GADMA2.0.2

An update to the version 2.0.1, which has a bug and is not possible to run. Description from GADMA2.0.1:

GADMA was updated and tested on Python3.10 with the latest versions of dependencies.

Changelog since 2.0.0:

• Add lower bounds for first and second splits (see #92)
• Create pyproject.toml and setup.cfg
• Add dependencies including moments-popgen, demes and demesdraw to setup - they will be automatically installed.
• Change code to work with last version of moments.
• Drop support for Gpy and GPyOpt bayesian optimization
• Tests for SMAC bayesian optimization does not run on GitHub Actions - need to upgrade code for the last smac version (TODO).
• Update params_file template
• Update docs

GADMA2.0.1

GADMA was updated and tested on Python3.10 with the latest versions of dependencies.

Changelog since 2.0.0:

• Add lower bounds for first and second splits (see #92)
• Create pyproject.toml and setup.cfg
• Add dependencies including moments-popgen, demes and demesdraw to setup - they will be automatically installed.
• Change code to work with last version of moments.
• Drop support for Gpy and GPyOpt bayesian optimization
• Tests for SMAC bayesian optimization does not run on GitHub Actions - need to upgrade code for the last smac version (TODO).
• Update params_file template
• Update docs

Official release of GADMA2.0.0

Final official release of GADMA2. It includes all previous pre-releases (2.0.0rc1 - 2.0.0rc26).

Changelog since 2.0.0rc26:

• Catch cases when theta and ancestral population size are negative for moments and dadi engines (issue #84). Fix optimization routine to ignore such parameters.
• Fix GitHub Action tests and PyPi publishing.
• Add documentation (regarding issues #60, #75, #85)
• Add note when SFS is build from less than 90% of given SNPs.
• Option Split fraction is set to be False by default.
• Update code according with new version of moments.LD that has nus in steady_state.

Minor bug fix

Fix float problem with new versions of numpy.

Minor fix for demes draw

Demes engine had an issue to multiply time twice by the generation time. It was fixed with small change.

Minor fix for claic evaluations and new messages in cmd

2.0.0rc24

Fix claic bug

Minor bug fix and new features

• Fix bug with momentsLD engine for models with exponential or linear change
• Restrict momi2 to use only one core
• Use another scipy function for Nelder_mead algorithm (local)
• Make all histories with different parameters when structure is changed (e.g. from 1,1 to 2,1)
• Allow usage of models specified using gadma API

Official release with Bayesian optimization

• Fix bug when failed model is reported as best (Issue #73 )
• Add additional checks for Bayesian optimization
• Add documentation about BO

Final changes that were planed

• Add linear extrapolation for dadi (Issue #68 ).
• Engine momi is renamed in momi2.
• Add dominance rate in the params file interface.
• Fix bug with CLAIC evaluation (for any eps it was taken as 1e-2).
• We changed hyperparameters of GADMA2
• Fix minor bugs.
• Fix documentation

Minor changes

This is rather small release with some fixes.

• We have removed bug that was caused by new moments version.
• GA now can be run after BO
• Momi engine can read .gz files now.