fixed freud bond issue

[chrisiacovella]

PR Summary:

This addresses issue #1125 whereby the freud_generate_bonds routine was not finding all bonds when looking for bonds between two different species

As detailed in the issue, this was caused by the way in which we pass the particles to freud during the calculation of neighbors. Ultimately, the fix for this is relatively straight forward to implement. If name_a == name_b, then exclude_ii = True; If name_a != name_b, then exclude_ii = False. This is now automatically toggled by the code, and users no longer have the option to change this.

An additional test is included now that looks at a system where the two specifies are unique, as the original tests did not include this.

PR Checklist

---

• Includes appropriate unit test(s)
• Appropriate docstring(s) are added/updated
• Code is (approximately) PEP8 compliant
• Issue(s) raised/addressed?

[codecov]

Codecov Report

Patch coverage: 100.00% and no project coverage change.

Comparison is base (738bf49) 87.12% compared to head (0096908) 87.13%.

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #1127   +/-   ##
=======================================
  Coverage   87.12%   87.13%           
=======================================
  Files          62       62           
  Lines        6448     6451    +3     
=======================================
+ Hits         5618     5621    +3     
  Misses        830      830           

Impacted Files	Coverage Δ
mbuild/compound.py	97.12% <100.00%> (+<0.01%)	⬆️

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[chrisiacovella]

Some tests are failing due to newly released hoomd 4. #1126

[daico007]

LGTM!