Openpathsampling

* Interface constrained shooting, an efficient technique in TIS
* Better ways to load trajectories for the OpenMM engine (especially from Gromacs trajectories)
* bugfix for minus interface ensemble in cases where the transition is not particularly rare

New features
* Tools to get correctly reduced box vectors for OpenMM (799)
* Simple function to load TRR files (799)
* "Part-In-B" network (used in TPS rate calculation) (796)
* Interface constrained shooting (788, 791, 790, 800) [parts by bolhuis]

Bugs fixed
* maskedarray fixes (803)
* bugfix in minus ensemble (803)
* Attempt to fix for old openmmtools as well as new (768)
* Fix push-docs-to-s3 for pip 10 (785)

Miscellaneous improvements
* Updates to Examples (798)
* Fix notebook tests (797)
* Updates to docs (795, 793)
* Changes to .gitignore files (792)
* Fixes for continuous integration (802)

Bugs fixed
* Only keep existing value stores in attribute_list (783)
* Omit using rejected paths in correlation visualization (782)
* Fix problems in notebook tests (776)
* Fix problem with netCDF not playing nicely with `simtk.unit` (776)
* Volumes should only be bounded on one side (772)
* Fix `TISEnsemble` so it allows 0 frames between interface and state B (772)

Miscellaneous improvements
* Fix pandas deprecation warning : replace df.as_matrix() with df.values (781)
* Update minus ensemble implementation (772)
* Fix openmmtools.RestorableIntegrator error (764)
* Better source code organization and management (754, 760)
* Add acknowledgments to docs (766)

* New ability to include velocities when creating an OPS trajectory from an MDTraj trajectory
* New default colors in visualizations (better visibility for the most common type of color blindness)
* Significant updates to the documentation
* Major improvements in Python 3 support
* Critical bug fix in the direct MD flux calculation
* Critical bug fix in two-way shooting

Details on all improvements below.

New features
* Add velocities as input to `trajectory_from_mdtraj` (750)
* Tools for converting flux to `pandas` structures (735)

Bugs fixed
* Allow unicode for string options in engine option check (757)
* Fix bug in `BackwardFirstTwoWayShooting` (752)
* Fix problem with `HistogramPlotter2D` limits (732)
* Fix bug in `snapshot.md box_vectors` (731)
* Fix bug in `DirectSimulation` flux (726)

Miscellaneous improvements
* Default path tree colors are better for color-blind (733)
* Improvements to documentation (751, 748, 744, 737, 729, 723)
* Improved Python 3 compatibility (743, 741, 739, 738)
* Improvements to examples (746, 743, 719 [by bolhuis])
* Behind-the-scenes upates to CI, testing, and deployment (758, 749, 747, 745, 742)
* Dev install for simple developer installs (728)
* Code readability updates (724)

Long-overdue release, with several new features and lots of little fixes. Includes significant progress toward Python 3 support, which should be fully complete within the next few releases.

New features

* Velocity direction modifiers (traditional delta-p) for 2-way shooting (650)
* Channel analysis tools to study switching between reaction channels (or different transitions) (658)
* `resampling_statistics` module to get uncertainties from `pandas.DataFrame` results (684)
* `safemode` to load CVs without loading the stored functions (695)
* `PseudoAttribute`s: caching storage for generalized `CollectiveVariable`-like functions (not just of snapshots) (691)
* New TIS analysis subsystem in `openpathsampling.analysis.tis` (686)

Miscellaneous improvements
* Major progress toward Python 3 support (690, 696, 708, 713)
* `storage.tags` works, as well as `storage.tag` (698)
* Faster ensemble check for the case that the trajectory was generated using `can_append`/`can_prepend` (669)
* Refactor `CommittorSimulation` into reusable `ShootFromSnapshotsSimulation` (667)
* Miscellaneous storage improvements
* Miscellaneous performance improvements
* Miscellaneous updates to docs, testing, and continuous integration procedures

Bugs fixed

* Fix bug in OpenMM instantaneous temperature (649)
* Fix (rare) bug in acceptance probability for 2-way shooting (652)
* Fix bug in deserialization/reloading of OpenMMTools integrators (675)
* Fix bug in multiple state rate calculation from `DirectSimulation` (706)

A few new features and some significant clean-up as we prepare for 1.0.

Note that the changes in the `Details` object have the potential to break compatibility with older code. Please check PRs 629 and 633 if that is likely to be a problem for you.

Changes in this release include:
- Added two-way shooting (600)
- Clean-up of how `Details` are handled (details are only for move changes; not samples) (629, 633)
- Load a trajectory to OPS (via MDTraj) with `ops_load_trajectory` (645)
- Items from storage can be loaded with negative numbers, following Python list index convention (612)
- CSS for visualizations moved to separate file (574)
- New conveniences for restarting a simulation (616)
- `RandomVelocities` respects constraints (618)
- Miscellaneous bugfixes, documentation improvements, and other minor improvements

Continuing clean-up and adding conveniences as we prepare for 1.0.

Some improvements new in this release:
- switch JSON library to `ujson` (582)
- `masses`, `n_degrees_of_freedom`, and `instantaneous_temperature` snapshot features (579, 589)
- renamings surrounding what used to be `live_visualization` (596)
- end checking for "safe imports" in CVs (599)
- improvements to the committor calculation (601)

In addition, we removed lots of unnecessary/outdated code, reorganized several sections for better modularity, cleaned up our examples, and gave the documentation a long-overdue update.