setup for docs build

Author: ChrisRackauckas

.buildkite/publish_tutorials_output.sh

@@ -11,7 +11,7 @@ temp_dir=$(mktemp -d)
 git -C "${temp_dir}" clone [email protected]:SciML/SciMLTutorialsOutput .
 
 # Copy our output artifacts into it:
-for d in html markdown notebook pdf script; do
+for d in docs html notebook pdf script markdown; do
     cp -vRa "${d}/" "${temp_dir}"
 done
 cp -va *.md *.bib "${temp_dir}"

.buildkite/run_tutorial.yml

@@ -35,12 +35,13 @@ steps:
             - ./*.toml
           outputs:
             - html/**/*.html
+            - markdown/**/figures/*.png
             - markdown/**/*.md
             - notebook/**/*.ipynb
             - pdf/**/*.pdf
             - script/**/*.jl
           s3_prefix: s3://julialang-buildkite-artifacts/scimltutorials
-    timeout_in_minutes: 360
+    timeout_in_minutes: 1000
     commands: |
       # Instantiate, to install the overall project dependencies
       echo "--- Instantiate"
@@ -62,7 +63,7 @@ steps:
           files:
             - .buildkite/ssh_deploy.key
       - JuliaCI/julia#v1:
-          version: 1.6
+          version: 1.7
       - staticfloat/sandbox:
           rootfs_url: "https://jc-rootfs-images.s3.amazonaws.com/aws_uploader-2021-11-12.x86_64.tar.gz"
           rootfs_treehash: "986217e5b36efd3b3b91ed90df8e36d628cf543f"
@@ -76,6 +77,7 @@ steps:
           input_from: "tutorial-{SANITIZED_PATH}"
           outputs:
             - html/**/*.html
+            - markdown/**/figures/*.png
             - markdown/**/*.md
             - notebook/**/*.ipynb
             - pdf/**/*.pdf

.buildkite/test_sciml.yml

@@ -2,10 +2,10 @@ agents:
   queue: "juliaecosystem"
 
 steps:
-  - label: ":julia: Run tests on 1.6"
+  - label: ":julia: Run tests on 1.7"
     plugins:
       - JuliaCI/julia#v1:
-          version: 1.6
+          version: 1.7
       - JuliaCI/julia-test#v1:
     timeout_in_minutes: 20
     artifact_paths:

docs/Project.toml

@@ -0,0 +1,2 @@
+[deps]
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"

docs/make.jl

@@ -0,0 +1,25 @@
+using Documenter, SciMLTutorialsOutput
+
+dir = @__DIR__() * "/.."
+
+@show dir
+@show readdir(dir)
+
+include("pages.jl")
+
+makedocs(
+    sitename="The SciML Tutorials",
+    authors="Chris Rackauckas",
+    modules=[SciMLTutorialsOutput],
+    clean=true, doctest=false,
+    format=Documenter.HTML(#analytics = "UA-90474609-3",
+        assets=["assets/favicon.ico"],
+        canonical="https://tutorials.sciml.ai/stable/"),
+    pages=pages
+)
+
+deploydocs(;
+    repo="github.com/SciML/SciMLTutorialsOutput",
+    devbranch="main",
+    branch="main"
+)

docs/pages.jl

@@ -0,0 +1,66 @@
+# This file assumes `dir` is the directory for the package! dir = @__DIR__() * "/.."
+
+dir = @__DIR__() * "/.."
+
+cp(joinpath(dir, "markdown"), joinpath(dir, "docs", "src"), force=true)
+cp(joinpath(dir, "README.md"), joinpath(dir, "docs", "src", "index.md"), force=true)
+tutorialsdir = joinpath(dir, "docs", "src")
+
+pages = Any["SciMLTutorials.jl: Tutorials for Scientific Machine Learning (SciML), Equation Solvers, and AI for Science"=>"index.md"]
+
+for folder in readdir(tutorialsdir)
+    newpages = Any[]
+    if folder[end-2:end] != ".md" && folder != "Testing" && folder != "figures"
+        for file in filter(x -> x[end-2:end] == ".md", readdir(
+            joinpath(tutorialsdir, folder)))
+            try
+                filecontents = readlines(joinpath(tutorialsdir, folder, file))
+                title = filecontents[3][9:end-1]
+
+                # Cut out the first 5 lines from the file to remove the Weave header stuff
+                open(joinpath(tutorialsdir, folder, file), "w") do output
+                    println(output, "# $title")
+                    for line in Iterators.drop(filecontents, 4)
+                        println(output, line)
+                    end
+                end
+                push!(newpages, title => joinpath(folder, file))
+            catch e
+                @show folder, file, e
+            end
+        end
+        push!(pages, folder => newpages)
+    end
+end
+
+#=
+# The result is in alphabetical order, change to the wanted order
+
+permute!(pages,
+    [1, 8, 11, 17, 3, 4, 7, 5, 9, 12, 18, 10, 16, 6, 15, 13, 14, 2]
+)
+
+names = [
+    "SciMLBenchmarks.jl: Benchmarks for Scientific Machine Learning (SciML) and Equation Solvers",
+    "Multi-Language Wrapper Benchmarks",
+    "Non-Stiff Ordinary Differential Equations",
+    "Stiff Ordinary Differential Equations",
+    "Biological Differential Equations",
+    "Differential-Algebraic Equations (DAEs)",
+    "Method of Lines Partial Differential Equations (PDEs)",
+    "Dynamical ODEs (Hamiltonian and Second Order)",
+    "N-Body Problem Benchmarks",
+    "Non-Stiff Stochastic Differential Equations",
+    "Stiff Stochastic Differential Equations",
+    "Non-Stiff Delay Differential Equations",
+    "Stiff Delay Differential equations",
+    "Jump Process Equations (Gillespie Benchmarks)",
+    "Parameter Estimation and Inverse Problem Benchmarks",
+    "Physics-Informed Neural Network (Neural Network PDE Solver) Cost Function Benchmarks",
+    "Physics-Informed Neural Network (Neural Network PDE Solver) Optimizer Benchmarks",
+    "SDE Adaptivity Benchmarks"]
+
+for i in 1:length(pages)
+    pages[i] = names[i] => pages[i][2]
+end
+=#