[Biopython] Biopython 1.54b test failures

[Peter]

On Sat, Apr 3, 2010 at 12:05 AM, Christoph Gohlke <cgohlke at uci.edu> wrote:
> Hello,
>
> I get two test failures (see below) when running 'setup.py test' for
> biopython 1.54b on win-amd64-py2.6 (built with msvc9). These are
> related to line ending style.

It is a known issue - a simple work around is just run something
like unix2dos on the SCOP test files, and then the tests pass.

> Maybe it would be a good idea to use Python's universal
> newline support (available since 2.3) when opening text
> files for iteration over lines.

I had tried that in the past without success...

> All tests pass after the following changes:
>
> BIO/SCOP/Raf.py
>
> line 104:
>        f = open(self.filename, 'rU')
>
> line 121:
>        f = open(self.filename, 'rU')
>
> BIO/SCOP/Cla.py
>
> line 103:
>        f = open(self.filename, 'rU')
>
> line 123:
>        f = open(self.filename, 'rU')
>
> line 72 (inconsistent indentation):
>            h.append("=".join(map(str,ht)))
>

I recall trying the universal read lines thing before without
success in the SCOP tests - maybe it was this line 72 thing
that I missed. I'll take another look at this next week (when
I have access to a Windows machine).

Thanks,

Peter