#8547: implement hidden markov models in Cython from scratch (so can remove the
GHMM standard package from Sage)
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Reporter: was | Owner: amhou
Type: enhancement | Status: needs_review
Priority: major | Milestone: sage-4.4
Component: statistics | Keywords:
Author: | Upstream: N/A
Reviewer: | Merged:
Work_issues: |
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Comment(by jason):
Some notes from reading through the code looking at stylistic issues. I
really wish we had line-by-line commenting like rietveld for this sort of
thing.
1. Lots of cdef'd functions do not have doctests. I thought the policy
from discussions on sage-devel was that *every* function (including cdef
functions) should have doctests (but, of course, these doctests would have
to either indirectly test the cdef'd function or would have to test a
wrapper of the cdef function). Some functions (_baum_welch_gamma, for
example) don't even have docstrings.
1. I'm curious why IntList.!__getitem!__ does not use the
sage.misc.misc_c.normalize_index function to deal with slices. How much
of a performance penalty is there? Can this "python semantics" part be
extracted out to be a more general cdef'd counterpart to normalize_index,
so that matrices, vectors, and other types can use it better to implement
!__getitem!__? Also, as a future enhancement, it doesn't seem that much
harder for !__setitem!__ to also support slices. At the very least, the
doctests for normalize_index probably ought to be run on the !__getitem!__
function, as they exercise a number of corner cases for the python
semantics.
1. IntList.sum() does not have a doctest for the overflow case
--
Ticket URL: <http://trac.sagemath.org/sage_trac/ticket/8547#comment:10>
Sage <http://www.sagemath.org>
Sage: Creating a Viable Open Source Alternative to Magma, Maple, Mathematica,
and MATLAB
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