FAIRmat-NFDI / nomad-parser-plugins-simulation / 21718692669

71%

Build Type

push

github

Committed by web-flow

Commit Message

Rename annotation keys (#141)

* Rename annotation keys

* Fix h5md schema

* Update src/nomad_simulation_parsers/schema_packages/quantumespresso/common.py

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

* Update src/nomad_simulation_parsers/schema_packages/quantumespresso/common.py

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

* Close abinit parsers

---------

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

 1. Annotation Key Namespacing (30 files)
  - Generic keys like 'out', 'xml', 'dos' are now prefixed with parser names
  - Examples:
    - 'out' → 'quantumespresso_out' (Quantum ESPRESSO)
    - 'xml' → 'vasp_xml' (VASP)
    - 'gpw' → 'gpaw_gpw' (GPAW)
    - 'out' → 'abinit_out' (ABINIT)

  2. Schema Reload Removal
  - Removes all reload(schema_module) calls from parsers
  - Previously, parsers were reloading schema packages to refresh annotations at runtime
  - This suggests annotations are now properly registered at import time

  3. Annotation Cleanup Removal
  - Removes calls to remove_mapping_annotations()
  - No longer needs to clean up annotations after parsing

  4. Resource Management Improvements
  - Adds missing close() calls for parsers (GPAW, Octopus, FHI-aims)
  - Ensures proper cleanup of file contexts

  5. Quantum ESPRESSO Refactoring (src/nomad_simulation_parsers/schema_packages/quantumespresso/common.py)
  - Introduces shared OUT_KEY = 'quantumespresso_out' constant
  - Refactors from manual m_annotations manipulation to using add_mapping_annotation() helper

Run Details

82 of 84 new or added lines in 22 files covered. (97.62%)

27 existing lines in 4 files now uncovered.

5266 of 7899 relevant lines covered (66.67%)

0.67 hits per line