PySB native reaction generation

[FFroehlich]

• Adds constructors for ReactionPattern/ComplexPattern/MonomerPattern from graphs
• Adds functionality to compute action of Rules on species using graph differences
• Adds functionality to compute reaction rates the action of Rules on the action of individual species
• Adds tests of the newly added functionality by regenerating reactions for most bng validation models that can be imported

[codecov-commenter]

Codecov Report

Merging #506 into master will increase coverage by 0.65%.
The diff coverage is 96.80%.

@@            Coverage Diff             @@
##           master     #506      +/-   ##
==========================================
+ Coverage   80.24%   80.90%   +0.65%     
==========================================
  Files         101      103       +2     
  Lines       10650    11064     +414     
==========================================
+ Hits         8546     8951     +405     
- Misses       2104     2113       +9     

Impacted Files	Coverage Δ
pysb/core.py	88.87% <92.90%> (+0.14%)	⬆️
pysb/tests/test_network_generation.py	97.82% <97.82%> (ø)
pysb/network_generation.py	98.72% <98.72%> (ø)
pysb/pattern.py	89.97% <100.00%> (+1.54%)	⬆️
pysb/tests/test_pattern.py	100.00% <100.00%> (ø)

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[codecov-io]

Codecov Report

Merging #506 (b8d0941) into master (8819eaa) will decrease coverage by 77.41%.
The diff coverage is 3.40%.

@@            Coverage Diff             @@
##           master    #506       +/-   ##
==========================================
- Coverage   80.33%   2.92%   -77.42%     
==========================================
  Files         101     100        -1     
  Lines       10832   10667      -165     
==========================================
- Hits         8702     312     -8390     
- Misses       2130   10355     +8225     

Flag	Coverage Δ
os-macos-latest	?
os-ubuntu-latest	?
os-windows-latest	2.92% <3.40%> (+0.02%)	⬆️
python-3.10	2.92% <3.40%> (-77.42%)	⬇️
python-3.7	?
python-3.8	2.92% <3.41%> (-77.40%)	⬇️
python-3.9	2.92% <3.41%> (-77.40%)	⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
pysb/network_generation.py	0.00% <0.00%> (ø)
pysb/pattern.py	0.00% <0.00%> (-88.34%)	⬇️
pysb/tests/test_network_generation.py	0.00% <0.00%> (ø)
pysb/tests/test_pattern.py	0.00% <0.00%> (-100.00%)	⬇️
pysb/core.py	22.78% <10.32%> (-65.87%)	⬇️
pysb/tests/__init__.py	0.00% <0.00%> (-100.00%)	⬇️
pysb/tests/test_bng.py	0.00% <0.00%> (-100.00%)	⬇️
pysb/tests/test_util.py	0.00% <0.00%> (-100.00%)	⬇️
pysb/tests/test_kappa.py	0.00% <0.00%> (-100.00%)	⬇️
pysb/examples/michment.py	0.00% <0.00%> (-100.00%)	⬇️
... and 81 more

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