Simupop

- NEW: allow taggers to write pedigree files
- NEW: introduce pedigreeParentsChooser to choose parents according to a given pedigree
- NEW: introduce pedigreeMating to mate according to a given pedigree
- NEW: add infoTagger, sexTagger, affectionTagger
- NEW: add pedigree information handling functions
- CHG: add more options to functions in hapMapUtil.py
- CHG: remove MPI related setup, build and source code (revert to r1393 to retrieve the
MPI related code).
- BUG: Fix a bug of setting individual visibility of populations loaded from disk file.
- NEW: improve the efficiency of MergePopulations and MergePopulationsByLoci when
a lot of populaitons are involved.

- BUG: Fix saveFstat in simuUtil.py
- NEW/CHG: rewrite pyMating, which now accepts a parents chooser, and an offspring generator.
- NEW: add heteroMating to allow allow different mating scheme used for different
subpopulations, or proportions of individuals
- NEW: add selfMating mating scheme.
- NEW: add various parent choosers.
- NEW: add various offspring generators.
- NEW: add null, duplicate, info, genotype, proportion splitters
- NEW: add splitter interface to populations.

- NEW: Allow len(pops) == 1 in MergePopulationsByLoci(pops) and
MergePopulations(pops)
- BUG: Use /dev/urandom for unix users. os.path.isfile('/dev/urandom')
returns false even if this file does exist.
- BUG: Fix the handling of binary option in command line, and handling of short
arguments.
- NEW: Use a checkbox for binary options in the parameter dialogs.
- NEW: make use of second to last inforFields passed to pyPenetrance
and pySelector to pass specified information fields to user-defined
functions.
- BUG: Fix a few functions in hapMapUtil.py
- BUG: stop displaying full path name in the title of the parameter dialog.
- NEW: add chromName(), chromNames(), chromByName() to genotypic structure, and
chromNames parameter to population constructor.
- NEW: Some documentation improvement.

- Reference manual overhaul
- Rename outputHelper to pyOutput, and alleleType to AlleleType for consistency.
- NEW: Respect environmental variable GSL_RNG_TYPE for the choice of RNG

- NEW: add subPop(s) parameters to selectors, allowing different selection pressure
in different subpopulations
- NEW: add subPops parameter to intializers, working the same as subPop
- NEW: extending pyIndOperator with handling of loci and infoFields
- BUG: fix a crash of postOps in dryrun mode by applying operator in the order given.
- BUG: fix scripts/simuViewPop.py
- NEW: add optional option destructive=False to simulator::getPopulation, as
a way to retrieve a population more efficiently.
- NEW: rewrite pyMigrator to allow for changing migration rates, and more subtle
control of migration using individual genotype.
- NEW: rename parameter atLoci to loci for all mutators (atLoci becomes obsolete, but is
still usable)
- BUG: fix a mutator crash when locus index difference exceeds the range of integer,
for cases, for example, with 10k loci and 100k individuals.
- NEW: add src/hapMapUtil.py to add some utility functions to handle HapMap data
- NEW: add parameter byChromosome to population::mergePopulationByLoci and
MergePopulationsByLoci to allow chromosome to chromosome merge.

- BUG: fix a memory leak bug with LoadPopulation
- BUG: fix a newPopByIndID bug where keepAncestralPops is not respected.
- NEW: nuclearFamilySampler operator and function
- NEW: add MATE_UniformDistribution number of offspring type
- BUG: fix a useAncestralGen bug in largePedigreeSample (Does not affect output).
- BUG: fix a typo in function SaveLinkage, I really need to test these functions as well.
- BUG: fix a SWIG option bug that prevents help messages of member functions to display.
- BUG: fix a memory leak bug with stat operator during allele frequency calculation
- NEW: make sure alleleFreq[x][0] and alleleFreq[x][1] exist, even if there is no
allele 1. This is avoid trouble in binary form. (maybe not a good idea).
- NEW: throw an exception when multiple selectors are applied at the same time.
- NEW: add population::mergePopulation, population::mergePopulationByLoci,
MergePopulations, MergePopulationsByLoci, population::resize
- NEW: add population::insertLoci, population::insertLocus, population::appendLoci,
population::appendLocus
- NEW: add genoStruTrait::locusByName, genoStruTrait::lociByName
- NEW: swig 1.3.32 compatibility
- NEW: add scripts/loadHapMap.py
- NEW: add pyTagger operator, which can be used to trace trait values.
- NEW: update comments, in preparation for the 0.8.0 release
- NEW: disallow change of genotypic structure of populations in a simulator.
- NEW: add simulator::addInfoField, simulator::addInfoFields, simulator::setAncestralDepth
and related tests and documents.
- BUG: fix a bug when stat() tries to remove non-existings variables
caused by population split.