Openpathsampling

OpenPathSampling 1.7.0 contains several pieces of new functionality and some bug fixes. Most significant is probably the experimental new path tree functionality, which works with data stored from SimStore ("experimental" storage, now recommended for most use cases).

Enhancements

* Add `restart_at_step` for `ExternalEngine` (for numeric filenames) ([1105](https://github.com/openpathsampling/openpathsampling/pull/1105))
* Custom `PathDensityHistogram._add_ops_trajectory` ([1154](https://github.com/openpathsampling/openpathsampling/pull/1154) #refactor)
* Volume shooting point selector ([1151](https://github.com/openpathsampling/openpathsampling/pull/1151))

Experimental (beta) features

* SimStore performance improvements and fixes ([1157](https://github.com/openpathsampling/openpathsampling/pull/1157) #enhancement)
* New path tree ([1048](https://github.com/openpathsampling/openpathsampling/pull/1048) #enhancement)

Bugs fixed
* Fix `SQLStorageBackend.load_storable_function_table` ([1153](https://github.com/openpathsampling/openpathsampling/pull/1153) #experimental)
* Fix histogram xvals ([1150](https://github.com/openpathsampling/openpathsampling/pull/1150))

Miscellaneous improvements

* Let UUID determine equality for ensembles ([1155](https://github.com/openpathsampling/openpathsampling/pull/1155))
* Improvements to continuous integration / automated testing ([1149](https://github.com/openpathsampling/openpathsampling/pull/1149), [#1156](https://github.com/openpathsampling/openpathsampling/pull/1156))
* Improvements to documentation ([1159](https://github.com/openpathsampling/openpathsampling/pull/1159))

OpenPathSampling 1.6.1 is a minor update, primarily focused on allowing OPS to run/be tested on Python 3.12. In practice, that means removing dependency on tools that prevented Python 3.12 support. In particular, this removes `nose` from our testing requirements, and deprecates our integration with PyEMMA, which is no longer maintained.

**DEPRECATION:** As of OPS 1.6.1, we no longer recommend the use of `PyEMMAFeaturizerCV`. PyEMMA is no longer maintained. Please do not create collective variables based on PyEMMA.

Miscellaneous improvements

* Test against Python 3.12; deprecate PyEMMA ([1145](https://github.com/openpathsampling/openpathsampling/pull/1145) #Deprecations)
* Cut off `nose` ([1141](https://github.com/openpathsampling/openpathsampling/pull/1141) #upstream_changed)
* Fix a few more setup -> setup_method tests ([1142](https://github.com/openpathsampling/openpathsampling/pull/1142) #upstream_changed)

This is a long-overdue (and huge) release for OPS. While the only highlight feature is the addition of S-Shooting, this release contains many updates to maintain usability of OPS as its dependencies change, as well as a number of important bug fixes that are recommended for all users.

**Deprecations:** The `FileSetter` for external engines (e.g., Gromacs) will be changing from a sequential numeric value to a random string. See 1102 for details.

New features

* S-shooting ([787](https://github.com/openpathsampling/openpathsampling/pull/787) singraber)

Other enhancements

* Clear old ExternalMDSnapshots during `iter_generate` ([1066](https://github.com/openpathsampling/openpathsampling/pull/1066))
* New analysis testing utilities ([1068](https://github.com/openpathsampling/openpathsampling/pull/1068))
* Account for modifier acceptance in engine movers ([1075](https://github.com/openpathsampling/openpathsampling/pull/1075))
* add no_copy option to NoModifier and Deprecate 'subset_mask' ([1079](https://github.com/openpathsampling/openpathsampling/pull/1079))
* Take care of coordinate modifcation in selector probability_ratio ([1076](https://github.com/openpathsampling/openpathsampling/pull/1076))

Experimental (beta) features

* improvements to unpatch after using SimStore ([1065](https://github.com/openpathsampling/openpathsampling/pull/1065))
* add simstore table access via slice ([1050](https://github.com/openpathsampling/openpathsampling/pull/1050))

Bugs fixed

* Use MDTraj codecs in SimStore JSON serialization ([1116](https://github.com/openpathsampling/openpathsampling/pull/1116))
* Prevent double monkey-patching experimental storage ([1109](https://github.com/openpathsampling/openpathsampling/pull/1109))
* Actually check for CVDefinedVolume.lambda_max == "inf" ([1092](https://github.com/openpathsampling/openpathsampling/pull/1092))
* SimStore: Fix storable function serialization ([1088](https://github.com/openpathsampling/openpathsampling/pull/1088))
* SimStore: Fix issue with internalized snapshot box vectors ([1086](https://github.com/openpathsampling/openpathsampling/pull/1086))
* OpenMMEngine: use masses from mdtraj topolgy directly ([1085](https://github.com/openpathsampling/openpathsampling/pull/1085) hejung)
* unbreak API call to selector.probability_ratio ([1082](https://github.com/openpathsampling/openpathsampling/pull/1082))

