GitLab

* updateParametersInContext() can change tabulated functions

* Fixed error in building C wrappers

* updateParametersInContext() can change tabulated functions for CustomCentroidBondForce

* CustomNonbondedForce can update tabulated functions

* CustomGBForce can update tabulated functions

* CustomManyParticleForce can update tabulated functions

* CustomHbondForce can update tabulated functions

* Added lots of checks for invalid parameter values

* Fixed test failures

* More checks for incorrect parameters

* Fixed test failures

* Created MonteCarloFlexibleBarostat

* Improved test cases

* Documentation for MonteCarloFlexibleBarostat

* Added a missing include

* Serialization for MonteCarloFlexibleBarostat

* Added MonteCarloFlexibleBarostat to C++ API docs index

* Added citation for MonteCarloFlexibleBarostat

* Allow querying current step count

* Fixed error building Python wrapper

* Proof of concept matching current behaviour with Breathe

* Reorganise C++ API docs to work without autosummary

* Revert to Sphinx-native search

* Move remaining pip deps to conda

* Remove unnecessary lunrsearch templates

* Remove lunrsearch from cmake

* Tidy up layout of API docs

* Get code blocks to work with Breathe

Breathe doesn't seem to support the Doxygen <preformatted> tag.
It does support the <code> tag, but better yet it supports using
<verbatim> tags to embed rst into docstrings. This commit changes
all <pre> tags to use RST verbatim, and updates the Python
documentation machinery to support it too.

* Clarified some language

* Have doxygen exclude undocumented classes and have sphinx fail on warnings for C++ API docs

* List custom forces and integrators last

* Add breathe to documentation CI

* Typo

* Fix link to custom forces in extras.rst

* Have Breathe process only public classes

* Strip OpenMM:: prefix from rst files to avoid colons in links

* Remove existing private classes from EXCLUDE_SYMBOLS

* Add comment to C++ cmake describing why we promote warnings to errors

* Revise documentation build instructions for new dependencies

* Deleted the default copy-constuctor for ContextImpl.

* Deleted the default copy assignment operator for ContextImpl.

* Began implementing geometric functions on points

* Started common implementation of point functions

* Completed implementation of point functions for CustomCompoundBondForce

* Implemented point functions for CustomCentroidBondForce

* Implemented point functions for CustomManyParticleForce

* Use point functions to simplify implementation of custom forces

* Removed unnecessary code

* Fixed typo

* Initial fixes for Apple silicon

Doesn't work yet

* assume vec4 is supported on apple

* Trust the user with env variables

* Fix macos-version-min logic

* Improved documentation for LangevinMiddleIntegrator

* Fixed a unicode character that caused problems on Windows

This is not added in SSE, because comparing two fvec4s results in an
fvec4, not an ivec4

This helps pave the way to test wider SIMD ISAs, such as AVX-512.

* Cleaned up checkpointing code for NoseHooverIntegrator

* Fixed compilation error

* Fixed OpenCL compiler errors

* Fixed incorrect references to BAOAB

* Fixed a method that was incorrectly made public

* Convert Nose-Hoover into LF middle scheme by copying NH kernels

* Rebrand VelocityVerletIntegrator as NoseHooverIntegrator

* Consolidate NH tests

* NoseHooverChainKernel begone

* Make Windows builds happy

* Add missing header for Windows build

* Fix mistake in CommonKernels header

* Add 6th Yoshida-Suzuki and make it the default