merge with main

.github/workflows/TagBot.yml

@@ -8,13 +8,23 @@ on:
       lookback:
         default: 3
 permissions:
+  actions: read
+  checks: read
   contents: write
+  deployments: read
+  issues: read
+  discussions: read
+  packages: read
+  pages: read
+  pull-requests: read
+  repository-projects: read
+  security-events: read
+  statuses: read
 jobs:
   TagBot:
     if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
     runs-on: ubuntu-latest
     steps:
       - uses: JuliaRegistries/TagBot@v1
         with:
-          token: ${{ secrets.GITHUB_TOKEN }}
-          ssh: ${{ secrets.DOCUMENTER_KEY }}
+          token: ${{ secrets.RELEASE_TOKEN }}

.github/workflows/integration-issues.yml

@@ -5,6 +5,7 @@ on:
     types:
       - reopened
       - opened
+      - labeled
 
 jobs:
   add-to-project:

.github/workflows/julia_ci.yml

@@ -0,0 +1,50 @@
+name: Julia CI/CD
+
+on:
+  schedule:
+    - cron: 0 0 * * *
+  push:
+    branches: ["main"]
+    tags: ["*"]
+  pull_request:
+  workflow_dispatch:
+    inputs:
+      action:
+        description: "Action"
+        required: true
+        default: "test"
+        type: choice
+        options:
+          - test
+          - release
+      version:
+        description: "Tag and release version:"
+        required: false
+
+permissions:
+  actions: read
+  checks: read
+  contents: write
+  deployments: read
+  discussions: read
+  issues: read
+  packages: read
+  pages: read
+  pull-requests: write
+  repository-projects: read
+  security-events: read
+  statuses: read
+
+jobs:
+  CI:
+    if: github.event_name == 'pull_request' || github.event_name == 'push' || (github.event_name == 'workflow_dispatch' && inputs.action == 'test')
+    uses: AlgebraicJulia/.github/.github/workflows/julia_ci.yml@main
+    secrets: inherit
+  CompatHelper:
+    if: github.event_name == 'schedule'
+    uses: AlgebraicJulia/.github/.github/workflows/julia_compat.yml@main
+    secrets: inherit
+  Release:
+    if: github.event_name == 'workflow_dispatch' && inputs.action == 'release' && inputs.version != ''
+    uses: AlgebraicJulia/.github/.github/workflows/julia_release.yml@main
+    secrets: inherit

.gitignore

@@ -13,11 +13,6 @@ deps/downloads/
 deps/usr/
 deps/src/
 
-# Build artifacts for creating documentation generated by the Documenter package
-docs/build/
-docs/site/
-docs/src/examples
-
 # Editor/IDE specific ignores
 .vscode/
 

Project.toml

@@ -2,26 +2,28 @@ name = "AlgebraicPetri"
 uuid = "4f99eebe-17bf-4e98-b6a1-2c4f205a959b"
 license = "MIT"
 authors = ["Micah Halter <[email protected]>"]
-version = "0.8.6"
+version = "0.9.0"
 
 [deps]
 Catlab = "134e5e36-593f-5add-ad60-77f754baafbe"
 GeneralizedGenerated = "6b9d7cbe-bcb9-11e9-073f-15a7a543e2eb"
 LabelledArrays = "2ee39098-c373-598a-b85f-a56591580800"
-LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
-Requires = "ae029012-a4dd-5104-9daa-d747884805df"
-StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
+
+[weakdeps]
+Catalyst = "479239e8-5488-4da2-87a7-35f2df7eef83"
+ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
+OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
+
+[extensions]
+AlgebraicPetriCatalystExt = "Catalyst"
+AlgebraicPetriModelingToolkitExt = "ModelingToolkit"
+AlgebraicPetriOrdinaryDiffEqExt = "OrdinaryDiffEq"
 
 [compat]
-Catalyst = "^13.0.0"
-Catlab = "^0.14.14"
+Catalyst = "13"
+Catlab = "0.15.1"
 GeneralizedGenerated = "0.3"
-LabelledArrays = "^1"
-Requires = "^1"
-StatsBase = "^0.33"
-julia = "1.6"
-
-[extras]
-Catalyst = "479239e8-5488-4da2-87a7-35f2df7eef83"
-Petri = "4259d249-1051-49fa-8328-3f8ab9391c33"
-Tables = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
+LabelledArrays = "1"
+ModelingToolkit = "8"
+OrdinaryDiffEq = "6"
+julia = "1.9"

README.md

@@ -1,8 +1,8 @@
 # AlgebraicPetri.jl
 
-[![Documentation](https://github.com/AlgebraicJulia/AlgebraicPetri.jl/workflows/Documentation/badge.svg)](https://algebraicjulia.github.io/AlgebraicPetri.jl/dev/)
-![Tests](https://github.com/AlgebraicJulia/AlgebraicPetri.jl/workflows/Tests/badge.svg)
-[![Code Coverage](https://codecov.io/gh/AlgebraicJulia/AlgebraicPetri.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/AlgebraicJulia/AlgebraicPetri.jl)
+[![Stable Documentation](https://img.shields.io/badge/docs-stable-blue.svg)](https://AlgebraicJulia.github.io/AlgebraicPetri.jl/stable)
+[![Development Documentation](https://img.shields.io/badge/docs-dev-blue.svg)](https://AlgebraicJulia.github.io/AlgebraicPetri.jl/dev)
+[![CI/CD](https://github.com/AlgebraicJulia/AlgebraicPetri.jl/actions/workflows/julia_ci.yml/badge.svg)](https://github.com/AlgebraicJulia/AlgebraicPetri.jl/actions/workflows/julia_ci.yml)
 [![DOI](https://zenodo.org/badge/275202510.svg)](https://zenodo.org/badge/latestdoi/275202510)
 
