Releases: molpopgen/fwdpy11
0.17.0, second alpha release
0.17.0a1 Rename conditional_models.track_mutation to conditional_models.track_…
First alpha release of 0.17.0
First alpha version: several bug fixes and draft API of fwdpy11.conditional_models.
Point release
Point release
Minor release--some documentation fixes and a better str
for fwdpy11.Mutation
Several "demes" model fixes
Most of the issues/PRs are collected under milestone 0.16.0
From the change log:
Bug fixes
- An integer type in the infinitely-many sites mutation model was changed from unsigned to signed.
This does not affect previous results because unsigned overflow doing the "right thing" ended up with final values being correct.
PR {pr}766
Issue {issue}765
- Fix a bug where stopping/restarting the evolution of demographic models at time points
where a deme goes extinct.
It is not possible that this bug affected results from earlier versions, as attempting to stop/start at these time points raised exceptions.
Issue {issue}775
PR {pr}774
- Fix bugs in C++ back-end for discrete demographic models.
In some cases, we were using the wrong vector of deme sizes to update the model,
leading to runtime exceptions.
PR {pr}802
PR {pr}803
- Fix error in
demes
models where "replacement" models had 1 generation of overlap between ancestral/derived demes.
Issue {issue}814
PR {pr}815
{user}apragsdale
{user}molpopgen
Behavior changes
- If a demographic model is evolved, pickled, unpickled, and then used to evolve,
it is now possible that exceptions will raise.
This change is due to the fix for Issue {issue}775
introduced in PR {pr}774
.
See issue {issue}777
for more background. - Mass migration events implemented via {func}
fwdpy11.copy_individuals
and {func}fwdpy11.move_individuals
now occur after sampling within a generation.
This change makes the timings consistent with all other events and also makes
certain operations easier/feasible.
{pr}809
- Calling {func}
fwdpy11.infinite_sites
during a simulation now raisesRuntimeError
.
{pr}820
{issue}769
- Models imported from
demes
now start the forward-time portion of the model 1 (one) generation before the most ancient end time of an ancestral deme.
{pr}818
{user}apragsdale
{user}molpopgen
New features
- Add {func}
fwdpy11.DiploidPopulation.add_mutation
.
PR {pr}764
PR {pr}799
- Add {class}
fwdpy11.NewMutationData
.
PR {pr}764
- Add
__copy__
and__deepcopy__
to {class}fwdpy11.DiploidPopulation
.
PR {pr}770
- Add
__deepcopy__
to {class}fwdpy11.DiscreteDemography
.
PR {pr}773
C++ back-end
- A population can now be checked that it is- or is not- being simulated.
PR {pr}762
- {class}
fwdpy11.discrete_demography.DiscreteDemography
now stores the migration matrix as a stack-allocated object and not aunique_ptr
.
PR {pr}785
{issue}781
Build system
- All GCC builds and CI tests on Ubuntu + GCC now apply a much stricter set of compiler options.
{pr}779
{issue}778
Dependencies
- Bump
pillow
version in doc/requirements.txt.
{pr}763
{pr}811
- Bump all lib dependencies and some doc dependencies.
{pr}807
Point release with two bug fixes
Point release with a bug fix
Improved interaction with tskit
This release contains several improvements relating to exporting simulations to tskit and then dealing with the exported objects.
The details of this release are collected under the 0.15.0 milestone and are detailed in the change log, which is found in the docs.
Documentation update
Small release to push new docs re: demes.
Support for "demes"
This release includes support for defining demographic models using demes. @apragsdale contributed the code to convert from the demes.Graph
objects to fwdpy11 objects.
Other changes are collected in the 0.14.0 milestone or the change log in the manual.