v0.19.0a2

Rewrite vignette on importing mutations from tskit

v0.19.0a1

0.19.0a1

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.

v0.19.0a0

Alpha relase

0.19.0a0

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.

Bug fix

Fixes #990

Minor bug fix, CI changes, back end tweaks.

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

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

Minor bug fix

Fix bug in the display of effect size distributions (#885)

Several bug fixes

This is a somewhat large release -- see the change log over in the manual. Lots of bug fixes, deprecations removed, etc..

Big thanks to @apragsdale for lots of help on this one.

Point release

Fixes a bug where some selective sweep models took to long to figure out that the mutation was gone. This error did not give incorrect results. Rather, it resulted in less efficient work flows. See #893

0.17.0

First stable release of the fwdpy11.conditional_models module.

This module allows simulations conditioning on events like sweeps,
mutations with minimal ages, etc..

The API is somewhat preliminary, and the docs minimal.

Fifth alpha release of 0.17.0

Bump tskit to ~0.4.0 (#874)

* bump tskit to ~=0.4.0 and rebuld pip lock files

* Update change log