FAIRmat-NFDI / nomad-simulations

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Build # 24843349547

Build Type

push

github

Committed by web-flow

Commit Message

patches during normalization migration (#373)

  Critical fixes and improvements for migrating normalizers to nomad-simulations
  and enabling CLI-based parsing workflows.

  ## Normalization & Schema Fixes

  - Fix context-dependent output-system linking to support CLI parsing (nomad parse)
  - Patch spectral profile for full DOS pipeline (parsing + visualization)
  - Add fallback for setting workflow tasks when outputs are missing
  - Remove spectral_profile.py fallback route after normalization improvements
  - Re-add guard to protect against result duplication

  ## Topology & Representation Detection

  - Fix representation detection and outputs linking for complex H5MD topologies
  - Refactor _get_molecular_bead_groups for better maintainability
  - Add duck-typing patches for robust type handling

  ## Performance & Optimization

  - Cache sibling section lookups to avoid repeated XPath traversals (15.5x speedup)
  - Refactor GeometryOptimization.map_tasks into 5 focused helper methods
  - Downgrade noisy sibling section warnings to debug level

  ## Type Safety & Configuration

  - Convert dos_energy_tolerance to pint.Quantity for type-safe comparisons
  - Fix Pydantic compatibility with pint.Quantity type annotations
  - Revert .tolist() removal to maintain mypy type compatibility

  ## Testing & Validation

  - Add comprehensive validation suite (test_pr_validation.py)
  - Add 8 new unit tests for GeometryOptimization helper methods
  - Add tests for sibling section caching functionality
  - Split and improve existing test organization
  - Fix test fixtures and imports for compatibility
  - Remove resolved TODO(normalization-robustness) comments

Coverage Stats

285 of 306 new or added lines in 14 files covered. (93.14%)

9 existing lines in 4 files now uncovered.

9161 of 10758 relevant lines covered (85.16%)

2.55 hits per line