Merge pull request #132 from Saityi/ipynb-regression-check

Run notebook examples in CI
AlgebraicJulia · Aug 22, 2024 · d636847 · d636847 · neonWhiteout · Aug 22, 2024
2 parents b83f45c + fa49986
commit d636847
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diff --git a/.github/workflows/validate-notebooks.yml b/.github/workflows/validate-notebooks.yml
@@ -0,0 +1,25 @@
+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:
+      - uses: actions/checkout@v3
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: 1.9
+      - uses: julia-actions/cache@v1
+      - uses: julia-actions/julia-buildpkg@v1
+      - name: Create Julia files from Jupyter Notebook examples
+        run: |
+          mkdir ./jlexamples
+          ./ipynb-to-jl.sh "full_fledged_schema_examples"
+          ./ipynb-to-jl.sh "full_fledged_schema_examples_new"
+      - name: Validate notebook examples by running
+        run: julia -p auto --project="." -e 'include("./run_notebooks.jl")'
+      - name: Clean up Julia files from Jupyter Notebook examples
+        run: rm -rf jlexamples
diff --git a/.gitignore b/.gitignore
@@ -2,35 +2,22 @@
 *.jl.cov
 *.jl.mem
 
-examples/.ipynb_checkpoints/
-
+.vscode
 .DS_Store
 
-examples/primitive schema examples/.ipynb_checkpoints/
-
-examples/primitive_schema_examples/.ipynb_checkpoints/
-
-
-
-examples/primitive_schema_examples/practises/.ipynb_checkpoints/SEIRVD model hard-checkpoint.ipynb
-
-examples/primitive_schema_examples/practises/.ipynb_checkpoints/SEIRVD model-checkpoint.ipynb
-
-examples/primitive_schema_examples/practises/.ipynb_checkpoints/SIRV composition model simple-checkpoint.ipynb
-
-examples/primitive_schema_examples/practises/.ipynb_checkpoints/SIRV composition model-checkpoint.ipynb
-
-examples/primitive_schema_examples/practises/solutions/.ipynb_checkpoints/SIRV composition model-checkpoint.ipynb
-
-examples/full_fledged_schema_examples/.ipynb_checkpoints/composed open population SIRV model-checkpoint.ipynb
-
-examples/full_fledged_schema_examples/.ipynb_checkpoints/
+Manifest.toml
+.#*
 
-examples/full_fledged_schema_examples/composition/.ipynb_checkpoints/
+# Jupyter notebook checkpoints
+.ipynb_checkpoints
+**/*.ipynb_checkpoints
 
-examples/full_fledged_schema_examples/stratification/.ipynb_checkpoints/
+# Vim temporary files:
+*~
+*.swp
+*.swo
 
-examples/full_fledged_schema_examples/CaulsalLoopDiagrams/.ipynb_checkpoints/
+# Emacs temporary files
+\#*\#
+.\#*
 
-Manifest.toml
-.#*
diff --git a/.vscode/settings.json b/.vscode/settings.json
diff --git a/Project.toml b/Project.toml
@@ -9,9 +9,7 @@ AlgebraicRewriting = "725a01d3-f174-5bbd-84e1-b9417bad95d9"
 Catlab = "134e5e36-593f-5add-ad60-77f754baafbe"
 Combinatorics = "861a8166-3701-5b0c-9a16-15d98fcdc6aa"
 CompTime = "0fb5dd42-039a-4ca4-a1d7-89a96eae6d39"
-GraphViz = "f526b714-d49f-11e8-06ff-31ed36ee7ee0"
 Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
-Graphviz_jll = "3c863552-8265-54e4-a6dc-903eb78fde85"
 JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 LabelledArrays = "2ee39098-c373-598a-b85f-a56591580800"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
@@ -29,7 +27,6 @@ AlgebraicRewriting = "0.2.1 - 0.3.2, 0.4"
 Catlab = "0.15.5 - 0.16.8, 0.16"
 Combinatorics = "1.0.2"
 CompTime = "0.1"
-GraphViz = "0.2"
 Graphs = "1.9.0"
 JSON = "0.21.0"
 LabelledArrays = "^1"

