Raise Mooncake compat floor to 0.5.36 (fix Downgrade resolution)

.github/dependabot.yml

@@ -5,6 +5,14 @@ updates:
     directory: "/" # Location of package manifests
     schedule:
       interval: "weekly"
-    ignore:
-      - dependency-name: "crate-ci/typos"
-        update-types: ["version-update:semver-patch", "version-update:semver-minor"]
+  - package-ecosystem: "julia"
+    directories:
+      - "/"
+      - "/docs"
+      - "/test"
+    schedule:
+      interval: "daily"
+    groups:
+      all-julia-packages:
+        patterns:
+          - "*"

.github/workflows/DependabotAutoMerge.yml

@@ -0,0 +1,9 @@
+name: "Dependabot Auto-merge"
+on: pull_request
+permissions:
+  contents: write
+  pull-requests: write
+jobs:
+  automerge:
+    uses: "SciML/.github/.github/workflows/dependabot-automerge.yml@v1"
+    secrets: "inherit"

.github/workflows/DocPreviewCleanup.yml

@@ -0,0 +1,10 @@
+name: "Doc Preview Cleanup"
+on:
+  pull_request:
+    types: [closed]
+permissions:
+  contents: write
+jobs:
+  cleanup:
+    uses: "SciML/.github/.github/workflows/docs-preview-cleanup.yml@v1"
+    secrets: "inherit"

.github/workflows/Documentation.yml

@@ -0,0 +1,21 @@
+name: "Documentation"
+
+on:
+  pull_request:
+    branches:
+      - main
+      - 'release-'
+  push:
+    branches:
+      - main
+    tags: '*'
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ github.ref_name != github.event.repository.default_branch || github.ref != 'refs/tags/v*' }}
+
+jobs:
+  docs:
+    name: Documentation
+    uses: "SciML/.github/.github/workflows/documentation.yml@v1"
+    secrets: "inherit"

.github/workflows/Downgrade.yml

@@ -0,0 +1,32 @@
+name: Downgrade
+
+on:
+  pull_request:
+    branches:
+      - main
+      - 'release-'
+    paths-ignore:
+      - 'docs/**'
+  push:
+    branches:
+      - main
+    paths-ignore:
+      - 'docs/**'
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ github.ref_name != github.event.repository.default_branch || github.ref != 'refs/tags/v*' }}
+
+jobs:
+  downgrade:
+    name: Downgrade
+    strategy:
+      fail-fast: false
+      matrix:
+        group:
+          - Core
+    uses: "SciML/.github/.github/workflows/downgrade.yml@v1"
+    with:
+      group: "${{ matrix.group }}"
+      julia-version: "lts"
+    secrets: "inherit"

.github/workflows/FormatCheck.yml

@@ -1,13 +1,16 @@
-name: "Format Check"
+name: format-check
 
 on:
   push:
     branches:
+      - 'master'
       - 'main'
+      - 'release-'
     tags: '*'
   pull_request:
 
 jobs:
-  format-check:
-    name: "Format Check"
-    uses: "SciML/.github/.github/workflows/format-suggestions-on-pr.yml@v1"
+  runic:
+    name: Runic
+    uses: "SciML/.github/.github/workflows/runic.yml@v1"
+    secrets: "inherit"

.github/workflows/RunicSuggestions.yml

@@ -0,0 +1,9 @@
+name: "Runic Suggestions"
+on: pull_request
+permissions:
+  contents: read
+  pull-requests: write
+jobs:
+  runic-suggestions:
+    uses: "SciML/.github/.github/workflows/runic-suggestions-on-pr.yml@v1"
+    secrets: "inherit"

.github/workflows/SpellCheck.yml

@@ -0,0 +1,9 @@
+name: Spell Check
+
+on: [pull_request]
+
+jobs:
+  typos-check:
+    name: Spell Check with Typos
+    uses: "SciML/.github/.github/workflows/spellcheck.yml@v1"
+    secrets: "inherit"

.github/workflows/TagBot.yml

@@ -1,15 +1,9 @@
-name: TagBot
+name: "TagBot"
 on:
   issue_comment:
-    types:
-      - created
+    types: [created]
   workflow_dispatch:
 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 }}
+  tagbot:
+    uses: "SciML/.github/.github/workflows/tagbot.yml@v1"
+    secrets: "inherit"

.github/workflows/Tests.yml

@@ -18,39 +18,6 @@ concurrency:
   cancel-in-progress: ${{ github.ref_name != github.event.repository.default_branch || github.ref != 'refs/tags/v*' }}
 
 jobs:
-  test:
-    name: "Tests"
-    strategy:
-      fail-fast: false
-      matrix:
-        version:
-          - '1'
-          - 'lts'
-          - 'nightly'
-        arch:
-          - x64
-    uses: "SciML/.github/.github/workflows/tests.yml@v1"
-    with:
-      julia-version: "${{ matrix.version }}"
-      julia-arch: "${{ matrix.arch }}"
+  tests:
+    uses: "SciML/.github/.github/workflows/grouped-tests.yml@v1"
     secrets: "inherit"
-
-  docs:
-    name: Documentation
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - uses: julia-actions/setup-julia@v2
-        with:
-          version: '1'
-      - uses: julia-actions/julia-buildpkg@v1
-      - uses: julia-actions/julia-docdeploy@v1
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
-      - run: |
-          julia --project=docs -e '
-            using Documenter: DocMeta, doctest
-            using FunctionWrappersWrappers
-            DocMeta.setdocmeta!(FunctionWrappersWrappers, :DocTestSetup, :(using FunctionWrappersWrappers); recursive=true)
-            doctest(FunctionWrappersWrappers)'

