Issue 20: Improving the example script

.github/workflows/test.yml

@@ -15,21 +15,21 @@ jobs:
       matrix:
         include:
           # Ubuntu x64
-          - version: '1.10'
+          - version: '1.11'
             os: ubuntu-latest
             arch: x64
           - version: '1'
             os: ubuntu-latest
             arch: x64
           # Windows x64
-          - version: '1.10'
+          - version: '1.11'
             os: windows-latest
             arch: x64
           - version: '1'
             os: windows-latest
             arch: x64
           # macOS (use default arch - Apple Silicon on latest runners)
-          - version: '1.10'
+          - version: '1.11'
             os: macOS-latest
             arch: aarch64
           - version: '1'

.gitignore

@@ -386,4 +386,4 @@ doc_development.md
 test_development.md
 
 # Tutorial images
-!docs/src/assets/tutorial/*.png
+!docs/src/vignettes/*.png

Project.toml

@@ -18,4 +18,4 @@ Dates = "1.10"
 LinearAlgebra = "1.10"
 LogExpFunctions = "0.3.29"
 ProgressMeter = "1.10"
-julia = "1.10"
+julia = "1.11"

README.md

@@ -30,13 +30,13 @@ Pkg.add(url="https://github.com/CDCgov/NowcastAutoGP.jl")
 
 `NowcastAutoGP.jl` allows the user to incorporate nowcasting with ensemble Gaussian process (GP) forecasting provided by `AutoGP.jl`. In the example below, we show forecasting with the "naive" belief that the most recent reported data is accurate and final, compared to forecasting that incorporates simple nowcasting that accounts for a reporting multiplicative factor based on historical reporting patterns.
 
-![Naive forecasting showing underestimation](docs/src/assets/tutorial/cell-10-output-1.png)
+![Naive forecasting showing underestimation](docs/src/vignettes/getting-started-19.png)
 *Naive forecasting consistently underestimates due to reporting delays*
 
-![Forecasts with simple nowcasting](docs/src/assets/tutorial/cell-14-output-1.png)
+![Forecasts with simple nowcasting](docs/src/vignettes/getting-started-31.png)
 *Forecasts incorporating simple nowcasting show improved accuracy*
 
-![Performance comparison](docs/src/assets/tutorial/cell-17-output-1.png)
+![Performance comparison](docs/src/vignettes/getting-started-37.png)
 *Score ratios demonstrate clear performance improvements with nowcasting*
 
 ## Documentation

docs/Project.toml

@@ -1,12 +1,16 @@
 [deps]
+AutoGP = "6eb593e7-dfb4-4e48-b98e-d7222cdf0053"
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
 CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
 NowcastAutoGP = "7e9f7f4b-f590-4c14-8324-de4fcbed18f7"
+Parameters = "d96e819e-fc66-5662-9728-84c9c7592b0a"
+ProgressMeter = "92933f4c-e287-5a05-a399-4b506db050ca"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 TidierData = "fe2206b3-d496-4ee9-a338-6a095c4ece80"
 
 [sources]
-NowcastAutoGP = {path = "./.."}
+NowcastAutoGP = {path = ".."}

docs/make.jl

@@ -1,6 +1,13 @@
 using Documenter
 using NowcastAutoGP
 
+# Doc pages
+pages = [
+    "Home" => "index.md",
+    "Getting Started" => "vignettes/getting-started.md",
+    "API Reference" => "api.md",
+]
+
 makedocs(
     sitename = "NowcastAutoGP.jl",
     authors = "Centers for Disease Control and Prevention",
@@ -11,11 +18,7 @@ makedocs(
         assets = ["assets/material-theme.css", "assets/material-theme.js"],
         mathengine = Documenter.MathJax3()
     ),
-    pages = [
-        "Home" => "index.md",
-        "Getting started" => "vignettes/tutorial.md",
-        "API Reference" => "api.md",
-    ],
+    pages = pages,
     clean = true,
     checkdocs = :exports
 )

docs/make_vignettes.jl

@@ -0,0 +1,16 @@
+using Literate
+vignettes_to_make = ["getting-started.jl"]
+
+# Generate markdown with executed output from Literate.jl scripts.
+# Uses CommonMarkFlavor so Documenter.jl won't re-evaluate code blocks.
+# Run this locally when vignettes change; commit the generated .md and images.
+for vignettefile in vignettes_to_make
+    Literate.markdown(
+        joinpath(@__DIR__, "vignettes", vignettefile),
+        joinpath(@__DIR__, "src", "vignettes");
+        execute = true,
+        flavor = Literate.CommonMarkFlavor(),
+        mdstrings = true,
+        credit = true
+    )
+end

docs/src/index.md

@@ -27,7 +27,7 @@ Pkg.add(url="https://github.com/CDCgov/NowcastAutoGP.jl")
 
 ## Getting Started
 
-- **[Getting started example](vignettes/tutorial.md)**: A getting started guide demonstrating basic usage for combining forecasting and nowcasting on NHSN covid-19 hospitalization data.
+- **[Getting started example](vignettes/getting-started.md)**: A getting started guide demonstrating basic usage for combining forecasting and nowcasting on NHSN covid-19 hospitalization data.
 
 ## API Reference and Resources