diff --git a/.github/dependabot.yml b/.github/dependabot.yml index cd7b7f249..39cbdba74 100644 --- a/.github/dependabot.yml +++ b/.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: diff --git a/.github/workflows/Documentation.yml b/.github/workflows/Documentation.yml index aa3839c3d..fb51f43a6 100644 --- a/.github/workflows/Documentation.yml +++ b/.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" diff --git a/.github/workflows/Downgrade.yml b/.github/workflows/Downgrade.yml index 54db9bada..0626e961d 100644 --- a/.github/workflows/Downgrade.yml +++ b/.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" diff --git a/.github/workflows/SpellCheck.yml b/.github/workflows/SpellCheck.yml index 746b039a1..a134515e2 100644 --- a/.github/workflows/SpellCheck.yml +++ b/.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 \ No newline at end of file + name: "Spell Check with Typos" + uses: "SciML/.github/.github/workflows/spellcheck.yml@v1" + secrets: "inherit" diff --git a/_typos.toml b/_typos.toml new file mode 100644 index 000000000..14be96fa8 --- /dev/null +++ b/_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" diff --git a/docs/old/getting_started.md b/docs/old/getting_started.md index 3192de0cb..4a5bbbae7 100644 --- a/docs/old/getting_started.md +++ b/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 diff --git a/test/save_positions.jl b/test/save_positions.jl index 13413b5b2..d23e209b8 100644 --- a/test/save_positions.jl +++ b/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)