* Test new catlab branch to fix compose version resolution
* Fix syntax
* Fix trailing paren
* Fixed export of object that doesn't exist and updated examples
* Added second simple example
* First attempt at codecov
* update catlab dev branch
* Added code coverage badge
* Use newest version of catlab
* rate functions can be a function of the current state and time
* version bump
* Added backwards compatibility with old method of just time dependent rate function
* Made tagbot run more frequently
* bump documentation julia version
* Fix typo in github actions
* Added install of compose to hopefully get the latest version
* grasping at straws now...
* Change colors in visualization
Species in #6C9AC3
Reactions in #E28F41
* Minor version bump for fixed visualization and colors
Co-authored-by: Micah Halter <micah.halter@gtri.gatech.edu>
* Moved to github workflows and changed doc folder to docs
* Worked on removing dependencies and cleaning up code
* Added documentation
* Added badges
* Removed jupyter temp files
* Started cleaning up test and examples
* Removed old julia versions because they are broken
* Finished up cleanup
* Version bump
* Last addition to the docs
* Updated README
* add symbolic_symplify routine for simplification of Exprs
* add OpenModels support from SemanticModels
this commit requires Catlab support.
* add visualization code to Petri.jl from SemanticModels.
we can now draw a PetriNet with Graphviz
* fix visualization code to draw the in/output vertices correctly
* add tests and light refactoring
* add CT tests
* refactor Petri.jl and add stochastic tests
add ParamProblem and AbstractProblem
* move more tests from CT to stochastic
* fix CT tests
currently not included because they depend on Catlab and SemanticModels.
* reduce test verbosity
* add test dependencies, bump version
* refactor tests and reduce DifferentialEquations Dependency
* add example and readme images
* make subdirectory for example images
* use relative links for github
* use SVG for web ready images
* github blocks SVGs in readmes
* add connections to ACT
* add images from last commit
* use correct figure for seirs
* add mk_function to avoid calling eval and improve performance
add examples showing high performance usage
* remove Manifest.toml because Petri is a library not application
* using codegen to build a specialized simulation for the stochastic version
works with eval, but not mk_function
* add tests and light refactoring
* add CT tests
* refactor Petri.jl and add stochastic tests
add ParamProblem and AbstractProblem
* move more tests from CT to stochastic
* fix CT tests
currently not included because they depend on Catlab and SemanticModels.
* reduce test verbosity
* add test dependencies, bump version
* refactor tests and reduce DifferentialEquations Dependency
* add example and readme images
* make subdirectory for example images
* use relative links for github
* use SVG for web ready images
* github blocks SVGs in readmes
* add connections to ACT
* add images from last commit
* use correct figure for seirs
* add mk_function to avoid calling eval and improve performance
add examples showing high performance usage
* remove Manifest.toml because Petri is a library not application
* add tests and light refactoring
* add CT tests
* refactor Petri.jl and add stochastic tests
add ParamProblem and AbstractProblem
* move more tests from CT to stochastic
* fix CT tests
currently not included because they depend on Catlab and SemanticModels.
* reduce test verbosity
* add test dependencies, bump version
* refactor tests and reduce DifferentialEquations Dependency
* add example and readme images
* make subdirectory for example images
* use relative links for github
* use SVG for web ready images
* github blocks SVGs in readmes
* add connections to ACT
* add images from last commit
* use correct figure for seirs
James
James