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src/c/o/cogent-1.5.3/cogent/maths/scipy_optimisers.py   cogent(Download)
#!/usr/bin/env python
 
from __future__ import division
import numpy, math, warnings
from cogent.maths.scipy_optimize import fmin_bfgs, fmin_powell, fmin, brent
        fb = func(xb)
    assert xb != xa, "Can't find a second in-bounds point on this line"
    return brent(func, brack=(xa, xb), **kw)
 
 

src/p/y/pycogent-HEAD/cogent/maths/scipy_optimisers.py   pycogent(Download)
#!/usr/bin/env python
 
from __future__ import division
import numpy, math, warnings
from cogent.maths.scipy_optimize import fmin_bfgs, fmin_powell, fmin, brent
        fb = func(xb)
    assert xb != xa, "Can't find a second in-bounds point on this line"
    return brent(func, brack=(xa, xb), **kw)
 
 

src/c/o/cogent-1.5.3/cogent/seqsim/usage.py   cogent(Download)
        of the one scipy function that still needs to be removed
"""
from cogent.maths.scipy_optimize import fmin, brent
from cogent.util.array import scale_trace, norm_diff, \
    has_neg_off_diags, sum_neg_off_diags, with_diag, without_diag
                def similarity_f(t):
                    return abs(sum(diagonal(expm(q)(t)*freqs))-similarity)
        return brent(similarity_f)
 
    def toSimilarProbs(self, similarity, freqs=None):

src/p/y/pycogent-HEAD/cogent/seqsim/usage.py   pycogent(Download)
        of the one scipy function that still needs to be removed
"""
from cogent.maths.scipy_optimize import fmin, brent
from cogent.util.array import scale_trace, norm_diff, \
    has_neg_off_diags, sum_neg_off_diags, with_diag, without_diag
                def similarity_f(t):
                    return abs(sum(diagonal(expm(q)(t)*freqs))-similarity)
        return brent(similarity_f)
 
    def toSimilarProbs(self, similarity, freqs=None):