 `AlgebraicPetri.jl` is a Julia library for building Petri Net models

docs/.gitignore

@@ -0,0 +1,2 @@
+build/
+src/generated/

docs/Project.toml

@@ -2,11 +2,12 @@
 AlgebraicPetri = "4f99eebe-17bf-4e98-b6a1-2c4f205a959b"
 Catlab = "134e5e36-593f-5add-ad60-77f754baafbe"
 DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa"
+DisplayAs = "0b91fe84-8a4c-11e9-3e1d-67c38462b6d6"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 LabelledArrays = "2ee39098-c373-598a-b85f-a56591580800"
 Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
+Markdown = "d6f4376e-aef5-505a-96c1-9c027394607a"
 OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
-Petri = "4259d249-1051-49fa-8328-3f8ab9391c33"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 PrettyTables = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d"

examples/covid/_covid.jl → docs/literate/covid/_covid.jl

@@ -1,6 +1,6 @@
 # # [Multi-City COVID-19 Model](@id covid_example)
 #
-#md # [![](https://img.shields.io/badge/show-nbviewer-579ACA.svg)](@__NBVIEWER_ROOT_URL__/examples/covid/covid.ipynb)
+#md # [![](https://img.shields.io/badge/show-nbviewer-579ACA.svg)](@__NBVIEWER_ROOT_URL__/generated/covid/covid.ipynb)
 
 using AlgebraicPetri
 using AlgebraicPetri.Epidemiology
@@ -61,7 +61,7 @@ seird_city = to_hom_expr(FreeBiproductCategory, seird_city)
 
 display_wd(seird_city)
 # -
-Graph(decoration(F(seird_city)))
+to_graphviz(decoration(F(seird_city)))
 
 # create a multi-city SEIRD models
 
@@ -72,7 +72,7 @@ pc_seird_3 = F(seird_3)
 p_seird_3 = decoration(pc_seird_3)
 display_wd(seird_3)
 # -
-Graph(p_seird_3)
+to_graphviz(p_seird_3)
 
 # Define time frame and initial parameters
 

examples/covid/_generate_figs.jl → docs/literate/covid/_generate_figs.jl

@@ -2,6 +2,7 @@
 include("epidemiology.jl")
 
 using OrdinaryDiffEq
+using Catlab.Graphics
 using Catlab.Graphics.Graphviz: run_graphviz
 
 # +
@@ -41,7 +42,7 @@ end
 # -
 
 save_wd(sir, "sir.svg")
-save_graph(Graph(p_sir), "sir_graph.svg")
+save_graph(to_graphviz(p_sir), "sir_graph.svg")
 
 # define initial states and transition rates
 u0 = [10.0, 1, 0]
@@ -53,7 +54,7 @@ sol = OrdinaryDiffEq.solve(prob,Tsit5())
 splot(sol, "sir_soln.svg")
 
 save_wd(seir, "seir.svg")
-save_graph(Graph(p_seir), "seir_graph.svg")
+save_graph(to_graphviz(p_seir), "seir_graph.svg")
 
 # define initial states and transition rates
 u0 = [10.0, 1, 0, 0]
@@ -65,7 +66,7 @@ sol = OrdinaryDiffEq.solve(prob,Tsit5())
 splot(sol, "seir_soln.svg")
 
 save_wd(seird, "seird.svg")
-save_graph(Graph(p_seird), "seird_graph.svg")
+save_graph(to_graphviz(p_seird), "seird_graph.svg")
 
 # define initial states and transition rates
 u0 = [10.0, 1, 0, 0, 0]
@@ -78,16 +79,16 @@ splot(sol, "seird_soln.svg")
 
 include("covid.jl")
 
-[save_graph(Graph(Petri.Model(decoration(p))), pname) for (p,pname) in [(spontaneous_petri, "spont.svg"),
+[save_graph(to_graphviz(Petri.Model(decoration(p))), pname) for (p,pname) in [(spontaneous_petri, "spont.svg"),
                                                (transmission_petri, "transmission.svg"),
                                                (exposure_petri, "exposure.svg"),
                                                (travel_petri, "travel.svg")]]
 
 save_wd(seird_city, "seird_city.svg")
-save_graph(Graph(Petri.Model(decoration(F(seird_city)))), "seird_graph.svg")
+save_graph(to_graphviz(Petri.Model(decoration(F(seird_city)))), "seird_graph.svg")
 
 save_wd(seird_3, "seird_3.svg")
-save_graph(Graph(p_seird_3), "seird_3_graph.svg")
+save_graph(to_graphviz(p_seird_3), "seird_3_graph.svg")
 
 pltdims = [4,9, 14]
 # Define time frame, 3 months