Miscellaneous improvements

* Support Python 3.10; Python 3.11 ([1133](https://github.com/openpathsampling/openpathsampling/pull/1133))
* Fix Dropbox download of precalculated results ([1128](https://github.com/openpathsampling/openpathsampling/pull/1128))
* revert openmmtools import guard from test notebook ([1106](https://github.com/openpathsampling/openpathsampling/pull/1106))
* clarify error message on missing units ([1122](https://github.com/openpathsampling/openpathsampling/pull/1122))
* update copyright to 2022 ([1097](https://github.com/openpathsampling/openpathsampling/pull/1097))
* Improved implementation of shooting point selector pick (avoid model that might introduce index error in subclasses) ([1110](https://github.com/openpathsampling/openpathsampling/pull/1110) hejung)
* Add FutureWarning for default filesetter external engines ([1102](https://github.com/openpathsampling/openpathsampling/pull/1102) #Deprecations)
* make a missed string into a rawstring ([1096](https://github.com/openpathsampling/openpathsampling/pull/1096))
* Guard against openmm import warnings (including those from OpenMMTools) ([1091](https://github.com/openpathsampling/openpathsampling/pull/1091))
* Add CITATIONS.md ([1064](https://github.com/openpathsampling/openpathsampling/pull/1064))
* Prevent non-string names in StorableNamedObject ([1052](https://github.com/openpathsampling/openpathsampling/pull/1052))
* Updates in response to changes in dependencies ([1137](https://github.com/openpathsampling/openpathsampling/pull/1137), [#1136](https://github.com/openpathsampling/openpathsampling/pull/1136), [#1134](https://github.com/openpathsampling/openpathsampling/pull/1134), [#1132](https://github.com/openpathsampling/openpathsampling/pull/1132), [#1129](https://github.com/openpathsampling/openpathsampling/pull/1129), [#1114](https://github.com/openpathsampling/openpathsampling/pull/1114), [#1130](https://github.com/openpathsampling/openpathsampling/pull/1130), [#1126](https://github.com/openpathsampling/openpathsampling/pull/1126), [#1093](https://github.com/openpathsampling/openpathsampling/pull/1093))
* Improvements to continuous integration and testing ([1123](https://github.com/openpathsampling/openpathsampling/pull/1123), [#1100](https://github.com/openpathsampling/openpathsampling/pull/1100), [#1089](https://github.com/openpathsampling/openpathsampling/pull/1089), [#1081](https://github.com/openpathsampling/openpathsampling/pull/1081), [#1078](https://github.com/openpathsampling/openpathsampling/pull/1078), [#1073](https://github.com/openpathsampling/openpathsampling/pull/1073), [#1058](https://github.com/openpathsampling/openpathsampling/pull/1058))
* Improvements to documentation ([1090](https://github.com/openpathsampling/openpathsampling/pull/1090), [#1087](https://github.com/openpathsampling/openpathsampling/pull/1087), [#1083](https://github.com/openpathsampling/openpathsampling/pull/1083), [#1057](https://github.com/openpathsampling/openpathsampling/pull/1057) bdice)

Thanks always to maintainers sroet and dwhswenson.

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](https://github.com/openpathsampling/openpathsampling/pull/1046))
* Raise FileNotFoundError if sql backend tries to read a file that does not exist ([1045](https://github.com/openpathsampling/openpathsampling/pull/1045)) #experimental

Miscellaneous improvements
* Fixes for OpenMM 7.6 RC ([1051](https://github.com/openpathsampling/openpathsampling/pull/1051)) #upstream_changed
* Fix syntax warning ([1044](https://github.com/openpathsampling/openpathsampling/pull/1044))

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](https://github.com/openpathsampling/openpathsampling/pull/1035)) #experimental
* Fix bug in live visualizer setup with implicit hooks ([1034](https://github.com/openpathsampling/openpathsampling/pull/1034) hejung)

Miscellaneous improvements
* Fix OpenMM engine docs on n_frames_max ([1037](https://github.com/openpathsampling/openpathsampling/pull/1037) hejung) #docs
* Fix DataFrame.sort_index future warning ([1036](https://github.com/openpathsampling/openpathsampling/pull/1036)) #upstream_changed

