0.1.11-patch2

Fixed

• Fixed error in calculate_full_transition_matrix. The previous implementation tried to calculate the fitness for
  strategies with 0 counts in the population. This would lead to an error when calculating the probability of group
  forming. Now, we calculate directly the probability of a strategy with 0 counts increasing by 1 individual in the
  population, i.e., prob = (n_decreasing_strategy / population_size) * (mu / (1 - nb_strategies)).

What's Changed

• Bump ncipollo/release-action from 1.11.1 to 1.11.2 by @dependabot in #38

Full Changelog: v0.1.11-patch1...v0.1.11-patch2

0.1.11-patch1

Fixed

• Fixed issue with changing mutation rate in StochDynamics. When the mutation rate was updated
  using evolver.mu = new_value, the variable evolver.not_mu was not udpated. This variable was used
  by calculate_full_stationary_distribution and it created an error. Now not_mu is calculated inside
  of calculate_full_stationary_distribution.
• Fixed issue with binomialCoeff implemented in c++. In some cases, the intermediary calculations were overflowing
  an uint64_t type when calling it from multivariateHypergeometricPDF. Now, we no longer calculate the exact value
  in multivariateHypergeometricPDF, instead use double types. This will be improved in the new version by
  using boost/multiprecision uint128_t types.

Changed

• Bump robinraju/release-downloader from 1.5 to 1.6 by @dependabot in #36

Full Changelog: v0.1.11...v0.1.11-patch1

0.1.11

Fixed

• fixed errors in docstrings examples
• fixed missing headers
• fixed error in full_fitness_difference_group and calculate_fulll_transition_matrix. There was a missing
  multiplying factor in the probability of transition due to mutation. The probability of selecting the strategy to dies
  must also be taken into account. There was also an issue when instantiating the multi_hypergeometric_distribution
  class from scipy. It does not copy the array containing the counts of each strategy. Now we create a copy before
  passing the state vector to avoid the issue.
• fixed issue with AbstractNPlayerGame. For N-player games it was not a good idea to calculate the fitness in Python
  as this part of the class becomes a bottleneck, as it will be called more often then in the 2-player case (because
  there are more states - so less likely the fitness will be stored in cache). For this reason we now implemented this
  abstract class in C++ and the fitness calculation is done in this language. Everything else remains the same, and it
  should be equally easy to create new games.
• fixed issues of missing initialization of internal parameters of some egttools.games.NormalForm.TwoAction
  strategies. Internal parameters should be initialized when time == 0, i.e., at the beginning of each game.

Changed

• changed egttools to src-layout. This should help fix issues with tests and make the overall structure of the
  library cleaner.
• moved C++ code to the cpp folder. This way the code is more organized.
• Bump pypa/cibuildwheel from 2.8.1 to 2.11.1
• Bump pypa/cibuildwheel from 2.11.1 to 2.11.2
• Bump robinraju/release-downloader from 1.4 to 1.5
• Bump ncipollo/release-action from 1.10.0 to 1.11.1
• removed support for win32 and manylinux_i686 for Python > 3.7

Added

• added new controls to draw_stationary_distribution
• added enhancement_factor parameter to CRDGame. This parameter serves as a multiplying factor for the payoff of
  each player in case the target is achieved. If enhancement_factor = 1 the CRDGame behaves as usual.
  For enhancement_factor > 1, we are incentivizing strategies that reach the target.
• added MemoryOneStrategy to egttools.games.NormalForm.TwoAction strategies.
• added CommonPoolResourceDilemma game - However it has still not been extensively tested!!
• added ninja as a requirement for the build.
• added TimeBasedCRDStrategy to egttools.games.CRD strategies. These strategies make contributions to the Public
  Good in function of the round of the game.
• added sdist to build.
• added labels to the lines plot by plot_gradients so that several lines can be plotted.
• added more unit testing, but this still needs a lot of improvement.
• added missing libraries on C++ code.

Full Changelog: v0.1.10...v0.1.11

0.1.10

Fixed

• fixed issue with the comparison of different types in PairwiseMoran
• fixed issue with colorbar so that now the axis is passed to maptlolib colorbar, this way it will be plotted correctly
  when drawing multiple subplots
• fixed issue with hardcoded x-axis in plot_gradients
• fixed error on calculate_full_transition_matrix. The error happened when calculating the transition probability:
  • a) although the literature is a bit confusing on this, the original paper by Traulsen 2006 says that for the transition we consider that the strategies to reproduce and die are pricked simultaneously (so both with probability 1/Z).
  • b) the is more accumulated numerical error when doing probability of transitioning from A to B P(A, B) = fermi(-beta, B - A) than when doing fermi(beta, A - B). This is probably specific to Python and Numpy, but must be taken into account in the future.
  • c) The schur decomposition (egttools.utils.calculate_stationary_distribution_non_hermitian) works better in this case (although still has a slight numerical error) and should be used for full transition matrices).
• normalized transition probabilities to use the definition in Traulsen et al. 2006
  • now we assume that both death and birth individuals are selected simultaneously with probability n_i/Z, where n_i is the number of individuals of that strategy in the population

