qcscine/heron: Release 2.0.0

Abstract

Changes: Add SCINE Chemoton tab to run explorations from within Heron Add tab to run the Chemoton Steering Wheel Add SCINE ReaDuct tab to carry out any ReaDuct task (e.g., structure optimizations) Modify Interactive to run with any SCINE backend calculator Add QM/MM capabilities, SFAM parametrization, and automated QM region selection to Interactive including database support Add option to construct Chemoton aggregate and reactive site filters Add option to store and generate reaction templates for SCINE Art Add possibility to slice trajectories Select and move multiple atoms in Interactive Add activate/deactive buttons to compounds in network view for rudimentary exploration control Allow direct connection to a database at start-up from the command line Introduce binary and human readable save formats for some tabs Added package variants for easier installation of optional requirements Generate graph of the entire CRN or import graph of the CRN for efficient processing purposes Introduced cache for every local CRN around a centroid; once built, it can be easily accessed again Enable fast filtering on barriers, flux, or date created (can be easily expanded to other filters) Reactions trajectory consistently extends from the center to the outer node Highlighting connected nodes when clicking on them Add new color style, legacy, based on Chemoton 1.0 colors Carry out steering wheel preview in background with progress bar with time estimate. The preview query can be aborted should it take too long Format reaction equation in path energy level widget Add timeout option for shortest path search, allowing users to easily interrupt lengthy searches if needed Add support for StructureFilter Add support for changed GearOptions Add AggregateFilter to database viewer tab Extend graph building capabilities Improve visualization of (shortest) path searches Improve error messaging Moved database queries to the SCINE Database module Rename 'Molecular Viewer' to 'Interactive' Node positions are now efficiently determined by algorithms implemented in Networkx Status bar in graph traversal is now identical to the main status bar Implement new caching logic for shortest paths, storing paths with and without two reactions in a path Add support for ElementaryStepFilter and ReactionFilter required by Chemoton 4.0.0. Handle the case of loading a completely empty database Prevent overlapping nodes in reactions Implement plateaus in spline representation to enhance visualization Being capable of representing local CRNs with more than 100 nodes Removed complicated code for positioning compound and reaction nodes, improving code readability and maintainability Functionalized individual parts to render and position nodes Functionalized reaction profile and cleaned up redundant code Employed energy diagram class for plateaus in reaction profile Removed substep_callback in Worker Update address in license