nomad-coe / nomad-simulations / 19530124068

82%

Build Type

push

github

Committed by web-flow

Commit Message

Replace `GeometricSpace` and `Cell` by `Representation` (#263)

  # Refactor Cell/AtomicCell into unified Representation architecture

  Replace nested Cell/AtomicCell subsections with direct geometric property access through Representation inheritance. `ModelSystem` now exposes geometric properties directly while supporting
  alternative representations for primitive/conventional cells.

  **Architecture Changes:**
  - Move `lattice_vectors`, `periodic_boundary_conditions`, `fractional_coordinates` directly to `ModelSystem`
  - Move `positions` from `Representation` to `ModelSystem` to enforce consistency across representations
  - Remove `GeometricSpace`, `Cell`, and `AtomicCell` classes
  - Restructure `Representation` as base class for geometric properties
  - Add `AlternativeRepresentation` subsection for different cell views

  **Implementation:**
  - Implement `compute_fractional_coordinates()` with tests
  - Improve `from_ase_atoms()` to leverage normalization and support velocities, charges, volumes
  - Extend volume detection to different dimensionalities
  - Improve `ChemicalSymbols` generation via particle labels

  **Testing & Compatibility:**
  - Add backwards compatibility layer for parsers
  - Modernize tests and remove backward compatibility
  - Fix test helpers: remove dead `type` parameter, add `representation_name`
  - Fix mypy type annotations throughout

  **Documentation:**
  - Add comprehensive `model_system.md` guide
  - Add `representation.md` technical documentation
  - Add `representation-squash-commit.md` design history and migration guide
  - Restructure `mkdocs.yml` navigation

Run Details

312 of 374 new or added lines in 12 files covered. (83.42%)

30 existing lines in 3 files now uncovered.

7073 of 8615 relevant lines covered (82.1%)

2.46 hits per line