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 raises `RuntimeError`.
{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 a `unique_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`