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@dwhswenson dwhswenson released this Aug 24, 2021

OpenPathSampling 1.5.2 is a minor release. It includes updates to support OpenMM 7.6, as well as some small bugfixes.

Bugs fixed

  • Prevent errors in ShootingPointAnalysis with invalid (e.g., max length) trajectories (#1046)
  • Raise FileNotFoundError if sql backend tries to read a file that does not exist (#1045) #experimental

Miscellaneous improvements

  • Fixes for OpenMM 7.6 RC (#1051) #upstream_changed
  • Fix syntax warning (#1044)
Assets 2

@dwhswenson dwhswenson released this Jul 24, 2021

OpenPathSampling 1.5.1 is a minor bugfix release. It fixes a bug in SimStore's ability to store/reload some CV types (specifically, CVs that save NumPy arrays). It also fixes a backward compatibility problem with live visualizations in scripts written for OPS before 1.5.0.

We're also happy to welcome @sroet as a maintainer of OPS, and as a "standard contributor." As a maintainer, @sroet has merge access to OPS repositories. As a standard contributor, PRs from @sroet will no longer be tagged with his username in release notes.

Bugs fixed

  • Fix bug with SimStore CVs storing NumPy arrays (#1035) #experimental
  • Fix bug in live visualizer setup with implicit hooks (#1034 @hejung)

Miscellaneous improvements

  • Fix OpenMM engine docs on n_frames_max (#1037 @hejung) #docs
  • Fix DataFrame.sort_index future warning (#1036) #upstream_changed
Assets 2

@dwhswenson dwhswenson released this Jul 6, 2021

OpenPathSampling 1.5 is a significant release, including many new features and enhancements. Highlights of this release are the implementation of Spring Shooting and the development of new "hooks" where users can patch in custom code during the simulation process, enabling much greater flexibility.

Note that the hooks are still considered beta code, and therefore some aspects of that API may change.

DEPRECATION: As of OPS 1.5, MDTrajTopology should be imported from openpathsampling.engines, not from openpathsampling.engines.openmm.

New features and enhancements

  • Spring Shooting mover/move scheme (#850 @sroet)
  • "Hooks" to enable more simulation flexibility (#755, #911 @hejung)
  • Gracious Kill Hook (#914 @hejung)
  • Warn if CVDefinedVolume CVs return iterables (#1030)
  • Shooting point selector with arbitrary bias (#1024)
  • Add global random number generator; support in shooting pt selectors and pathmovers (#998 @sroet, #1008 @sroet #1015)
  • Move n_dofs to engine; add engine.has_constraints() (#979)

Experimental (beta) features

Bugs fixed

  • Make histogramming more robust (#1029 @sroet)
  • Fix problem with repeated ensemble names in MISTIS (#988)
  • Fix MISTIS minus ensemble not forbidding other states (#983)
  • Fix problem with Histogram.bin_range not getting set (#972)

Miscellaneous improvements

Assets 2

@dwhswenson dwhswenson released this Jan 30, 2021

OPS 1.4.2 is a bugfix release, most importantly fixing a bug in TIS analysis for interface sets with more than 10 interfaces.

Bugs fixed

  • Fix simtk JSON storage in SimStore (#961)
  • Fix broken WHAMing if an InterfaceSet has more than 10 interfaces (#967 @sroet)

Miscellaneous improvements

  • Update ujson pin (#965)
  • Make more deterministic test for shooting point selector (#964 @sroet)
  • Fix broken link in Readme.md of toy mstis examples (#963 @sroet)
  • Switch to CI GitHub Actions (#959, #966 @sroet)
Assets 2

@dwhswenson dwhswenson released this Dec 31, 2020

OPS 1.4.1 is a minor release to fix issues with imports when not all integrations are installed.

Miscellaneous improvements

  • Remove nose from test_helpers (#958)
  • Fix so SimStore tests pass without simtk.unit (#957)
  • fix omt is None error in test suite (#954 @sroet)
Assets 2

@dwhswenson dwhswenson released this Dec 24, 2020

OpenPathSampling 1.4 introduces SimStore, our (experimental) new storage system. It is faster and more flexible than the old storage system, and will be the only storage in OPS 2.0. As an experimental addition, its API is not locked. However, the parts that are likely to change deal with extending SimStore (e.g., supporting new types). Regular usage to save and load results of simulations should now be stable.

In addition, OPS 1.4 adds a reactive flux (Bennett-Chandler) calculation, plus many small improvements and bug fixes.

New features and enhancements

  • Reactive flux (#924 @singraber)
  • Internalized snapshots; random filenames for external snapshots (#933)

Experimental (beta) features

  • SimStore: Simplify OPS Storage constructor (#950)
  • SimStore: Support for OpenMM snapshots (#949)
  • SimStore: Type identification (#947)
  • Fix bug in SimStore when appending to non-existent files (#941) #bugfix
  • SimStore: Tags (#940)
  • SimStore part 2: Storable functions (and more) (#929)
  • SimStore: New storage subsystem (part 1) (#928)

Bugs fixed

  • fix for filename counter of gromacs engine (#946 @hejung)
  • OpenMM instantaneous temp should work if positions not set (#938)
  • Fix: OPS hangs when external engine errors/exits unexpectedly (#913 @oliverdutton)

Miscellaneous improvements

Assets 2

@dwhswenson dwhswenson released this Sep 26, 2020

The highlights of OpenPathSampling 1.3 are the PLUMED wrapper CVs for OPS (previously an external repository), and the optional progress indicators for analysis. In addition, OPS 1.3 brings several bugfixes, and adds support for newer versions of dependencies.

