Fwdpy11

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 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`