Bio::Root back in master

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Bio::Root back in master

Fields, Christopher J
All,

Just a note that we decided the split out of Bio::Root was causing too many headaches, so decided to merge the code back into the master branch as of today (in commit c5b1cf8a).  

Major thanks to Brian Osborne for doing the work on merging the code back in on a branch (including changes made in the now-defunct Bio-Root repo)!

chris
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Re: Bio::Root back in master

Brian Osborne-2
Chris,

Looks good, all tests pass for me using “master” except for this familiar one:

not ok 78 # TODO The nodes are garbage-collected away b/c Tree isn't retained in memory
#   Failed (TODO) test at t/Tree/TreeIO.t line 342.
#          got: '0'
#     expected: '198'

What was the deal on this one, something to do with Perl version? Mine is 5.14.3.

BIO

On Sep 17, 2015, at 12:07 AM, Fields, Christopher J <[hidden email]> wrote:

All,

Just a note that we decided the split out of Bio::Root was causing too many headaches, so decided to merge the code back into the master branch as of today (in commit c5b1cf8a).  

Major thanks to Brian Osborne for doing the work on merging the code back in on a branch (including changes made in the now-defunct Bio-Root repo)!

chris
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Re: Bio::Root back in master

Fields, Christopher J
Yes, that’s a TODO test for a ‘bug’ (it will pass normally but warns that it needs to be addressed in some way). It’s subjective whether this is a true issue:

=========================================
...
$root = Bio::TreeIO->new(-format => 'newick',
               -verbose => $verbose,
               -file   => test_input_file('bug2869.tree'),
               -no_cleanup => 1)->next_tree->get_root_node;

isa_ok($root, 'Bio::Tree::NodeI');

TODO: {
    local $TODO = 'The nodes are garbage-collected away b/c Tree isn\'t retained in memory';
    my $total2 = 0;
    for my $child ($root->get_Descendents) {
        $total2++;
    }
   
    is($total2, $total1);
}

=========================================

Note the way the tree object is not retained, but the root node is; the Bio::Tree::Tree is not retained, and thus the list of nodes for the tree are not retained except the root node.  Here’s the original report:

https://redmine.open-bio.org/issues/2869

chris

> On Sep 17, 2015, at 3:23 PM, Brian Osborne <[hidden email]> wrote:
>
> Chris,
>
> Looks good, all tests pass for me using “master” except for this familiar one:
>
> not ok 78 # TODO The nodes are garbage-collected away b/c Tree isn't retained in memory
> #   Failed (TODO) test at t/Tree/TreeIO.t line 342.
> #          got: '0'
> #     expected: '198'
>
> What was the deal on this one, something to do with Perl version? Mine is 5.14.3.
>
> BIO
>
>> On Sep 17, 2015, at 12:07 AM, Fields, Christopher J <[hidden email]> wrote:
>>
>> All,
>>
>> Just a note that we decided the split out of Bio::Root was causing too many headaches, so decided to merge the code back into the master branch as of today (in commit c5b1cf8a).  
>>
>> Major thanks to Brian Osborne for doing the work on merging the code back in on a branch (including changes made in the now-defunct Bio-Root repo)!
>>
>> chris
>> _______________________________________________
>> Bioperl-l mailing list
>> [hidden email]
>> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>


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