Add support for torus QPU graph variations

[jackraymond]

The primary purpose of this pull request is to provide generators for the instances evaluated in https://arxiv.org/abs/2202.03044 [BBRR].

The pull request:

• Adds support for torus graph variations upon Chimera, Pegasus and Zephyr as used in _[BBRR], _[RH].
• Corrects errors associated to special edge cases in use of check_edge_list and check_node_list in zephyr_graph, pegasus_graph and chimera_graph
• Refactors some bibliography entries, and corrects for some associated errors in elimination_order.py
• Simplifies one line in coloring.py to suppress a type error.

[codecov-commenter]

Codecov Report

Merging #225 (ededd31) into main (b0dee61) will increase coverage by 0.47%.
The diff coverage is 95.00%.

@@            Coverage Diff             @@
##             main     #225      +/-   ##
==========================================
+ Coverage   75.18%   75.66%   +0.47%     
==========================================
  Files          31       30       -1     
  Lines        2112     2174      +62     
==========================================
+ Hits         1588     1645      +57     
- Misses        524      529       +5     

Impacted Files	Coverage Δ
dwave_networkx/algorithms/elimination_ordering.py	85.57% <ø> (ø)
dwave_networkx/generators/chimera.py	87.16% <93.33%> (+0.46%)	⬆️
dwave_networkx/generators/common.py	95.45% <93.33%> (-4.55%)	⬇️
dwave_networkx/generators/pegasus.py	89.60% <93.75%> (-0.01%)	⬇️
dwave_networkx/algorithms/coloring.py	96.47% <100.00%> (ø)
dwave_networkx/generators/zephyr.py	97.27% <100.00%> (+0.22%)	⬆️
dwave_networkx/__init__.py

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[JoelPasvolsky]

I'm making this PR review in slices to help you get it in quickly. This first one is mostly on the chimera.py updates

[JoelPasvolsky]

Comments for another slice: pegasus.py

[JoelPasvolsky]

Third slice (for Zephyr). I think that should cover most of what I'll spend time looking at

Very nice addition, @jackraymond

[boothby]

lgtm

[jackraymond]

Implemented review comments in full. Some docstring issues remained in edge_list and node_list, these have been subsequently simplified. Some other minor formatting and compliance issues were addressed.

[randomir]

Tests could use some PEP8 love, but otherwise LGTM!