feat: add SciMLJacobianOperators package

.JuliaFormatter.toml

@@ -2,4 +2,3 @@ style = "sciml"
 format_markdown = true
 annotate_untyped_fields_with_any = false
 format_docstrings = true
-join_lines_based_on_source = false

.buildkite/pipeline.yml

@@ -1,15 +1,25 @@
 steps:
-  - label: "Julia 1"
+  - label: "Julia 1 (NonlinearSolve)"
     plugins:
       - JuliaCI/julia#v1:
           version: "1"
-      - JuliaCI/julia-test#v1:
-          coverage: true
       - JuliaCI/julia-coverage#v1:
           codecov: true
           dirs:
             - src
             - ext
+    command: |
+      julia --color=yes --code-coverage=user --depwarn=yes --project=. -e '
+        import Pkg;
+        Pkg.Registry.update();
+        # Install packages present in subdirectories
+        dev_pks = Pkg.PackageSpec[];
+        for path in ("lib/SciMLJacobianOperators",)
+            push!(dev_pks, Pkg.PackageSpec(; path));
+        end
+        Pkg.develop(dev_pks);
+        Pkg.instantiate();
+        Pkg.test(; coverage=true)'
     agents:
       queue: "juliagpu"
       cuda: "*"
@@ -20,6 +30,4 @@ steps:
 env:
   GROUP: CUDA
   JULIA_PKG_SERVER: "" # it often struggles with our large artifacts
-  RETESTITEMS_NWORKERS: 4
-  RETESTITEMS_NWORKER_THREADS: 2
   SECRET_CODECOV_TOKEN: "HC7K/ymhi62KUQ5OLU4DOl+11gaQt4JhXX/2nfTGlTsBB8mEMxQ8R+sHIp/2HjEup5eSXAN2IWQDQ7RDBuQvVp0T1UVtr2e4YNZFztKnsJXrFO15hXxYShJodI//X/8DzhlQd/lyTDOAOJu3eznsc3sC2CUgJzXZxLUtQN9YaZ1i3a+NoN1mO5UpkkHVhXigwF5gjy+0tei8fCdcP+SIhG0EanS5yd9q/SurtCpMHsHyUG97+ZVPglSKgdaqr31+PdmiPJ+ynp4+Hnc/esosxUSHSIL+ryRTO+28RNwPTiNf99J51RJLQmz1knWTR1ky6tiYIZ5218O6wvNil0SqNw==;U2FsdGVkX18nBY3t4LZYlEIz3EVKjpqCd994JNeJGt006up+sAjXEssI0tgCVXnfXsenVsP3NCCEoOS1GXc44g=="

.github/workflows/CI_NonlinearSolve.yml

@@ -0,0 +1,80 @@
+name: CI (NonlinearSolve)
+
+on:
+  pull_request:
+    branches:
+      - master
+    paths:
+      - "src/**"
+      - "ext/**"
+      - "test/**"
+      - "Project.toml"
+      - ".github/workflows/CI_NonlinearSolve.yml"
+      - "lib/SciMLNonlinearOperators/**"
+  push:
+    branches:
+      - master
+
+concurrency:
+  # Skip intermediate builds: always.
+  # Cancel intermediate builds: only if it is a pull request build.
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        group:
+          - Core
+          - Downstream
+          - Misc
+          - Wrappers
+        version:
+          - "min"
+          - "1"
+        os:
+          - ubuntu-latest
+          - macos-latest
+          - windows-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
+        with:
+          version: ${{ matrix.version }}
+      - uses: actions/cache@v4
+        env:
+          cache-name: cache-artifacts
+        with:
+          path: ~/.julia/artifacts
+          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
+          restore-keys: |
+            ${{ runner.os }}-test-${{ env.cache-name }}-
+            ${{ runner.os }}-test-
+            ${{ runner.os }}-
+      - name: "Install Dependencies and Run Tests"
+        run: |
+          import Pkg
+          Pkg.Registry.update()
+          # Install packages present in subdirectories
+          dev_pks = Pkg.PackageSpec[]
+          for path in ("lib/SciMLJacobianOperators",)
+              push!(dev_pks, Pkg.PackageSpec(; path))
+          end
+          Pkg.develop(dev_pks)
+          Pkg.instantiate()
+          Pkg.test(; coverage=true)
+        shell: julia --color=yes --code-coverage=user --depwarn=yes --project=. {0}
+        env:
+          GROUP: ${{ matrix.group }}
+      - uses: julia-actions/julia-processcoverage@v1
+        with:
+          directories: src,ext,lib/SciMLJacobianOperators/src
+      - uses: codecov/codecov-action@v4
+        with:
+          file: lcov.info
+          token: ${{ secrets.CODECOV_TOKEN }}
+          verbose: true
+          fail_ci_if_error: true

