Merge pull request #597 from ChrisRackauckas-Claude/centralize-ci

Centralize CI on SciML reusable workflows

Author: ChrisRackauckas

.github/dependabot.yml

@@ -5,14 +5,11 @@ 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"
+      - "/test/gpu"
     schedule:
       interval: "daily"
     groups:

.github/workflows/Documentation.yml

@@ -9,23 +9,6 @@ on:
 
 jobs:
   build:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v6
-      - uses: julia-actions/setup-julia@latest
-        with:
-          version: '1'
-      - name: Install dependencies
-        run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
-      - name: Build and deploy
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # For authentication with GitHub Actions token
-          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # For authentication with SSH deploy key
-          GKSwstype: "100" # https://discourse.julialang.org/t/generation-of-documentation-fails-qt-qpa-xcb-could-not-connect-to-display/60988
-        run: julia --project=docs/ --code-coverage=user docs/make.jl
-      - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v6
-        with:
-          file: lcov.info
-          token: ${{ secrets.CODECOV_TOKEN }}
-          fail_ci_if_error: true
+    name: "Documentation"
+    uses: "SciML/.github/.github/workflows/documentation.yml@v1"
+    secrets: "inherit"

.github/workflows/Downgrade.yml

@@ -11,22 +11,12 @@ on:
     paths-ignore:
       - 'docs/**'
 jobs:
-  test:
+  downgrade:
     if: false  # Disabled: waiting on OrdinaryDiffEq updates. See issue for details.
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        downgrade_mode: ['alldeps']
-        julia-version: ['1.10']
-    steps:
-      - uses: actions/checkout@v6
-      - uses: julia-actions/setup-julia@v2
-        with:
-          version: ${{ matrix.julia-version }}
-      - uses: julia-actions/julia-downgrade-compat@v2
-        with:
-          skip: Pkg,TOML
-      - uses: julia-actions/julia-buildpkg@v1
-      - uses: julia-actions/julia-runtest@v1
-        with:
-          ALLOW_RERESOLVE: false
+    name: "Downgrade"
+    uses: "SciML/.github/.github/workflows/downgrade.yml@v1"
+    with:
+      julia-version: "1.10"
+      skip: "Pkg,TOML"
+      allow-reresolve: false
+    secrets: "inherit"

.github/workflows/SpellCheck.yml

@@ -4,10 +4,6 @@ on: [pull_request]
 
 jobs:
   typos-check:
-    name: Spell Check with Typos
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout Actions Repository
-        uses: actions/checkout@v6
-      - name: Check spelling
-        uses: crate-ci/typos@v1.18.0 
+    name: "Spell Check with Typos"
+    uses: "SciML/.github/.github/workflows/spellcheck.yml@v1"
+    secrets: "inherit"

_typos.toml

@@ -0,0 +1,11 @@
+[default.extend-words]
+# Surname of an author cited in the SortingDirect references (McCollum et al.)
+Collum = "Collum"
+# Name of the LambaEM integrator from OrdinaryDiffEq
+Lamba = "Lamba"
+# Internal function name resetted_jump_problem
+resetted = "resetted"
+# "IMA J Numer Anal" journal abbreviation in a citation
+Numer = "Numer"
+# setp from SymbolicIndexingInterface
+setp = "setp"

docs/old/getting_started.md

@@ -96,7 +96,7 @@ jump = ConstantRateJump(rate, affect!)
 There are many types of jumps. Some of them allow for variable rates. You can
 read about [different jump types in this page](@ref jump_types).
 
-Once the jump is defined, we initialize the `JumpProblem`. _Aggegators_ are
+Once the jump is defined, we initialize the `JumpProblem`. _Aggregators_ are
 algorithms that determines jump times. We call them _aggregators_ because they
 aggregate all jump callbacks into a single callback. Alternatively, we can think
 of aggregators as the jump simulation algorithms. In this case we use the

test/save_positions.jl

@@ -10,7 +10,7 @@ let
 
         dprob = DiscreteProblem(u0, tspan)
         # set the rate to 0, so that no jump ever occurs; but urate is positive so
-        # Coevolve will consider many candidates before the end of the simmulation.
+        # Coevolve will consider many candidates before the end of the simulation.
         # None of these points should be saved.
         jump = VariableRateJump((u, p, t) -> 0, (integrator) -> integrator.u[1] += 1;
             urate = (u, p, t) -> 1.0, rateinterval = (u, p, t) -> 5.0)