[Biopython-dev] Post Biopython 1.62 release, clean-up after dropping Python 2.5

Peter Cock p.j.a.cock at googlemail.com
Fri Aug 30 10:49:23 UTC 2013

Hello Biopythoneers,

I've outlined another relatively simple improvement for potential
new contributors to try below....

On Thu, Aug 29, 2013 at 5:33 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
>> On Wed, Aug 28, 2013 at 7:53 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
>>> Hello all - especially newcomers,
>>> There are going to be several boring but useful things to do to
>>> the Biopython code base once we're finished with Python 2.5
>>> (the imminent release of Biopython 1.62 has been clearly
>>> described as the final Biopython release to support it).
>>> ...
>>> (4) Scan over the code base looking for any comments
>>> about Python 2.5 (e.g. using the grep command), and
>>> reviewing them one by one to see if there is an old
>>> workaround we can now remove.
>> Lenna had a quick look, there should be some easy one here.
>>> (5) More advanced code review, for example looking
>>> for places we can better take advantage of context
>>> managers (with statements) for file handles.
>> Another new one, related to (5), and fairly easy:
>> (6) Reviewing examples in the docstrings and Tutorial
>> where it would make sense to use a 'with' for file handles.
>> This should also solve many of the ResourceWarning:
>> unclosed file ... warnings visible running the full test
>> suite under Python 3, e.g. see:
>> http://testing.open-bio.org/biopython/builders/Linux%2064%20-%20Python%203.3/builds/298/steps/shell/logs/stdio
> On Thu, Aug 29, 2013 at 11:30 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
>> ... I have come up with another easy task instead,
>> (7) Update exception style

(7) was done by Chris Mitchell,

> (8) Excluding doctests and the Tutorial, use print function
> rather than print statement. e.g. replace this:

(8) is being looked at by Sergei Lebedev.


Here's another idea, under the general issue (5) of taking
advantage of context managers (with statements), which
I would judge to be fairly easy (but not trivial).

(9) Use context managers (with statements) for temporary
warning filters in the unit tests.

Currently many of our unit tests add simple filters to ignore
a warning, and then restore the old filters using pop(). This
mostly works, but is fragile and the filter list is global so this
can have strange side effects. See:

$ grep "warnings." Tests/*.py

The idea here is to replace this:

warnings.simplefilter('ignore', PDBConstructionWarning)
#some code which may trigger the warning

with this:

with warnings.catch_warnings():
    warnings.simplefilter("ignore", PDBConstructionWarning)
    #some code which may trigger the warning

Note the indentation - these changes will not give nice
clean diffs, so this will not be so easy to review.

I would therefore suggest editing just one test file at a
time (i.e. limit each commit to changing a single file), as
that makes it easier to selectively apply your changes

Please make sure you test this Python 2.6 which is most
likely to have problems with this "new" style ;)

(Again, if anyone plans to work on this, please let the list
know to minimised duplicated effort.)

If you're not familiar with our test suite, there is a chapter
introducing this in the main Tutorial & Cookbook,



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