.github/workflows/CI.yml → .github/workflows/CI_SciMLJacobianOperators.yml

@@ -1,28 +1,30 @@
-name: CI
+name: CI (SciMLJacobianOperators)
+
 on:
   pull_request:
     branches:
       - master
+    paths:
+      - "lib/SciMLJacobianOperators/**"
+      - ".github/workflows/CI_SciMLJacobianOperators.yml"
   push:
     branches:
       - master
+
 concurrency:
   # Skip intermediate builds: always.
   # Cancel intermediate builds: only if it is a pull request build.
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
+
 jobs:
   test:
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        group:
-          - Core
-          - Downstream
-          - Misc
-          - Wrappers
         version:
+          - "min"
           - "1"
         os:
           - ubuntu-latest
@@ -43,16 +45,16 @@ jobs:
             ${{ runner.os }}-test-${{ env.cache-name }}-
             ${{ runner.os }}-test-
             ${{ runner.os }}-
-      - uses: julia-actions/julia-buildpkg@v1
-      - uses: julia-actions/julia-runtest@v1
-        env:
-          GROUP: ${{ matrix.group }}
-          JULIA_NUM_THREADS: 11
-          RETESTITEMS_NWORKERS: 4
-          RETESTITEMS_NWORKER_THREADS: 2
+      - name: "Install Dependencies and Run Tests"
+        run: |
+          import Pkg
+          Pkg.Registry.update()
+          Pkg.instantiate()
+          Pkg.test(; coverage=true)
+        shell: julia --color=yes --code-coverage=user --depwarn=yes --project=lib/SciMLJacobianOperators {0}
       - uses: julia-actions/julia-processcoverage@v1
         with:
-          directories: src,ext
+          directories: lib/SciMLJacobianOperators/src
       - uses: codecov/codecov-action@v4
         with:
           file: lcov.info

.github/workflows/Documentation.yml

@@ -17,7 +17,17 @@ jobs:
         with:
           version: '1'
       - name: Install dependencies
-        run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
+        run: |
+          import Pkg
+          Pkg.Registry.update()
+          # Install packages present in subdirectories
+          dev_pks = Pkg.PackageSpec[]
+          for path in ("lib/SciMLJacobianOperators", ".")
+              push!(dev_pks, Pkg.PackageSpec(; path))
+          end
+          Pkg.develop(dev_pks)
+          Pkg.instantiate()
+        shell: julia --color=yes --project=docs/ {0}
       - name: Build and deploy
         env:
           JULIA_DEBUG: "Documenter"

.github/workflows/Downgrade.yml

@@ -26,7 +26,3 @@ jobs:
           skip: Pkg,TOML
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1
-        env:
-          JULIA_NUM_THREADS: 11
-          RETESTITEMS_NWORKERS: 4
-          RETESTITEMS_NWORKER_THREADS: 2

.github/workflows/Downstream.yml

@@ -55,9 +55,6 @@ jobs:
             @info "Not compatible with this release. No problem." exception=err
             exit(0)  # Exit immediately, as a success
           end
-        env:
-          RETESTITEMS_NWORKERS: 4
-          RETESTITEMS_NWORKER_THREADS: 2
       - uses: julia-actions/julia-processcoverage@v1
         with:
           directories: src,ext

Project.toml

@@ -1,7 +1,7 @@
 name = "NonlinearSolve"
 uuid = "8913a72c-1f9b-4ce2-8d82-65094dcecaec"
 authors = ["SciML"]
-version = "3.14.0"
+version = "3.15.0-DEV"
 
