unify exception handling, improve sanity checks and code coverage #126
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…o calculate_HH and other functions, fix missing lines from lib/lattice and tutorials
jngrad
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May 16, 2025
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besides suggested changes, LGTM
jngrad
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May 16, 2025
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May 21, 2025
…MBE-dev#126) * add sanity checks, unify exceptions with loggins, add full coverage to calculate_HH and other functions, fix missing lines from lib/lattice and tutorials * remove verbose * fix pylint issues * speed up HH unit test * remove force capping from energy relaxation * address JN suggestions, fix relaxation issues with hydrogel functional test
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Fixes
lib/lattice.pythat were removed in Add a hydrogel builder #103, which were breaking the lattice tutorial.tutorials/pyMBE_tutorial.ipynb.calculate_HH.testsuite/henderson_hasselbalch_tests.py.Changed
logginsand hard errors byraisestatements. Fixes Improve exception handling #115pmb_type = "peptide"instead than sharing type with custom moleculespmb_type = "molecule". This simplifies handling cases in which both objects behave differently.Removed
lib/handy_functions.relax_espresso_systemno longer supports force capping because it causes instabilities when relaxing bonded systems.verboseoptional argument have been removed from most methods except from those that need to silence verbose from espresso.Adds