change the stop criteration of a ContinuousTimeModel simulation.
Minor fix  in ContinuousTimeModel for the euclidean distance automata
tests.
Add of a test for stop criteria simulation of ContinousTimeModel
(unit/simulation_stop_criteria).

All tests passed.

It computes the euclidean distance and finish the simulation if the
distance is above the tolerance epsilon.
I ha to change some function signature of types in core/model.jl but it
was minor changes.
I add a new test + change some others related to automata.
A minor rewriting core/model for better readability

The solution is to use FunctionWrappers.jl which provides a high
interface for C function pointers.

All tests passed.

update_state functions but performance gets worst.
With bench/pkg/abstract_arrays.jl i've highligthed each time a function
is in a collection performance gets worst.

implemetend in the package.
A lot of files has been modified because some of the internal syntax has
changed. But the top level methods should still work.

Two tests about the plots of synchronized oscillatory simulations have
been added.

All tests passed.

This commit groups the change operated to the creation of models and
simulate function of a ContinuousTimeModel.
The general idea is to create a concrete type and a simulate function
 per model creation by metaprogramming.
- Now, ContinuousTimeModel is an abstract type. Each creation of a model
defines a concrete type T <: ContinuousTimeModel by meta programming.
- f! and isabsorbing ContinuousTimeModel fields are Symbols.
- simulate(::ContinuousTimeModel) is run by multiple dispatch, according
to the type of the model.

Can't run the whole tests for now but unit/simulate_available_models.jl
runs properly (i've updated the list of models in this commit), and I've
manually checked in the repl that simulations run correctly (distributed
/ plots).

check_constraint and update_state functions are created inside
create_automaton_*(), by the evaluation of meta_elementary_functions <:
Expr. check_constraint and update_state don't depend on constants::Dict
anymore: constants are interpolated inside the expression.

Add of tests for euclidean distance automaton.
Add a new function euclidean_distance that computes the euclidean
distance of a Trajectory compared to observations along a discrete
timeline.

automata and proba moels are differents. This bug was introduced after
we change the structure of automata in order to better distributed
programming.
It leads to a restructuration of automata. In fine, the structure is
more stable and consistent. It is possible it is more computationally
efficient, but for now it is not well tested.

2) Creation of functions that collects data along with a timeline
over a trajectory + unit test vectorize.

3) Very small fix in plots and abc smc.

Fix in simulation of macro generated models. Small changes with variables types of the pkg. Small change in test of macro models.

Modification of print of models + renaming macro for creation of models in order to be more inclusive.

to define CTMC with the biochemical network.

copyto! is implemented for LHA states.

Automaton G works almost well, a bias in the distance is identified
compared to Cosmos when one of the model parameters is zero.

Implementation of volatile_simulate, which simulates SynchronizedModel
without saving values: it only returns the last LHA state of the
simulation.

Implementation of distributed computations of variable automata with
volatile_simulate.

Tests passed.

Fix about methods of SynchronizedTrajectory + tests.

Simulation for ParametricModel works.

First bricks of the automaton_abc algorithm.

Add several convenient methods for parameters of model.

Next step: implementation of simulate with resize!.

order to replace vcat by push!.

The benchmarks are at least equal, and better when the buffer size is
small. However, no significative difference of performance with adequate
buffer size.

My opinion the gain can be seen when simulations are going to be very
long with more complicated models than we have implemented for now.

All tests passed.

Add of set_time_bound!
Add of a first notebook example to explain the package.

Add of a major test based on Cosmos: tests/cosmos/distance_F/ER_1D.jl

The LHA distance F of this package is tested with Cosmos.
For several parameters in R1, R2, R3 experiments (see Bentriou,
Ballarini, Cournede 2018), Cosmos is called to
compute an average distance. Then we collect the number of simulations
and the estimated value computed by Cosmos.
We compute an average distance by the package methods with the same
number of simulations done by Cosmos

Then the two average distances are compared to each others with
regard to the width of the confidence interval set in Cosmos.
Test passed.

Add of a new type of Trajectory: SynchronizedTrajectory which is created
by the simulation of a synchronized model with an LHA.

Simulate function for SynchronizedModel executes and is tested by two
simple models.

Next step : Cosmos based tests.

Add of several useful functions for access values of model, lha and
trajectory objects.

an object.

Type stability of simulate, dist, read_trajectory seems to be preserved.

First implementation of LHA.
Synchronized simulation not yet tested.
Reading of trajectories with LHA seems to work with one test basted on
simulations that checks that the last value is well read.

Major fix of type unstabilities which improved performances.
For now on, we observe for pygmalion benchmarks:
+2x speed simulation compared to simulation of models.
100x speed in terms of reading values (no allocations).

Fix of a major issue in the simulation: sometimes the number of states
wasn't consistent. Add of test to check the consistency of the
Trajectory structure (unit/check_trajectory_consistency).

Implementation of the lp distance for trajectories.
Add of unit tests for lp distance.

can be set by the user. Changes of SIR and ER.