nomad-coe / nomad-simulations / 19170712288

82%

Build Type

push

github

Committed by web-flow

Commit Message

Migrate md (#261)

* initial migration, restructuring, etc.

* updating Rg, modularizing MDOutputs.normalize

* further work on MDOutputs.normalize

* save for testing

* fix compile errors and restructure get_mol_rgs

* rename model to method, results to outputs, time to simulationoutputs throughout

* clean MD imports

* more renaming

* reverted outputs renaming to results

* fix remaining tests

* reinsert final_outputs in tests and comment for now

* working old h5md tests

* some renaming and refinement

* fix mypy error

* more mypy errors

* ruff

* ruff format

* add MDAnalysis as dependency

* start review fixes

* fix imports and tests

* add basic md tests

* fix mypy errors

* ruff

* fix ruff version

* try better typing for bond_list

* ruff

* pytest_asyncio dep

* fix 3.11 mypy

* proxy type instead of cond import

* finish review edits

* updated beyond_hf workflows naming

* missed updates

* mypy fix

* further fix num settings

* improve optional dep treatment in utils

* done with review of util MD

* done with workflow/md.py

* comment out archive_to_universe till updated

* ruff

* reimplement dummy archive to universe

* diff fix

* replace missing comment

* pull max mol warn out of loop

* small code formatting

* test cond dep

* generalize get_diffusion_constant

* add typed dicts to results

* update cond import approach for MD schema

* mypy adjustments

* ruff format

Run Details

595 of 1314 new or added lines in 44 files covered. (45.28%)

1 existing line in 1 file now uncovered.

6598 of 7983 relevant lines covered (82.65%)

2.48 hits per line