FAIRmat-NFDI / nomad-parser-plugins-simulation / 21077212708
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LAST BUILD BRANCH: rename-annotation.keys
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Files 77
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coverage: 62.608% (-0.7%) from 63.286%
21077212708

Pull #129

github

ndaelman-hu 
Fix parser test isolation issues by removing annotation contamination

This commit addresses two related test isolation problems:

1. VASP tests failing after exciting/fhiaims/h5md run
   - Removed remove_mapping_annotations() calls from exciting, fhiaims, h5md
   - These were removing annotations from shared parent classes, breaking VASP

2. Quantum Espresso tests failing in full suite due to annotation accumulation
   - Multiple parsers (abinit, ams, crystal, octopus, QE) use key 'out'
   - Annotations accumulated across parsers (~111 annotations before QE)
   - Added remove_annotation_key() utility to selectively clear specific keys
   - QE now clears 'out' key before parsing to get clean slate

Changes:
- parsers/exciting/parser.py: Remove remove_mapping_annotations() call
- parsers/fhiaims/parser.py: Remove remove_mapping_annotations() call
- parsers/h5md/parser.py: Remove remove_mapping_annotations() call
- parsers/quantumespresso/parser.py: Add remove_annotation_key('out') before parsing
- schema_packages/utils.py: Add remove_annotation_key() helper function

Documentation:
- VASP_TEST_ISOLATION_FIX.md: Comprehensive investigation and fix documentation
- PARSER_ANNOTATIONS.md: Analysis of annotation key collisions across parsers

Test results: All 42 parser tests now pass (previously 40 passed, 2 failed)
Pull Request #129: Add pseudopot parsing

128 of 195 new or added lines in 9 files covered. (65.64%)

79 existing lines in 5 files now uncovered.

4365 of 6972 relevant lines covered (62.61%)

0.63 hits per line

New Missed Lines in Diff

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 -3.01% src/nomad_simulation_parsers/parsers/__init__.py
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 -9.76% src/nomad_simulation_parsers/parsers/vasp/outcar_parser.py
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61.54
 -23.65% src/nomad_simulation_parsers/parsers/vasp/xml_parser.py

Uncovered Existing Lines

Lines Coverage ∆ File
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 -0.78% src/nomad_simulation_parsers/parsers/quantumespresso/parser.py
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74.39
 -9.76% src/nomad_simulation_parsers/parsers/vasp/outcar_parser.py
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46.81
 -31.91% src/nomad_simulation_parsers/parsers/quantumespresso/pwscf/parser.py
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 -52.23% src/nomad_simulation_parsers/schema_packages/utils.py
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 0.36% src/nomad_simulation_parsers/parsers/utils/mdparserutils.py
Jobs
ID Job ID Ran Files Coverage
1 21077212708.1 77
62.61
 GitHub Action Run
Source Files on build 21077212708