🚀 Release 0.10.0. Release notes update. (#1038)

Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
Co-authored-by: Ivy Zhang <35546250+zhang-ivy@users.noreply.github.com>
Co-authored-by: John Chodera <john.chodera@choderalab.org>

docs/changelog.rst

@@ -11,9 +11,39 @@ The full release history can be viewed `at the GitHub perses releases page <http
 0.10.0 - Release
 ----------------
 
+New command line interface (CLI), many enhancements for the API (especially the ``PointMutationExecutor``) and improved testing.
+
+Bugfixes
+^^^^^^^^
+- Bug in geometry engine's ``_determine_extra_torsions``: when ``topology_index_map``, which contains the atom indices involved in a particular torsion, is None -- fixed by not trying to add that torsion when ``topology_index_map`` is ``None``. (`#855 <https://github.com/choderalab/perses/pull/855>`_)
+- Bug generated by changes upstream in the ``openmm`` package -- default method for calculating solvent padding changed, which resulted in smaller boxes. Fixed by adding more padding to the simulation box, it is now 1.1 nm. Openmm issue `#3502 <https://github.com/openmm/openmm/issues/3502>`_. Perses issue `#949 <https://github.com/choderalab/perses/issues/949>`_ (`#953 <https://github.com/choderalab/perses/pull/953>`_)
+- Fixed energy bookkeeping in test of ``HybridTopologyFactory`` when a ring amino acid is involved in transformation. (`#969 <https://github.com/choderalab/perses/pull/969>`_)
+- Avoid changing the global context cache behavior on module imports. Issue `#968 <https://github.com/choderalab/perses/issues/968>`_ (`#977 <https://github.com/choderalab/perses/pull/977>`_).
+- Benchmark free energy plots now shift data to experimental mean. (`#981 <https://github.com/choderalab/perses/pull/981>`_)
+- Skip introduction of counterion for charge changing mutations in vacuum and fix typo in the phase name in ``test_resume_protein_mutation_no_checkpoint`` (`#991 <https://github.com/choderalab/perses/pull/991>`_).
+- Recovered logging capabilities respecting the ``LOGLEVEL`` environment variable. Issue `#1018 <https://github.com/choderalab/perses/issues/1018>`_ (`#1032 <https://github.com/choderalab/perses/pull/1032>`_).
+
+
 Enhancements
-------------
-- Introduce ``unsampled_endstates`` boolean option in input YAML file, for enabling/disabling creation of unsampled endstates long-range sterics correction. Issue `#1033 <https://github.com/choderalab/perses/issues/1033>`_ (`#1037 <https://github.com/choderalab/perses/pull/1037>`_).
+^^^^^^^^^^^^
+- Improved continuous integration (CI) performance. (`#961 <https://github.com/choderalab/perses/pull/961>`_)
+- ``PointMutationExecutor`` now accepts both solute and solvated PDBs (previously only accepted solute PDBs). (`#967 <https://github.com/choderalab/perses/pull/967>`_)
+- Tests and examples are now using ``openff-2.0.0`` force field instead of ``openff-1.0.0``. (`#971 <https://github.com/choderalab/perses/pull/971>`_)
+- Use names (instead of indices) for fetching the force components of a system, avoiding issues with force reordering upstream in ``openmm``. Issue `#993 <https://github.com/choderalab/perses/issues/993>`_ (`#976 <https://github.com/choderalab/perses/pull/976>`_ and `#1007 <https://github.com/choderalab/perses/pull/1007>`_)
+- Increase stability of simulations by decreasing the default hydrogen mass to 3 amu in the ``PointMutationExecutor``. Issue `#982 <https://github.com/choderalab/perses/issues/982>`_ (`#983 <https://github.com/choderalab/perses/pull/983>`_).
+- Improved CI tests on both CPU and GPU. Better handling of temporary directories, closing opened reporter files when tests are finished, and using same environments for CPU and GPU (`#985 <https://github.com/choderalab/perses/pull/985>`_ `#989 <https://github.com/choderalab/perses/pull/989>`_ `#1012 <https://github.com/choderalab/perses/pull/1012>`_)
+- Performance increase when retrieving the old or new positions from the hybrid positions. Issue `#1005 <https://github.com/choderalab/perses/issues/1005>`_ (`#1020 <https://github.com/choderalab/perses/pull/1020>`_)
+- Use of unique names for force components in ``HybridTopologyFactory`` (`#1022 <https://github.com/choderalab/perses/pull/1022>`_).
+- New function ``create_endstates_from_real_systems()`` for creating unsampled endstates for currently supported hybrid topology factories (`#1023 <https://github.com/choderalab/perses/pull/1023>`_).
+- Improve the readability and usability of ``PointMutationExecutor`` and updates how parameters are specified for solvation (`#1024 <https://github.com/choderalab/perses/pull/1024>`_).
+
+New features
+^^^^^^^^^^^^
+- Introduce ``RESTCapableHybridTopologyFactory``. Hybrid factory that allows for REST scaling, alchemical scaling, and 4th dimension softcore. So far, only working for protein mutations (`#848 <https://github.com/choderalab/perses/pull/848>`_ `#992 <https://github.com/choderalab/perses/pull/992>`_).
+- New perses command line interface (CLI) ``perses-cli`` using ``click``. Allowing a more friendly interface for users. It tests the running environment, sets the platform for the simulation and allows interactive overriding arbitrary options in the input YAML file. Former ``perses-relative`` CLI entry point is now deprecated (`#972 <https://github.com/choderalab/perses/pull/972>`_ `#1021 <https://github.com/choderalab/perses/pull/1021>`_ `#1027 <https://github.com/choderalab/perses/pull/1027>`_).
+- Support for handling charge changes (by transforming a water into a counterion) for both protein mutations and ligands transformations. `#862 <https://github.com/choderalab/perses/issues/862>`_ (`#973 <https://github.com/choderalab/perses/pull/973>`_).
+- Hybrid topology factory class name can now be specified using the ``hybrid_topology_factory`` parameter in the input YAML file (`#988 <https://github.com/choderalab/perses/pull/988>`_).
+- Introduce ``unsampled_endstates`` boolean option in input YAML file, which enables/disables creation of unsampled endstates with long-range sterics correction. Issue `#1033 <https://github.com/choderalab/perses/issues/1033>`_ (`#1037 <https://github.com/choderalab/perses/pull/1037>`_).
 
 0.9.5 - Release
 ---------------