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nomad-coe / nomad-simulations / 19530124068
82%

Build:
DEFAULT BRANCH: develop
Ran 20 Nov 2025 08:16AM UTC
Jobs 3
Files 102
Run time 1min
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20 Nov 2025 08:15AM UTC coverage: 82.101% (-0.3%) from 82.412%
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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

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

New Missed Lines in Diff

Lines Coverage ∆ File
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75.09
-0.09% src/nomad_simulations/schema_packages/numerical_settings.py
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1.03% tests/conftest.py
11
97.92
-1.48% tests/test_model_system.py
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78.69
-6.14% src/nomad_simulations/schema_packages/model_system.py

Uncovered Existing Lines

Lines Coverage ∆ File
1
77.35
1.03% tests/conftest.py
2
75.09
-0.09% src/nomad_simulations/schema_packages/numerical_settings.py
27
78.69
-6.14% src/nomad_simulations/schema_packages/model_system.py
Jobs
ID Job ID Ran Files Coverage
1 19530124068.1 20 Nov 2025 08:16AM UTC 102
82.1
GitHub Action Run
2 19530124068.2 20 Nov 2025 08:16AM UTC 102
82.1
GitHub Action Run
3 19530124068.3 20 Nov 2025 08:17AM UTC 102
82.1
GitHub Action Run
Source Files on build 19530124068
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  • Changed 8
  • Source Changed 0
  • Coverage Changed 8
Coverage ∆ File Lines Relevant Covered Missed Hits/Line
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