Merge branch 'master' into i-1067-generic-stochastic-model

Author: phumtutum

CHANGELOG.md

@@ -2,10 +2,28 @@
 
 All notable changes to this project will be documented in this file.
 
-## [Unreleased]
+## Unreleased
 
 ### Added
 - [#1417](https://github.com/pints-team/pints/pull/1417) Added a module `toy.stochastic` for stochastic models. In particular, `toy.stochastic.MarkovJumpModel` implements Gillespie's algorithm for easier future implementation of stochastic models.
+- [#1420](https://github.com/pints-team/pints/pull/1420) The `Optimiser` class now distinguishes between a best-visited point (`x_best`, with score `f_best`) and a best-guessed point (`x_guessed`, with approximate score `f_guessed`). For most optimisers, the two values are equivalent. The `OptimisationController` still tracks `x_best` and `f_best` by default, but this can be modified using the methods `set_f_guessed_tracking` and `f_guessed_tracking`.
+
+### Changed
+- [#1424](https://github.com/pints-team/pints/pull/1424) Fixed a bug in PSO that caused it to use more particles than advertised.
+- [#1424](https://github.com/pints-team/pints/pull/1424) xNES, SNES, PSO, and BareCMAES no longer use a `TriangleWaveTransform` to handle rectangular boundaries (this was found to lead to optimisers diverging in some cases).
+
+### Deprecated
+
+### Removed
+- [#1424](https://github.com/pints-team/pints/pull/1424) Removed the `TriangleWaveTransform` class previously used in some optimisers.
+
+### Fixed
+
+
+## [0.4.0] - 2021-12-07
+
+### Added
+- [#1409](https://github.com/pints-team/pints/pull/1409) The `OptimisationController` now accepts a callback function that will be called at every iteration; this can be used for easier customisation or visualisation of the optimiser trajectory.
 - [#1383](https://github.com/pints-team/pints/pull/1383) Added a method `toy.TwistedGaussianDistribution.untwist` that turns samples from this distribution into samples from a multivariate Gaussian.
 - [#1322](https://github.com/pints-team/pints/pull/1322) Added a method `sample_initial_points` that allows users to generate random points with finite metrics (either log-probabilities or error measures) to use as starting points for sampling or optimisation.
 - [#1243](https://github.com/pints-team/pints/pull/1243) Added testing for Python 3.9.
@@ -21,6 +39,7 @@ All notable changes to this project will be documented in this file.
 - [#1025](https://github.com/pints-team/pints/pull/1025) Added a stochastic logistic growth problem for use with ABC.
 
 ### Changed
+- [#1420](https://github.com/pints-team/pints/pull/1420) The `OptimisationController` now logs a best and a current score.
 - [#1375](https://github.com/pints-team/pints/pull/1375) Changed all arguments called `transform` to `transformation` for consistency.
 - [#1365](https://github.com/pints-team/pints/pull/1365) Dropped support for Python 2.7. PINTS now requires Python 3.5 or higher.
 - [#1360](https://github.com/pints-team/pints/pull/1360) The `ParallelEvaluator` will now set a different (pre-determined) random seed for each task, ensuring tasks can use randomness, but results can be reproduced from run to run.
@@ -32,6 +51,7 @@ All notable changes to this project will be documented in this file.
 - [#1112](https://github.com/pints-team/pints/pull/1112) The `pints.Logger` can now deal with `None` being logged in place of a proper value.
 
 ### Deprecated
+- [#1420](https://github.com/pints-team/pints/pull/1420) The methods `pints.Optimisation.xbest()` and `fbest()` are deprecated in favour of `x_best()` and `f_best()`.
 - [#1201](https://github.com/pints-team/pints/pull/1201) The method `pints.rhat_all_params` was accidentally removed in 0.3.0, but is now back in deprecated form.
 
 ### Removed

docs/source/optimisers/boundary_transformations.rst

@@ -16,7 +16,6 @@ or the :class:`OptimisationController` class.
     running
     base_classes
     convenience_methods
-    boundary_transformations
     cmaes_bare
     cmaes
     gradient_descent