Merge branch 'upstream' of https://github.com/Shreyas-Ekanathan/Ordin…

…aryDiffEq.jl
Shreyas-Ekanathan · Aug 15, 2024 · 30cc947 · 30cc947
2 parents 67bb0fe + ba80b06
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diff --git a/.buildkite/pipeline.yml b/.buildkite/pipeline.yml
@@ -3,6 +3,13 @@ steps:
     plugins:
       - JuliaCI/julia#v1:
           version: "1"
+      - staticfloat/metahook:
+          pre-command: |
+            julia --project=. -e '
+              using Pkg;
+              Pkg.develop(map(path ->Pkg.PackageSpec.(;path="$(@__DIR__)/lib/$(path)"), readdir("./lib")));
+              Pkg.instantiate();
+            '
       - JuliaCI/julia-test#v1:
            coverage: false # 1000x slowdown
     agents:
@@ -33,6 +40,13 @@ steps:
       GROUP: "{{matrix.group}}"
     plugins:
       - JuliaCI/julia#v1
+      - staticfloat/metahook:
+          pre-command: |
+            julia --project=. -e '
+              using Pkg;
+              Pkg.develop(map(path ->Pkg.PackageSpec.(;path="$(@__DIR__)/lib/$(path)"), readdir("./lib")));
+              Pkg.instantiate();
+            '
       - JuliaCI/julia-test#v1:
           coverage: false
           julia_args: "--threads=auto"

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -22,12 +22,39 @@ jobs:
           - AlgConvergence_II
           - AlgConvergence_III
           - Downstream
-          - Symplectic
-          - Extrapolation
-          - StabilizedRK
-          - StabilizedIRK
           - ODEInterfaceRegression
           - Multithreading
+
+          - OrdinaryDiffEqAdamsBashforthMoulton
+          - OrdinaryDiffEqBDF
+          - OrdinaryDiffEqCore
+          - OrdinaryDiffEqDefault
+          - OrdinaryDiffEqDifferentiation
+          - OrdinaryDiffEqExplicitRK
+          - OrdinaryDiffEqExponentialRK
+          - OrdinaryDiffEqExtrapolation
+          - OrdinaryDiffEqFIRK
+          - OrdinaryDiffEqFeagin
+          - OrdinaryDiffEqFunctionMap
+          - OrdinaryDiffEqHighOrderRK
+          - OrdinaryDiffEqIMEXMultistep
+          - OrdinaryDiffEqLinear
+          - OrdinaryDiffEqLowOrderRK
+          - OrdinaryDiffEqLowStorageRK
+          - OrdinaryDiffEqNordsieck
+          - OrdinaryDiffEqPDIRK
+          - OrdinaryDiffEqPRK
+          - OrdinaryDiffEqQPRK
+          - OrdinaryDiffEqRKN
+          - OrdinaryDiffEqRosenbrock
+          - OrdinaryDiffEqSDIRK
+          - OrdinaryDiffEqSSPRK
+          - OrdinaryDiffEqStabilizedIRK
+          - OrdinaryDiffEqStabilizedRK
+          - OrdinaryDiffEqSymplecticRK
+          - OrdinaryDiffEqTsit5
+          - OrdinaryDiffEqVerner
+
         version:
           - '1'
     steps:
@@ -45,7 +72,15 @@ jobs:
             ${{ runner.os }}-test-${{ env.cache-name }}-
             ${{ runner.os }}-test-
             ${{ runner.os }}-
-      - uses: julia-actions/julia-buildpkg@v1
+      # Explicitly develop the libraries first before running the tests for now.
+      # This is necessary since the tests are likely to fail otherwise, given that all
+      # the libs haven't been registered yet.
+      - name: "Develop the libraries since they haven't been registered yet"
+        run: |
+          julia --project=. -e '
+              using Pkg;
+              Pkg.develop(map(path ->Pkg.PackageSpec.(;path="$(@__DIR__)/lib/$(path)"), readdir("./lib")));
+          '
       - uses: julia-actions/julia-runtest@v1
         env:
           GROUP: ${{ matrix.group }}

diff --git a/.github/workflows/Documentation.yml b/.github/workflows/Documentation.yml
@@ -15,6 +15,15 @@ jobs:
       - uses: julia-actions/setup-julia@latest
         with:
           version: '1'
+      # Explicitly develop the libraries first before running the tests for now.
+      # This is necessary since the tests are likely to fail otherwise, given that all
+      # the libs haven't been registered yet.
+      - name: "Develop the libraries since they haven't been registered yet"
+        run: |
+          julia --project=. -e '
+              using Pkg;
+              Pkg.develop(map(path ->Pkg.PackageSpec.(;path="$(@__DIR__)/lib/$(path)"), readdir("./lib")));
+          '
       - name: Install dependencies
         run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
       - name: Build and deploy

