[Biopython-dev] used local in Tests/test_Nexus.py

[Peter Cock]

Thanks Brad,

Done: https://github.com/biopython/biopython/commit/eccc10d2190ce3904c8625639ccba91bd1799f6a

Peter

On Fri, Dec 4, 2015 at 3:27 PM, Brad Chapman <chapmanb at 50mail.com> wrote:
>
> Vincent and Peter;
> My guess is the tests there make sure it can read the ts2 tree, then the
> int_node_labels.nwk file. We don't really need to assign to the `tree` local
> variable since we don't do anything with it. As Peter said, separating the
> tests or adding some assertions would help make this more clear.
>
> Brad
>
>
>> Hi Vincent,
>>
>> Did you mean a reused local variable in the email title?
>>
>> It looks like Brad added this test some time back,
>> https://github.com/biopython/biopython/commit/bba8b8ded8964e5dd2484303d78a0f69efa756dc
>>
>> Certainly the final int_node_labels.nwk snippet seems like
>> it could be a separate test method, perhaps expanded with
>> a sanity test like the number of leaves?
>>
>> Peter
>>
>> On Fri, Dec 4, 2015 at 1:09 AM, Vincent Davis <vincent at vincentdavis.net> wrote:
>>> Posting this here just to be sure I am not missing something.
>>>
>>> Starting at lin
>>> e
>>> 386
>>> https://github.com/biopython/biopython/blob/master/Tests/test_Nexus.py#L386
>>> ...
>>>
>>> tree = Trees.Tree(ts2)
>>>
>>> large_ex_handle = open(os.path.join(self.testfile_dir,
>>>     "int_node_labels.nwk"))
>>> tree = Trees.Tree(large_ex_handle.read())
>>> large_ex_handle.close()
>>>
>>> ...
>>>
>>> Vincent Davis
>>> 720-301-3003
>>>
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