molpopgen/fwdpy11: v0.19.0

This is a major back end release:

• rust and demes-rs integration
• main functionality is built into a core shared library

Two bug fixes.

One new feaure: importing mutation from tskit tree sequences.

0.19.0

Differences from the last stable release also include entries for all alpha releases listed below

Documentation

• Add new vignettes. See {ref}here <varying_fitness_conditions_across_demes_intro> PR {pr}950

Bug fix

• Add runtime checks for invalid models where effect sizes vary across demes. PR {pr}1047

Testing

• Disable wheel build workflow for PRs PR {pr}1048

0.19.0a5

Deployment

• Add missing , to docker tag names PR {pr}1042

Testing

• Remove stray return statement in a test. PR {pr}1043

0.19.0a4

Deployment

• Add a version name tag to releases PR {pr}1041

Documentation

• Describe podman and give singularity example in deployment section. PR {pr}1040

Testing

• Fix logic error in testing mutation import from tskit. PR {pr}1039

0.19.0a3

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

0.19.0a2

Documentation

• Rewrite {ref}vignette <import_mutations_from_tskit_vignette>. PR {pr}1026.

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.

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.