Fwdpy11

Deployment

* Update docker base image to `ubuntu:jammy`.
PR {pr}`1031`
* Docker images now installs into a venv rather than globablly.
PR {pr}`1031`
* Fix docker tags so that `latest` means the latest release.
PR {pr}`1036`

Documentations

* Document how to build core library in isolation.
PR {pr}`1038`
* Document `cbindgen` requirement for development.
PR {pr}`1030`

Back end changes

* C++ back ends of Region/Sregion now validate their coordinates at run time.
PR {pr}`1032`
* Add wrapper to `gsl_ran_flat` to avoid returning max value.
PR {pr}`1035`

Testing

* Separate Python tests requiring compiled C++ modules to
another directory.
PR {pr}`1037`

Rewrite vignette on importing mutations from tskit

New features

* Ability to import tree sequences with mutations from tskit.
A new {ref}`vignette <import_mutations_from_tskit_vignette>` describes the procedure.
PR {pr}`1026`.

Bug fixes

* Fix bug in sweep models.
The fix in PR {pr}`1020` was incomplete.
Tree span is now accounted for.
PR {pr}`1026`.
* Fix Python-side constructors in Mutation re: integer types.
No previous results were affected.
PR {pr}`1023`.

Documentation

* Update developer docs.
PR {pr}`1021`.

Bug fixes

* Fix bug in sweep models.
The previous implementation chose acceptable branches for mutation placement uniformly.
The new method chooses proportionally to branch length.
PR {pr}`1020`.

API changes

* Remove deprecated `WrappedTreeSeqeuence`
PR {pr}`978`.
* Add Python-level checks that "regions" don't contain positions extending past the genome ends.
PR {pr}`987`.

Dependencies

* Bump pybind11 to 2.10.0
PR {pr}`986`.

Build system and CI

* Remove all use of automake/autoconf.
PR {pr}`971`.
* Build core library as shared library.
PR {pr}`961`.
* Allow for standalone cmake builds.
PR {pr}`966`.
* Add rust crate `demes-forward-capi` to core lib.
PR {pr}`962`.
PR {pr}`1001`.
* Build C++ tests with cmake.
PR {pr}`967`.
* Use `python -m build .` for Ubuntu CI.
PR {pr}`970`.
* Build all C++ targets in one command on Ubuntu CI.
PR {pr}`972`.
* Test docker work flow on CI.
PR {pr}`979`.
* Add cancel actions to all work flows.
PR {pr}`982`.
PR {pr}`985`.
* Wheels are now based on `manylinux_2_28`
PR {pr}`994`.
* move `fwdpy11/src` to `cpp/`
PR {pr}`996`.
* Add dependabot for GitHub actions
PR {pr}`1002`.
* Fix warnings from `python -m build .`
PR {pr}`1018`.

Back end changes

* Move evolve code to core library.
PR {pr}`974`.
* Clean up implementation of individual and mutation metadata decoding.
PR {pr}`1015`.
* Tidy up a lot of `mypy` errors.
PR {pr}`1016`.

Testing

* Remove many C++ files from tests/
PR {pr}`976`.
* Test that we can load YAML files from demes-spec
into our rust-based ForwardDemesGraph.
PR {pr}`975`.
* move `fwdpy11.ezparams` module to tests/
PR {pr}`977`.
* Add C++ tests of our new "forward demes graph".
PR {pr}`980`.
PR {pr}`983`.
PR {pr}`984`.
PR {pr}`989`.
PR {pr}`999`.

Fixes 990

Fixes a bug in demes models with zero burn-in length. 949

for other changes, see the change log in the manual.