Merge pull request #308 from choderalab/cut0133

Cut 0.13.3 critical bug fix release for SamplerState

appveyor.yml

@@ -6,24 +6,24 @@ environment:
     CMD_IN_ENV: "cmd /E:ON /V:ON /C .\\devtools\\appveyor\\run_with_env.cmd"
 
   matrix:
-    #- PYTHON: "C:\\Python33_32"
-    #  PYTHON_VERSION: "3.3"
-    #  PYTHON_ARCH: "32"
-    #  CONDA_PY: "33"
-    #  CONDA_NPY: "19"
+    - PYTHON: "C:\\Python35_64"
+      PYTHON_VERSION: "3.5"
+      PYTHON_ARCH: "64"
+      CONDA_PY: "35"
+      CONDA_NPY: "112"
 
-    - PYTHON: "C:\\Python34_32"
-      PYTHON_VERSION: "3.4"
-      PYTHON_ARCH: "32"
-      CONDA_PY: "34"
-      CONDA_NPY: "19"
+    - PYTHON: "C:\\Python36_64"
+      PYTHON_VERSION: "3.6"
+      PYTHON_ARCH: "64"
+      CONDA_PY: "36"
+      CONDA_NPY: "112"
 
 install:
   # this installs the appropriate Miniconda (Py2/Py3, 32/64 bit),
   # as well as pip, conda-build, and the binstar CLI
   - ps: . ".\\devtools\\appveyor\\install.ps1"
   - "SET PATH=%PYTHON%;%PYTHON%\\Scripts;%PATH%"
-  - conda config --add channels http://conda.binstar.org/omnia
+  - conda config --add channels omnia
   - conda config --add channels conda-forge
 
