[Biopython-dev] Biopython 1.68 plans (mid August?)

[Lluís Revilla]

Hi all,
I ran  python2.7 setup.py test and all the test passed or where skipped as
expected. However here are outputs I found strange:

running test
Python version: 2.7.6 (default, Jun 22 2015, 17:58:13)
[GCC 4.8.2]
Operating system: posix linux2
...
test_GenomeDiagram ... Warn: Can't find .pfb for face 'Times-Roman'
ok
test_GraphicsBitmaps ... skipping. Check the fonts needed by ReportLab if
you want bitmaps from Bio.Graphics
Can't setFont(Times-Roman) missing the T1 files?
Originally <type 'exceptions.TypeError'>: makeT1Font() argument 2 must be
string, not None
...
test_PAML_baseml ...
Error: Number of sequences different in tree and seq files..
ok
test_PAML_codeml ...
Error: Number of sequences different in tree and seq files..
ok
...
test_SeqIO_PdbIO ...
/home/lluis/Downloads/biopython-1.68/build/lib.linux-x86_64-2.7/Bio/SeqIO/PdbIO.py:187:
BiopythonWarning: First line is not a 'HEADER'; can't determine PDB ID.
Line: 'TITLE     STRUCTURE OF THE COMPLEX OF LAC REPRESSOR HEADPIECE AND
AN\n'
  "Line: %r" % firstline, BiopythonWarning)
/home/lluis/Downloads/biopython-1.68/build/lib.linux-x86_64-2.7/Bio/SeqIO/PdbIO.py:187:
BiopythonWarning: First line is not a 'HEADER'; can't determine PDB ID.
Line: 'REMARK INTRODUCED BUGS IN RESIDUES 2,3,4 AND WAT 67\n'
  "Line: %r" % firstline, BiopythonWarning)
ok


All the rest seems ok and I could import it correctly on python2.7. I could
test it for 3.4 too if no one can.

Lluís

On 25 August 2016 at 19:13, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> On Thu, Aug 25, 2016 at 5:57 PM, Peter Cock <p.j.a.cock at googlemail.com>
> wrote:
> > I'm about to do the MSI for Python 2.6 and 2.7 which for some reason
> > were not on the "script" - which with the new website setup is now extra
> > cumbersome: http://biopython.org/wiki/Building_a_release
>
> Now I recall why:
>
> http://mailman.open-bio.org/pipermail/biopython-dev/2015-
> October/021121.html
>
> This worked for Python 2.7, where https://bugs.python.org/issue1128
> was fixed via https://bugs.python.org/issue7639 but not Python 2.6
> where perhaps I patched my copy manually?
>
> https://github.com/biopython/biopython.github.io/commit/
> a42161f002f97f530c89e1870c4e631dbc702282
>
> I might try that tomorrow, but consider it quite a low priority.
>
> Peter
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>
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