Add option to reset child labels in Compound.remove()

[jaclark5]

Two changes are made:

1. Add keyword argument to Compound.remove() for resetting the labels to achieve two goals. First, if all children of some category are removed, the parent category label will inherently be removed, while the ports are also renumbered.
2. In Compound.add() if a single Compound is added without a label, the Compound.name attribute is used instead of Compound.class.name to align with the default behavior in:
   • lib/atoms/n4.py : line 14
   • conversion.py : line 586, 700
   • lib/recipes/tiled_compound.py : line 139

PR Summary:

Resolves #1172

Using the code in the issue where the last line is now, Molecule.remove(remove_array, reset_labels=True), the results are now:

Before ['C', 'C[0]', 'H', 'H[0]', 'H[1]', 'C[1]', 'H[2]', 'H[3]', 'O', 'O[0]', 'down', 'up']
After Flatten ['monomer', 'H', 'C', 'C[0]', 'H[2]', 'H[3]', 'C[1]', 'H[4]', 'H[5]', 'O', 'O[0]', 'H[6]', 'H[7]']
After Remove H ['C', 'C[0]', 'C[1]', 'O', 'O[0]', 'port', 'port[0]', 'port[1]', 'port[2]', 'port[3]', 'port[4]', 'port[5]']

After

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

All modified and coverable lines are covered by tests ✅

Project coverage is 87.32%. Comparing base (df74ac1) to head (d9c2cfa).

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1173      +/-   ##
==========================================
+ Coverage   87.28%   87.32%   +0.04%     
==========================================
  Files          62       62              
  Lines        6502     6525      +23     
==========================================
+ Hits         5675     5698      +23     
  Misses        827      827              

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[chrisjonesBSU]

I left one suggestion, but this looks good to me. Thank you @jaclark5!

[daico007]

LGTM! Found a new bug (unrelated to this PR) that we need to fix though when reset_labels=False. The gist is if you removed all particle of a specific type (in this example all H of the ethane6 molecule, there is still the "H" in ethane6.labels. If we try to print it out, it will error out, since all the underlying object has been removed. This is bug in the remove method, basically we need a better of pruning the references to the removed object. This bug was basically fixed with the reset_label=True, since the new label dict was re-generated with only existing object.

[CalCraven]

We should potentially add in a future PR a deprecation warning for reset_index