diff --git a/docs/Project.toml b/docs/Project.toml
@@ -2,7 +2,6 @@
 AlgebraicRewriting = "725a01d3-f174-5bbd-84e1-b9417bad95d9"
 Catlab = "134e5e36-593f-5add-ad60-77f754baafbe"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
-GraphViz = "f526b714-d49f-11e8-06ff-31ed36ee7ee0"
 JSON3 = "0f8b85d8-7281-11e9-16c2-39a750bddbf1"
 LabelledArrays = "2ee39098-c373-598a-b85f-a56591580800"
 Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"

diff --git a/...full_fledged_schema_examples_new/CasualLoopDiagrams/convert_from_SEIR_stockFlowDiagram.jl b/...full_fledged_schema_examples_new/CasualLoopDiagrams/convert_from_SEIR_stockFlowDiagram.jl
@@ -1,7 +1,5 @@
 # # Convert from SEIR Stock Flow Diagram
 
-using GraphViz
-
 using StockFlow
 using StockFlow.Syntax
 

diff --git a/docs/literate/full_fledged_schema_examples_new/composition/COVID_full_model.jl b/docs/literate/full_fledged_schema_examples_new/composition/COVID_full_model.jl
@@ -1,7 +1,5 @@
 # # COVID Full Model
 
-using GraphViz
-
 using StockFlow
 using StockFlow.Syntax
 

diff --git a/...terate/full_fledged_schema_examples_new/composition/SEIR_full_model_measles_chickenpox.jl b/...terate/full_fledged_schema_examples_new/composition/SEIR_full_model_measles_chickenpox.jl
@@ -1,7 +1,5 @@
 # # SEIR Full Model Measles Chickenpox
 
-using GraphViz
-
 using StockFlow
 using StockFlow.Syntax
 

diff --git a/...erate/full_fledged_schema_examples_new/composition/composed_open_population_SIRV_model.jl b/...erate/full_fledged_schema_examples_new/composition/composed_open_population_SIRV_model.jl
@@ -1,7 +1,5 @@
 # # Composed Open Population SIRV Model
 
-using GraphViz
-
 using StockFlow
 using StockFlow.Syntax
 

diff --git a/...ll_fledged_schema_examples_new/composition/curable_sexually_transmitted_diseases_model.jl b/...ll_fledged_schema_examples_new/composition/curable_sexually_transmitted_diseases_model.jl
@@ -1,7 +1,5 @@
 # # Curable Sexually-Transmitted Diseases Model
 
-using GraphViz
-
 using StockFlow
 using StockFlow.Syntax
 

diff --git a/docs/literate/full_fledged_schema_examples_new/composition/diabetes_model.jl b/docs/literate/full_fledged_schema_examples_new/composition/diabetes_model.jl
@@ -1,7 +1,5 @@
 # # Diabetes Model
 
-using GraphViz
-
 using StockFlow
 using StockFlow.Syntax
 

diff --git a/docs/literate/full_fledged_schema_examples_new/stratification/diabetes_diagnose.jl b/docs/literate/full_fledged_schema_examples_new/stratification/diabetes_diagnose.jl
@@ -1,7 +1,5 @@
 # # Diabetes Diagnose
 
-using GraphViz
-
 using StockFlow
 using StockFlow.Syntax
 

diff --git a/docs/literate/full_fledged_schema_examples_new/stratification/sir_linear_stratification.jl b/docs/literate/full_fledged_schema_examples_new/stratification/sir_linear_stratification.jl
@@ -1,7 +1,5 @@
 # # SIR Linear Stratification
 
-using GraphViz
-
 using StockFlow
 using StockFlow.Syntax
 

diff --git a/...te/full_fledged_schema_examples_new/stratification/sir_linear_stratification.md b/...te/full_fledged_schema_examples_new/stratification/sir_linear_stratification.md
@@ -1,5 +1,3 @@
-using GraphViz
-
 using StockFlow
 using StockFlow.Syntax
 

diff --git a/docs/literate/full_fledged_schema_examples_new/stratification/sir_standard_stratification.jl b/docs/literate/full_fledged_schema_examples_new/stratification/sir_standard_stratification.jl
@@ -1,7 +1,5 @@
 # # SIR Standard Stratification
 