Changed

• updated installation instructions
• updated to PEP 621 syntax
• updated setup.py since now scikit-build supports VS2019
• updated draw_stationary_distribution to make the display of labels optional
• changed stability calculation for the replicator dynamics to use the Jacobian matrix
• updated plot_gradients to check for all possible types of roots (stable, unstable and saddle)
• removed stability checks for the stochastic dynamics
  • if T+ is too small, phi will be approximated to infinity and the fixation probability will be approximated to 0.
  • This may not be correct, since if p_minus is also very small or equal to p_plus, the outcome would be different.
    So it might change in a future version
• updated default language for documentation to en
• updated docstrings
• changed colorbar default label to gradient of selection
• droped pin to Sphinx <= 4.5.0
• updated variable name in AbstractGame
• changed name of variable in calculate_fitness method of Abstract game

Added

• added input parameter checks for run and evolve methods of PairwiseMoran
• created a method to calculate roots
• created a method to check the stability of the replicator dynamics through the Jacobian matrix
• added a check for the limit case in which the only non-negative eigenvalue is close to atol
• added new notebook with examples of use
• added an extra check when calculating fixation probabilities
• added Python 3.10 binary - except for Windows and manylinuxi686 as non numpy or scipy builds yet available
• added new CRD strategy
• added extra tolerance controls in check_replicator_stability_pairwise_games
• added new abstract game classes to simplify game implementation
• added NPlayerStagHunt game

Full Changelog: v0.1.9...v0.1.10

0.1.9-patch6

Fixed

• There was a problem with setting a geometric_distribution in C++ as a private variable for OpenMP which caused some
  errors when estimating stationary distributions. This was fixed by setting it as a shared variable.
• Fixed error on version formatting, it should be 0.1.9.dev6 instead of 0.1.9.patch6.
• Fixed wrong version tag on git.

Added

• Binder links to run examples and updated notebooks
• Add a Gitter chat badge to README.md by @gitter-badger in #12

Full Changelog: v0.1.9...v0.1.9-patch3

0.1.9-patch3

Added

• Added gitter chat and binder launch.

Fixed

• Added missing seaborn dependency. This dependency is only needed to be able to automatically generate colorblind
  colors to plot the invasion diagram, so it might be dropped in the future. But, for the moments, it provides the
  easiest way to do this.

Changed

• Updated docs and notebooks to use the latest egttools API.

Full Changelog: v0.1.9...v0.1.9-patch3

0.1.9-patch2

Fixed

• This release fixes an issue with a modulo operation that was causing an index error when calculating stability for plotting dynamics on a simplex.

Full Changelog: v0.1.9...v0.1.9-patch2

0.1.9-patch1

Fixes

This release fixes an issue with CITATION.cff which prevented zenodo from publishing a new doi.

Full Changelog: v0.1.9...v0.1.9-patch1

0.1.9

This releases fixes some bugs and simplifies the Simplex plotting.

Added

• Added plot_replicator_dynamics_in_simplex and plot_moran_dynamics_in_simplex to simplify the plotting of 2
  Simplexes when using replicator_equation and StochDynamics provided in egttools.
• Added an extra example to the docs to showcase the simplified plotting.

Fixed

• Fixed wrong numpy use in egttools.utils.calculate_stationary_distribution. Instead of numpy.eig the correct use
  is numpy.linalg.eig.
• Fixed issue with plotting edges which have random drift.
  Before egttools.plotting.helpers.calculate_stationary_points would logically find many roots in an edge with random
  drift and Simplex2D.draw_stationary_points would attempt to draw all of them. Now, we first search of edges in which
  there is random drift, and mask them, so that no stationary points nor trajectories are plot in the edge. Instead, we
  draw a dashed line to represent the random drift.

Changed

• Updated Readme.md to use the simplified plot_replicator_dynamics_in_simplex in the example of 2 Simplex plotting.

Full Changelog: v0.1.8...v0.1.9

0.1.8

The major feature of this update is to add a class to visualize evolutionary dynamics in 2-Simplexes.

Added

• Added Simplex2D class which can be used to plot the evolutionary dynamics in a 2-Simplex.
• Added OneShotCRD game.
• Added egttools.utils.calculate_stationary_distribution_non_hermitian which uses scipy.linalg.schur instead
  of numpy.linalg.eig. This function should be used when the transition matrix is not Hermitian (not symmetric if all
  the values are real). This may happen when studying the full state-space in a simplex of higher than 3 dimensions.

Fixed

• Fixed issue with extending AbstractGame in Python.
• Fixed bug in egttools.utils.get_payoff_function.

Changed

• Updated output of StochDynamics.transition_and_fixation_matrix so that the correct fixation probabilities are
  returned, instead of fixation_probabilities/(1/Z).
• draw_stationary_distribution was also updated so that it expects the fixation probabilities as input and
  not fixation_probabilities/(1/Z).
• Several improvements in documentation and docstrings.

Full Changelog: v0.1.6.dev7...v0.1.8