Point release

0.21.3

Deprecations

• Constructing {class}fwdpy11.ModelParams without a demographic object is now deprecated
  and raises a warning.
  This will be a hard error in a future release.
  PR {pr}1219

Documentation

• Minor updates to manual.
  Some formatting issues fixed.
  PR {pr}1222
  PR {pr}1223

Python back end

• Use tskit.NODE_IS_SAMPLE constant instead of relying on the numeric value
  when exporting to tskit.
  PR {pr}1218

Bug fix

0.21.2

Bug fixes

• Fix internal error validating distributions of effect sizes for multi-deme models
  with correlations in effect sizes between demes.
  PR {pr}1210.

Examples

• Update examples to latest API and run them in CI.
  PR {pr}1211.

Dependencies

• Bump pybind11 to 2.11.11.
  PR {pr}1172.
• Require tskit >= 0.5.6
  PR {pr}1206.
• Add cmake dependency to pyproject.toml.
  PR {pr}1177.
• Bump demes-forward-capi to depend on latest version.
  PR {pr}1182.

Deprecations

The following are deprecated:

• fwdpy11.GSS
• fwdpy11.GSSmo
• fwdpy11.MutivariateGSS
• fwdpy11.MutivariateGSSmo

Their functionality is replaced with {class}fwdpy11.GaussianStabilizingSelection.

PR {pr}1166.
Issue {issue}{463}.

Version 0.21.0

0.21.0

Breaking changes

• Refactor {class}fwdpy11.conditional_models.SimulationStatus as an enum.
  This change makes correct use much easier.
  PR {pr}1161.
  Issue {issue}934.

Fixes

• {class}fwdpy11.conditional_models.ConditionalModelOutput now contains
  fields allowing one to distinguish if the tracked mutation is still present
  in {attr}fwdpy11.DiploidPopulation.mutations and/or {attr}fwdpy11.DiploidPopulation.fixations
  PR {pr}1163.
  Issue {issue}1160.

New features

• {func}fwdpy11.DiploidPopulation.create_from_tskit is now able to restore
  individual metadata, populating {attr}fwdpy11.DiploidPopulation.diploid_metadata
  and {attr}fwdpy11.DiploidPopulation.ancient_sample_metadata.
  PR {pr}1157.
  Issue {issue}1130.

CI changes

• Remove tests using conda environments.
  This removal was a pragmatic decision to speed up CI time.
• Test macOS/x86 using brew instead of conda
• Reduce number of work flows run for PRs into the dev branch.
  Several work flows are only needed when merging into main.
• Reduce number of work flows running upon push to main/dev.
  We now use branch protection, so in theory any changes merging
  have passed their CI requirements.

Bug fix release

Fixes bug #1153 via pr #1155.
Improves issues with build system (issue #1154, pr #1156).

v0.20.0

This is the first stable release of the 0.20.x series.

The main change is that a rust implementation of demes is used by the C++ back end to manage the internal state of the demographic model.

The CHANGELOG is extensive for this one!

Second alpha of 0.20.0

0.20.0a1

New features

• Add {class}fwdpy11.BinomialIntervalMap.
  PR {pr}1142

Back end

• Improve test suite run times.
  PR {pr}1136
• Refactor some C++ test fixtures.
  PR {pr}1139
• Python tests now treat warnings as errors.
  PR {pr}1135

Documentation

• Improve docs related to {class}fwdpy11.ForwardDemesGraph.
  PR {pr}1133
  PR {pr}1137

0.20.0 alpha 0

0.20.0a0

New features

• {func}fwdpy11.DiploidPopulation.create_from_tskit now uses the generation field from top-level metadata to restore all times to their forward-in-time values.
  PR {pr}1129
• Discrete demographic models are now managed by
  {class}fwdpy11.ForwardDemesGraph
  See {ref}here <demes_vignette>.
  PR {pr}1101
  PR {pr}1103
  PR {pr}1121
  PR {pr}1123
  PR {pr}1124
• Add support for Python 3.11
  PR {pr}1108
• Allow suppressing of residual selfing.
  See {ref}here <demes_details>.
  PR {pr}1117
  PR {pr}1118

Deprecations

• Deprecate use of {class}fwdpy11.Region for recombination
  PR {pr}1126

Breaking changes

• Drop support for Python 3.7
  PR {pr}1108
• Removed deprecated discrete demography API
  PR {pr}1101
  PR {pr}1116

Documentation

• Give link to examples of lists of "gvalue" objects
  PR {pr}1127
• Rewrite demes-related documentation
  PR {pr}1124

Documentation improvement

Rewrote a vignette to focus only on what it is trying to document.

#1119, issue #1104

Bug fix

Bug fix:

• When building a population from a tskit tree sequence, we now correctly handle the origin times of mutations generated from within fwdpy11.
• This fix allows evolve/export/import/evolve work flows

PR #1113

Bug fix / new feature (matter of perspective)

Added support for creating a population from a tskit tree sequence output from a previous fwdpy11 run.

PR #1110 / issue #1109