Fwdpy11

Bug fix:

* Raise error when simulating neutral mutations and
tracking mutation counts suppresses table indexing.
(PR {pr}`1342`)

Removes an unintended `print` statement from the C++ back end code.

Bug fixes:

Fix bug in handling fixation removal in generations
when simplification occurs. (PR {pr}`1326`)

Back end changes:

* Improve runtime validation of inputs to GSL discrete
lookup tables. (PR {pr}`1330`)
* Throw an exception if ALL diploid fitness values are 0. (PR {pr}`1330`)
* Throw an exception if ALL diploid fitness values are 0 within a single deme. (PR {pr}`1330`)
* Fix a warning relating to code not accepted in C++20. (PR {pr}`1333`)

Bug fixes:

Fix bug in handling fixation removal (1323)

* In effect, flags to remove fixations were ignored.
This likely occurred when modifying the back end
to support demes graphs, but I have not bothered to
bisect out the source of the error.
* Added explicit C++ and Python tests of removing fixations
* Updated Python tests of selective sweeps, including
fixing some logic errors in the tests that led them
to pass "by luck" rather than by design.

This bug does not affect simulation results for multiplicative
models. For such models, relative fitness is what matters
and not removing fixations still maintains relative fitness.

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`.