Simupop

- DOC: Adjust reference output for simuPOP classes.
- CHG: Rename genoStruTrait::haplodiploid to isHaplodiploid.
- CHG: Rename genoStruTrait::sexChrom to hasSexChrom.
- CHG: Remove the maxAllele parameter of population.
- CHG: Remove outputHelper operator, which has been replaced by pyOutput.
- CHG: Remove read support for XML and Binary formats.
- CHG: Completely change the way sex chromosomes are handled, and add
initial support for customized chromosome.
- CHG: Rename class vsp to vspID.
- CHG: Merge population::subPopSize and population::virtualSubPopSize.
- CHG: Change parameter of population::virtualSubPopName().
- CHG: Merge population::individuals(sp) and population::individuals(sp, vsp).
- CHG: Remove genoStruTrait::maxAllele(). Use MaxAllele() instead.
- CHG: Make pedigree a subclass of population and move population::locateRelatives
and population::setRelativeIndex to this class.
- CHG: Temporarily disable all pedigree related features such as pedigree parent
chooser, pedigree mating scheme, and all samplers.
- CHG: Rename population::useAncestralPop to population::useAncestralGen.
- CHG: Replace population::mergePopulation by population::addIndFromPop.
- CHG: Replace population::mergePopulationByLoci by population::addChromFromPop
and population::addLociFromPop.
- CHG: Remove removeEmptySubPops parameter from population::mergeSubPops.
- CHG: Adjust interface to population::removeLoci.
- CHG: Adjust interface to population::removeSubPops.
- NEW: Allow indInfo, setInfo etc to access virtual subpopulation.
- CHG: Merge parameter virtualSubPop with subPop in mating schemes.
- NEW: Add simuProgress class to simuUtl.
- CHG: Remove simulator::applyOpToStoppedReps and simulator::stopIfOneRepStops
- NEW: Add StopEvolution exception and add simulator::stopIfOneRepStops to terminators.
- CHG: Remove operator terminator and continueIf.
- CHG: Reset file format number. No longer support previous file formats.
- NEW: add simulator::populations().
- NEW: Allow the use of multiple replicates for an operator. Remove REP_ALL (now []),
and REP_LAST (now -1).
- CHG: Replace simulator::getPopulation by simulator::population and
simulator::extract.

- CHG: Remove the replicate group feature.
- NEW: Allow mapSelector to work for all ploidy.
- DOC: Add keyword applicability to indicate applicability of operators.
- DOC: Document applicability of mating schemes.
- DOC: Fix bibtex references of user's guide and reference manual.
- CHG: indiviudal::arrGenotype, individual::arrInfo are marked obsolete
and will be removed later.
- NEW: add individual::genotype (previously called arrGenotype) and
individual::arrGenotype.
- CHG: genoStruTrait::arrLociPos is marked obsolete and will be removed
later.
- CHG: population arrGenotype are marked obsolete and will be removed
later.
- NEW: add population::genotype and population::setGenoytpe.
- BUG: Fix a bug in simuRPy.py that prevents varPlotter from plotting
images.
- NEW: Support Python 2.6.

- NEW: allow the use of a list to specify a virtual subpopulation.
- NEW: change the return type of allele() so that no boolean value (True or False)
will be returned from the binary modules.
- DOC: Correct documentation about variables related to genotype and heterozygote frequency.
- BUG: Fix a bug when a zero-sized virtual subpopulation has weight -1.
- BUG: Fix a bug when calculating expected heterozygosity with increased
number of subpopulations.
- BUG: Fix a bug in controlled random mating where number of affected alleles
are calculated from current instead of offspring populations.
- CHG: Only write (compressed if possible) in text format. simuPOP can still
read binary and xml formats.
- BUG: Fix a bug that is related to the calculation of Fst in populations with
unordered individuals.
- BUG: Fix activation and deactivation of combinedVirtualSplitter.
- BUG: Fix a bug that prevents simuPOP from compressing population files.
- NEW: Make boost 1.36.0 the default built-in boost version.
- BUG: Fix a carray genotype slice assignment bug under windows and python2.5.
- NEW: Stop distributing zlib1.dll by building zlib from source under
windows.

- NEW: Polish command line arguments output in a configuration file.
- NEW: add a function ForwardFreqTrajetory to simulate trajectory of varying
population size and selection pressure.
- BUG: Fix a minor simuOpt::saveConfigFile bug
- BUG: reveal RNG::randMultinomial and RNG::randMultinomialVar
- BUG: fix a bug that is related to reference count of loaded lists.
- CHG: allow sample size > population size (give a warning rather than error)
- CHG: allow recombination rate > 0.5 (adjust to 0.5 and issue a warning)
- NEW: allow longarg names in option jump and jumpIfFalse in simuOpt.py
- NEW: load fine-scale recombinate rate and set variable genDist in loaded
HapMap populations. (loadHapMap.py)
- CHG: polish tkInter and wxPython parameter input dialog.
- CHG: Remove parameter order from information field related functions.
- BUG: Fix a information field + migration bug.
- NEW: add operation resizeSubPops.
- BUG: Fix a NuclearfamilySample bug regarding parameter minAffected.
- NEW: separate sex initialization from initByFreq, initByValue and pyInit
and add a new operator initSex.
- BUG: Fix a iterator bug that affects populations with ancestralDepth > 1
during evolution.
- CHG: Remove subpopulation specific virtual subpopulation. This is no longer
needed with combined virtual splitter.
- NEW: Add population::ancestor(ind, gen) and population::ancestor(ind, subPop, gen)
to access an individual in an ancestory generation directly.
- NEW: support virtual subpopulation in fromSubPop parameter of a migrator.
This allows sex-specific migraton and more complicated migration
schemes.
- NEW: add functions population::locateRelatives and population::setIndexesOfRelatives
- NEW: add functions individual::indInfo(idx) and individual::indInfo(name)
- NEW: add a new parent chooser infoParentsChooser and a new mating scheme
consanguineousMating, along with an example doc/cookbook/Mating_consanguineous.py.

- BUG: fix a bug that prevents a cloned simulator from evolving again.
- NEW: add parameter numMale and sexMode to all offspring generator and
mating schemes, to control the sex of offspring exactly.
- NEW: add gene conversion to recombinator, using parameter convMode, convProb and convParam.
- NEW: add convenience functions GenoStruTrait::distLeft and GenoStruTrait::lociLeft.
- NEW: add random parent chooser without replacement and/or with alpha individuals,
haplodiploidOffspringGenerator, monogamousMating, polygamousMating, alphaMating,
and haplodiploidMating mating schemes.
- NEW: add haplodiploid option to GenoStructure. Recombinator now handles such
populations correctly.
- CHG: make the subPop parameter of population() function obsolete.
- CHG: add parameter gen, and make parameter end in simulator::evolve obsolete.

- NEW: add support for other posix systems like HP-UX
- NEW: automatically download HapMap data in loadHapMap.py and simuAdmixture.py.
- NEW: add two operators infoEval and infoExec that can be used to manipulate
information fields during evolution.
- NEW: operator stator popSize=True also calculates virtual subpop size using
variable virtualPopSize.
- BUG: fix a bug in the re-initialization of pyParentsChooser.
- CHG: inheritTagger will inherit the first, instead of the second, information
field from mother in TAG_Maternal mode.
- CHG: population::numVirtualSubPop() returns 0 instead 1 when there is no
virtual subpopulation.
- NEW: allow multiple genotype in the same virtual subpopulation split by
genotypeSplitter
- NEW: add combinedSplitter