ImportError: cannot import name 'Mapping' from 'collections'

[Phlya]

Above error appears in python 3.10. As usual with collections, import should be fixed with this change: from collections.abc import Mapping.
I haven't checked from which version of python this would work and whether we can just simply change it or it would break in earlier versions.

File /tungstenfs/scratch/ggiorget/ilya/condaenvs/hic/lib/python3.10/site-packages/pairtools/__init__.py:116, in <module>
    113         return func(*args, **kwargs)
    114     return wrapper
--> 116 from .pairtools_dedup import dedup
    117 from .pairtools_sort import sort
    118 from .pairtools_flip import flip

File /tungstenfs/scratch/ggiorget/ilya/condaenvs/hic/lib/python3.10/site-packages/pairtools/pairtools_dedup.py:14, in <module>
     12 from . import _dedup, _fileio, _pairsam_format, _headerops, cli, common_io_options
     13 from .pairtools_markasdup import mark_split_pair_as_dup
---> 14 from .pairtools_stats import PairCounter
     17 UTIL_NAME = 'pairtools_dedup'
     19 # you don't need to load more than 10k lines at a time b/c you get out of the 
     20 # CPU cache, so this parameter is not adjustable

File /tungstenfs/scratch/ggiorget/ilya/condaenvs/hic/lib/python3.10/site-packages/pairtools/pairtools_stats.py:10, in <module>
      6 import click
      8 import numpy as np
---> 10 from collections import OrderedDict, Mapping
     12 from . import _fileio, _pairsam_format, cli, _headerops, common_io_options
     14 UTIL_NAME = 'pairtools_stats'

ImportError: cannot import name 'Mapping' from 'collections' (/tungstenfs/scratch/ggiorget/ilya/condaenvs/hic/lib/python3.10/collections/__init__.py)

[Phlya]

I fixed it in #107
Also there is no OrderedDict in recent (3.10?) python, so I just changed it all to regular dicts, since they are now ordered.

[agalitsyna]

Hi, OrderedDict is present in Python 3.10 and even in 3.11. It is actually actively maintained and constantly improved. E.g. it was recently made 2x times faster.
You can simply do from collections import OrderedDict as it was before.

Another point is that I benchmarked OrderedDict against dict, and simple iteration over d.items() is ~3-5 times slower for OrderedDict (Python 3.10). Adding to the dict/accessing by the key have the same performance on simple test set.

Just to make sure: we do not support Python below 3.7, so it's safe to replace the OrderedDict by dict (which started to be ordered from Python 3.7)?

Ipersonally like the idea to stick to an old implementation that makes the "ordering" feature explicit. But it's up to you. If you decide to remove OrderedDict, please, fix also the documentation, now there are many mentions of OrderedDict class in the docstrings.

[golobor]

i second the idea to move from OrderedDict to dict, as ordering is now guaranteed in dicts : https://stackoverflow.com/questions/39980323/are-dictionaries-ordered-in-python-3-6