Fwdpy11

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`}.

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.

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

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

The main change is that a [rust implementation](https://github.com/molpopgen/demes-rs) of [demes](https://popsim-consortium.github.io/demes-spec-docs/main/introduction.html) is used by the C++ back end to manage the internal state of the demographic model.

The [CHANGELOG](https://molpopgen.github.io/fwdpy11/misc/changelog.html) is extensive for this one!

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`

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`