Importing ABCs from collections.abc

[abhiShandy]

Fixes #2605

Changes made in this Pull Request:

• Importing ABCs from collections.abc instead of deprecated direct method in collections.MutableMapping

I ran lib/test_util.py::TestFlattenDict locally to confirm that the corresponding deprecation warning is eliminated.

PR Checklist

• Tests?
• Docs?
• CHANGELOG updated?
• Issue raised/referenced?

[codecov]

Codecov Report

Merging #2607 into develop will decrease coverage by 0.11%.
The diff coverage is 100.00%.

@@             Coverage Diff             @@
##           develop    #2607      +/-   ##
===========================================
- Coverage    90.71%   90.60%   -0.12%     
===========================================
  Files          174      174              
  Lines        23549    23256     -293     
  Branches      3072     3066       -6     
===========================================
- Hits         21363    21070     -293     
  Misses        1565     1565              
  Partials       621      621              

Impacted Files	Coverage Δ
package/MDAnalysis/lib/util.py	88.16% <100.00%> (-0.11%)	⬇️
package/MDAnalysis/auxiliary/base.py	88.19% <0.00%> (-0.74%)	⬇️
package/MDAnalysis/coordinates/chain.py	87.37% <0.00%> (-0.59%)	⬇️
package/MDAnalysis/coordinates/TRZ.py	83.46% <0.00%> (-0.38%)	⬇️
package/MDAnalysis/coordinates/base.py	93.46% <0.00%> (-0.36%)	⬇️
package/MDAnalysis/coordinates/DMS.py	88.23% <0.00%> (-0.34%)	⬇️
package/MDAnalysis/coordinates/GMS.py	85.41% <0.00%> (-0.30%)	⬇️
package/MDAnalysis/coordinates/INPCRD.py	90.62% <0.00%> (-0.29%)	⬇️
package/MDAnalysis/coordinates/GSD.py	86.95% <0.00%> (-0.28%)	⬇️
package/MDAnalysis/coordinates/TXYZ.py	90.10% <0.00%> (-0.22%)	⬇️
... and 32 more

---

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[abhiShandy]

Travis CI failed since my change is not reverse compatible with Python 2.7
Should I make it reverse compatible?

[IAlibay]

@abhiShandy unfortunately MDA must support py2.7 until at least v1.0.0 (if I'm remembering the roadmap correctly). An option that would cover py2.7 through tto 3.8 would be appreciated if possible.

[lilyminium]

Do we need MutableMapping? So far as I can tell, flatten_dict is only used once in groups.py, on a dict.

mdanalysis/package/MDAnalysis/core/groups.py

Lines 1726 to 1745 in d9a78a4

	res = dict()
	if isinstance(topattrs, (string_types, bytes)):
	attr=topattrs
	if isinstance(topattrs, bytes):
	attr = topattrs.decode('utf-8')
	ta = getattr(self, attr)
	return {i: self[ta == i] for i in set(ta)}
	else:
	attr = topattrs[0]
	ta = getattr(self, attr)
	for i in set(ta):
	if len(topattrs) == 1:
	res[i] = self[ta == i]
	else:
	res[i] = self[ta == i].groupby(topattrs[1:])
	return util.flatten_dict(res)

[abhiShandy]

Do we need MutableMapping? So far as I can tell, flatten_dict is only used once in groups.py, on a dict.

mdanalysis/package/MDAnalysis/core/groups.py

Lines 1726 to 1745 in d9a78a4

	res = dict()
	if isinstance(topattrs, (string_types, bytes)):
	attr=topattrs
	if isinstance(topattrs, bytes):
	attr = topattrs.decode('utf-8')
	ta = getattr(self, attr)
	return {i: self[ta == i] for i in set(ta)}
	else:
	attr = topattrs[0]
	ta = getattr(self, attr)
	for i in set(ta):
	if len(topattrs) == 1:
	res[i] = self[ta == i]
	else:
	res[i] = self[ta == i].groupby(topattrs[1:])
	return util.flatten_dict(res)

Good point.

• changed it to isinstance(v, dict) to check if it's nested.
• Removed unnecessary collections from that file.

Locally, lib/test_util and core/test_groups passed with Python 3.8

[abhiShandy]

@MDAnalysis/gsoc-mentors can someone review this?

[orbeckst]

Looks good to me.

Please also

• add yourself to AUTHORS
• add a note to Fixes in CHANGELOG (referencing the issue)

[orbeckst]

Please ping me @orbeckst for a final review when you have addressed my review and all tests pass. Thank you for your contribution!

[abhiShandy]

@orbeckst it's ready

[orbeckst]

Thank you very much, @abhiShandy !