Maintenance release

0.22.2

Maintenance release

C++ back end:

• Clear table collection indexes early each generation.
  PR {pr}1272

Build system

• Use scikit-build as the build backend.
  PR {pr}1284
• Remove boutique arguments from setup.py.
  PR {pr}1288
• Remove setup.py.
  PR {pr}1291

CI and deployment

Several PRs resulted in the following changes:

• macos CI now runs on Apple Silicon runners
• macos wheels are now built for two recent Python versions for both
  x86 and arm64 platforms
• cibuildwheel is used to build wheels.
• docker images are only pushed for releases and not for each commit
  to main.

Bug fix

0.22.0

Bug fixes:

• Fixed incorrect handling of models with end times > 0 in a demes Graph.
  When exporting to tskit, alive node times were treated as 0.0, causing
  potential problems for some use cases.
  Issue {issue}1253
  PR {issue}1255

Deprecations

• Deprecate the demes_graph argument to {func}fwdpy11.DiploidPopulation.dump_tables_to_tskit
  PR {issue}1265
• Deprecate using a dict for the the model_params argument to {func}fwdpy11.DiploidPopulation.dump_tables_to_tskit
  PR {issue}1265

Set time_units in output tree sequence

Data output to tskit now sets the time_units to generations.

Python 3.12 support

Add support for Python 3.12, including wheels for Linux and macOS/x86.

Point release

0.21.4

Behavior changes:

• {func}fwdpy11.DiploidPopulation.add_mutation now considers the overlap
  with the desired interval when calculating weights.
  PR {pr}1228
  Issue {issue}1180
• Raise warnings when removing selected fixations may
  not be the right thing to do during a simulation.
  PR {pr}1235

Documentation

• Remove deprecated API use from manual.
  PR {pr}1233

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!