New features and enhancements

  • PLUMED Collective Variables in OPS (#910 @apdealbao)
  • Gromacs engine and example updates (#909)
  • Progress indicators for analysis (#895, #902, #906)
  • storage.filename is now an absolute path and a read-only property (#903 @hejung)

Bugs fixed

  • Pin ujson<2 (bug in later versions can break reloading) (#926)
  • use uuid instead of 'is' for selecting ensembles in rate calculation (#919 @sroet)
  • Fix missing names in ExternalMDSnapshot (#908)
  • DirectSimulation should use engine.start/.stop (#905)

Miscellaneous improvements

Assets 2

@dwhswenson dwhswenson released this Jan 31, 2020

OpenPathSampling 1.2 brings several small improvements, including a new method to facilitate equilibration in path sampling, and some under-the-hood updates that will facilitate features intended for future releases.

New features and enhancements

  • Refactor RandomVelocity so engine can do the randomization (#890)
  • Add PathSampling.run_until_decorrelated (#884, #894)
  • Add progress meter adapter classes (#882)

Miscellaneous improvements

  • Fix pandas API change: set_value -> at (#896) #upstream_changed
  • Improvements to the documentation (#865, #887, #893)
  • Improvements to the CI (#893)
Assets 2

@dwhswenson dwhswenson released this Dec 12, 2019

The marquee feature in OPS 1.1 is the addition of GROMACS support. That also introduces the external engine framework, which can be used by other MD engines.

Another important change is that OPS is now pip-installable and can be installed through conda's conda-forge channel (starting with 1.1, new versions of OPS will not be in the omnia channel). Also note that many tools that previously were bundled with OPS now are not. In particular, if you want to use any of the following packages, you must install them separately:

  • OpenMM
  • OpenMMTools
  • PyEMMA
  • MSMBuilder
  • Jupyter

They're all just a conda install away, and as soon as they're in your environment, OPS will interface with them as before.

Deprecations: CVs based on MSMBuilder featurizers are deprecated. MSMBuilder can no longer be tested in our standard test setup. We haven't removed support, but we can't recommend using it.

New features

  • External Engine (#144)
  • Gromacs engine (#819)
  • Path density: Bresenham interpolation (#875)
  • Simplify Trajectory.__getattr__ (#879)
  • Add information to MinusMove change.details (#874)

Bugs fixed

  • Fix bug with left_bin_edge in histogram (#851 @sroet)
  • Fix problems with storage for nonperiodic systems (#835 [part from @ajsilveira])
  • Fix Py3 bug in getting function name when CV storage raises error (#830 @ajsilveira)

Miscellaneous improvements

  • Reduce install requirements; make PyPI/conda-forge possible(#867, #876)
  • Use Autorelease for version/release management (#883)
  • Add subpackages as a space for user contributions (#849)
  • Some toy engine reprs (#880)
  • Various improvements to documentation (#881 @sroet, #859, #856 @sroet, #847, #770 @hejung)
  • Various improvements to CI/testing (#877, #866, #848)
  • Deprecate MSMBuilder (#853) #Deprecations
Assets 2

@dwhswenson dwhswenson released this Jul 22, 2019

OpenPathSampling 1.0 is ready for release! Major changes since 0.9.6 include:

  • New license! OPS is now under the MIT license. Versions of OPS prior to 1.0 are still licensed under LGPL 2.1 or later.
  • Officially supported Python versions are now 2.7, 3.6, and 3.7
  • Significant refactoring to clean up many parts of the code. In unusual circumstances, these could lead to API breaks. For details, see PRs linked under "Miscellaneous improvements -> Refactoring and API cleanup" below.

Deprecations: Use the generic Details object instead of MoveDetails, which adds no additional functionality.

New features

  • "Visit all states" ensemble (#826)
  • Make WHAM's lnZ accessible from outside (#825)
  • Add engine property to OneWayShooting (#805)

Miscellaneous improvements

  • Switch to MIT License (#844)
  • Switch to 2.7/3.6/3.7; deploy docs on 3.7 (#815, #824)
  • Update developer install process (#840, #842, #843)
  • Improve performance on trajectory_from_mdtraj (#839) #performance
  • Additions and improvements in the documentation (#820, #825, #828, #831, #838)
  • snapshot_from_pdb uses same code path as other functions (#833)
  • Improve continuous integration (#808, #811, #814, #829)
  • Shooting selector tests (#827)
  • Refactoring and API cleanup (#809, #816, #818, #821, #823)
Assets 2