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OpenFF overhaul #32

Merged
merged 36 commits into from
Dec 3, 2024
Merged

OpenFF overhaul #32

merged 36 commits into from
Dec 3, 2024

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timbernat
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@timbernat timbernat commented Dec 3, 2024 •
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Description

Consolidating and improving robustness of mdtools.openfftools

Todos

Notable points that this PR has either accomplished or will accomplish.

Status

  • Tests passed
  • CI actions complete

@timbernat
Added importutils submodule for dynamically checking module dependencies
2a19f18
@timbernat
Moved importutils tests into dedicated tests.gentutils.importutils su…
129a7b1 
…bdirectory
@timbernat
Reimplemented find_module() with importlib.util.find_spec() to avoid …
d077bd4 
…actual import during check
@timbernat
Wrte unit tests for importutils.dependencies
ff82901
@timbernat
Standardized docstrings
c7ac3f7
@timbernat
Added unit tests module for mdutils.openfftools.partialcharge.molchar…
e14afd7 
…gers
@timbernat
Filled out unit tests for molchargers
1a1b702
@timbernat
Ignored GNN charge model ".model.pt" junk files
84964f1
@timbernat
Added extra arg to specify custom Exception type raised for missing d…
121e61c 
…ependencies
@timbernat
Updated MolCharger "CHARGING_METHOD" class attribute to be handled by…
e13ffe2 
… decorators.classmod.register_abstract_class_attrs()
@timbernat
Made MolCharger subclasses aware of package dependences, directly mak…
eba751b 
…e use of respective ToolkitWrappers
@timbernat
Updated and pinned NAGL tooling and model versions in env
1cc2743
@timbernat
Strengthened openff.nagl package dependencies
b27c4ab
@timbernat
Mae unit tests aware of installed packages (avoid erroneous errors ca…
458a841 
…used by dependencies, rather than code)
@timbernat
Added OpenFF Toolkit-specific exceptions to package requirement decor…
e102159 
…ations
@timbernat
Re-added OpenFF Toolkit-specific exceptions to package requirement de…
e51f1d3 
…corations
@timbernat
Added provisional module for smart OpenFF ToolkitWrapper registration
0ec3e00
@timbernat
Reworked type hints to deprecate external dependency on typetools
844fa03
@timbernat
Removed dependency on typetools
9dda6bf
@timbernat
Fixed ambertools package check, TOOLKITS_BY_CHARGE_METHOD population …
4943e10 
…loop
@timbernat
Added dynamic ToolkitRegistry and name-based toolkit wrapper registra…
4062ab4 
…tion
@timbernat
Added submodule for SMIRNOFF force field registrations
589c495
@timbernat
Relativized imports, broke up logic blocks among respective OpenFf de…
fbd98c1 
…pendencies
@timbernat
Inserted author and email tags
aa2cd54
@timbernat
Deprecated chargemethods submodule in favor of direct registry import…
c1393ac 
… from _toolkits
@timbernat
Cleaned up openfftools subpackage-level __init__ with openff dependen…
61e3980 
…cy precheck and relative registry improts
@timbernat
Fixed back-to-front imports for offxml getter functions
b4afb52
@timbernat
Shunted openff.units dependency into mdtools.openfftools subpackage
a2d3881
@timbernat
Created openfftools subpackage for OpenMM interoperability, absorbed …
8bc7326 
…relevant functionality in backwards-compatible manner
@timbernat
Added unit test placeholder for omminter
43836a3
@timbernat timbernat self-assigned this Dec 3, 2024
@timbernat timbernat merged commit 2a979ed into dev Dec 3, 2024
2 checks passed
This was referenced Dec 3, 2024
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Closed
@timbernat timbernat deleted the openff-cleanup branch December 3, 2024 04:17
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