-using GraphViz
-
 using StockFlow
 using StockFlow.Syntax
 

diff --git a/.../convert_from_SEIR_stockFlowDiagram.ipynb → .../convert_from_SEIR_stockFlowDiagram.ipynb b/.../convert_from_SEIR_stockFlowDiagram.ipynb → .../convert_from_SEIR_stockFlowDiagram.ipynb
@@ -1342,21 +1342,21 @@
     }
    ],
    "source": [
-    "Graph(seir_causalLoop)"
+    "GraphCL(seir_causalLoop)"
    ]
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Julia 1.9.2",
+   "display_name": "Julia 1.10.4",
    "language": "julia",
-   "name": "julia-1.9"
+   "name": "julia-1.10"
   },
   "language_info": {
    "file_extension": ".jl",
    "mimetype": "application/julia",
    "name": "julia",
-   "version": "1.9.2"
+   "version": "1.10.4"
   }
  },
  "nbformat": 4,

diff --git a/...Diagrams/create_a_causalLoopDiagram.ipynb → ...Diagrams/create_a_causalLoopDiagram.ipynb b/...Diagrams/create_a_causalLoopDiagram.ipynb → ...Diagrams/create_a_causalLoopDiagram.ipynb
@@ -110,8 +110,8 @@
    "source": [
     "# test the causal loop diagram\n",
     "si_causalLoop=CausalLoop(\n",
-    "    (:S,:i,:I),\n",
-    "    (:S=>:i,:i=>:S,:i=>:I,:I=>:i)\n",
+    "    [:S,:i,:I],\n",
+    "    [:S=>:i,:i=>:S,:i=>:I,:I=>:i]\n",
     ")"
    ]
   },
@@ -186,21 +186,21 @@
     }
    ],
    "source": [
-    "Graph(si_causalLoop)"
+    "GraphCL(si_causalLoop)"
    ]
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Julia 1.7.3",
+   "display_name": "Julia 1.10.4",
    "language": "julia",
-   "name": "julia-1.7"
+   "name": "julia-1.10"
   },
   "language_info": {
    "file_extension": ".jl",
    "mimetype": "application/julia",
    "name": "julia",
-   "version": "1.7.3"
+   "version": "1.10.4"
   }
  },
  "nbformat": 4,

diff --git a/...d_schema_examples/SIR_example_function_structure_test_compostion_and_stratification.ipynb b/...d_schema_examples/SIR_example_function_structure_test_compostion_and_stratification.ipynb
@@ -946,7 +946,7 @@
    "source": [
     "# define a foot of the structured multicospan\n",
     "footS=foot(:S, :N, :S=>:N)\n",
-    "Graph(footS;schema=\"C0\")"
+    "StockFlow.Graph(footS;schema=\"C0\")"
    ]
   },
   {
@@ -970,7 +970,7 @@
    "source": [
     "# define a foot of the structured multicospan\n",
     "footI=foot(:I, :N, :I=>:N)\n",
-    "Graph(footI;schema=\"C0\")"
+    "StockFlow.Graph(footI;schema=\"C0\")"
    ]
   },
   {
@@ -2114,9 +2114,7 @@
   {
    "cell_type": "code",
    "execution_count": 15,
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -2543,9 +2541,7 @@
   {
    "cell_type": "code",
    "execution_count": 19,
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -6059,9 +6055,7 @@
   {
    "cell_type": "code",
    "execution_count": 34,
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -9921,9 +9915,7 @@
   {
    "cell_type": "code",
    "execution_count": 46,
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -10756,21 +10748,21 @@
    ],
    "source": [
     "causalloop=convertToCausalLoop(SIRstructure)\n",
-    "Graph(causalloop)"
+    "GraphCL(causalloop)"
    ]
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Julia 1.9.2",
+   "display_name": "Julia 1.10.4",
    "language": "julia",
-   "name": "julia-1.9"
+   "name": "julia-1.10"
   },
   "language_info": {
    "file_extension": ".jl",
    "mimetype": "application/julia",
    "name": "julia",
-   "version": "1.9.2"
+   "version": "1.10.4"
   }
  },
  "nbformat": 4,