 build: false

docs/releasehistory.rst

@@ -1,4 +1,229 @@
 Release History
 ===============
 
-These are new features and improvements of note in each release.
+0.13.3 - Critical Bugfix to SamplerState Context Manipulation
+=============================================================
+
+Critical Fixes
+--------------
+
+- ``SamplerState.apply_to_context()`` applies box vectors before positions are set to prevent a bug on non-Reference
+  OpenMM Platforms which can re-order system atoms. (`#305 <https://github.com/choderalab/openmmtools/issues/305>`_)
+
+Additional Fixes
+----------------
+
+- LibYAML is now optional (`#304 <https://github.com/choderalab/openmmtools/issues/304>`_)
+- Fix AppVeyor testing against Python 3.4 (now Python 3.5/3.6 and NumPy 1.12)
+  (`#307 <https://github.com/choderalab/openmmtools/issues/307>`_)
+- Release History now included in online Docs
+
+
+0.13.2 - SamplerState Slicing and BitWise And/Or Ops
+====================================================
+
+Added support for SamplerState slicing (`#298 <https://github.com/choderalab/openmmtools/issues/298>`_)
+Added bit operators ``and`` and ``or`` to ``math_eval`` (`#301 <https://github.com/choderalab/openmmtools/issues/301>`_)
+
+
+
+0.13.1 - Bugfix release
+=======================
+
+- Fix pickling of ``CompoundThermodynamicState`` (`#284 <https://github.com/choderalab/openmmtools/issues/284>`_).
+- Add missing term to OBC2 GB alchemical Force (`#288 <https://github.com/choderalab/openmmtools/issues/288>`_).
+- Generalize ``forcefactories.restrain_atoms()`` to non-protein receptors
+  (`#290 <https://github.com/choderalab/openmmtools/issues/290>`_).
+- Standardize integrator global variables in ContextCache
+  (`#291 <https://github.com/choderalab/openmmtools/issues/291>`_).
+
+
+
+OpenMMTools 0.13.0
+==================
+
+New Features
+------------
+
+- Storage Interface module with automatic disk IO handling
+- Option for shifted or switched Reaction Field
+- ``LangevinSplittingDynamic`` MCMC move with specifiable sub step ordering
+- Nose-Hoover Chain Thermostat
+
+Bug Fixes
+---------
+
+- Many doc string cleanups
+- Tests are based on released versions of OpenMM
+- Tests also compare against development OpenMM, but do not fail because of it
+- Fixed bug in Harmonic Oscillator tests' error calculation
+- Default collision rate in Langevin Integrators now matches docs
+
+
+
+0.12.1 - Add virtual sites support in alchemy
+=============================================
+
+
+- Fixed AbsoluteAlchemicalFactory treatment of virtual sites that were previously ignored
+  (`#259 <https://github.com/choderalab/openmmtools/issues/259>`_).
+- Add possibility to add ions to the WaterBox test system
+  (`#259 <https://github.com/choderalab/openmmtools/issues/259>`_).
+
+
+
+0.12.0 - GB support in alchemy and new forces module
+====================================================
+
+New features
+------------
+
+- Add AbsoluteAlchemicalFactory support for all GB models
+  (`#250 <https://github.com/choderalab/openmmtools/issues/250>`_)
+- Added ``forces`` and ``forcefactories`` modules implementing ``UnishiftedReactionFieldForce`` and
+  ``replace_reaction_field`` respectively. The latter has been moved from ``AbsoluteAlchemicalFactory``
+  (`#253 <https://github.com/choderalab/openmmtools/issues/253>`_)
+- Add ``restrain_atoms`` to restrain molecule conformation through an harmonic restrain
+  (`#255 <https://github.com/choderalab/openmmtools/issues/255>`_)
+
+Bugfixes
+--------
+
+- Bugfix for ``testsystems`` that use implicit solvent (`#250 <https://github.com/choderalab/openmmtools/issues/250>`_)
+- Bugfix for ``ContextCache``: two consecutive calls retrieve the same ``Context`` with same thermodynamic state and no
+  integrator (`#252 <https://github.com/choderalab/openmmtools/issues/252>`_)
+
+
+Hotfix 0.11.2
+=============
+
+Hotfix in fringe Python2/3 compatibility issue when using old style serialization systems in Python 2
+
+
+
+Release 0.11.1: Optimizations
+=============================
+
+- Adds Drew-Dickerson DNA dodecamer test system (`#223 <https://github.com/choderalab/openmmtools/issues/223>`_)
+- Bugfix and optimization to ``ContextCache`` (`#235 <https://github.com/choderalab/openmmtools/issues/235>`_)
+- Compress serialized ``ThermodynamicState`` strings for speed and size
+  (`#232 <https://github.com/choderalab/openmmtools/issues/232>`_)
+- Backwards compatible with uncompressed serialized ``ThermodynamicStates``
+
+
+0.11.0
+======
+
+New Features:
+
+- ``LangevinIntegrator`` now sets ``measure_heat=False`` by default for increased performance
+  (`#211 <https://github.com/choderalab/openmmtools/issues/211>`_)
+- ``AbsoluteAlchemicalFactory`` now supports ``disable_alchemical_dispersion_correction`` to prevent 600x slowdowns with
+  nonequilibrium integration (`#218 <https://github.com/choderalab/openmmtools/issues/218>`_)
+- We now require conda-forge as a dependency for testing and deployment
+  (`#216 <https://github.com/choderalab/openmmtools/issues/216>`_)
+- Conda-forge added as channel to conda packages
+
+
+
+Release 0.10.0 - Optimizations of ThermodynamicState, renamed AlchemicalFactory
+===============================================================================
+
+- BREAKS API: Renamed AlchemicalFactory to AbsoluteAlchemicalFactory
+  (`#206 <https://github.com/choderalab/openmmtools/issues/206>`_)
+- Major optimizations of ThermodynamicState (`#200 <https://github.com/choderalab/openmmtools/issues/177>`_,
+  `#205 <https://github.com/choderalab/openmmtools/issues/205>`_)
+
+    * Keep in memory only a single System object per compatible state
+    * Fast copy/deepcopy
+    * Enable custom optimized serialization for multiple states
