GitLab

* added type checking for Simulation.step()

* changed how to check if step is an integer number

* allow for dicts to be returned from Reporter.describeNextReport
remove deprecated getState parameters ( #4437 )

* convert old format into new format

* update docstring

* nested set comprehension to set.union

* Allow 'periodic':None
update describeNextReport in all occurrences in the code

* debug

* update documentation

* add a reporter for energyParameterDerivative

* Revert "add a reporter for energyParameterDerivative"

This reverts commit 1d44dc3f60153defb6252ab56a3b85350fa24826.

* Edit documentation

* XTCReporter overwrite existing xtc file

* add position size check for xtcfile

* fix formal charge reading and writing in pdb files; store formal charge in topology

* use formalCharge in public api

* permissive reading

* fix writing

* fix

* add test for formal charges

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Co-authored-by: Alex Izvorski <alex@genesistherapeutics.ai>

* Support numpy 2

* Debugging

* Removed debugging code

* Don't require importlib_metadata

* Handle older versions of importlib

* Fix import of netcdf_file for scipy 1.14

* Fix indentation

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Co-authored-by: Timothy Palpant <tim@atommapper.com>

* addHydrogens() allows specifying exactly what hydrogens to add

* Prevent CI from using numpy 2.0

* Allow multiple registrations of the same atom type if definitions identical

* Different short-circuiting logic

Co-authored-by: FloLangenfeld <florent.langenfeld@peptinov.fr>

* added type checking for Simulation.step()

* changed how to check if step is an integer number

* Avoid overflow in large XTC files

* Also cast box indices to size_t

* Created DebuggingReporter class

* Fixed description

* Can use getPlatform() instead of getPlatformByName()

* More concise arguments for getState()

* Replaces sub tags for python API docs

* Changes string to pathlib

* Adds support for sup html tags

* Corrects function description

* Faster algorithm for DrudeSCFIntegrator

* Minor code simplification

* Reduced default error tolerance

* Fixed errors on NVIDIA

Added CustomCentroidBondForce.addTabulatedFunction to STEAL_OWNERSHIP table in Python wrapper configuration script (#4340)
Co-authored-by: Evan Pretti <evan@pretti.net>

* Optimizations to reporters

* Removed unneeded imports

* Py wrapper: preserve bond data in Modeller operations

* regression tests for add(), delete(), deleteWater(), addSolvent()

* Tests for addHydrogens and addExtraParticles

* Cosmetic

* A single regression test spanning a whole workflow

* Remove now-redundant tests

* Test also deleteWater and addHydrogens. Remove excessive assertions.

* Remove support for Gromacs implicit solvent

* Removed tests of implicit solvent

* Replace distutils with setuptools

* Replace more uses of distutils

* Implemented MinimizationReporter

* PythonAPI for MinimizationReporter

* Improved test case

* SWIG fix

* Reporter returns a bool instead of throwing an exception

* Support GROMOS bond and angle types

* Support NBFIX with geometric combining rule

* Continuing GROMOS support

* Bug fixes

* Fixes to test case

* Update wrappers/python/openmm/app/gromacstopfile.py
Co-authored-by: Jason Swails <jason@entos.ai>

* Improve logic for handling dihedraltypes

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Co-authored-by: Jason Swails <jason@entos.ai>