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ReusedBondError when bond binds >2 sites within Complex #466

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merged 2 commits into from Oct 16, 2019

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alubbock commented Oct 15, 2019

Each bond number can connect at most two sites, otherwise an error occurs in both BNG and Kappa. This PR adds a check for this as part of the dangling bond check, during ReactionPattern instantation. E.g., the following will now generate a ReusedBondError:

as_reaction_pattern(A(a=1) % B(b=1) % B(b=1))

Fixes: #465

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codecov-io commented Oct 15, 2019

Codecov Report

Merging #466 into master will increase coverage by 0.02%.
The diff coverage is 100%.

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@@            Coverage Diff             @@
##           master     #466      +/-   ##
==========================================
+ Coverage   79.71%   79.73%   +0.02%     
==========================================
  Files          98       98              
  Lines       10059    10069      +10     
==========================================
+ Hits         8019     8029      +10     
  Misses       2040     2040
Impacted Files Coverage Δ
pysb/core.py 88.29% <100%> (+0.02%) ⬆️
pysb/pattern.py 88.2% <100%> (+0.1%) ⬆️
pysb/tests/test_core.py 95.52% <100%> (+0.06%) ⬆️

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@alubbock alubbock merged commit a2fcbc1 into pysb:master Oct 16, 2019
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@alubbock alubbock deleted the alubbock:reused_bonds branch Oct 16, 2019
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