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Releases: molpopgen/fwdpy11

Bug fix release

15 Mar 20:35
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Bug fix release

10 Mar 23:33
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Bug fix

  • Fix error in conditional models when sampling ancient
    samples throughout the focal mutation sojourn.
    PR #1094
    Issue #1093

v0.19.5

08 Mar 14:28
b3c405f
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Bug fix in the new implementations of binomial crossover types released in 0.19.4

PR #1088

major performance improvement

07 Mar 21:20
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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

23 Feb 12:36
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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

12 Jan 19:08
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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

29 Nov 18:00
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Fixes the generation of the source distributions uploaded to PyPi.

v0.19.0

14 Nov 23:18
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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

12 Nov 23:54
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v0.19.0a5 Pre-release
Pre-release

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

12 Nov 22:13
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v0.19.0a4 Pre-release
Pre-release

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