slendr 1.4.0

• A visualization bug in plotting "truncated" backwards time models using plot_model() has been fixed. (issue #189)

• Two new arguments of gene_flow() specifying the magnitude of migration have been implemented, clarifying confusion in the original implementation (see #99 for an example):

1. migration_rate specifies the rate of gene flow per unit of time of the given gene-flow time window;
2. proportion specifies the total amount of ancestry received by a population from the given source population over the time span of the gene-flow event (this is, effectively, what the rate argument meant until this point, somewhat confusingly unless the user looked at the manpage of the gene_flow() function).

• As far as the original argument rate is concerned, setting the value of this argument in a gene_flow() call will now issue an informative warning message about its deprecation in a future major release. However, old code will remain working without any change for the foreseeable future. Furthermore, gene_flow() now includes a guard against a given migration_rate potentially resulting in a proportion of ancestry higher than 1.0 (when aggregated over the total span of the gene-flow window), meaning than users' code will not run into hidden bugs even after the eventual deprecation of rate.

(PR #188)

• tskit used by slendr's internal Python environment has been updated to version 1.0.0. As a result, updating slendr to version 1.4.0 will require re-running setup_env(). We note that the tskit update does not come with any apparent backwards incompatibility issues.
  (PR #190)

• Due to issues on a user's system with the Python 3.13 binary installed by conda (related to the built-in pyexpat module), slendr now reverted to Python 3.12. As far as we can tell, this is related to either a broken Python 3.13 distributed by conda for some architectures, or an issue with reticulate's interaction with this Python version. Either way, downgrading to Python 3.12 does not affect any of the functionality of slendr and so its worth doing as a defensive measure in case users in the future run into a similar problem.
  (#b2e5c6)