Ionbench

Initial state setting bug remaining in the previous release. Fixed here.

Bug fix in initial state setting to allow optimisation of remaining problems.

Improvements and updates made to profile likelihood. Markov model staircase problem no longer features noise as it interferes with the identifiability.

Tracker now records and saves the times for each of the model solves, separated into cost and gradient solves.

Added many more optimisers. Introduced lists of approaches to loop through and run everything. Added more features to the Tracker (now tracks time for model solves, reports if model was solve multiple times at the same parameters, and tracks the best parameters). Added more tests for the optimisers through a new problem specifically for ensuring all optimisers can optimise a simple problem. All problems now simulate from steady state for current parameters, rather than steady state for true parameters. Gradient calculator doesn't yet account for this.

Upgraded the gradient calculator to calculate the gradient of the cost function (or jacobian of the residuals) with respect to the parameters using myokit sensitivities. Added more optimisers which make use of this, such as a new SPSA algorithm, better matching the original from Spall 1998. Also added conjugate gradient descent, simulated annealing by Vanier 1999 and curvilinear gradient descent by Dokos 2004.