Merge branch 'AlgebraicJulia:master' into foot_error_messages

.github/workflows/tests.yml

@@ -9,7 +9,6 @@ jobs:
       matrix:
         julia-version: ['1.9']
         os: [ubuntu-latest, macOS-latest]
-
     steps:
       - uses: actions/checkout@v2
       - uses: julia-actions/setup-julia@latest

.github/workflows/validate-notebooks.yml

@@ -0,0 +1,50 @@
+name: Check notebook examples for regressions
+
+on: [push, pull_request]
+
+env:
+  JULIA_NUM_THREADS: 'auto'
+jobs:
+  notebooks-examples-regression-test:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+      - name: Setup Julia
+        uses: julia-actions/setup-julia@v1
+        with:
+          version: 1.9
+      - name: Cache Julia dependencies
+        uses: julia-actions/cache@v1
+      - name: Add IJulia Jupyter kernel
+        run: julia --color=yes --project=. -e 'ENV["JULIA_PKG_PRECOMPILE_AUTO"]=0; using Pkg; pkg"add IJulia"'
+      - name: Install Julia dependencies
+        run: julia --color=yes --project=. -e 'import Pkg; Pkg.instantiate(); Pkg.resolve(); Pkg.precompile()'
+      - uses: yaananth/run-notebook@v2
+        env:
+          RUNNER: ${{ toJson(runner) }}
+          SECRETS: ${{ toJson(secrets) }}
+          GITHUB: ${{ toJson(github) }}
+        with:
+          notebook: "examples/full_fledged_schema_examples_new/stratification/diabetes_diagnose.ipynb"
+      - uses: yaananth/run-notebook@v2
+        env:
+          RUNNER: ${{ toJson(runner) }}
+          SECRETS: ${{ toJson(secrets) }}
+          GITHUB: ${{ toJson(github) }}
+        with:
+          notebook: "examples/full_fledged_schema_examples_new/composition/diabetes_model.ipynb"
+      - uses: yaananth/run-notebook@v2
+        env:
+          RUNNER: ${{ toJson(runner) }}
+          SECRETS: ${{ toJson(secrets) }}
+          GITHUB: ${{ toJson(github) }}
+        with:
+          notebook: "examples/full_fledged_schema_examples_new/CausalLoopDiagrams/convert_from_SEIR_stockFlowDiagram.ipynb"
+      - uses: actions/upload-artifact@v3
+        if: always()
+        with:
+          name: output
+          path: ${{ RUNNER.temp }}/nb-runner
+        env:
+          RUNNER: ${{ toJson(runner) }}

docs/.gitignore

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

docs/make.jl

@@ -0,0 +1,59 @@
+using Documenter
+using Literate
+
+const literate_dir = joinpath(@__DIR__, "literate")
+const generated_dir = joinpath(@__DIR__, "src", "generated")
+
+@info "Loading StockFlow.jl"
+using StockFlow
+
+const no_literate = "--no-literate" in ARGS
+if !no_literate
+  @info "Building Literate.jl docs"
+
+  # XXX: Work around old LaTeX distribution in GitHub CI.
+  if haskey(ENV, "GITHUB_ACTIONS")
+    import TikzPictures
+    TikzPictures.standaloneWorkaround(true)
+  end
+
+  # Set Literate.jl config if not being compiled on recognized service.
+  config = Dict{String,String}()
+  if !(haskey(ENV, "GITHUB_ACTIONS") || haskey(ENV, "GITLAB_CI"))
+    config["nbviewer_root_url"] = "https://nbviewer.jupyter.org/github/AlgebraicJulia/StockFlow.jl/blob/gh-pages/dev"
+    config["repo_root_url"] = "https://github.com/AlgebraicJulia/StockFlow.jl/blob/main/docs"
+  end
+
+  for (root, dirs, files) in walkdir(literate_dir)
+    out_dir = joinpath(generated_dir, relpath(root, literate_dir))
+    for file in files
+      if last(splitext(file)) == ".jl"
+        Literate.markdown(joinpath(root, file), out_dir;
+                          config=config, documenter=true, credit=false)
+        Literate.notebook(joinpath(root, file), out_dir;
+                          execute=true, documenter=true, credit=false)
+      end
+    end
+  end
+end
+
+@info "Building Documenter.jl docs"
+makedocs(
+  modules     = [StockFlow],
+  format      = Documenter.HTML(
+                                assets = ["assets/analytics.js"],
+                               ),
+  sitename    = "StockFlow.jl",
+  doctest     = false,
+  checkdocs   = :none,
+  pages       = Any[
+    "StockFlow.jl" => "index.md",
+  ]
+)
+
+@info "Deploying docs"
+deploydocs(
+  target = "build",
+  repo   = "github.com/AlgebraicJulia/StockFlow.jl.git",
+  branch = "gh-pages"
+)

docs/src/index.md

@@ -0,0 +1,10 @@
+# [StockFlow](@id StockFlow)
+
+```@autodocs
+Modules = [
+    StockFlow,
+    StockFlow.Syntax,
+    StockFlow.PremadeModels
+]
+Private = false
+```