GitLab

* addHydrogens() allows specifying exactly what hydrogens to add

* Prevent CI from using numpy 2.0

* 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.

* add swm4-ndp water to addSolvent

* add equilibrated box

* typo of water radius

* fixed addSolvent description

* add swm4 to tests

* Added GLYCAM

* Improved tests and documentation

* Fixed incorrect external bonds

* Top level Python module is now "openmm"

* Updated module names in examples

* Updated module names in documentation

* Updated module in CI scripts

* Added deprecation warning