Build petri net agent based models compositionally https://algebraicjulia.github.io/AlgebraicPetri.jl/stable/
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* [WIP] implementation of whole-grained Petri nets (#12) * implementation of whole-grained Petri nets * ENH: Some cleanup of basic Petri net implementation Co-authored-by: Owen Lynch <email@example.com> * Updated reaction network definition * Catch up petset to master (#16) * Updated catlab interface (#14) * Updated catlab interface * patch version bump to fix broken catlab * Don't dev catlab for docs * Updated petri to fix graphing * Update examples to match new interface * Change test versions * Added code coverage (#15) * Added code coverage * Fix documentation dependency incorrect resolution * Use newest version of catlab * Updated Catlab API * Working on CSet implementation of Petri nets * Added better constructor for building petri nets * Updated to newer cset type definitions * Improve interface to work with both Petri and ReactionNets * Added labelled petri nets * Added more nice constructors for building petri nets * Finished constructors and cleaned up duplicate code a little * Updated comment of example code * Added interface for Petri.jl * Added chime toy model * Removed unnecessary comments * Separated time span to variable for clearer definition * Added JSON generation * Added final json form and cleaned up * Added executable CHIME model using CSet implementation as well as JSON generation with code * Cleaned up code some more * Final code clean up for this example * Fix typo * Added chime model folder * Updated README * Updated documentation for CHIME models * Updated README * Updated README * Updated types with new patch in Catlab * Update to catlab 0.8 and petri 1.2.1 * Added looser codecov rules * Moved open petri nets to use the cset implementation * Updated examples * Updated chime-cset imports * Updated examples * Added more testing * Fix julia v1.0 support * Simplified each row iterator * Fix dimensionality mismatch in rate_eq * Added support for labelled petri net vector field generation * Split out vectorfield generation using multiple dispatch * Removed duplicate function * Moved to LabelledArrays to fix diffeq bug with dictionaries * Fix typo and update tests * final push on petsets * Fixed typo in epi: Co-authored-by: olynch <firstname.lastname@example.org> Co-authored-by: Owen Lynch <email@example.com>
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