Simupop

- BUG (build): add solaris support. This OS does not have stdint.h.
- BUG (build): add support for python 2.5 on 64 bit machines (new Py_ssize_t type for python2.5)
- NEW: add SaveSolarFrqFile in simuUtil.py
- NEW: separate SaveQTDT in SaveMerlinDatFile, SaveMerlinMapFile and SaveMerlinPedFile
SaveQTDT now calls these three functions.
- NEW: rewrite newPopByIndID and speed up sample generation considerably.
- NEW: add scripts/simuHWE.py that demonstrate the temorary deviation from HWE in a
population with unequal male and female allele frequencies, from Yaji Xu.
- BUG: fix a bug in the calculation of D'
- NEW: add LD measurement delta^2
- NEW: add LD_param parameter to have finer control over how LD is calculated
- NEW: add exphetero_param, Fst_param, alleleFreq_param etc to have better
control over the calculation of these statistics.
- CHG: midValues of LD is replaced by LD_param={'midValues':True}
- NEW: add association statistics (ChiSq, UC_U, CramerV)
- BUG: fix passing of relMethod parameter of stat operator
- CHG: NO_CONVERSION is no longer the default for rpy

- BUG: fix broken user interactive input
- BUG: fix help feature of tkinter dialog
- NEW: bundle boost 1.33.1 with source package
- BUG (build): fix a SConstruct bug with MSVC environment variables
- NEW: add other LD measurements to simuLDDecay.py
- NEW: optionally add header to QTDT ped file
- BUG: fix the combine parameter of SaveQTDT

-NEW (build): bring scons build system on par with python setup.py
-NEW (build): scons build now accepts options prefix, include-dirs and library-dirs
-NEW (build): try really hard to search proper boost libraries. One usually
does not have to specify boost inc and lib paths to build simuPOP.
-NEW (build): prune files from source package
-NEW: add ancestralGen to penetrance and qtrait operators
-NEW: change pySelector and allow a second parameter gen for the fitness function
This allows varying selection pressure.
-CHG: individual comparison does not compare information fields
-CHG: adjust individual representation (actually output genotype)
-BUG: fix a bug in loading some files saved in binary module from standard modules
-BUG: fix an affected sibpair sampler bug introduced in 0.7.5
MPI modules:
-NEW: add hasInfoField() function
-NEW: MPI module pass 00, 01, 06 test scripts
-NEW: Only head node can print to cout

-NEW: change file format for binary modules, resulting much faster save/load.
-NEW: fix adjustGenotype (efficiency)
-BUG: fix simulator::clone(), introduced in 0.7.5
-NEW: disable compression under windows due to a boost bug.
-BUG: make simuRPy works with the latest R and rpy.
-NEW: several new chapters in the user's guide.

- NEW: experimental MPI modules.
- BUG: None is treated as False now in Py_Object_As_Bool.
- NEW: (internal) Optimize binary allele handling. Copying of alleles are now
faster than regular alleles.
- NEW (internal): Optimize BernulliTrials and recombination. Recombination
under certain conditions is 1/3 faster now.
- NEW (internal): Using vector<bool> instead of dynamic_bitset for BernulliTrials
cache internal point for performance purposes. This also fixes a windows
dynamic_bitset related bug (never figure out what was wrong).
- NEW: add the missing simulator.clone() function
- CHG: stop embedding zlib since the source does not work under windows.
The installation process is changed as well.

- BUG: fix simulator.population() function
- NEW/CHG: add order parameter to population arr function series.
Changed functions are:
C++ level: population::genoBegin(true), genoBegin(sp, true)
population::infoBegin(idx, order), infoBegin(idx, subPop, order)
Python level: population::arrGenotype(True), arrGenotype(sp, True)
population::indInfo(idx, order), indInfo(idx, subPop, order)
population::arrIndInfo(order), arrIndInfo(subPop, order)
- NEW: test/test_21_performance is added to keep track of performance
improvements.
- NEW: (minor) performance improvement of randomMating and maSelector.
- NEW: significant performance improvement of mating schemes.
controlled randomMating: typically 150s => 90s
- NEW: add instruction for using intel c++ compiler, which usually improve
performance by 20% to 30%.
- BUG: recombinator set sex in a wrong way.
- NEW: experimental large pedigree sampling largePedigreeSample
- NEW: experimental support for merlin/vc and merlin regression
- CHG (internal): overhaul of ascertainment operators and file save stuff.
- NEW: add 'useDefault' option to simuOpt paramter specification.