Turn off identify_connected_components default

[daico007]

Per discussion stemmed from #757, this PR turned off the default identify_connected_components option in the parameterize.apply.

[codecov]

Codecov Report

Patch coverage: 100.00% and project coverage change: +0.01% 🎉

Comparison is base (0011e15) 92.06% compared to head (75b0a11) 92.07%.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #760      +/-   ##
==========================================
+ Coverage   92.06%   92.07%   +0.01%     
==========================================
  Files          67       67              
  Lines        6892     6890       -2     
==========================================
- Hits         6345     6344       -1     
+ Misses        547      546       -1     

Files Changed	Coverage Δ
gmso/utils/specific_ff_to_residue.py	89.66% <ø> (ø)
gmso/parameterization/parameterize.py	100.00% <100.00%> (ø)
gmso/parameterization/topology_parameterizer.py	97.67% <100.00%> (-0.04%)	⬇️

... and 1 file with indirect coverage changes

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[CalCraven]

Per this discussion, a few other changes may as well be made here:

    identify_connected_components: bool, optional, default=False
        A flag which will speed up atomtyping for systems with many repeated molecules in
        the system. Specifically useful if `top.unique_site_labels()` isn't properly identifying 
        repeated. However, if the molecules are identified, then it is recommended to use
        use_molecule_info.
        molecules.

Also, I would set use_molecule_info to True as default, since that shouldn't add any overhead, since it's just checking the molecule tags. The use_molecule_info text should also be changed. Maybe something like:
A flag to determine whether or not to look at site.molcule_name to look for repeated molecules, and copy the parameters out to the remaining molecules.

I was also thinking we could rename these parameters. There are three potential speedup methods:
identify_connected_components=True
use_molecule_info=True
fast_copy=True

What if we named them something something more cohesive so it was clear if things are running slow for you, you should try to use of of these flags?
Something:
speedup_idmolecules
speedup_molecule_tag
speedup_copyexpressions

While we're here, what do we think about reformatting assert_x_parameters as well. What if we condensed it to assert_parameter_connections, and you pass a dict instead of 4 different bools? Might reduce how lengthy this function docstring is.

[chrisjonesBSU]

I like the idea of using speedup in the parameter names to help convey the idea of what these parameters are doing.

[daico007]

Good idea! I think we can go with speedup_by_moltag and speedup_by_molgraph? (short for molecule tag and molecule graph, i.e., connected components)?

[daico007]

Regarding the assert_x_parameters, I agree that we should to put them in one place/parameter. But I am thinking we could reverse it a little bit, instead of the user assert a set of parameters exist, we could turn it into ignore_pararameters, which could take a list/tuple of ('bond', 'angle', 'dihedral', 'improper'). So in the default case, the ignore_parameters will just be ('improper').

[daico007]

I included the proposed changes in the latest commit, lmk what y'all think.

[chrisjonesBSU]

I left a couple comments for some small changes.

[CalCraven]

Once those few changes are in, this looks good to me.

[daico007]

I should have addressed all the comments by @chrisjonesBSU and @CalCraven in the last commit.

[chrisjonesBSU]

LGTM! I made one commit to change True to False in the doc string for speedup_by_molgraph

[CalCraven]

Few more minor doc string changes and this is good to merge.