diff --git a/.github/workflows/Downstream.yml b/.github/workflows/Downstream.yml
@@ -41,7 +41,15 @@ jobs:
         with:
           version: ${{ matrix.julia-version }}
           arch: x64
-      - uses: julia-actions/julia-buildpkg@latest
+      # Explicitly develop the libraries first before running the tests for now.
+      # This is necessary since the tests are likely to fail otherwise, given that all
+      # the libs haven't been registered yet.
+      - name: "Develop the libraries since they haven't been registered yet"
+        run: |
+          julia --project=. -e '
+              using Pkg;
+              Pkg.develop(map(path ->Pkg.PackageSpec.(;path="$(@__DIR__)/lib/$(path)"), readdir("./lib")));
+          '
       - name: Clone Downstream
         uses: actions/checkout@v4
         with:

diff --git a/.github/workflows/Invalidations.yml b/.github/workflows/Invalidations.yml
@@ -20,7 +20,15 @@ jobs:
       with:
         version: '1'
     - uses: actions/checkout@v4
-    - uses: julia-actions/julia-buildpkg@v1
+    # Explicitly develop the libraries first before running the tests for now.
+    # This is necessary since the tests are likely to fail otherwise, given that all
+    # the libs haven't been registered yet.
+    - name: "Develop the libraries since they haven't been registered yet"
+      run: |
+        julia --project=. -e '
+            using Pkg;
+            Pkg.develop(map(path ->Pkg.PackageSpec.(;path="$(@__DIR__)/lib/$(path)"), readdir("./lib")));
+        '
     - uses: julia-actions/julia-invalidations@v1
       id: invs_pr
 

