run_treeshrink.py fails with python 3.10

[nylander]

FYK,

After a recent local upgrade of my Ubuntu Linux OS --- which brought python to version 3.10.4 --- run_treeshrink.py no longer works.

The reason seems to be an outdated version of dendropy's file utility/container.py in the TreeShrink repo. Apparently, there was a change between python 3.9 and 3.10 involving the library collections (see, e.g., https://www.datasciencelearner.com/attributeerror-module-collections-has-no-attribute-mutablemapping/, and https://github.com/jeetsukumaran/DendroPy/blob/main/src/dendropy/utility/container.py).

Some details:

$ cat /etc/lsb-release 
DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=22.04
DISTRIB_CODENAME=jammy
DISTRIB_DESCRIPTION="Ubuntu 22.04.1 LTS"
$ python -V
Python 3.10.4
$ git clone https://github.com/uym2/TreeShrink.git
$ cd TreeShrink
$ python setup.py install --user
$  python run_treeshrink.py 
Traceback (most recent call last):
  File "/home/nylander/tmp/TreeShrink/run_treeshrink.py", line 5, in <module>
    from treeshrink.optimal_filter_lib import TreeFilter
  File "/home/nylander/tmp/TreeShrink/treeshrink/optimal_filter_lib.py", line 2, in <module>
    from dendropy.datamodel.treemodel import Tree
  File "/home/nylander/tmp/TreeShrink/dendropy/__init__.py", line 24, in <module>
    from dendropy.dataio.nexusprocessing import get_rooting_argument
  File "/home/nylander/tmp/TreeShrink/dendropy/dataio/__init__.py", line 20, in <module>
    from dendropy.dataio import newickreader
  File "/home/nylander/tmp/TreeShrink/dendropy/dataio/newickreader.py", line 29, in <module>
    from dendropy.dataio import nexusprocessing
  File "/home/nylander/tmp/TreeShrink/dendropy/dataio/nexusprocessing.py", line 30, in <module>
    from dendropy.utility import container
  File "/home/nylander/tmp/TreeShrink/dendropy/utility/container.py", line 356, in <module>
    class CaseInsensitiveDict(collections.MutableMapping):
AttributeError: module 'collections' has no attribute 'MutableMapping'

[V-Z]

I can confirm, Python 3.9 seems to be the last Python version working with TreeShrink.

With Python 3.10 I get:

$ run_treeshrink.py -h
Traceback (most recent call last):
  File "/home/vojta/.local/bin/run_treeshrink.py", line 4, in <module>
    __import__('pkg_resources').run_script('TREESHRINK==1.3.9', 'run_treeshrink.py')
  File "/usr/lib/python3.10/site-packages/pkg_resources/__init__.py", line 720, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/usr/lib/python3.10/site-packages/pkg_resources/__init__.py", line 1559, in run_script
    exec(code, namespace, namespace)
  File "/home/vojta/.local/lib/python3.10/site-packages/TREESHRINK-1.3.9-py3.10.egg/EGG-INFO/scripts/run_treeshrink.py", line 5, in <module>
    from treeshrink.optimal_filter_lib import TreeFilter
  File "/home/vojta/.local/lib/python3.10/site-packages/TREESHRINK-1.3.9-py3.10.egg/treeshrink/optimal_filter_lib.py", line 2, in <module>
    from dendropy.datamodel.treemodel import Tree
  File "/home/vojta/.local/lib/python3.10/site-packages/TREESHRINK-1.3.9-py3.10.egg/dendropy/__init__.py", line 24, in <module>
    from dendropy.dataio.nexusprocessing import get_rooting_argument
  File "/home/vojta/.local/lib/python3.10/site-packages/TREESHRINK-1.3.9-py3.10.egg/dendropy/dataio/__init__.py", line 20, in <module>
    from dendropy.dataio import newickreader
  File "/home/vojta/.local/lib/python3.10/site-packages/TREESHRINK-1.3.9-py3.10.egg/dendropy/dataio/newickreader.py", line 29, in <module>
    from dendropy.dataio import nexusprocessing
  File "/home/vojta/.local/lib/python3.10/site-packages/TREESHRINK-1.3.9-py3.10.egg/dendropy/dataio/nexusprocessing.py", line 30, in <module>
    from dendropy.utility import container
  File "/home/vojta/.local/lib/python3.10/site-packages/TREESHRINK-1.3.9-py3.10.egg/dendropy/utility/container.py", line 356, in <module>
    class CaseInsensitiveDict(collections.MutableMapping):
AttributeError: module 'collections' has no attribute 'MutableMapping'

So for now I stay with Python 3.9.

[V-Z]

My easy PR https://github.com/uym2/TreeShrink/pull/40 should fix it. You can try it.

[uym2]

Thank you very much for pointing out the error snf fixing it. I will do some tests and will merge.

On Thu, Apr 27, 2023 at 5:42 AM V-Z @.***> wrote:

My easy PR #40 https://github.com/uym2/TreeShrink/pull/40 should fix it. You can try it.

— Reply to this email directly, view it on GitHub https://github.com/uym2/TreeShrink/issues/33#issuecomment-1525290417, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB6MKWQO6RX46Q3GVPM6OI3XDI5RJANCNFSM56ZU6EXQ . You are receiving this because you are subscribed to this thread.Message ID: @.***>

[smirarab]

ping!

[chrisjackson-pellicle]

Hi - won't this PR break compatibility with Python <= 3.9, though?

In the link provided in the opening post (https://www.datasciencelearner.com/attributeerror-module-collections-has-no-attribute-mutablemapping/), solution 2 suggests a dynamic approach i.e.:

import collections 
if sys.version_info.major == 3 and sys.version_info.minor >= 10

    from collections.abc import MutableMapping
else 
    from collections import MutableMapping

Then, CaseInsensitiveDict(collections.MutableMapping) can be changed to CaseInsensitiveDict(MutableMapping). It should then work with e.g. either Python 3.9 or 3.10.

Cheers,

Chris

[nylander]

Hi, for the dendropy code shipped with TreeShrink, the code suggested by @chrisjackson-pellicle will work given that sys is imported before checking for version and after adding the missing colons for the pythonic if: else: :-) I would have liked to see the whole dendropy folder updated though. Most probably more work... Cheers Johan

import sys
import collections 
if sys.version_info.major == 3 and sys.version_info.minor >= 10:
    from collections.abc import MutableMapping
else: 
    from collections import MutableMapping

Then, CaseInsensitiveDict(collections.MutableMapping) can be changed to CaseInsensitiveDict(MutableMapping). It should then work with e.g. either Python 3.9 or 3.10.