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FAIRmat-NFDI / nomad-simulations
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DEFAULT BRANCH: develop
Repo Added 02 Jan 2026 09:31AM UTC
Token NlHfzWOWVbn6VpwLJzAj4wHjNVcmQ4tGZ regen
Build 290 Last
Files 129
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  • 240-disambiguate-crystal-symmetry-symbols-port
  • add-bsdft
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23 Apr 2026 03:18PM UTC coverage: 85.155% (+0.5%) from 84.641%
24843349547

push

github

web-flow
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

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

Relevant lines Covered
Build:
Build:
10758 RELEVANT LINES 9161 COVERED LINES
2.55 HITS PER LINE
Source Files on develop
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  • List 129
  • Changed 13
  • Source Changed 0
  • Coverage Changed 13
Coverage ∆ File Lines Relevant Covered Missed Hits/Line

Recent builds

Builds Branch Commit Type Ran Committer Via Coverage
24843349547 develop 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... push 23 Apr 2026 03:19PM UTC web-flow github
85.16
24834622967 norm-migration Fix ruff lint issues in test_pr_validation.py - Add sys import - Replace exit() with sys.exit() - Auto-format with ruff Pull #373 23 Apr 2026 12:16PM UTC ndaelman-hu github
85.13
24767155520 orb-volume add a draft imülementation of the orbital volume visualization Pull #378 22 Apr 2026 08:00AM UTC EBB2675 github
84.1
24734289512 norm-migration Refactor GeometryOptimization.map_tasks into smaller helper methods Split the large 76-line map_tasks method into focused helper methods: - _map_tasks_from_outputs(): Handles task creation from outputs - _map_tasks_from_model_system(): Handles f... Pull #373 21 Apr 2026 04:34PM UTC ndaelman-hu github
85.13
24722944380 norm-migration Fix test_resolve_normalization_factor by using fixture properly The test now uses the fixture's properly normalized structure directly instead of trying to manually construct a new hierarchy. This preserves the metainfo parent relationships neede... Pull #373 21 Apr 2026 12:43PM UTC ndaelman-hu github
84.88
24663972854 norm-migration Apply ruff formatting Pull #373 20 Apr 2026 11:29AM UTC ndaelman-hu github
84.84
24662498139 norm-migration Address remaining reviewer feedback - Simplify parent section name check in spectral_profile.py (remove intermediate variable) - Move early return optimization before magnitude extractions (performance) - Add reference to issue #377 for get_sibli... Pull #373 20 Apr 2026 10:52AM UTC ndaelman-hu github
84.84
24561843463 norm-migration Revert .tolist() removal - required for mypy type compatibility The moltypes variable is typed as list[str] | None, so removing .tolist() causes a mypy error on Python 3.11+ since np.unique returns ndarray. mypy error: src/nomad_simulations/sche... Pull #373 17 Apr 2026 11:04AM UTC ndaelman-hu github
84.84
24560526806 norm-migration Fix test failures: correct imports and task name pattern - Fix RadialDistributionFunction import path (workflow.molecular_dynamics) - Fix task name pattern assertion (Step instead of Geometry Optimization) Pull #373 17 Apr 2026 10:30AM UTC ndaelman-hu github
84.84
24284002975 norm-migration Merge branch 'norm-migration-patch' into norm-migration Pull #373 11 Apr 2026 02:00PM UTC JFRudzinski github
84.76
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