Refactor workflows with shared module architecture

[eurunuela]

Summary

This PR refactors the tedana workflow files to use a new shared module architecture (tedana/workflows/shared/). The goal is to improve code organization, reduce duplication, and make the codebase more maintainable.

Key Changes

• New workflows/shared/ submodule with focused, reusable components:

  • containers.py - Typed dataclasses (MultiEchoData, MaskData, DecayMaps, OptcomData)
  • setup.py - Workflow setup/teardown utilities (logging, output directory, command saving)
  • data_loading.py - Multi-echo data loading and TR validation
  • masking.py - Adaptive mask creation for denoising and classification
  • fitting.py - T2*/S0 decay model fitting
  • combination.py - Optimal echo combination
  • output.py - Result writing, tedort, MIR, metadata generation
  • reporting.py - Static figures and dynamic report generation

• Refactored all three workflows to use the shared modules:

  • tedana.py - Now uses shared functions and returns a results dictionary
  • t2smap.py - Simplified using shared data loading, masking, and fitting
  • ica_reclassify.py - Simplified using shared output and reporting functions

Benefits

• Separation of concerns: Each shared module handles a specific aspect of the workflow
• Type safety: Dataclasses provide clear interfaces between workflow stages
• Reduced duplication: Common operations are now shared across all workflows
• Easier testing: Individual modules can be tested in isolation
• Better maintainability: Changes to shared functionality only need to be made once

Changes Summary

File	Change
workflows/shared/*.py	New shared modules (8 files)
workflows/tedana.py	Refactored to use shared modules, added type hints, returns results dict
workflows/t2smap.py	Simplified using shared modules
workflows/ica_reclassify.py	Simplified using shared modules

Test plan

• Run existing test suite to ensure no regressions
• Verify t2smap workflow produces identical outputs
• Verify tedana workflow produces identical outputs
• Verify ica_reclassify workflow produces identical outputs
• Test with different parameter combinations

🤖 Generated with Claude Code

[eurunuela]

This is an alternative to #1280.

[codecov]

Codecov Report

❌ Patch coverage is 90.26316% with 37 lines in your changes missing coverage. Please review.
✅ Project coverage is 89.97%. Comparing base (e093290) to head (d35d9ad).

Files with missing lines	Patch %	Lines
tedana/workflows/shared/masking.py	75.60%	8 Missing and 2 partials ⚠️
tedana/workflows/shared/containers.py	89.18%	8 Missing ⚠️
tedana/workflows/tedana.py	89.39%	5 Missing and 2 partials ⚠️
tedana/workflows/shared/data_loading.py	80.95%	2 Missing and 2 partials ⚠️
tedana/workflows/shared/setup.py	89.74%	4 Missing ⚠️
tedana/workflows/ica_reclassify.py	86.66%	2 Missing ⚠️
tedana/workflows/shared/combination.py	89.47%	1 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1281      +/-   ##
==========================================
+ Coverage   89.73%   89.97%   +0.24%     
==========================================
  Files          29       37       +8     
  Lines        4403     4560     +157     
  Branches      730      735       +5     
==========================================
+ Hits         3951     4103     +152     
- Misses        299      302       +3     
- Partials      153      155       +2     

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