Fwdpy11

Data output to tskit now sets the time_units to generations.

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

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`

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.