openpathsampling/openpathsampling: OpenPathSampling 0.9.4

OpenPathSampling 0.9.4 includes a few new features, several important bug fixes, and a lot of minor improvements. A few highlights include:

• New ability to include velocities when creating an OPS trajectory from and 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.

• Add velocities as input to trajectory_from_mdtraj (#750)
• Tools for converting flux to pandas structures (#735)

• 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)

• 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)