 [deps]
 ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b"
@@ -23,6 +23,7 @@ Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 RecursiveArrayTools = "731186ca-8d62-57ce-b412-fbd966d074cd"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
+SciMLJacobianOperators = "19f34311-ddf3-4b8b-af20-060888a46c0e"
 SimpleNonlinearSolve = "727e6d20-b764-4bd8-a329-72de5adea6c7"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 SparseDiffTools = "47a9eef4-7e08-11e9-0b38-333d64bd3804"
@@ -73,12 +74,14 @@ FastLevenbergMarquardt = "0.1"
 FiniteDiff = "2.22"
 FixedPointAcceleration = "0.3"
 ForwardDiff = "0.10.36"
+Hwloc = "3"
+InteractiveUtils = "<0.0.1, 1"
 LazyArrays = "1.8.2, 2"
 LeastSquaresOptim = "0.8.5"
 LineSearches = "7.2"
 LinearAlgebra = "1.10"
 LinearSolve = "2.30"
-MINPACK = "=1.2"
+MINPACK = "1.2"
 MaybeInplace = "0.1.3"
 ModelingToolkit = "9.15.0"
 NLSolvers = "0.5"
@@ -96,6 +99,7 @@ RecursiveArrayTools = "3.8"
 Reexport = "1.2"
 SIAMFANLEquations = "1.0.1"
 SciMLBase = "2.34.0"
+SciMLJacobianOperators = "0.1"
 SimpleNonlinearSolve = "1.8"
 SparseArrays = "1.10"
 SparseDiffTools = "2.19"
@@ -120,6 +124,8 @@ Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9"
 ExplicitImports = "7d51a73a-1435-4ff3-83d9-f097790105c7"
 FastLevenbergMarquardt = "7a0df574-e128-4d35-8cbd-3d84502bf7ce"
 FixedPointAcceleration = "817d07cb-a79a-5c30-9a31-890123675176"
+Hwloc = "0e44f5e4-bd66-52a0-8798-143a42290a1d"
+InteractiveUtils = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
 LeastSquaresOptim = "0fc2ff8b-aaa3-5acd-a817-1944a5e08891"
 MINPACK = "4854310b-de5a-5eb6-a2a5-c1dee2bd17f9"
 ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
@@ -141,4 +147,4 @@ Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
 
 [targets]
-test = ["Aqua", "BandedMatrices", "BenchmarkTools", "CUDA", "Enzyme", "ExplicitImports", "FastLevenbergMarquardt", "FixedPointAcceleration", "LeastSquaresOptim", "MINPACK", "ModelingToolkit", "NLSolvers", "NLsolve", "NaNMath", "NonlinearProblemLibrary", "OrdinaryDiffEq", "Pkg", "Random", "ReTestItems", "SIAMFANLEquations", "SpeedMapping", "StableRNGs", "StaticArrays", "Sundials", "Symbolics", "Test", "Zygote"]
+test = ["Aqua", "BandedMatrices", "BenchmarkTools", "CUDA", "Enzyme", "ExplicitImports", "FastLevenbergMarquardt", "FixedPointAcceleration", "Hwloc", "InteractiveUtils", "LeastSquaresOptim", "MINPACK", "ModelingToolkit", "NLSolvers", "NLsolve", "NaNMath", "NonlinearProblemLibrary", "OrdinaryDiffEq", "Pkg", "Random", "ReTestItems", "SIAMFANLEquations", "SpeedMapping", "StableRNGs", "StaticArrays", "Sundials", "Symbolics", "Test", "Zygote"]

docs/Project.toml

@@ -14,6 +14,7 @@ OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
+SciMLJacobianOperators = "19f34311-ddf3-4b8b-af20-060888a46c0e"
 SimpleNonlinearSolve = "727e6d20-b764-4bd8-a329-72de5adea6c7"
 SparseDiffTools = "47a9eef4-7e08-11e9-0b38-333d64bd3804"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
@@ -36,6 +37,7 @@ OrdinaryDiffEq = "6"
 Plots = "1"
 Random = "<0.0.1, 1"
 SciMLBase = "2.4"
+SciMLJacobianOperators = "0.1"
 SimpleNonlinearSolve = "1"
 SparseDiffTools = "2.14"
 StaticArrays = "1"

docs/make.jl

@@ -1,6 +1,7 @@
 using Documenter, DocumenterCitations
 using NonlinearSolve, SimpleNonlinearSolve, Sundials, SteadyStateDiffEq, SciMLBase,
       DiffEqBase
+using SciMLJacobianOperators
 
 cp(joinpath(@__DIR__, "Manifest.toml"),
     joinpath(@__DIR__, "src/assets/Manifest.toml"), force = true)
@@ -13,8 +14,8 @@ bib = CitationBibliography(joinpath(@__DIR__, "src", "refs.bib"))
 
