, detailed changes, keyword modifications, validation results, and testing confirmation. All template sections are properly documented.
Linked Issues check	✅ Passed	The PR fully addresses all requirements from issues #10, #11, #12: creates three anatomy prompt templates (hip, ankle, wrist), extends detect_anatomy() with relevant keywords including German terms, removes over-broad 'gelenk' keyword, updates tests (+5 new tests).
Out of Scope Changes check	✅ Passed	All changes are directly scoped to the linked issues: three new anatomy templates, keyword pattern updates in detect_anatomy(), CHANGELOG update, and unit tests. No extraneous modifications detected.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

_{✏️ Tip: You can configure your own custom pre-merge checks in the settings.}

✨ Finishing Touches

📝 Generate docstrings

• Create stacked PR
• Commit on current branch

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch claude/repo-issues-features-3ZLdb

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.

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[coderabbitai]

🧹 Nitpick comments (2)

src/medcheck/pipeline/preprocess.py (2)

22-22: 💤 Low value

The "carpal" keyword may match metacarpal scans.

"Metacarpal" (hand/finger bones) contains "carpal" and would incorrectly classify as wrist. If the system processes hand/finger MRIs separately, consider using a word boundary anchor or a more specific pattern.

♻️ Proposed refinement using word boundaries

-    (r"wrist|handgelenk|carpal|tfcc|scaphoid", "wrist"),
+    (r"wrist|handgelenk|\bcarpal\b|tfcc|scaphoid", "wrist"),

Alternatively, if metacarpal scans are rare or always labeled with more specific terms (e.g., "metacarpophalangeal"), the current pattern may be acceptable.

🤖 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 `@src/medcheck/pipeline/preprocess.py` at line 22, The regex mapping that maps
("wrist") currently includes "carpal" which will match "metacarpal"; update the
pattern in the tuple that contains (r"wrist|handgelenk|carpal|tfcc|scaphoid",
"wrist") to use word-boundary anchors (e.g., \bcarpal\b or wrap each wrist token
with \b...\b) or otherwise make "carpal" more specific so it won't match
"metacarpal"; locate and modify this pattern in preprocess.py where the wrist
mapping tuple is defined (the tuple with the regex and "wrist") and adjust the
regex accordingly.

---

21-21: ⚡ Quick win

Tighten the generic foot match in the ankle regex (line 21)

Repo-wide search only finds the foot token in this regex (no other description examples to gauge actual DICOM wording), so false-positive risk can’t be quantified here—but it’s still safer to restrict foot (e.g., to a whole-word/anchored match) to avoid mapping more specific terms like “forefoot/midfoot” or “foot_*” into ankle.

🤖 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 `@src/medcheck/pipeline/preprocess.py` at line 21, The current ankle mapping
regex tuple (r"ankle|sprunggelenk|achilles|foot|fuß|fuss|calcaneus|hindfoot",
"ankle") is too permissive for the token "foot" and can false-match terms like
"forefoot" or "midfoot"; update that regex in
src/medcheck/pipeline/preprocess.py (the ankle mapping tuple) to restrict "foot"
to a whole-word match (e.g., replace the plain foot/füß/fuss token with a
word-boundary form such as \bfoot\b and similarly \bfuß\b/\bfuss\b in the raw
string) so only standalone “foot” maps to ankle while preserving the other
alternatives.

🤖 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 `@src/medcheck/pipeline/preprocess.py`:
- Line 22: The regex mapping that maps ("wrist") currently includes "carpal"
which will match "metacarpal"; update the pattern in the tuple that contains
(r"wrist|handgelenk|carpal|tfcc|scaphoid", "wrist") to use word-boundary anchors
(e.g., \bcarpal\b or wrap each wrist token with \b...\b) or otherwise make
"carpal" more specific so it won't match "metacarpal"; locate and modify this
pattern in preprocess.py where the wrist mapping tuple is defined (the tuple
with the regex and "wrist") and adjust the regex accordingly.
- Line 21: The current ankle mapping regex tuple
(r"ankle|sprunggelenk|achilles|foot|fuß|fuss|calcaneus|hindfoot", "ankle") is
too permissive for the token "foot" and can false-match terms like "forefoot" or
"midfoot"; update that regex in src/medcheck/pipeline/preprocess.py (the ankle
mapping tuple) to restrict "foot" to a whole-word match (e.g., replace the plain
foot/füß/fuss token with a word-boundary form such as \bfoot\b and similarly
\bfuß\b/\bfuss\b in the raw string) so only standalone “foot” maps to ankle
while preserving the other alternatives.

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ℹ️ Review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro Plus

Run ID: 357f4b29-8ce5-425c-9e0a-0ee58e9fbc2d

📥 Commits

Reviewing files that changed from the base of the PR and between fd38b79 and 64e0870.

📒 Files selected for processing (7)

• CHANGELOG.md
• src/medcheck/pipeline/preprocess.py
• src/medcheck/prompts/anatomy/ankle.txt
• src/medcheck/prompts/anatomy/hip.txt
• src/medcheck/prompts/anatomy/wrist.txt
• tests/unit/test_pipeline/test_preprocess.py
• tests/unit/test_pipeline/test_vision_analysis.py