0.8.0

This release incorporates numerous revisions and bugfixes:

• Alchemical functionality is now encapsulated in a separate module called alchemy
• Support for YAML-based specification of calculations has been added. This uses an AmberTools-based pipeline under the hood.
• Lots of bugfixes

Alchemical Hamiltonian replica exchange overhaul

This version features a complete overhaul of how alchemical Hamiltonian replica exchange is implemented.
Now, a single Context object is used for all alchemical states, and only the context parameters are updated for each state.
Startup should be much faster and the simulations should run more efficiently.

Last revision before alchemical repex overhaul

This is the last revision before alchemical repex overhaul to give major speedup.

0.6.2

Temporary pre-release for tutorial session and testing various upstream dependencies.

Adds mpi4py dependency to conda recipe

Merge pull request #183 from jchodera/update-conda-recipe

Updated conda recipe to install mpi4py

0.6

Merge pull request #172 from kyleabeauchamp/del

Deleted several more unused functions.

Partially stable development release (in use by some collaborators)

This version is being frozen as a release because it is in use by several collaborators, including the Geerke lab.