Refactor non-standard object identity test

[ahkole]

• Closes Non-standard object identity test in SparseOrbital.iter_nnz #995
• Changes documented in changes/996.dev.rst

It also refactors all other occurrences of not [object_name] is None to [object_name] is not None.

[zerothi]

If you think this should be fixed, then there are plenty of other places where this is done:

grep "is None" **/*.py | grep not | grep -v "is not None" 

[ahkole]

If you think this should be fixed, then there are plenty of other places where this is done:

grep "is None" **/*.py | grep not | grep -v "is not None" 

Ah okay, I see now yes. I personally think object is not None is easier to read than not object is None. If you agree maybe I could just replace all of them?

[codecov]

Codecov Report

❌ Patch coverage is 88.46154% with 6 lines in your changes missing coverage. Please review.
✅ Project coverage is 86.64%. Comparing base (fc153f0) to head (b606152).

Files with missing lines	Patch %	Lines
src/sisl/_core/_ufuncs_grid.py	50.00%	1 Missing ⚠️
src/sisl/_core/sparse_geometry.py	50.00%	1 Missing ⚠️
src/sisl/io/openmx/omx.py	0.00%	1 Missing ⚠️
src/sisl/io/siesta/stdout.py	66.66%	1 Missing ⚠️
src/sisl/io/tbtrans/se.py	0.00%	1 Missing ⚠️
src/sisl/physics/hamiltonian.py	50.00%	1 Missing ⚠️

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #996   +/-   ##
=======================================
  Coverage   86.64%   86.64%           
=======================================
  Files         414      414           
  Lines       54741    54741           
=======================================
  Hits        47430    47430           
  Misses       7311     7311           

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[zerothi]

yeah, it would make sense to catch them all, while at it. Also, I wouldn't call it a fix, but a refactor/maintenance. So your changes should be named <>.dev.rst, so users don't think it will affect their code.

[ahkole]

I have used sed to replace all occurrences of not [object_name] is None to [object_name] is not None. Hopefully that should catch all of them.

I also checked after the replacement with your suggested grep command and the only remaining matches are lines that I agree should not be changed, either because they were false positives or the current expression is actually more readable.

Finally I also updated the PR title and the news fragment to call this a refactor instead of a fix.

[zerothi]

thank!