OpenPathSampling 1.5 is a significant release, including many new features and enhancements. Highlights of this release are the implementation of [Spring Shooting](http://dx.doi.org/10.1063/1.4965882) 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](https://github.com/openpathsampling/openpathsampling/pull/850) sroet)
* "Hooks" to enable more simulation flexibility ([755](https://github.com/openpathsampling/openpathsampling/pull/755), [#911](https://github.com/openpathsampling/openpathsampling/pull/911) hejung)
* Gracious Kill Hook ([914](https://github.com/openpathsampling/openpathsampling/pull/914) hejung)
* Warn if CVDefinedVolume CVs return iterables ([1030](https://github.com/openpathsampling/openpathsampling/pull/1030))
* Shooting point selector with arbitrary bias ([1024](https://github.com/openpathsampling/openpathsampling/pull/1024))
* Add global random number generator; support in shooting pt selectors and pathmovers ([998](https://github.com/openpathsampling/openpathsampling/pull/998) sroet, [#1008](https://github.com/openpathsampling/openpathsampling/pull/1008) sroet [#1015](https://github.com/openpathsampling/openpathsampling/pull/1015))
* Move n_dofs to engine; add engine.has_constraints() ([979](https://github.com/openpathsampling/openpathsampling/pull/979))

Experimental (beta) features

* SimStore: Periodic CVs ([990](https://github.com/openpathsampling/openpathsampling/pull/990))
* SimStore: Make storable function modes customizable ([1004](https://github.com/openpathsampling/openpathsampling/pull/1004))
* SimStore bug fixes and minor improvements ([985](https://github.com/openpathsampling/openpathsampling/pull/985), [#995](https://github.com/openpathsampling/openpathsampling/pull/995), [#1002](https://github.com/openpathsampling/openpathsampling/pull/1002), [#1003](https://github.com/openpathsampling/openpathsampling/pull/1003), [#1016](https://github.com/openpathsampling/openpathsampling/pull/1016), [#1027](https://github.com/openpathsampling/openpathsampling/pull/1027)) #bugfix

Bugs fixed
* Make histogramming more robust ([1029](https://github.com/openpathsampling/openpathsampling/pull/1029) sroet)
* Fix problem with repeated ensemble names in MISTIS ([988](https://github.com/openpathsampling/openpathsampling/pull/988))
* Fix MISTIS minus ensemble not forbidding other states ([983](https://github.com/openpathsampling/openpathsampling/pull/983))
* Fix problem with Histogram.bin_range not getting set ([972](https://github.com/openpathsampling/openpathsampling/pull/972))

Miscellaneous improvements

* Move MDTrajTopology into `engines.topology` ([1012](https://github.com/openpathsampling/openpathsampling/pull/1012) sroet, [#1014](https://github.com/openpathsampling/openpathsampling/pull/1014)) #Deprecations
* Reduce unnecessary object creation ([975](https://github.com/openpathsampling/openpathsampling/pull/975), [#976](https://github.com/openpathsampling/openpathsampling/pull/976) sroet, [#978](https://github.com/openpathsampling/openpathsampling/pull/978) sroet)
* Fix problems with PyEMMA tests ([997](https://github.com/openpathsampling/openpathsampling/pull/997), [#1009](https://github.com/openpathsampling/openpathsampling/pull/1009), [#1018](https://github.com/openpathsampling/openpathsampling/pull/1018) sroet, [#1022](https://github.com/openpathsampling/openpathsampling/pull/1022) sroet, [#1023](https://github.com/openpathsampling/openpathsampling/pull/1023) sroet)
* make test less flaky ([999](https://github.com/openpathsampling/openpathsampling/pull/999) sroet)
* Switch notebook tests to nbval ([987](https://github.com/openpathsampling/openpathsampling/pull/987))
* Add automatic testing against OpenMM release candidates ([1019](https://github.com/openpathsampling/openpathsampling/pull/1019), [#1020](https://github.com/openpathsampling/openpathsampling/pull/1020), [#1021](https://github.com/openpathsampling/openpathsampling/pull/1021))
* Improve interactions with CodeCov ([980](https://github.com/openpathsampling/openpathsampling/pull/980), [#991](https://github.com/openpathsampling/openpathsampling/pull/991), [#1025](https://github.com/openpathsampling/openpathsampling/pull/1025))
* Improvements to the documentation ([939](https://github.com/openpathsampling/openpathsampling/pull/939), [#970](https://github.com/openpathsampling/openpathsampling/pull/970), [#1010](https://github.com/openpathsampling/openpathsampling/pull/1010) sroet)
* Pin OpenMM != 7.5.1 ([1017](https://github.com/openpathsampling/openpathsampling/pull/1017))
* Pin sqlalchemy!=1.4.0 ([996](https://github.com/openpathsampling/openpathsampling/pull/996))
* Add Python 3.8, 3.9 to testing matrix ([993](https://github.com/openpathsampling/openpathsampling/pull/993))
* fix numpy 1.20 DeprecationWarnings ([974](https://github.com/openpathsampling/openpathsampling/pull/974))