error with interval-tree

[mkohram]

After installing using python 3.5.1 I get this error:

Traceback (most recent call last):
  File "/Users/kohb9m/tmp/genmod/env/bin/genmod", line 9, in <module>
    load_entry_point('genmod==3.5.1', 'console_scripts', 'genmod')()
  File "/Users/kohb9m/tmp/genmod/env/lib/python3.5/site-packages/pkg_resources/__init__.py", line 558, in load_entry_point
    return get_distribution(dist).load_entry_point(group, name)
  File "/Users/kohb9m/tmp/genmod/env/lib/python3.5/site-packages/pkg_resources/__init__.py", line 2682, in load_entry_point
    return ep.load()
  File "/Users/kohb9m/tmp/genmod/env/lib/python3.5/site-packages/pkg_resources/__init__.py", line 2355, in load
    return self.resolve()
  File "/Users/kohb9m/tmp/genmod/env/lib/python3.5/site-packages/pkg_resources/__init__.py", line 2361, in resolve
    module = __import__(self.module_name, fromlist=['__name__'], level=0)
  File "/Users/kohb9m/tmp/genmod/env/lib/python3.5/site-packages/genmod/commands/__init__.py", line 3, in <module>
    from .build_annotation import build as build_command
  File "/Users/kohb9m/tmp/genmod/env/lib/python3.5/site-packages/genmod/commands/build_annotation.py", line 32, in <module>
    from genmod.annotate_regions import parse_annotations
  File "/Users/kohb9m/tmp/genmod/env/lib/python3.5/site-packages/genmod/annotate_regions/__init__.py", line 10, in <module>
    from .parse_annotations import parse_annotations
  File "/Users/kohb9m/tmp/genmod/env/lib/python3.5/site-packages/genmod/annotate_regions/parse_annotations.py", line 69, in <module>
    from interval_tree import interval_tree
  File "/Users/kohb9m/tmp/genmod/env/lib/python3.5/site-packages/interval_tree/__init__.py", line 1, in <module>
    from interval_tree import IntervalTree
ImportError: cannot import name 'IntervalTree'

Any ideas?

EDIT: Looks like from interval_tree.interval_tree import IntervalTree would work.

[moonso]

Hi,

could you try pip install -U interval_tree?

Måns

[mkohram]

No luck. Everything works fine with python2.7. Haven't had time to investigate other versions.

[mkohram]

Here is what is happening. I think essentially you would need to change the __init__.py in interval_tree to

from .interval_tree import IntervalTree

[moonso]

Thanks for the fix, I'll update requirements in genmod soon. Meanwhile you can upgrade interval_tree to 0.3.4.

[mkohram]

Thanks!