Upgraded to MEDS v0.4

[mmcdermott]

Closes #180. Will require a major release to incorporate.

Summary by CodeRabbit

• Refactor
  • Updated internal references to schema field names to use centralized schema classes, improving consistency across the application.
• Chores
  • Broadened the acceptable version range for a key dependency, enhancing compatibility with future releases.
• Tests
  • Adjusted test code to utilize schema classes for field names, reducing reliance on hardcoded strings.

[coderabbitai]

Walkthrough

The changes update the codebase to use the new LabelSchema class from the meds package for all label schema references, replacing scattered constants and string literals. The dependency on meds is updated to allow versions compatible with 0.4.0. Test code is refactored to use centralized schema classes.

Changes

File(s)	Change Summary
pyproject.toml	Updated meds dependency from ==0.3.3 to ~=0.4.0.
src/aces/run.py	Replaced direct constant imports with LabelSchema class; updated all label schema references; used LabelSchema.align() for schema alignment.
tests/test_meds.py	Replaced string constants and field names with DataSchema and LabelSchema class attributes; refactored test data and schema alignment logic.

Sequence Diagram(s)

sequenceDiagram
    participant ACES_Run
    participant MEDS_LabelSchema

    ACES_Run->>MEDS_LabelSchema: Import LabelSchema
    ACES_Run->>MEDS_LabelSchema: Use LabelSchema attributes for schema validation
    ACES_Run->>MEDS_LabelSchema: Call LabelSchema.align(df)
    MEDS_LabelSchema-->>ACES_Run: Return aligned DataFrame/Table

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Assessment against linked issues

Objective	Addressed	Explanation
Upgrade to MEDS v0.4 (#180)	✅

Possibly related PRs

• Match MEDS label schema as per #72 #80: Introduces initial schema validation; this PR builds on and centralizes schema handling.
• Update to support MEDS v0.3.2 #108: Updates for MEDS v0.3.2 and subject ID renaming; both PRs address MEDS compatibility and schema references.

Suggested labels

Impacts Benchmark

Suggested reviewers

• justin13601

Poem

In fields of code where schemas grow,
The LabelSchema now steals the show.
No more strings that roam or stray,
All fields aligned the MEDS way.
With tests and benchmarks hopping right,
This bunny’s code is clean and bright!
🐇✨

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📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL
Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 58dd44d and c802d98.

📒 Files selected for processing (3)

• pyproject.toml (1 hunks)
• src/aces/run.py (8 hunks)
• tests/test_meds.py (9 hunks)

🔇 Additional comments (16)

pyproject.toml (1)

29-29: Update confirmed for MEDS package dependency.

The dependency specification for meds has been appropriately updated to use the compatible release operator ~=, allowing any version from 0.4.0 up to (but not including) 0.5.0. This change aligns with the project's upgrade to MEDS version 0.4.

src/aces/run.py (9)

14-14: Updated import to use centralized schema classes.

Replacing individual constant imports with the LabelSchema class is a good approach for centralizing schema references.

---

23-24: Schema constants now use LabelSchema reference.

Using LabelSchema.subject_id_name provides a more maintainable and centralized approach for schema references.

---

27-32: Schema constants migrated to LabelSchema references.

All optional type references have been updated to use the appropriate LabelSchema attributes, making the code more maintainable.

---

71-72: Type correction in docstring example.

The type for float_value was correctly changed from double to float in the example docstring to match the actual output.

---

83-84: Updated schema validation to use LabelSchema.

References to prediction time field now use the centralized LabelSchema.prediction_time_name attribute.

---

95-95: Updated error message to reference Label DataFrame.

Error message now correctly refers to "MEDS Label DataFrame" instead of "MEDS Data DataFrame".

---

118-118: Simplified schema alignment using LabelSchema.align.

The previous manual conversion and casting has been replaced with a cleaner call to LabelSchema.align(), leveraging the functionality provided by the updated MEDS package.

---

148-153: Updated column mapping to use LabelSchema references.

The column name mappings in the rename operation now use the centralized LabelSchema attributes instead of hardcoded strings.

---

154-159: Updated subject_id check using LabelSchema reference.

The check for the existence of the subject_id column and the creation of an empty column now use the LabelSchema.subject_id_name attribute.

tests/test_meds.py (6)

10-10: Updated import to use centralized schema classes.

Importing both DataSchema and LabelSchema from meds for centralizing schema references in tests.

---

39-43: MEDS_PL_SCHEMA now uses DataSchema references.

Schema field definitions now use DataSchema attributes instead of hardcoded string constants.

---

47-56: Label schema types now use LabelSchema references.

Both mandatory and optional label schema type definitions now use LabelSchema attributes.

---

115-115: Simplified schema alignment using LabelSchema.align.

Similar to the change in run.py, the function now uses LabelSchema.align() to handle alignment.

---

133-133: Updated time column reference using DataSchema.

Time column access now uses DataSchema.time_name instead of a hardcoded string.

---

162-359: Updated test data to use standard schema column names.

All test YAML strings have been updated to use standard schema column names without variable interpolation, which is more maintainable.

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[Copilot]

Pull Request Overview

This PR upgrades the MEDS dependency to v0.4 and refactors the code to use the new DataSchema and LabelSchema naming conventions. Key changes include:

• Updating test imports and schema definitions in tests/test_meds.py to use DataSchema and LabelSchema.
• Refactoring schema references, error messages, and column renames in src/aces/run.py.
• Adjusting the MEDS dependency version in pyproject.toml.

Reviewed Changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 1 comment.

File	Description
tests/test_meds.py	Updated import statements and schema usage to align with MEDS v0.4.
src/aces/run.py	Refactored schema references and error messages for consistency.
pyproject.toml	Updated MEDS dependency version to ~0.4.0.

Comments suppressed due to low confidence (1)

src/aces/run.py:71

• Verify that changing the cast from 'double' to 'float' for the 'float_value' field aligns with the MEDS v0.4 specification and does not introduce precision issues.

float_value: float

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.

Files with missing lines	Coverage Δ
src/aces/run.py	100.00% <100.00%> (ø)

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