v0.19.5

Bug fix in the new implementations of binomial crossover types released in 0.19.4

PR #1088

major performance improvement

Massive improvement to the performance of simulations using genetic maps with a large number of PoissonInterval classes.

These changes mean that simulations with many regions will give different results for the same random number seed.

#1087 (see issue #1082)

This release also include several back-end changes getting ready to use demes models directly.
See the detailed change log in the manual.

v0.19.3

0.19.3

Deprecations

• The low-level Python API for defining demographic events
  is now deprecated and will raise warnings.
  No action has to be taken yet.
  There is no replacement API to migrate to.
  PR {pr}1064.

Back end changes

• Prepare to refactor C++ code to evolve directly from demes graphs.
  PR {pr}1063.
  PR {pr}1067.
• Boolean flags affecting simulation behavior collected into struct.
  PR {pr}1061.

Documentation improvement

This release updates one of the vignettes:

• Fix an error where the vignette says we cannot import tskit tree sequences with mutations.
• Add a link to the vignette showing exactly how to create/import such tree sequences.

0.19.2

Documentation

• Add link between vignettes regarding
  importing tree sequences from tskit.
  PR {pr}1054.
• Force notebooks to be executed during doc builds.
  PR {pr}1058.

Testing/CI

• Docs workflow updated to run with Python 3.10.
  PR {pr}1056.

Bug fix release

Fixes the generation of the source distributions uploaded to PyPi.

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.

v0.19.0a5

0.19.0a5

Deployment

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

Testing

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

v0.19.0a4

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

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.