Releases: molpopgen/fwdpy11
Releases · molpopgen/fwdpy11
Alpha release of 0.1.3
Bug fixes:
- Issue #2 on GitHub fixed. [commit] (562a4d3)
- The attributes of :class:
fwdpy11.fwdpp_types.Mutation
are now read-only, addressing Issue #5 on GitHub. commit
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 - 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
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 - 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. 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
- fwdpy11.model_params now uses try/except rather than isinstance to check that rates are float-like types.commit
Integration w/numpy via buffer protocol
This release has a few bug fixes, but the main high points are:
- Better integration with Numpy via Python's buffer protocol. This means better speed
- Lots of new documentation.
Major update with lots of cool new stuff...
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.
(e715fb7). - Fix bug recording fixation times. If a population was evolved multiple times, fixation times from the later rounds of
evolution were incorrect.
(9db14d8) - Fix issue #1, related to fixations in quantitative trait sims. (6a27386)
- 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
. (i639c8de999679140fad6a976ff6c1996b25444aa) - Custom stateless fitness/genetic value calculations may now be implemented with a minimal amount of C++ code. See
:ref:customgvaluecpp
.
(a75166d) - Custom fitness/genetic value calculations now allowed in pure Python, but they are quite slow (for now). See
:ref:customgvalues
. (5549286) - Stateful trait value models enabled for qtrait sims. (161dfce)
- Refactor evolution functions so that stateful fitness models behave as expected. Enable compiling in a debug mode.
Fix bug in operator== for diploid type. (a726c05) - fwdpy11.util added, providing :func:
fwdpy11.util.add_mutation
. (17b92db) - Simulations now parameterized using classes in fwdpy11.model_params. (18e261c) and (eda7390)
- Added multi-locus simulation of quantitative traits.(fcad8de)
- Refactoring of type names. (632477c)
- Refactoring internals of single-region fitnes/trait value typess. (d55d636)
- Allow selected mutations to be retained in fwdpy11.wright_fisher.evolve_regions_sampler_fitness. (dcc1f2f)
More build system fixes re: os x
I think we finally have a robust setup.py for OS X/clang and OS X/gcc.
Clean up for build system
Now GCC is required on OS X.
Debugging symbols are not generated. This results in much smaller library files.
Clean up for OS X builds
Allows OS X builds via clang/llvm.
First official release.
Corresponds to first PyPi release.