Openpathsampling

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)

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
* Improve CV storage error message about missing templates (935)
* Fixes for deprecation warnings and syntax warnings (923 sroet, 936 sroet, 944 bdice)
* Improvements to documentation (932, 937, 939)
* Miscellaneous cleanup (951)

The highlights of OpenPathSampling 1.3 are the PLUMED wrapper CVs for OPS (previously an [external repository](https://gitlab.e-cam2020.eu/apdealbao/plumed_wrapper/)), 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
* Support for ujson 3 ((917 sroet, 921 hejung)
* Improvements and maintenance of devtools (912, 926, 927)
* Support for pandas 1.0 (898 sroet, 925)
* Improvements to documentation (901, 909)
* make tqdm optional for tests (916 sroet)
* Fix missing newline in the VisitAllStatesEnsemble (900)

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)

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

* 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)