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Releases: molpopgen/fwdpy11

Alpha release of 0.1.3

21 Aug 20:10
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Pre-release

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

19 Jun 21:05
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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.

Major update with lots of cool new stuff...

01 Jun 19:58
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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

14 Apr 18:04
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I think we finally have a robust setup.py for OS X/clang and OS X/gcc.

Clean up for build system

13 Apr 23:18
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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

11 Apr 01:34
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Allows OS X builds via clang/llvm.

First official release.

10 Apr 19:38
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Corresponds to first PyPi release.