choderalab/yank: YANK 0.14.1: Early Access 1.0 Release

This release marks the early access phase for YANK 1.0. We intend for this to be a formal release for users to test YANK and its functionality while we refactor the underlying Python API.

In this release:

• YAML Syntax Structure Frozen. YANK YAML Version 1.0. All YAML scripts from this version will be compatible with future versions until YAML 2.0 New features may appear in the time meantime, but scripts will be forwards compatible.
• Initial support for OpenMM XML systems and PDB files
• Support for separate solvent configurations for the two phases when defined from amber/gromacs/openmm files
• clearance in YAML no mandatory parameter of explicit solvent, but only when molecule setup goes through pipeline
• Boresch Orientational Restraints fully implemented and documented.
• Long range anisotropic dispersion correction improved to work on both ends of thermodynamic cycle leg
• Documentation updated with better algorithms and theory sections.
• Full walkthroughs of yank-examples added to online documentation
• Various other documentation improvements
• Support for upcoming OpenMM 7.1 Release and features (still works with 7.0.1)
• YANK now on MIT License
• Many bugfixes