+
+- Added readthedocs documentation (`#191 <https://github.com/choderalab/openmmtools/issues/191>`_)
+- Bugfix for serialization of context when NaN encountered
+  (`#199 <https://github.com/choderalab/openmmtools/issues/199>`_)
+- Added tests for Python 3.6 (`#184 <https://github.com/choderalab/openmmtools/issues/184>`_)
+- Added tests for integrators (`#186 <https://github.com/choderalab/openmmtools/issues/186>`_,
+  `#187 <https://github.com/choderalab/openmmtools/issues/187>`_)
+
+
+Release 0.9.4 - Nonequilibrium integrators overhaul
+===================================================
+
+Major changes
+-------------
+
+- Overhaul of ``LangevinIntegrator`` and subclasses to better support nonequilibrium integrators
+- Add true reaction-field support to ``AlchemicalFactory``
+- Add some alchemical test systems
+
+Updates to ``openmmtools.integrators.LangevinIntegrator`` and friends
+---------------------------------------------------------------------
+
+API-breaking changes
+^^^^^^^^^^^^^^^^^^^^
+
+- The nonequilibrium integrators are now called ``AlchemicalNonequilibriumLangevinIntegrator`` and
+  ``ExternalPerturbationLangevinIntegrator``, and both are subclasses of a common ``NonequilibriumLangevinIntegrator``
+  that provides a consistent interface to setting and getting ``protocol_work``
+- ``AlchemicalNonequilibriumLangevinIntegrator`` now has a default ``alchemical_functions`` to eliminate need for every
+  test to treat it as a special case (`#180 <https://github.com/choderalab/openmmtools/issues/180>`_)
+- The ``get_protocol_work()`` method allows you to retrieve the protocol work from any
+  ``NonequilibriumLangevinIntegrator`` subclass and returns a unit-bearing work. The optional ``dimensionless=True``
+  argument returns a dimensionless float in units of kT.
+- Integrator global variables now store all energies in natural OpenMM units (kJ/mol) but the new accessor methods
+  (see below) should b used instead of getting integrator global variables for work and heat.
+  (`#181 <https://github.com/choderalab/openmmtools/issues/181>`_)
+- Any private methods for adding steps to the integrator have been prepended with ``_`` to hide them from the public
+  API.
+
+New features
+^^^^^^^^^^^^
+
+- Order of arguments for all ``LangevinIntegrator`` derivatives matches ``openmm.LangevinIntegrator`` so it can act as a drop-in
+  replacement. (`#176 <https://github.com/choderalab/openmmtools/issues/176>`_)
+- The ``get_shadow_work()`` and ``get_heat()`` methods are now available for any ``LangevinIntegrator`` subclass, as
+  well as the corresponding properties ``shadow_work`` and heat. The functions also support ``dimensionless=True.``
+  (`#163 <https://github.com/choderalab/openmmtools/issues/163>`_)
+- The ``shadow_work`` and ``heat`` properties were added to all LangevinIntegrator subclasses, returning the values of
+  these properties (if the integrator was constructed with the appropriate ``measure_shadow_work=True`` or
+  ``measure_heat=True`` flags) as unit-bearing quantities
+- The ``get_protocol_work()`` and ``get_total_work()`` methods are now available for any
+  ``NonequilibriumLangevinIntegrator``, returning unit-bearing quantities unless ``dimensionless=True`` is provided in
+  which case they return the work in implicit units of kT. ``get_total_work()`` requires the integrator to have been
+  constructed with ``measure_shadow_work=True``.
+- The ``protocol_work`` and ``total_work`` properties were added to all ``NonequilibriumLangevinIntegrator`` subclasses,
+  and return the unit-bearing work quantities. ``total_work`` requires the integrator to have been constructed with
+  ``measure_shadow_work=True``.
+- The subclasses have been reworked to support any kwargs that the base classes support, and defaults have all been made
+  consistent.
+- Various reset() methods have been added to reset statistics for all ``LangevinIntegrator`` subclasses.
+- All custom integrators support ``.pretty_format()`` and ``.pretty_print()`` with optional highlighting of specific
+  step types.
+
+Bugfixes
+^^^^^^^^
+
+- Zero-step perturbations now work correctly (`#177 <https://github.com/choderalab/openmmtools/issues/177>`_)
+- ``AlchemicalNonequilibriumLangevinIntegrator`` now correctly supports multiple ``H`` steps.
+
+Internal changes
+^^^^^^^^^^^^^^^^
+
+- Adding new LangevinIntegrator step methods now uses a ``self._register_step_method(step_string, callback_function, supports_force_groups=False)`` call to simplify this process.
+- Code duplication has been reduced through the use of calling base class methods whenever possible.
+- ``run_nonequilibrium_switching()`` test now uses BAR to test dragging a harmonic oscillator and tests a variety of
+  integrator splittings ``(["O { V R H R V } O", "O V R H R V O", "R V O H O V R", "H R V O V R H"])``.
+- Integrator tests use deterministic PME and mixed precision when able.
+
+Updates to openmmtools.alchemy.AlchemicalFactory
+------------------------------------------------
+
+- Reaction field electrostatics now removes the shift, setting ``c_rf = 0``.
+
+- A convenience method AlchemicalFactory.replace_reaction_field() has been added to allow fully-interacting systems to
+  be modified to force ``c_rf = 0`` by recoding reaction-field electrostatics as a ``CustomNonbondedForce``
+
+New ``openmmtools.testsystems`` classes
+---------------------------------------
+
+- AlchemicalWaterBox was added, which has the first water molecule in the system alchemically modified

setup.py

@@ -15,7 +15,7 @@
 
 ########################
 VERSION = "0.13.3"
-ISRELEASED = False
+ISRELEASED = True
 __version__ = VERSION
 ########################
 CLASSIFIERS = """\