Simupop

NEW FEATURES:
* Expose type defdict so that users can use this type directly.
* Add event based demographic models.

BUG FIXES:
* Fix a bug with MultiStageModel when the population does not start from generation 0.

MAJOR NEW FEATURES:
* Add a new mating scheme [[https://github.com/BoPeng/simuPOP/manual_svn/build/refManual_ch2_sec3.html#class-conditionalmating|ConditionalMating]] to apply different matings schemes to populations with different properties. ([[https://github.com/BoPeng/simuPOP/manual_svn/build/userGuide_ch6_sec1.html#conditional-mating-schemes|Example]]

NEW FEATURES:
* Support compiling simuPOP using clang under MacOSX Maverick
* Allow function passed to PyMutator to accept parameter locus.
* Allow the use of varying recombination rates rates=[...] with loci=ALL_AVAIL in operator Recombinator.
* Raise an error if a demographic function returns a negative population size.
* Expose the chooseParents interface of parent [[https://github.com/BoPeng/simuPOP/manual_svn/build/refManual_ch2_sec3.html#class-sequentialparentchooser|choosers]] so that they could be used in PyParentsChooser. ([[https://github.com/BoPeng/simuPOP/manual_svn/build/userGuide_ch6_sec3.html#a-python-parent-chooser|Example]])
* Allow the passing of mutants (non-zero alleles) as a dictionary to user-provided function in call-back functions of PySelector, PyQuanTrait, and PyPenetrance. This can be more efficient for large genomes with few mutants.

BUGS:
* Fix a bug for random parent chooser (single parent) without replacement.
* Fix a memory leak bug for PyParentChooser.
* Fix a crash for Stat(min/maxInfo) with empty subpopulation

MAJOR NEW FEATURE:
* Add a new module simuPOP.demography, move migr functions from simuPOP.utils to this module and add a migration matrix generating function for 2D stepping stone model. Add demographic models InstantChangeModel, LinearGrowthModel, ExponentialGrowthModel and MultiStageModel, OutofAfricaModel, and SettlementOfNewWorldModel.

BUGS:
* Fix a bug in Population.addLoci when a locus is added to an empty chromosome (with 0 locus).
* Stop output details of mutations by default (> was set as default).
* Fix the use of virtual subpopulation in import/export functions.
* Add only one field if duplicated information fields are added.

NEW FEATURE:
* Add support for format ms to functions simuPOP.utils.importPopulation and simuPOP.utils.export.
* Add support for matplotlib in module simuPOP.plotter. Only VarPlotter is supported because other statistics related operators (e.g. BoxPlotter) reply on rpy for statistical analysis.
* Stop an evolutionary process if the demographic function returns an empty list. This allows the demographic models to stop evolution.
* Allow the passing of duplicated information fields to allow more flexibility in the design of external modules.

NEW FEATURE:
- Implement temporal estimates of effective population size for sampling plan 1. Add variables
Ne_tempoFS_P1, Ne_tempoFS_P2, Ne_waples97_P1 and Ne_waples97_P2. Variables Ne_tempoFS and
Ne_waples97 are now deprecated.
- A new file format to improve efficiency and reduce memory footprint of save/load of simuPOP populations.

BUG:
- Fix setOption(version) for minor simuPOP releases with version string ending with a, b, etc.
- Fix lociPos for positions that are very close to each other.
- Fix a bug in mutator that crashes with low mutation rate.
- Fix a bug in recombinator that crashes with low recombination intensity.

Major New Features:
- Add parameter effectiveSize to operator Stat to calculate effective population size.
Currently based on the moment method of Waples 1989, TempoFS method of Jorde
& Ryman 2007, a LD-based method from Waples 2006, and an esimate of the
demographic effectize size.

New Feature:
- Rename PER_LOCI to PER_ALLELE in InitLineage. PER_LOCI can still be used for backward compatibility.
- Allow empty value list in InitLineage. In this case, unique values will be provided for each case.
- Allow export in PED, MAP and Phylip format in operator utils.Exporter and function utils.export.

BUG:
- Fix a HWE test crash when one of the homozygote count is zero.
- Result of homoFreq should be a dictionary. A list is returned
in the current version.
- Fix InitGenotype(haplotypes) in multi-thread mode of the binary module.

Major New Features:
- Add an operator Exporter and function export to export a simuPOP population in STRUCTURE,
GenePop, FStat and CSV formats.

MAJOR BUG:
- Fix a bug that prevents females from selected correctly during random mating. The bug
was introduced in simuPOP 1.0.6.

BUG:
- Quit with proper error message when Population.save fails to write
- Fix a bug where applicability parameters in operators in parameter ops
for operators MlSelector and MlPenetrance are ignored.
- Results from Stat(heteroFreq) are now set one by one, and not as a default dictionary
- Fix a bug in Population.removeLoci() that will lead to incorrect population genotype.
- Fix compatibility bug with SWIG 2.0.8
- Allow IdTagger to work properly in Self mating when two parents have the same IDs

Minor improvement:
- Automatically create a directory if needed when a full path name is specified to parameter saveAs of plotters defined in simuPOP.plotter.
- Use simuPOP RNG in simuPOP.sampling so that users could get reproducable samples by setting RNG seed, regardless the way this module is imported.