Enable pattern matching with compartments

[FFroehlich]

Enable RulePatternMatcher and SpeciesPatternMatcher for models with compartments. Support was already there, just removed NotImplementedError - this is validated by including move_connected, which contains species with compartments, in the test_all_species generated test.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 78.43%. Comparing base (6d850c2) to head (07c25b0).

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #570      +/-   ##
==========================================
+ Coverage   78.28%   78.43%   +0.15%     
==========================================
  Files         106      106              
  Lines       11253    11301      +48     
==========================================
+ Hits         8809     8864      +55     
+ Misses       2444     2437       -7     

Flag	Coverage Δ
os-macos-latest	78.43% <100.00%> (+0.15%)	⬆️
os-ubuntu-latest	78.42% <100.00%> (+0.15%)	⬆️
os-windows-latest	2.76% <1.51%> (-0.02%)	⬇️
python-3.10	78.43% <100.00%> (+0.15%)	⬆️
python-3.11	78.43% <100.00%> (+0.15%)	⬆️
python-3.12	78.43% <100.00%> (+0.15%)	⬆️
python-3.8	78.42% <100.00%> (+0.15%)	⬆️
python-3.9	78.42% <100.00%> (+0.15%)	⬆️

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[alubbock]

LGTM overall, though it's been a while since I worked with compartments. Ideally it'd be good to see test coverage for the two lines highlighted by codecov - particularly pysb/core.py line 956.

[FFroehlich]

LGTM overall, though it's been a while since I worked with compartments. Ideally it'd be good to see test coverage for the two lines highlighted by codecov - particularly pysb/core.py line 956.

Ah! turns out adding the edges in line 956 is actually not even necessary, simply adding the species compartment node to the graph is sufficient. Removed the respective lines, added a test for the value error and simplified the code a bit further.