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

[Peter Cock]

On Thu, Aug 25, 2016 at 6:47 PM, Lluís Revilla <lluis.revilla at gmail.com> wrote:
> 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:
>

That's helpful, thank you!

> 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

I've seen this before - something odd going on with ReportLab.
It might cause you problems with using GenomeDiagram, but
otherwise don't worry about it.

> ...
> 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

That is strange. My guess is you have a different version of
PAML installed to us, and somehow it gives odd output.
Can you see what version you have for baseml and codeml?

> ...
> 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

Probably harmless warning, there's an open issue on this:
https://github.com/biopython/biopython/issues/838

> 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

That should be fine - thank you.

Any tests of the Windows installers would he helpful though...

Peter