* [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 <root@owenlynch.org>
* 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 <oclynch888@gmail.com>
Co-authored-by: Owen Lynch <root@owenlynch.org>
Micah Halter
eaa7cb8cdd