* Updated Petri and Catlab APIs

* Added compat entries and version bump for final release

* Removed v1.0 test

* Remove ModelingToolkit dependency from semanticmodels

* Updated to new Petri.jl interface

* Updated to new Petri.jl interface for petrimodels

* Began the great cleanup of 2020

* Removed pretty much everything else

* Forgot a couple

* Began restructuring

* Moved documentation to it's own project environment

* Added back some old expression based model functionality

* Began working on cleaning up examples

* Continued cleaning up examples

* Added ignoring of virtual environment folders

* More work cleaning up examples

* Stil working on cleaning up examples

* removed last manifest

* Removed unnecessary travis lines

* Updating travis

* travis automatically tests

* Fixed travis documentation typo

* Updated jupyter notebook examples

* Updated dockerfile

* Removed last of the unnecessary files

* Updated README

* Removed all documentation errors

* Added github actions

* Fixed missing light graphs dependency

* Added fixes for the covid example

* Hopefully "fixed" dependencies

* Add a theory for modeling SEIRD diseases primitive transmision model

* update covid example with operadic composition and SEIRD model

* Update catlab dependency

* Fix typo

* Updated dependency versions

* Updated catlab syntax and petri net syntax throughout files

* Updated packages

* attempt to update malaria example. Fixes problems with OpenPetri.model.model

* More fixes to malaria.ipynb

* fix the mk_function calls in malaria.ipynb

* update wd render to orientation from direction. update malaria example

* Add some TODOs to the CT api

* attempt to use the new CT API for petri composition.

* add implementation of Covid model without CT interface.

* figured out how to use the new API

* introduce PetriCospan instance, tests pass

* WIP saving state

* fix test failure on Death Sq

* fix compose_pushout attempt 1

* remove compose_pushout debug stmts

* collecting tests at the bottom of the file

* move covid example to bottom of file

* remove unnecessarily tight type constraint

* add tests for building SEI and SEIR models

* comment out drawing to make testing easier

* WIP building intercity flow model

* add more PetriCospan tests

* add covid model and parameter exploration

* refactor covid odemodel

* move covid images to a `img` folder

* ignore images in covid example directory

* add SEIRD case for COVID

* fix plotting

* add peakgap analysis of SEIRD multicity

* delete unused test file for catlab

* add Pseird city model to covid example

* update project.toml and tests

* add comments to odemodel.jl

* integrate PetriCospans into SemanticModels add tests

* ammend previous commit

* add estimate delay to odemodel.jl

* add SEIR vs SEIRD comparison based on gap

* add validation data generation script

Co-authored-by: Micah Halter <micah.halter@gtri.gatech.edu>

* Added julia compat

* Fix compatibility entries

* add StaticArray version

* Add diffeq compat requirements

* Fixed difeq requirements

* Added stochasticdiffeq compat

* Moving julia

* Added another compat

* Roll back to v0.3.0 for rerelease

* Added logo and fixed project compat

* Created full logo

* Added line

* Updated documentation index

* Removed old logo

* Version bump

add Lotka Volterra examples and elementary food web examples

* Fix redefined headfunction between typegraphs.jl and exprs.jl

* Fix test errors with package and function conflicts

* Added missing dependency

we need to retag

missing a file `examples/epicookbook/data/edges_from_code_1.jl`

automated with Documenter.jl so the tables in markdown reflect the CSV.