Releases: molpopgen/fwdpy11
Bug fix release
Bug fix release
v0.19.5
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.
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
tocpp/
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
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