Pyabc

-------------------

* In ABCSMC.run, allow a default infinite number of iterations, and log the
ESS in each iteration.
* Reformulate exponential temperature decay, allowing for a fixed number of
iterations or fixed ratios.
* Solve acceptance rate temperature match in log space for numeric stability.
* Perform temperation of likelihood ratio in log space for numeric stability
(all 221).
* Fix wrong maximum density value in binomial kernel.
* Allow not fixing the final temperature to 1 (all 223).
* Allow passing id to history directly (225).
* Pass additional arguments to Acceptor.update.
* Give optional min_rate argument to AcceptanceRateScheme (all 226).
* In plot functions, add parameter specifying the reference value color (227).

-------------------

* Fix extras_require directive.
* Fix error with histogram plot arguments.
* Extend test coverage for visualization (all 215).
* ABCSMC.{new,load,run} all return the history with set id for convenience.
* Document pickling paradigm of ABCSMC class (see doc/sampler.rst).
* Always use lazy evaluation in updates (all 216).
* Restructure run function of ABCSMC class (216, 218).
* Run notebooks on travis only on pull requests (217).
* Correct weighting in AcceptanceRateScheme (219).

-------------------

* Fix error that prevented using rpy2 based summary statistics with non rpy2
based models (213).

-------------------

* Introduce acceptor.StochasticAcceptor to encode the stochastic acceptance
step generalizing the standard uniform criterion.
* Introduce distance.StochasticKernel to encode noise distributions, with
several concrete implementations already.
* Introduce epsilon.Temperature to capture the temperature replacing the
traditional epsilons. In addition, multiple concrete
pyabc.epsilon.TemperatureSchemes have been implemented that handle the
calculation of the next temperature value (all 197).

-------------------

* Add high-level versions of the kde plotting routines (204).
* Add unit tests for common epsilon schemes (207).

-------------------

* Move to cffi>=1.13.1 after that bug was surprisingly quickly fixed (195).
* Create sub-module for epsilon (189).
* Add plots for sample and acceptance rate trajectories (193).