agents refactor

.gitignore

@@ -9,4 +9,6 @@ Manifest.toml
 .vscode/
 LocalPreferences.toml
 .DS_Store
-_*
+_*
+*.db
+*.db.wal

LICENSE

@@ -1,6 +1,6 @@
 The MIT License
 
-Copyright © 2022 Merck & Co., Inc., Rahway, NJ, USA and its affiliates. All rights reserved.
+Copyright © 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates. All rights reserved.
 
 Jan Bima (MSD), Otto Ritter (MSD), Sean L. Wu (Merck)
 

LICENSES_THIRD_PARTY

@@ -1,40 +1,10 @@
-ReactiveDynamics.jl depends on third-party Julia packages which may be distributed under different licenses. We have listed all of these third party packages and their licenses below. For the most up-to-date information, see `Project.toml`.
+ReactiveDynamics.jl depends on third-party Julia packages, which may be distributed under various licenses. For the most recent list of these packages, refer to `Project.toml` and consult the license terms of the individual packages.
 
-You must agree to the terms of these licenses, in addition to the ReactiveDynamics source code license, in order to use this software.
+You must agree to the terms of these licenses, in addition to the ReactiveDynamics.jl source code license, in order to use this software.
 
 --------------------------------------------------
 Third party software listed by License type
 --------------------------------------------------
 
 MIT License (or adaptations) (https://www.opensource.org/licenses/MIT)
-  * The Julia Language - https://github.com/JuliaLang/julia/blob/master/LICENSE.md
-  * BenchmarkTools.jl - https://github.com/JuliaCI/BenchmarkTools.jl
-  * CSV - https://github.com/JuliaData/CSV.jl
-  * Catlab - https://github.com/AlgebraicJulia/Catlab.jl
-  * ComponentArrays.jl - https://github.com/jonniedie/ComponentArrays.jl
-  * Crayons - https://github.com/KristofferC/Crayons.jl
-  * DataFrames.jl - https://github.com/JuliaData/DataFrames.jl
-  * DiffEqBase.jl - https://github.com/SciML/DiffEqBase.jl
-  * DifferentialEquations.jl - https://github.com/SciML/DifferentialEquations.jl
-  * Distributions.jl - https://github.com/JuliaStats/Distributions.jl
-  * Documenter - https://github.com/JuliaDocs/Documenter.jl
-  * DocumenterMarkdown - https://github.com/JuliaDocs/DocumenterMarkdown.jl
-  * GeneratedExpressions.jl - https://github.com/Merck/GeneratedExpressions.jl
-  * IJulia - https://github.com/JuliaLang/IJulia.jl
-  * JLD2 - https://github.com/JuliaIO/JLD2.jl
-  * JSON.jl - https://github.com/JuliaIO/JSON.jl
-  * MacroTools.jl - https://github.com/FluxML/MacroTools.jl
-  * NLopt - https://github.com/JuliaOpt/NLopt.jl
-  * OrdinaryDiffEq - https://github.com/SciML/OrdinaryDiffEq.jl
-  * Plots - https://github.com/JuliaPlots/Plots.jl
-  * Pluto.jl - https://github.com/fonsp/Pluto.jl
-  * Reexport - https://github.com/simonster/Reexport.jl
-  * SafeTestsets - https://github.com/YingboMa/SafeTestsets.jl
-  * Statistics.jl - https://github.com/JuliaStats/Statistics.jl
-  * StatsFuns.jl - https://github.com/JuliaStats/StatsFuns.jl
-  * Symbolics.jl - https://github.com/JuliaSymbolics/Symbolics.jl
-  * TOML.jl - https://github.com/JuliaLang/TOML.jl
-  * Tables.jl - https://github.com/JuliaData/Tables.jl
-
-The Unlicense (https://opensource.org/licenses/unlicense)
-  * PlutoUI.jl - https://github.com/JuliaPluto/PlutoUI.jl
+  * The Julia Language - https://github.com/JuliaLang/julia/blob/master/LICENSE.md

Project.toml

@@ -1,63 +1,54 @@
 name = "ReactiveDynamics"
 uuid = "c7456e7d-545a-4b79-91ea-6e93d96dd4d4"
-version = "0.2.7"
+version = "0.2.9"
 
 [deps]
+ACSets = "227ef7b5-1206-438b-ac65-934d6da304b8"
+AlgebraicAgents = "f6eb0ae3-10fa-40e6-88dd-9006ba45093a"
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
-Catlab = "134e5e36-593f-5add-ad60-77f754baafbe"
 ComponentArrays = "b0b7db55-cfe3-40fc-9ded-d10e2dbeff66"
 Crayons = "a8cc5b0e-0ffa-5ad4-8c14-923d3ee1735f"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
-DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e"
-DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
-Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
-DocumenterMarkdown = "997ab1e6-3595-5248-9280-8efb232c3433"
 GeneratedExpressions = "84d730a5-1eb9-4187-a799-27dd07f33a14"
 IJulia = "7073ff75-c697-5162-941a-fcdaad2a7d2a"
 JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
 JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 MacroTools = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09"
-NLopt = "76087f3c-5699-56af-9a33-bf431cd00edd"
-OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 Pluto = "c3e4b0f8-55cb-11ea-2926-15256bba5781"
 PlutoUI = "7f904dfe-b85e-4ff6-b463-dae2292396a8"
+Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 SafeTestsets = "1bc83da4-3b8d-516f-aca4-4fe02f6d838f"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 StatsFuns = "4c63d2b9-4356-54db-8cca-17b64c39e42c"
 Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7"
 TOML = "fa267f1f-6049-4f14-aa54-33bafae1ed76"
 Tables = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
-Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [compat]
-julia = "1.9"
-DifferentialEquations = "7.9"
-StatsFuns = "1.3"
-Catlab = "0.14"
-DataFrames = "1.6"
-PlutoUI = "0.7"
-Statistics = "1.9"
-DocumenterMarkdown = "0.2"
-ComponentArrays = "0.14"
-JLD2 = "0.4"
-GeneratedExpressions = "0.1"
-DiffEqBase = "6.128"
-JSON = "0.21"
-NLopt = "1.0"
-OrdinaryDiffEq = "6.55"
-Symbolics = "5.5"
-IJulia = "1.24"
-SafeTestsets = "0.1"
+julia = "1.11"
 CSV = "0.10"
-Plots = "1.39"
+Plots = "1.40"
+StatsFuns = "1.5"
+AlgebraicAgents = "0.3"
+ACSets = "0.2"
+Random = "1.11"
+DataFrames = "1.7"
+PlutoUI = "0.7"
+Statistics = "1.11"
 Reexport = "1.2"
 TOML = "1.0"
 MacroTools = "0.5"
+ComponentArrays = "0.15"
+JLD2 = "0.5"
 Crayons = "4.1"
-Documenter = "0.27"
-Tables = "1.10"
+GeneratedExpressions = "0.1"
+JSON = "0.21"
+Symbolics = "6.51"
+IJulia = "1.29"
+Tables = "1.12"
+SafeTestsets = "0.1"
 Distributions = "0.25"
-Pluto = "0.19"
+Pluto = "0.20"