Fwdpy11

Bug fixes:

* For multiplicative fitness models, "super lethal" mutations ("s" < -1.0)
could results in positive fitness values.
This is now fixed, and the fitness function returns as soon as "w" <= 0.
PR {pr}`1319`

Deprecations

* All previous deprecations have been removed. PR {pr}`1301`
* Site frequency spectrum calculations from tables are now deprecated.
PR {pr}`1292`
* Redundant methods for loading demes graphs are now deprecated.
PR {pr}`1304`

UI improvements

* Add {attr}`fwdpy11.ForwardDemesGraph.demes_graph`.
PR {pr}`1297`.
PR {pr}`1298`.
* Improve early detection of invalid optimum values.
See issue {issue}`1217` for context.
PR {pr}`1299`.

C++ back end:

* Code for genetic value calculations extracted into a location available
for C++ unit testing.
PR {pr}`1319`
* Run c++ test suite through valgrind in CI. PR {pr}`1296`

Dependencies

* pybind11 bumped to 2.12.0. PR {pr}`1313`
* demes-forward-capi bumped to 0.5.0. PR {pr}`1294`
* scipy dropped as a dependency. PR {pr}`1292`

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](https://cibuildwheel.pypa.io/en/stable/) is used to build wheels.
* `docker` images are only pushed for releases and not for each commit
to `main`.

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`

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`