[Biopython-dev] Versions of numpy/Numeric

[Peter]

> Hi,
> I just built and installed Python 2.6 with gcc version 4.3.2. I then
> installed numpy 1.2 with it (so no Numeric).

I thought you might be the first to try Biopython with python 2.6 was
I knew it was out.

> I did a cvs update on biopython and installed with Python 2.5.2 and Python
> 2.6.  In both cases I noticed many gcc warnings 'differ in signedness'
>  (should I file a bug report?) in Bio/cstringfnsmodule.c and Bio/trie.c and
> also Bio/triemodule.c has a couple of other warnings.

I've noticed differ in signedness warnings from trie before with an
older gcc - we propably should fix these so please file a (low
priority) bug for that.

> In both cases 'python setup.py test' opened graphical window - it did not do
> that before when I tested. What should the default be?

python setup.py test --no-gui

If the relevant GUI python framework isn't present, it defaults to no
GUI.  It has been suggested that we drop the GUI - as a relative new
comer to Biopython what do you think?

> All expected tests (ie I do not have biosql setup) passed with Python 2.5.2.

Excellent.

> With Python 2.6, running tests gave two warnings (should I file a bug
> report?):
> biopython/build/lib.linux-x86_64-2.6/Bio/Data/CodonTable.py:580:
> DeprecationWarning: the sets module is deprecated
>  from sets import Set

As of python 2.4, set (note lower case) became a built in function
(like list).  As we still support Python 2.3, avoiding this
deprecation would need something like:

try :
   #This should work on python 2.4+
    Set = set
except NameError:
   from sets import Set
#The remaining code can use Set as before...

Or something similar if we switch all the calls to Set() to the newer
set() instead.

> biopython/build/lib.linux-x86_64-2.6/Bio/Crystal/__init__.py:42:
> DeprecationWarning: BaseException.message has been deprecated as of Python
> 2.6
>  self.message = message

I'm not immediatley sure how to fix that, lets see if anyone on the
list has a quick suggestion.

> Also I got three errors with Python 2.6 (without the -3 flag as that
> provides warnings for Python 3) so I filed bug reports:
> test_CAPS
> test_PDB
> test_Restriction
>
> The failure for test_CAPS and and test_Restriction is due to the same line
> "Bio/Restriction/Restriction.py" (line 217).

OK - we'll have to look at those.

> Apart from these everything else passed.

Thanks.

Peter