 makedocs(; sitename = "NonlinearSolve.jl",
     authors = "Chris Rackauckas",
-    modules = [NonlinearSolve, SimpleNonlinearSolve,
-        SteadyStateDiffEq, Sundials, DiffEqBase, SciMLBase],
+    modules = [NonlinearSolve, SimpleNonlinearSolve, SteadyStateDiffEq,
+        Sundials, DiffEqBase, SciMLBase, SciMLJacobianOperators],
     clean = true,
     doctest = false,
     linkcheck = true,

docs/pages.jl

@@ -2,25 +2,61 @@
 
 pages = ["index.md",
     "Getting Started with Nonlinear Rootfinding in Julia" => "tutorials/getting_started.md",
-    "Tutorials" => Any["tutorials/code_optimization.md", "tutorials/large_systems.md",
-        "tutorials/modelingtoolkit.md", "tutorials/small_compile.md",
-        "tutorials/iterator_interface.md", "tutorials/optimizing_parameterized_ode.md"],
-    "Basics" => Any["basics/nonlinear_problem.md", "basics/nonlinear_functions.md",
-        "basics/solve.md", "basics/nonlinear_solution.md", "basics/autodiff.md",
-        "basics/termination_condition.md", "basics/diagnostics_api.md",
-        "basics/sparsity_detection.md", "basics/faq.md"],
-    "Solver Summaries and Recommendations" => Any["solvers/nonlinear_system_solvers.md",
-        "solvers/bracketing_solvers.md", "solvers/steady_state_solvers.md",
-        "solvers/nonlinear_least_squares_solvers.md", "solvers/fixed_point_solvers.md"],
-    "Native Functionalities" => Any["native/solvers.md", "native/simplenonlinearsolve.md",
-        "native/steadystatediffeq.md", "native/descent.md",
-        "native/globalization.md", "native/diagnostics.md"],
+    "Tutorials" => Any[
+        "tutorials/code_optimization.md",
+        "tutorials/large_systems.md",
+        "tutorials/modelingtoolkit.md",
+        "tutorials/small_compile.md",
+        "tutorials/iterator_interface.md",
+        "tutorials/optimizing_parameterized_ode.md"
+    ],
+    "Basics" => Any[
+        "basics/nonlinear_problem.md",
+        "basics/nonlinear_functions.md",
+        "basics/solve.md",
+        "basics/nonlinear_solution.md",
+        "basics/autodiff.md",
+        "basics/termination_condition.md",
+        "basics/diagnostics_api.md",
+        "basics/sparsity_detection.md",
+        "basics/faq.md"
+    ],
+    "Solver Summaries and Recommendations" => Any[
+        "solvers/nonlinear_system_solvers.md",
+        "solvers/bracketing_solvers.md",
+        "solvers/steady_state_solvers.md",
+        "solvers/nonlinear_least_squares_solvers.md",
+        "solvers/fixed_point_solvers.md"
+    ],
+    "Native Functionalities" => Any[
+        "native/solvers.md",
+        "native/simplenonlinearsolve.md",
+        "native/steadystatediffeq.md",
+        "native/descent.md",
+        "native/globalization.md",
+        "native/diagnostics.md"
+    ],
     "Wrapped Solver APIs" => Any[
-        "api/fastlevenbergmarquardt.md", "api/fixedpointacceleration.md",
-        "api/leastsquaresoptim.md", "api/minpack.md", "api/nlsolve.md", "api/nlsolvers.md",
-        "api/siamfanlequations.md", "api/speedmapping.md", "api/sundials.md"],
+        "api/fastlevenbergmarquardt.md",
+        "api/fixedpointacceleration.md",
+        "api/leastsquaresoptim.md",
+        "api/minpack.md",
+        "api/nlsolve.md",
+        "api/nlsolvers.md",
+        "api/siamfanlequations.md",
+        "api/speedmapping.md",
+        "api/sundials.md"
+    ],
+    "Sub-Packages" => Any[
+        "api/SciMLJacobianOperators.md",
+    ],
     "Development Documentation" => [
-        "devdocs/internal_interfaces.md", "devdocs/linear_solve.md",
-        "devdocs/jacobian.md", "devdocs/operators.md", "devdocs/algorithm_helpers.md"],
+        "devdocs/internal_interfaces.md",
+        "devdocs/linear_solve.md",
+        "devdocs/jacobian.md",
+        "devdocs/operators.md",
+        "devdocs/algorithm_helpers.md"
+    ],
     "Release Notes" => "release_notes.md",
-    "References" => "references.md"]
+    "References" => "references.md"
+]