Epydemic

- Refactored event taps to be more general
- Added events and new query methods to the Newman-Ziff percolation processes
- Changed the way Newman-Ziff results are returned in notebooks
- Added named sub-processes in process sequences
- Reformulated tutorial to avoid some confusions
- Added recipe on percolation

- Added recording of first hitting time for nodes
- Added options to CompartmentedMode.markOccupied() and CompartmentedModel.markHit()
to only record the first occupation and hitting times respectively,
and to ignore subsequent re-transmission or -infection
- Added tests to make sure epidemics happen (when they should) on a per-model
basis but under both dynamics
- Added more tests for generating functions
- Simplified experimental parameter names
- Small changes to the way topologies are marked in parameters
- Integrated opinion dynamics, vaccine-enhanced SIR, and anti-vax rumour models
- Removed all uses of multiple inheritance
- Added tutorial explanations of process composition
- Fixed CI job
- Added optional meaningful event names
- Added event taps sub-system, documentation, and implemntation note
- Added installing type stubs for Python 10
- Added InterSphinx links to the important parts of epyc, to make it easier to
understand what's going on in large-scale simulations
- Changed the generating function interface slightly, as well as its internals

- Fixed generating functions library not installing

- Changed implementation of Percolate to use the Newman-Ziff approach
- Refactored the setting of initial compartments in CompartmentedModel to
use changeInitialCompartment instead of changeCompartment, so that initial
behaviour can be different
- Changed the cookbook recipe on choosing which nodes to infect to include
more code
- Changed the exception raised by CompartmentedModel.initialCompartmentDistribution
in the case of an illegal distribution to ValueError
- Integrated the generating functions library
- Added type annotations to documentation format (makes reading the docs easier)
- Added "shuffle" process for rewiring edges
- Wrote implementation note on generating functions

- Added topology marker to parameters to capture the network generator used
- Changed names of network generation parameters to match the topology markers
- Added class inheritance diagram to documentation
- Added speed improvements to front page
- Added discussion of going from R values to SIR parameters

- Started maintaining simulation time in NetworkDynamics
- Changed the way Monitor represents its results, to avoid problems persisting
in HDF5 lab notebooks
- Lots of changes to typing and imports, for code style
- Upgraded Locus to get a major performance improvement
- Updated the cookbook recipe for parallelism and multicore
- Fixed typos in monitor recipe, added plotting code
- Added documentation for DrawSets