Upgrade biopython package to 1.54

[mhampton]

A new biopython package was released May 20, 2010.

[mhampton]

A first attempt is up at:  http://sage.math.washington.edu/home/mhampton/biopython-1.54.p0.spkg

I didn't change anything except upgrading the src folder and noting the upgrade in SPKG.txt.

[awebb]

My first look at it is good. I installed (SAGE_CHECK=yes) on two machines (32 and 64 bit Linux). The self test passed and my two test worksheets passed. One is just a short sheet and the other is the first three chapters of the tutorial.

Adam

[awebb]

I tried the new Phylo module and it is nice. I had a problem with one example with networkx. (files in Tests/PhyloXML)

sage: from Bio import Phylo
sage: import networkx, pylab
sage: tree = Phylo.read('example.xml', 'phyloxml')
sage: net = Phylo.to_networkx(tree)
sage: networkx.draw(net)
TypeError                                 Traceback (most recent call last)

/home/adamwebb/download/biopython-1.54.p0/src/Tests/PhyloXML/<ipython console> in <module>()

/home/math/sage/local/lib/python/networkx/drawing/nx_pylab.pyc in draw(G, pos, ax, hold, **kwds)
    108
    109     if pos is None:
--> 110         pos=networkx.drawing.spring_layout(G) # default to spring layout
    111
    112     cf=pylab.gcf()

/home/math/sage/local/lib/python/networkx/drawing/layout.pyc in fruchterman_reingold_layout(G, dim, pos, fixed, iterations, weighted, scale)
    209                                          weighted=weighted)
    210     except:
--> 211         A=networkx.to_numpy_matrix(G)
    212         pos=_fruchterman_reingold(A,
    213                                   pos=pos_arr,

/home/math/sage/local/lib/python/networkx/convert.pyc in to_numpy_matrix(G, nodelist, dtype, order)
    478         if (u in nodeset) and (v in nodeset):
    479             i,j = index[u],index[v]
--> 480             M[i,j] += attrs.get('weight', 1)
    481             if undirected:
    482                 M[j,i] = M[i,j]

TypeError: unsupported operand type(s) for +=: 'numpy.float64' and 'str'

The next line would be. sage: pylab.show()

I installed pygraphviz as well and the other graphing examples worked.

Adam

[jason]

Should this be "needs review"?

[mhampton]

I think it should be "positive review", but someone else should do that. I have been using it for weeks on linux and os x versions of sage with no problems. Given the upstream testing on this, and the fact that its an optional package, I don't see why it should be held back.

[awebb]

I was going to give it a positive review originally but was uncertain in regards to the networkx related error. Is this only on my setup? Should this be a ticket for networkx? The other plotting options worked for me so is this fine for an optional package? I assume that perfection is not required.

In any case, I think that the biopython package is fine as an optional package.

Adam

[rlm]

The optional biopython package on the website is already at .p0. Did someone already do this, or should the one here be a .p1?

[rlm]

Oops, nevermind, I see the version number change.

[rlm]

Not sure about the merged-in field, but why not?

"Updated on 2 July 2010."