Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Release 0.17 #396

Merged
merged 4 commits into from
Jan 24, 2019
Merged

Release 0.17 #396

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
ac2cd69
Update releasehistory.rst
andrrizzi Jan 24, 2019
aeec651
Fix formatting
andrrizzi Jan 24, 2019
5892ccf
Drop tests python 3.5 and activate python 3.7
andrrizzi Jan 24, 2019
eab00e5
Release 0.17
andrrizzi Jan 24, 2019
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 1 addition & 3 deletions .travis.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -36,10 +36,8 @@ script:

env:
matrix:
- python=3.5 CONDA_PY=35
# TODO: reactivate the devomnia when we switch back to official OpenMM release instead of dev.
- python=3.5 CONDA_PY=35 DEVOMNIA=true
- python=3.6 CONDA_PY=36
- python=3.7 CONDA_PY=37
global:
- ORGNAME="omnia" # the name of the organization
- PACKAGENAME="openmmtools" # the name of your package
Expand Down
24 changes: 8 additions & 16 deletions docs/releasehistory.rst
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -6,12 +6,9 @@ Release History

New features
------------
- Add ``GlobalParameterFunction`` that allows to enslave a ``GlobalParameter`` to an arbitrary function of controlling
variables (`#380 <https://github.com/choderalab/openmmtools/pull/380>`_).
- Allow to ignore velocities when building the dict representation of a ``SamplerState``. This can be useful for example
to save bandwidth when sending a ``SamplerState`` over the network and velocities are not required (`#386 <https://github.com/choderalab/openmmtools/pull/386>`_).
- Add ``DoubleWellDimer_WCAFluid`` and ``DoubleWellChain_WCAFluid`` test
systems (`#389 <https://github.com/choderalab/openmmtools/pull/389>`_).
- Add ``GlobalParameterFunction`` that allows to enslave a ``GlobalParameter`` to an arbitrary function of controlling variables (`#380 <https://github.com/choderalab/openmmtools/pull/380>`_).
- Allow to ignore velocities when building the dict representation of a ``SamplerState``. This can be useful for example to save bandwidth when sending a ``SamplerState`` over the network and velocities are not required (`#386 <https://github.com/choderalab/openmmtools/pull/386>`_).
- Add ``DoubleWellDimer_WCAFluid`` and ``DoubleWellChain_WCAFluid`` test systems (`#389 <https://github.com/choderalab/openmmtools/pull/389>`_).

Enhancements
------------
Expand All @@ -24,19 +21,14 @@ considerable speed improvement over the previous implementation (`#380 <https://

Bug fixes
---------
- Fixed a bug involving the ``NoseHooverChainVelocityVerletIntegrator`` with ``System`` with constraints. The constraints
were not taken into account when calculating the number of degrees of freedom resulting in the temperature not converging
to the target value. (`#384 <https://github.com/choderalab/openmmtools/pull/384>`_)
- Fixed a bug affecting ``reduced_potential_at_states`` when computing the reduced potential of systems in different
``AlchemicalState``s when the same alchemical parameter appeared in force objects split in different force groups. (`#385 <https://github.com/choderalab/openmmtools/pull/385>`_)
- Fixed a bug involving the ``NoseHooverChainVelocityVerletIntegrator`` with ``System`` with constraints. The constraints were not taken into account when calculating the number of degrees of freedom resulting in the temperature not converging to the target value. (`#384 <https://github.com/choderalab/openmmtools/pull/384>`_)
- Fixed a bug affecting ``reduced_potential_at_states`` when computing the reduced potential of systems in different ``AlchemicalState``s when the same alchemical parameter appeared in force objects split in different force groups. (`#385 <https://github.com/choderalab/openmmtools/pull/385>`_)

Deprecated and API breaks
-------------------------
- Python 2 is not supported anymore.
- The ``update_alchemical_charges`` attribute of ``AlchemicalState`, which was deprecated in 0.16.0, has now been removed
since it doesn't make sense with the new parameter offset implementation.
- The methods ``AlchemicalState.get_alchemical_variable`` and ``AlchemicalState.set_alchemical_variable`` have been
deprecated. Use ``AlchemicalState.get_alchemical_function`` and ``AlchemicalState.set_alchemical_function`` instead.
- Python 2 and 3.5 is not supported anymore.
- The ``update_alchemical_charges`` attribute of ``AlchemicalState`, which was deprecated in 0.16.0, has now been removed since it doesn't make sense with the new parameter offset implementation.
- The methods ``AlchemicalState.get_alchemical_variable`` and ``AlchemicalState.set_alchemical_variable`` have been deprecated. Use ``AlchemicalState.get_alchemical_function`` and ``AlchemicalState.set_alchemical_function`` instead.


0.16.0 - Py2 deprecated, GlobalParameterState class, SamplerState reads CVs
Expand Down
2 changes: 1 addition & 1 deletion setup.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@

########################
VERSION = "0.17.0"
ISRELEASED = False
ISRELEASED = True
__version__ = VERSION
########################
CLASSIFIERS = """\
Expand Down