Code

OpenFF overhaul#32

Code

Merged

timbernat merged 36 commits intodevtimbernat/polymerist:devfrom openff-cleanuptimbernat/polymerist:openff-cleanupCopy head branch name to clipboardDec 3, 2024

+678-207

Commits

Commits on Nov 20, 2024

• Added importutils submodule for dynamically checking module dependencies

  timbernat

  committed
  2a19f18

  Copy full SHA for 2a19f18

Commits on Nov 21, 2024

• Moved importutils tests into dedicated tests.gentutils.importutils subdirectory

  timbernat

  committed
  129a7b1

  Copy full SHA for 129a7b1

• Reimplemented find_module() with importlib.util.find_spec() to avoid actual import during check

  timbernat

  committed
  d077bd4

  Copy full SHA for d077bd4

• Wrte unit tests for importutils.dependencies

  timbernat

  committed
  ff82901

  Copy full SHA for ff82901

• Standardized docstrings

  timbernat

  committed
  c7ac3f7

  Copy full SHA for c7ac3f7

• Added unit tests module for mdutils.openfftools.partialcharge.molchargers

  timbernat

  committed
  e14afd7

  Copy full SHA for e14afd7

• Filled out unit tests for molchargers

  timbernat

  committed
  1a1b702

  Copy full SHA for 1a1b702

• Ignored GNN charge model ".model.pt" junk files

  timbernat

  committed
  84964f1

  Copy full SHA for 84964f1

• Added extra arg to specify custom Exception type raised for missing dependencies

  timbernat

  committed
  121e61c

  Copy full SHA for 121e61c

• Updated MolCharger "CHARGING_METHOD" class attribute to be handled by decorators.classmod.register_abstract_class_attrs()

  timbernat

  committed
  e13ffe2

  Copy full SHA for e13ffe2

• Made MolCharger subclasses aware of package dependences, directly make use of respective ToolkitWrappers

  timbernat

  committed
  eba751b

  Copy full SHA for eba751b

• Updated and pinned NAGL tooling and model versions in env

  timbernat

  committed
  1cc2743

  Copy full SHA for 1cc2743

• Strengthened openff.nagl package dependencies

  timbernat

  committed
  b27c4ab

  Copy full SHA for b27c4ab

• Mae unit tests aware of installed packages (avoid erroneous errors caused by dependencies, rather than code)

  timbernat

  committed
  458a841

  Copy full SHA for 458a841

• Added OpenFF Toolkit-specific exceptions to package requirement decorations

  timbernat

  committed
  e102159

  Copy full SHA for e102159

• Re-added OpenFF Toolkit-specific exceptions to package requirement decorations

  timbernat

  committed
  e51f1d3

  Copy full SHA for e51f1d3

• Added provisional module for smart OpenFF ToolkitWrapper registration

  timbernat

  committed
  0ec3e00

  Copy full SHA for 0ec3e00

Commits on Nov 22, 2024

• Reworked type hints to deprecate external dependency on typetools

  timbernat

  committed
  844fa03

  Copy full SHA for 844fa03

• Removed dependency on typetools

  timbernat

  committed
  9dda6bf

  Copy full SHA for 9dda6bf

Commits on Dec 2, 2024

• Fixed ambertools package check, TOOLKITS_BY_CHARGE_METHOD population loop

  timbernat

  committed
  4943e10

  Copy full SHA for 4943e10

• Added dynamic ToolkitRegistry and name-based toolkit wrapper registration

  timbernat

  committed
  4062ab4

  Copy full SHA for 4062ab4

• Added submodule for SMIRNOFF force field registrations

  timbernat

  committed
  589c495

  Copy full SHA for 589c495

• Relativized imports, broke up logic blocks among respective OpenFf dependencies

  timbernat

  committed
  fbd98c1

  Copy full SHA for fbd98c1

• Inserted author and email tags

  timbernat

  committed
  aa2cd54

  Copy full SHA for aa2cd54

• Deprecated chargemethods submodule in favor of direct registry import from _toolkits

  timbernat

  committed
  c1393ac

  Copy full SHA for c1393ac

• Cleaned up openfftools subpackage-level __init__ with openff dependency precheck and relative registry improts

  timbernat

  committed
  61e3980

  Copy full SHA for 61e3980

• Fixed back-to-front imports for offxml getter functions

  timbernat

  committed
  b4afb52

  Copy full SHA for b4afb52

Commits on Dec 3, 2024

• Shunted openff.units dependency into mdtools.openfftools subpackage

  timbernat

  committed
  a2d3881

  Copy full SHA for a2d3881

• Created openfftools subpackage for OpenMM interoperability, absorbed relevant functionality in backwards-compatible manner

  timbernat

  committed
  8bc7326

  Copy full SHA for 8bc7326

• Added unit test placeholder for omminter

  timbernat

  committed
  43836a3

  Copy full SHA for 43836a3

• Simplified and clarified typehints

  timbernat

  committed
  1f8fb8d

  Copy full SHA for 1f8fb8d

• Extended is_volume() to support Pint-style objects, clarified unit-like typehints

  timbernat

  committed
  c06c384

  Copy full SHA for c06c384

• Wrote unit tests for unitutils.dimensions

  timbernat

  committed
  8f0fbde

  Copy full SHA for 8f0fbde

• Added requirement for "pint" (the units package)

  timbernat

  committed
  ae9e8b4

  Copy full SHA for ae9e8b4

• Fixed indents on YAML header comments

  timbernat

  committed
  9f4b82c

  Copy full SHA for 9f4b82c

• Inverted import order to cause OpenFF installation error to raise prior to direct openff.toolkit imports

  timbernat

  committed
  00f5f97

  Copy full SHA for 00f5f97