trying to fix the within_inf problem

[zerothi]

Basically the isc did not respect the initial placement of the atomic coordinates, so if atoms were already outside of the unit-cell, then isc would be wrong.

@pfebrer I think this corrects your remarks in #649.
Comments?

• Closes within_inf returns wrong supercell indices? #649
• Added tests for new/changed functions?
• Ran isort . and black . [24.2.0] at top-level
• Documentation for functionality in docs/
• Changes documented in CHANGELOG.md

[codecov]

Codecov Report

Attention: Patch coverage is 94.28571% with 2 lines in your changes missing coverage. Please review.

Project coverage is 86.89%. Comparing base (bc41504) to head (e774c5a).
Report is 4 commits behind head on main.

Files with missing lines	Patch %	Lines
src/sisl/_core/_ufuncs_geometry.py	66.66%	1 Missing ⚠️
src/sisl/_core/geometry.py	95.45%	1 Missing ⚠️

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #850   +/-   ##
=======================================
  Coverage   86.89%   86.89%           
=======================================
  Files         403      403           
  Lines       52434    52450   +16     
=======================================
+ Hits        45561    45577   +16     
  Misses       6873     6873           

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[pfebrer]

This fixes the first code snippet in #649, but not the second one 😅

By the way, before getting this in, we have to remove these lines:

sisl/src/sisl/_core/geometry.py

Lines 3736 to 3738 in 614aadb

	# within_inf translates atoms to the unit cell to compute
	# supercell indices. Here we revert that
	ISC -= np.floor(self.fxyz[IA]).astype(int32)

[zerothi]

This fixes the first code snippet in #649, but not the second one 😅

By the way, before getting this in, we have to remove these lines:

sisl/src/sisl/_core/geometry.py

Lines 3736 to 3738 in 614aadb

	# within_inf translates atoms to the unit cell to compute
	# supercell indices. Here we revert that
	ISC -= np.floor(self.fxyz[IA]).astype(int32)

I think I tried that, but I'll double check! Thanks for the heads up of the blob, I'll add this to this PR then!