[Biopython-dev] Parsing efetch results from the Journals database through Bio.Entrez

[Peter]

On Mon, Sep 20, 2010 at 11:41 AM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
> Thanks for letting me know.
> Could you try with the latest version in the Python 2.6 series? This
> DeprecationWarning seems to be a bug in Python itself. I haven't seen
> this deprecation warning with either Python 2.6.5 or Python 2.7.
>

Using the Apple provided Python 2.6 on Mac OS X 10.6.4 "Snow Leopard",

$ python2.6
Python 2.6.1 (r261:67515, Feb 11 2010, 00:51:29)
[GCC 4.2.1 (Apple Inc. build 5646)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> class X(ValueError):
...     def __init__(self, message):
...         self.message = message
...
>>> raise X("Test")
__main__:3: DeprecationWarning: BaseException.message has been
deprecated as of Python 2.6
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
__main__.X
>>>

On one of our Linux machines,

$ python2.6 -Wall
Python 2.6.6 (r266:84292, Aug 31 2010, 16:21:14)
[GCC 4.1.2 20080704 (Red Hat 4.1.2-48)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> class X(ValueError):
...     def __init__(self, message):
...         self.message = message
...
>>> raise X("Test")
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
__main__.X
>>>

I did a little Google searching, and according to PEP 352 the BaseException
message attribute which was introduced in Python 2.5 was deprecated in
Python 2.6, http://www.python.org/dev/peps/pep-0352/

However, the initial implementation of the deprecation warning triggered
false positives (as in your code on Python 2.6.1), and this was fixed later
in the Python 2.6.x series: http://bugs.python.org/issue6844

There is a simple work around - avoid using message as the attribute
name. For example we could use msg, or simply a private attribute like
_message instead:

$ python2.6
Python 2.6.1 (r261:67515, Feb 11 2010, 00:51:29)
[GCC 4.2.1 (Apple Inc. build 5646)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> class X(ValueError):
...     def __init__(self, message):
...         self.msg = message
...
>>> raise X("Test")
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
__main__.X

Peter