print the hierarchy of a compound

[chrisiacovella]

PR Summary:

This refers to issue #1096 . This adds in functionality to print out the hierarchy using treelib (https://treelib.readthedocs.io/en/latest/).

An example output of a system with two ethane molecules is shown below. The function will automatically group together compounds at the same level that are identical in name, number and name of children and number and name of particles.

Compound, 16 particles, 14 bonds, 2 children
└── [Ethane x 2], 8 particles, 7 bonds, 2 children
    └── [CH3 x 2], 4 particles, 3 bonds, 4 children
        ├── [C x 1], 1 particles, 4 bonds, 0 children
        └── [H x 3], 1 particles, 1 bonds, 0 children

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 project coverage change: +0.10 🎉

Comparison is base (00d8c77) 89.29% compared to head (4a0434b) 89.39%.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1097      +/-   ##
==========================================
+ Coverage   89.29%   89.39%   +0.10%     
==========================================
  Files          61       61              
  Lines        6173     6235      +62     
==========================================
+ Hits         5512     5574      +62     
  Misses        661      661              

Impacted Files	Coverage Δ
mbuild/compound.py	96.95% <100.00%> (+0.18%)	⬆️

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[chrisiacovella]

Linux tests are being reported as failing, but it appears it is actually just being canceled when testing the silica interface. Basically, same thing as discussed in #1090 . I'm going to go ahead and comment out those tests of the next commit.

[daico007]

This looks great, some comment about the identifiers (to avoid false positive)

[daico007]

Also, pre-commit is failing due to docstring style issues

check yaml...............................................................Passed
fix end of files.........................................................Passed
trim trailing whitespace.................................................Passed
black....................................................................Passed
isort (python)...........................................................Passed
pydocstyle...............................................................Failed
- hook id: pydocstyle
- exit code: 1

mbuild/compound.py:283 in public method `print_hierarchy`:
        D205: 1 blank line required between summary line and description (found 0)
mbuild/compound.py:283 in public method `print_hierarchy`:
        D400: First line should end with a period (not 'e')
mbuild/compound.py:283 in public method `print_hierarchy`:
        D401: First line should be in imperative mood (perhaps 'Print', not 'Prints')
mbuild/compound.py:283 in public method `print_hierarchy`:
        D214: Section is over-indented ('Parameters')
mbuild/compound.py:283 in public method `print_hierarchy`:
        D215: Section underline is over-indented (in section 'Parameters')
mbuild/compound.py:283 in public method `print_hierarchy`:
        D214: Section is over-indented ('Returns')
mbuild/compound.py:283 in public method `print_hierarchy`:
        D409: Section underline should match the length of its name (Expected 7 dashes in section 'Returns', got 6)
mbuild/compound.py:283 in public method `print_hierarchy`:
        D215: Section underline is over-indented (in section 'Returns')
mbuild/compound.py:380 in private method `_get_hierarchy_nodup`:
        D205: 1 blank line required between summary line and description (found 0)

[chrisiacovella]

Ok, I think all comments are addressed. Read the docs is still failing because of the "unexpected" indents in some of the hoomd conversion files. Might need to do a separate PR to try to figure out why those are failing because nothing seems wrong.

[daico007]

LGTM!