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Examples v1 - #197
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Examples v1#197
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- Add CHANGELOG.md with v1.0 entry - Add docs/migration.md with breaking-change guide and SPARQL UPDATE - Replace stale root index.ipynb with index.md landing page - Expand README with installation, quickstart, citation (arXiv 2604.06230) - Wire migration + changelog into _toc.yml; un-orphan example 03 - Add module docstring + commit missing atomrdf/_version.py - Fix license.md (pyscal-rdf -> atomRDF)
- 04_point_defects: vacancy / interstitial / substitutional with PODO - 05_sparql_queries: raw SPARQL + term-builder + sample export - 06_persistence_and_visualisation: in-memory vs SQL vs Oxigraph stores - All three are smoke-tested end-to-end and registered in _toc.yml
…MPS outputs - Add KnowledgeGraph.reconstruct_workflow() and .reconstruct_workflow_by_sample() wrapper methods (they delegate to atomrdf.io.reconstruct functions) - Add _write_software_requirements(), _write_incar(), _write_lammps_input() helpers - reconstruct_workflow now detects DFT workflows: writes INCAR + POSCAR instead of trying to generate an executable Python script (which was unsupported) - reconstruct_workflow now detects LAMMPS: writes in.lammps with read_data + minimize blocks in addition to run_workflow.py - software_requirements.txt always written regardless of method - Structure format auto-detected from software list (VASP→POSCAR, LAMMPS→.lmp) - All 4 test_reconstruct tests now pass; full suite 84 passed, 2 skipped
- test_rotate.py: module-level pytest.importorskip('atomman') skips the
whole file when atomman is absent
- test_structure.py: _atomman_available flag + @pytest.mark.skipif on
test_stacking_fault
Codecov Report❌ Patch coverage is Additional details and impacted files@@ Coverage Diff @@
## main #197 +/- ##
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+ Coverage 52.32% 53.29% +0.96%
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Files 47 49 +2
Lines 5353 6048 +695
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+ Hits 2801 3223 +422
- Misses 2552 2825 +273 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
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Removed Python 3.9 from the testing matrix.
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