ERROR: type: apply: expected Function, got PyObject

[diegozea]

What is wrong here?

In Python:

>>> import Bio.pairwise2 as py_aln
>>> import Bio.SubsMat.MatrixInfo as py_mat
>>> py_aln.align.globalds
<Bio.pairwise2.alignment_function instance at 0x7f0db3da7998>
>>> py_aln.align.globalds("AHHH","HHHA",py_mat.ident,-0.25,-0.5)
[('AHHH-', '-HHHA', 17.5, 0, 5)]

In Julia:

julia> using PyCall
julia> @pyimport Bio.pairwise2 as py_aln
julia> @pyimport Bio.SubsMat.MatrixInfo as py_mat
julia> py_aln.align[:globalds]
PyObject <Bio.pairwise2.alignment_function instance at 0xaf48560>
julia> py_aln.align[:globalds]("AHHH","HHHA",py_mat.ident,-0.25,-0.5)
ERROR: type: apply: expected Function, got PyObject

[diegozea]

PyObject can be converted to Function. This works :) I don't close the issue because maybe is a real issue...

julia> a = py_aln.align[:globalds]
PyObject <Bio.pairwise2.alignment_function instance at 0xaf48680>

julia> aa = convert(Function,a)
fn (generic function with 1 method)

julia> aa("AHHH","HHHA",py_mat.ident,-0.25,-0.5)
1-element Array{Any,1}:
 ("AHHH-","-HHHA",17.5,0,5)

[stevengj]

You can also call pycall(a, PyAny, "AHHH","HHHA",py_mat.ident,-0.25,-0.5).

The problem is that PyCall is not automatically able to detect that alignment_function is a function type (and Julia doesn't allow one to overload apply (JuliaLang/julia#2403), because alignment_function is a BioPython-specific type that is not a subclass of types.FunctionType. I could check whether it is callable, but the problem is that a lot of objects are callable and I don't necessarily want to autoconvert all callable objects into opaque anonymous functions.