[Bioperl-l] 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 <bosborne11 at verizon.net> 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 <cjfields at illinois.edu> 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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>