Simupop

- CHG: change the allele type of long module to unsigned short, since
2^16 seems to be enough even for long allele cases.
- NEW: add -c option to simuCluster.py to allow it to se command instead
of the default qaub
- NEW: add reference count debugging in simulator.evolve (require
specially built python.)
- BUG: fix memory leaks in stator, util.cpp (pyExec) and simuPOP_common.i
- NEW: add pyMating operator
- NEW: add population::individuals() function that can be used to iterate
through all individuals (or in a subpopulation).
- NEW: add pyIndOperator

- CHG: remove demo and support for scipy's gplt package.
- NEW: add infoFields parameter to population and operators
- CHG: all populations must now explicitly state the information
fields for each individual.
- CHG: all qtrait and penetrance oeprators now use info fields of
individuals (they use variable before). penetrance field is
optional.
- CHG: (Internal) selectors now use info field (fitness) rather than
using its own population variable.
- NEW: add --useDefault parameter to use default parameters instead of
reading from stdin, if they can not be obtained from other methods.
- NEW: simuCluster.py now subst environmental variables, and stops if
there is remaining $ in the script.
- CHG: make 'configName' and 'prompt' of simuOpt options obsolete, use
'label' instead.
- BUG: fix starting allele problem in simuCDCV.py

- BUG: Fix a bug in backward trajectory simulation
- CHG: change the release/snapsot generating process
- NEW: add script/simuCluster.py which assists submission of jobs on cluster
machines.
- BUG: fix a random number generator bug on 64 bit machines.
- NEW: random number seed is generated in a much better way, and is
retrievable.
- NEW: fix analComplexDisease.py which was not up to date with
simuComplexDisease.py

- Check all scripts and test cases
- Check document
- release

- CHG: user's guide and reference manual revision
- NEW: add a local scons build system for developers
- BUG: fix the variable update bug.
- BUG: fix setRNG(seed) bug.
- CHG: rename setRNG() to SetRNG(), and listAllRNG() to ListAllRNG()

- NEW: Add trajectory simulation functions follows those from selSim
and geneArtisan.
- NEW: Add controlledMating that accept an generation only if allele
frequency at specified locus/loci fail in specified range.
- NEW: add test case for controlledMating. (No doc is avaiable yet.)
- NEW: implement trajectory simulation follows Slatkin 2001. This
works better than methods from both selSim and geneArtisan.
- CHG: (internal change) abort the original template design. This
will make the source less flexible but can dramatically improve
development time.
- CHG: add separator to simuOpt's parameter specification.
- NEW: add controlledRandomMating and controlledBinomialSelection which
implement a quicker alternative to controlledMating.
- CHG: simuComplexDisease.py has been re-written.
- NEW: add TurnOnDebugWithName(name) and the ability to set SIMUDEBUG
to turn on certain debug mode.
- BUG: fixed a bug about s_shallowCopied flag of population.
- CHG: Remove starting allele and let all allele start from 0. tests
and scripts have been modified. These changes can make binary
and other modules behave the same.
- CHG: (internal change) upgrade to boost 1.33.1. This allows me to use
boost::iostream for instant file compression.
- NEW: File format change that compress population genotype before it is
saved. This will greatly reduce the file size of saved populations.
- NEW: add compress=True option to savePopulation(). For a large file:
Before: txt: 496M, 58s load, 24s write
xml: 169M, 19s load, ? write
Now: txt: 66M, 25s load, 125s save
bin: 51M, 10s load, 70s write
Since load operation tends to happen more often than save,
this increased write time seems to be acceptable.
- NEW: let simuPOP handles file.txt.gz extensions directly. Using .gz will
be equilivalent to compress=True (although compress=True does not
add .gz extension to the filename supplied. )