.typos.toml

@@ -0,0 +1,143 @@
+[default.extend-words]
+# Julia-specific functions
+indexin = "indexin"
+findfirst = "findfirst"
+findlast = "findlast"
+eachindex = "eachindex"
+setp = "setp"
+getp = "getp"
+setu = "setu"
+getu = "getu"
+
+# Mathematical/scientific terms
+jacobian = "jacobian"
+hessian = "hessian" 
+eigenvalue = "eigenvalue"
+eigenvector = "eigenvector"
+discretization = "discretization"
+linearization = "linearization"
+parameterized = "parameterized"
+discretized = "discretized"
+vectorized = "vectorized"
+extrapolant = "extrapolant"
+# Person names in citations - these are correct spellings
+Sigal = "Sigal"  # Sigal Gottlieb is a real person/author
+Steinebach = "Steinebach"
+Protopapa = "Protopapa"
+Hairer = "Hairer"
+Wanner = "Wanner"
+Verwer = "Verwer"
+Sandu = "Sandu"
+Carmichael = "Carmichael"
+Potra = "Potra"
+Seinfeld = "Seinfeld"
+Dabdub = "Dabdub"
+Marzo = "Marzo"
+Loon = "Loon"
+RODASP = "RODASP"
+Rodas4P = "Rodas4P"
+Rodas5P = "Rodas5P"
+Rodas6P = "Rodas6P"
+Scholz = "Scholz"
+Veldhuizen = "Veldhuizen"
+Tsit5DA = "Tsit5DA"
+Kaps = "Kaps"
+Rentrop = "Rentrop"
+Rang = "Rang"
+Darmstadt = "Darmstadt"
+"Méthodes" = "Méthodes"
+"différentiels" = "différentiels"
+"algébriques" = "algébriques"
+"problèmes" = "problèmes"
+problemes = "problemes"  # French word in citation without accent
+Ono = "Ono"  # Hiroshi Ono, author of Ono10/Ono12 RK methods
+padd = "padd"  # variable name in analyticless_convergence_tests.jl
+Preprint = "Preprint"
+Nr = "Nr"
+Wouver = "Wouver"
+Sauces = "Sauces"
+Schiesser = "Schiesser"
+Vande = "Vande"
+BIT = "BIT"
+Numer = "Numer"
+Jcon = "Jcon"
+arXiv = "arXiv"
+
+# (Numer already declared above for "BIT Numer" context.)
+
+# Technical variable names
+dorder = "dorder"  # Parameter for delta order / order change
+
+
+# Common variable patterns in Julia/SciML
+ists = "ists"
+ispcs = "ispcs"
+osys = "osys"
+rsys = "rsys"
+usys = "usys"
+fsys = "fsys"
+eqs = "eqs"
+rhs = "rhs"
+lhs = "lhs"
+ode = "ode"
+pde = "pde"
+sde = "sde"
+dde = "dde"
+bvp = "bvp"
+ivp = "ivp"
+
+# Common abbreviations
+tol = "tol"
+rtol = "rtol"
+atol = "atol"
+idx = "idx"
+jdx = "jdx"
+prev = "prev"
+curr = "curr"
+init = "init"
+tmp = "tmp"
+vec = "vec"
+arr = "arr"
+dt = "dt"
+du = "du"
+dx = "dx"
+dy = "dy"
+dz = "dz"
+
+# Algorithm/type suffixes
+alg = "alg"
+prob = "prob"
+sol = "sol"
+cb = "cb"
+opts = "opts"
+args = "args"
+kwargs = "kwargs"
+
+# Scientific abbreviations
+ND = "ND"
+nd = "nd"
+MTK = "MTK"
+ODE = "ODE"
+PDE = "PDE"
+SDE = "SDE"
+
+# SDE-specific terms
+IIF = "IIF"  # Integrating Factor method (IIF1M, IIF2M, IIF1Mil)
+iif = "iif"
+currate = "currate"  # current rate variable in tau-leaping
+SIE = "SIE"  # SIEA/SIEB algorithm name prefix
+SME = "SME"  # SME algorithm name (Stochastic Modified Euler)
+resetted = "resetted"  # variable name in stepsize control
+strat = "strat"  # Stratonovich abbreviation
+
+# Variable names used in codebase
+yhat = "yhat"  # estimated y value
+accpt = "accpt"  # accepted step flag variable
+gam = "gam"  # gamma abbreviation in tableaux
+clos = "clos"  # closure abbreviation
+
+# Journal abbreviations in BibTeX citations
+Comput = "Comput"  # J. Comput. Phys. (Journal of Computational Physics)
+
+# Julia spelling convention
+inferrable = "inferrable"  # Julia uses "inferrable" not "inferable"