cdcapano / epsie / 356
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Birthdeath proposal (#26)

* add birthdeath proposal

* add .active support

* fix active proposal bug

* add suport for lists of act/inact props

* attempt at fixing PT bug

* rename files

* add reverse jump back

* Include multiple layesr jump

* update proposal description

* fix minor bugs in reverse jump

* hold list of active props

* working version for non-pt

* quick hack to allow parallel tempering

* make active proposals attributes of the chain

* working PT

* pep 8 issues

* more support for list of propols

* PT sampler + correct RJMCMC logpdf

* fix pep8

* fix overindent

* stop repeating in _start_pos blocks of code and store state in pos

* make transdimensional attribute of the base sampler

* remove 1/k factors

* stop requiring `transdimensional` argument

* remove assumption of all model proposals being the same

* rename

* remove transdimensinal list

* add suport for having global proposals

* add birth distributions support

* example notebook

* Support in chain for both standard and transdim proposals

* add support for vanishing decay RJMCMC

* fix renaming of a chain active props in ptchain

* test unit test

* test travis

* fix python2 RandomGenerator import

* finalise the unit test

* final pep8 checks

* move UniformBirthDistribution to nested_transdimensional.py

* chain when starting from state learn _positions dtypes from starting point

* do numpy.testing.assert_equal to compare positions in case some are NaNs

* add a way for proposals to keep track of number of steps within each model if transdimensional

* add unit tests for adaptation, seed, checkpoint and clear memory

* fix minor issues and pep8

* remove unwanted comments

* change some imports

* Make `nsteps` proposal attribute

* fix pep8

* Make base proposal keep nsteps

* pep8 comment issue

1563 of 1712 relevant lines covered (91.3%)

1.82 hits per line

Jobs
ID Job ID Ran Files Coverage
1 356.1 0
91.0
 Travis Job 356.1
2 356.2 0
91.0
 Travis Job 356.2
Source Files on build 356
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