Release 4.0.0

Changes:

• Move network refinement to separate folder
• Move all filters to separate folder
• Move reaction rules to separate folder
• Remove deprecated database queries
• Removed some gear options such as pre_refine_model in favor of the default model field
• Set the default model option with PlaceHolderModel and check if it is still present before launching the gear to make sure that an intended model is used
• Small changes to the default arguments of the kinetic modeling gear to facilitate its use in SCINE Heron
• Add StructureFilters derived from fitting AggregatesFilters.
• Assemble reactive complexes from two given molecules easily with an CLI.
• Elementary Step Gears can set up reaction trials for flasks.
• Almost all Aggregate and ReactiveSiteFilters are made suitable for flasks. If not, a note is included in the documentation.
• Add an AggregateFilter that filters based on substructure searches.
• Add an AggregateFilter that filters based on allowed / disallowed molecular charges.
• Add reverse option for some existing AggregateFilters.
• KineticsGear now has an option that allows to run it as many cycles as long as no new aggregates are activated and then stops itself.
• Add gear to carry out additional energy calculations.
• Kinetic modeling may now work with a mixture of electronic structure models.
• Energies may now be automatically referenced as formation energies from the atoms.
• The bond-based trial generator is now able to enable (enable exploration/analysis) the analysis of structures,
  elementary steps, etc. in the results of already completed calculations, i.e., the trial generator detects that
  it already set up a calculation previously. Instead of just continuing, it may then enable the results of this
  calculation. This simulates a step-wise exploration of already existing data in the DB that was disabled before
  and is intended to allow re-exploration with different reaction conditions such as temperature and pressure or
  recycle existing data after changing the kinetics gear (or kinetic modeling, pathfinder etc.).
• Add a framework to filter reactions (analogous to the aggregates filters) and filter elementary steps. These
  new filters can be applied to the refinement framework (e.g., barrier-screening, barrier-less reaction selection,
  concentrations etc.).
• The refinement is now split into 3 gears:
  • Calculation-based refinement looping over the calculations and refining elementary steps (structures etc).
  • Reaction-based refinement looping over reactions and selects elementary steps to be refined for each reaction
    (including energy window for the step selection).
  • Aggregate-based refinement looping over aggregates and refining the structures of these aggregates (including
    energy window for the selection of the structure).
• All refinement gears support the same enabling strategy as introduced to the bond-based trial generator.
• Add reaction filter-based kinetics gear.
• Add reaction filter to constrain the maximum energy encountered when exploring a single potential energy surface.
• Add an aggregate filter to enforce that the particle number is conserved during the exploration.
• Add feature that a running Network Expansion of the Steering Wheel can be interrupted and continued later.
• Rework the Engine / Gear interaction, by replacing the sent signals with shared memory members
• Add EngineHandler class to join any forked engines if a signal is sent, replacing the custom code in the main script; the class also allows for running all engines and stopping the processes gracefully
• Change the internal representation of some AggregateFilters from strings to enums in order to be faster.
• Add additional caches to some AggregateFilters for increased performance.
• Add more default settings.
• The MinimalConnectivityKinetics and BasicBarrierHeightKinetics did not consider reactions where all reactants on the right hand side were available, which lead to fewer activated aggregates
• GearOptions of the NetworkExpansion did not consider that there could be multiple gears of the same type but with different options in a protocol, hence their datastructure (including access keys) are now changed.
• Fix type annotations in the documentation.
• get_transition_state_free_energy in the reaction_wrapper now returns max(e_lhs, e_rhs) if the reaction is
  barrier-less.
• Add more typehints