Bug fixes + new features

Issues fixed: #268, #269, #267

New features: #272, #275, #279

Add SiteTable

This is an intermediate release as we are still working towards supporting more general demographic models.

Major changes include:

• Updating the fwdpp back-end to the pre-release code for fwdpp 0.8.0. Almost none of these changes are "user facing".
• Add :class:fwdpy11.SiteTable, :class:fwdpy11.Site and new fields to :class:fwdpy11.MutationRecord. #258 These changes affect the API for some function calls. See :ref:upgrade_path for details.

Even though this release changes some of the tree sequence data structures, we are still able to read in files generated by version 0.4.5! (This is actually unit tested.)

Minor changes include:

• Add :func:fwdpy11.gsl_version. :class:fwdpy11.MutationRecord.#256
• :attr:fwdpy11.Mutation.g is converted to the mutation's age when dumping table collections to tskit's format. #257
• New exception types from fwdpp registered as Python exceptions. #260
• Several updates to documentation and to continuous integration testing.

Fix behavior of DataMatrixIterator

Fixes handling of nested window coordinates. #244

Faster "sliding window" analysis from tree sequences

Added fwdpy11.DataMatrixIterator, which allows very fast traversal of multiple genomic intervals, retrieving the genotype matrix at each window.

Minor feature release

• Minor fixes to packaging of source distrubition.
• Add a YCM config file to source repo
• Allow mutation and recombination regions to be empty. PR 239

Minor tweak for VariantIterator

VariantIterator's __init__ now accepts arguments to skip neutral or selected variants.

More docs, some UI tweaks to improve consistency

Minor release:

• Added position ranges to tree traversal. #232
• Changed default type for range arguments for VariantIterator and data matrix generation. #233
• Skipping fixations is now optional in :func:fwdpy11.data_matrix_from_tables.
• The C++ back-end for population classes was changed to avoid deleting move constructors. #231
• Documentation updates

fwdpy11 0.4.0

This is a BIG release! Far too much to list here. The manual is re-written, and that's the best place to look.

Bug fix

Fixes #228

Bug fixes

Fixes #212 and some minor issues involving the C++ back-end.