nomad-coe / nomad-simulations / 17122209592

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180 check creation of composition formula (#239)

* a mess of preliminary changes, including new implementation of ModelSystem.symbols, get_bond_list, get_root, etc

* working tests

* clean comments

* type annotation for idx

* ruff

* idx type condition fix

* redo of resolve_comp_formula & symbols from review, still messy but tests work

* cleaned composition formula, added new functionality for missing branch labels,  and fixed typing issue in tests, updated test results

* refactor get_symbols

* is_root_system simplified

* get_root_system simplified

* bond_list is getter only

* robust sorting in get_composition

* fix util imports

* fixed utils mypy error

* ruff

* commented out get_symbols logger for now

* moved ArchiveSection out of type checking, utils

* ruff

* clean out old bond_list function

* remove get_formula from particles

* get composition formula for root

* new is_atomic criterion, new reassignment policy for ParticleStates

* one more logical tweak for particle_states reassignment and is_atomic

* clean are_valid_chemical_symbols() out

* fixed bug in test

105 of 108 new or added lines in 4 files covered. (97.22%)

2459 of 3701 relevant lines covered (66.44%)

0.66 hits per line