Fwdpy11

Bug fixes:
------------------------

* Issue 2 on GitHub fixed. [commit] (https://github.com/molpopgen/fwdpy11/commit/562a4d31947d9a7aae31f092ed8c014e94dc56db)
* The attributes of :class:`fwdpy11.fwdpp_types.Mutation` are now read-only, addressing Issue 5 on GitHub. [commit](https://github.com/molpopgen/fwdpy11/commit/f376d40788f3d59baa01d1d56b0aa99706560011)

API changes/new features:
------------------------------------------------

* :func:`fwdpy11.util.change_effect_size` added, allowing the "s" and "h" fields of :class:`fwdpy11.fwdpp_types.Mutation` to be changed. [commit](https://github.com/molpopgen/fwdpy11/commit/ba4841e9407b3d98031801d7eea92b2661871eb2)
* Trait-to-fitness mapping functions for quantitative trait simulations now take the entire population, rather than just the generation. This allows us to model things like truncation selection, etc. [commit](https://github.com/molpopgen/fwdpy11/commit/fa37cb8f1763bc7f0e64c8620b6bc1ca350fddb9)

Back-end changes
------------------------

* :mod:`fwdpy11.model_params` has been refactored, addressing issue 4 on GitHub. The new code base is more idiomatic w.r.to Python's OO methods.[commit](https://github.com/molpopgen/fwdpy11/commit/1b811c33ab394ae4c64a3c8894984f320b870f22)
* Many of the C++-based types can now be pickled, making model parameter objects easier to serialize. Most of the
changes are in [this commit](https://github.com/molpopgen/fwdpy11/commit/d0a3602e71a866f7ff9d355d62953ea00c663c5a). This mostly addresses Issue #3 on GitHub.
* Added magic numbers to keep track of compatibility changes to serialization formats.
* __str__ changed to __repr__ for region types [commit](https://github.com/molpopgen/fwdpy11/commit/2df859dd74d3de79d941a1cc21b8712a52bcf9ba)
* fwdpy11.model_params now uses try/except rather than isinstance to check that rates are float-like types.[commit](https://github.com/molpopgen/fwdpy11/commit/37112a60cd8fc74133945e522a47183314bf4085)

This release has a few bug fixes, but the main high points are:

1. Better integration with Numpy via Python's buffer protocol. This means better speed
2. Lots of new documentation.

Bug fixes:
---------------------
* Fixed bug in :func:`fwdpy11.sampling.DataMatrix.selected` that returned wrong data in best case scenario and could
have caused crash in worst case.
(https://github.com/molpopgen/fwdpy11/commit/e715fb74472555aa64e1d894563ec218ebba1a97).
* Fix bug recording fixation times. If a population was evolved multiple times, fixation times from the later rounds of
evolution were incorrect.
(https://github.com/molpopgen/fwdpy11/commit/9db14d8b3db1c744045e20bfc00ce37e7fb28dfb)
* Fix issue 1, related to fixations in quantitative trait sims. (https://github.com/molpopgen/fwdpy11/commit/6a27386498f056f0c4cc1fc6b8ea12f2b807636c)
* The "label" field of a diploid is now initialized upon constructing a population.

API and back-end changes:
------------------------------------------
* Added :func:`fwdpy11.sampling.matrix_to_sample` and :func:`fwdpy11.sampling.separate_samples_by_loci`. (https://github.com/molpopgen/fwdpy11/commit/i639c8de999679140fad6a976ff6c1996b25444aa)
* Custom stateless fitness/genetic value calculations may now be implemented with a minimal amount of C++ code. See
:ref:`customgvaluecpp`.
(https://github.com/molpopgen/fwdpy11/commit/a75166d9ff5471c2d18d66892f9fa01ebec5a667)
* Custom fitness/genetic value calculations now allowed in pure Python, but they are quite slow (for now). See
:ref:`customgvalues`. (https://github.com/molpopgen/fwdpy11/commit/5549286046ead1181cba684464b3bcb19918321e)
* Stateful trait value models enabled for qtrait sims. (https://github.com/molpopgen/fwdpy11/commit/161dfcef63f3abf28ad56df33b84a92d87d7750f)
* Refactor evolution functions so that stateful fitness models behave as expected. Enable compiling in a debug mode.
Fix bug in operator== for diploid type. (https://github.com/molpopgen/fwdpy11/commit/a726c0535a5176aab1df5211fee7bf0aeba5054b)
* fwdpy11.util added, providing :func:`fwdpy11.util.add_mutation`. (https://github.com/molpopgen/fwdpy11/commit/17b92dbe61ee85e2e60211e7dc0ed507a70dbd64)
* Simulations now parameterized using classes in fwdpy11.model_params. (https://github.com/molpopgen/fwdpy11/commit/18e261c8596bf63d2d4e1ef228effb87397b793e) and (https://github.com/molpopgen/fwdpy11/commit/eda7390adb9a98a5d96e6557ba1003488ebac511)
* Added multi-locus simulation of quantitative traits.(https://github.com/molpopgen/fwdpy11/commit/fcad8de9d37bcef5a71ba6d26b4e40e1b67b1993)
* Refactoring of type names. (https://github.com/molpopgen/fwdpy11/commit/632477c7b7592d956149a0cf44e4d26f2a67797e)
* Refactoring internals of single-region fitnes/trait value typess. (https://github.com/molpopgen/fwdpy11/commit/d55d63631d02fdb2193940475dbcffaa201cf882)
* Allow selected mutations to be retained in fwdpy11.wright_fisher.evolve_regions_sampler_fitness. (https://github.com/molpopgen/fwdpy11/commit/dcc1f2f6555eeada669efef8317f446e3cd0e46a)

I think we finally have a robust setup.py for OS X/clang and OS X/gcc.

Now GCC is required on OS X.

Debugging symbols are not generated. This results in much smaller library files.

Allows OS X builds via clang/llvm.