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -2,3 +2,33 @@
   - Please run `using JuliaFormatter, OrdinaryDiffEq; format(joinpath(dirname(pathof(OrdinaryDiffEq)), ".."))` before committing.
   - Add tests for any new features.
   - Additional help on contributing to the numerical solvers can be found at https://docs.sciml.ai/DiffEqDevDocs/stable/
+
+## Developing Locally
+
+OrdinaryDiffEq is a very large package and thus it uses a sublibrary approach to keep down
+the total number of dependencies per solver. As a consequence, it requires a bit of special
+handling compared to some other Julia packages. When running the full test suite, it's
+recommended that one has dev'd all of the relevant packages. This can be done via:
+
+```julia
+pathtolibrary = Pkg.pkgdir(OrdinaryDiffEq)
+sublibs = string.((pathtolibrary,), readdir(pathtolibrary))
+Pkg.develop(map(name -> Pkg.PackageSpec.(; path = name), sublibs));
+```
+
+and then running `Pkg.test("OrdinaryDiffEq")` will run the global tests locally. Each of the
+per-solver subtests, which includes convergence tests and other per-library handling,
+is then ran by using a specific solver set, such as
+`Pkg.test("OrdinaryDiffEqAdamsBashforthMoulton")`
+
+## Dependency Structure
+
+There is a tree dependency structure to the sublibraries of OrdinaryDiffEq. The core stepper
+lives in OrdinaryDiffEqCore.jl. Explicit methods only require the core. Then on top of the
+core is OrdinaryDiffEqDifferentiation.jl which defines the utilities used for differentiation
+and Jacobian construction. This is used directly by methods like Rosenbrock and exponential
+integrators, which use Jacobians but not implicit solvers. Finally there's
+OrdinaryDiffEqNonlinearSolve, which is the largest set of dependencies and pulls in the
+NonlinearSolve.jl stack for handling implicit equations, and is thus the core dependency
+of the implicit integrators. OrdinaryDiffEqNonlinearSolve relies on OrdinaryDiffEqDifferentiation
+which relies on OrdinaryDiffEqCore.
diff --git a/Project.toml b/Project.toml
@@ -18,7 +18,6 @@ FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b"
 FiniteDiff = "6a86dc24-6348-571c-b903-95158fe2bd41"
 ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
 FunctionWrappersWrappers = "77dc65aa-8811-40c2-897b-53d922fa7daf"
-IfElse = "615f187c-cbe4-4ef1-ba3b-2fcf58d6d173"
 InteractiveUtils = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
 LineSearches = "d3d80556-e9d4-5f37-9878-2ab0fcc64255"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
@@ -27,6 +26,36 @@ Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
 MacroTools = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09"
 MuladdMacro = "46d2c3a1-f734-5fdb-9937-b9b9aeba4221"
 NonlinearSolve = "8913a72c-1f9b-4ce2-8d82-65094dcecaec"
+OrdinaryDiffEqAdamsBashforthMoulton = "89bda076-bce5-4f1c-845f-551c83cdda9a"
+OrdinaryDiffEqBDF = "6ad6398a-0878-4a85-9266-38940aa047c8"
+OrdinaryDiffEqCore = "bbf590c4-e513-4bbe-9b18-05decba2e5d8"
+OrdinaryDiffEqDefault = "50262376-6c5a-4cf5-baba-aaf4f84d72d7"
+OrdinaryDiffEqDifferentiation = "4302a76b-040a-498a-8c04-15b101fed76b"
+OrdinaryDiffEqExplicitRK = "9286f039-9fbf-40e8-bf65-aa933bdc4db0"
+OrdinaryDiffEqExponentialRK = "e0540318-69ee-4070-8777-9e2de6de23de"
+OrdinaryDiffEqExtrapolation = "becaefa8-8ca2-5cf9-886d-c06f3d2bd2c4"
+OrdinaryDiffEqFIRK = "5960d6e9-dd7a-4743-88e7-cf307b64f125"
+OrdinaryDiffEqFeagin = "101fe9f7-ebb6-4678-b671-3a81e7194747"
+OrdinaryDiffEqFunctionMap = "d3585ca7-f5d3-4ba6-8057-292ed1abd90f"
+OrdinaryDiffEqHighOrderRK = "d28bc4f8-55e1-4f49-af69-84c1a99f0f58"
+OrdinaryDiffEqIMEXMultistep = "9f002381-b378-40b7-97a6-27a27c83f129"
+OrdinaryDiffEqLinear = "521117fe-8c41-49f8-b3b6-30780b3f0fb5"
+OrdinaryDiffEqLowOrderRK = "1344f307-1e59-4825-a18e-ace9aa3fa4c6"
+OrdinaryDiffEqLowStorageRK = "b0944070-b475-4768-8dec-fb6eb410534d"
+OrdinaryDiffEqNonlinearSolve = "127b3ac7-2247-4354-8eb6-78cf4e7c58e8"
+OrdinaryDiffEqNordsieck = "c9986a66-5c92-4813-8696-a7ec84c806c8"
+OrdinaryDiffEqPDIRK = "5dd0a6cf-3d4b-4314-aa06-06d4e299bc89"
+OrdinaryDiffEqPRK = "5b33eab2-c0f1-4480-b2c3-94bc1e80bda1"
+OrdinaryDiffEqQPRK = "04162be5-8125-4266-98ed-640baecc6514"
+OrdinaryDiffEqRKN = "af6ede74-add8-4cfd-b1df-9a4dbb109d7a"
+OrdinaryDiffEqRosenbrock = "43230ef6-c299-4910-a778-202eb28ce4ce"
+OrdinaryDiffEqSDIRK = "2d112036-d095-4a1e-ab9a-08536f3ecdbf"
+OrdinaryDiffEqSSPRK = "669c94d9-1f4b-4b64-b377-1aa079aa2388"
+OrdinaryDiffEqStabilizedIRK = "e3e12d00-db14-5390-b879-ac3dd2ef6296"
+OrdinaryDiffEqStabilizedRK = "358294b1-0aab-51c3-aafe-ad5ab194a2ad"
+OrdinaryDiffEqSymplecticRK = "fa646aed-7ef9-47eb-84c4-9443fc8cbfa8"
+OrdinaryDiffEqTsit5 = "b1df2697-797e-41e3-8120-5422d3b24e4a"
+OrdinaryDiffEqVerner = "79d7bb75-1356-48c1-b8c0-6832512096c2"
 Polyester = "f517fe37-dbe3-4b94-8317-1923a5111588"
 PreallocationTools = "d236fae5-4411-538c-8e31-a6e3d9e00b46"
 PrecompileTools = "aea7be01-6a6a-4083-8856-8a6e6704d82a"
@@ -53,25 +82,24 @@ DataStructures = "0.18"
 DiffEqBase = "6.147"
 DocStringExtensions = "0.9"
 EnumX = "1"
-ExponentialUtilities = "1.22"
+ExponentialUtilities = "1"
 FastBroadcast = "0.2, 0.3"
 FastClosures = "0.3"
 FillArrays = "1.9"
 FiniteDiff = "2"
-ForwardDiff = "0.10.3"
+ForwardDiff = "0.10"
 FunctionWrappersWrappers = "0.1"
-IfElse = "0.1"
 InteractiveUtils = "1.9"
 LineSearches = "7"
 LinearAlgebra = "1.9"
-LinearSolve = "2.1.10"
+LinearSolve = "2"
 Logging = "1.9"
 MacroTools = "0.5"
 MuladdMacro = "0.2.1"
-NLsolve = "4"
-NonlinearSolve = "3.12.3"
+NonlinearSolve = "3"
+OrdinaryDiffEqCore = "1"
 Polyester = "0.7"
-PreallocationTools = "0.4.15"
+PreallocationTools = "0.4"
 PrecompileTools = "1"
 Preferences = "1.3"
 RecursiveArrayTools = "2.36, 3"
@@ -81,8 +109,7 @@ SciMLOperators = "0.3"
 SciMLStructures = "1"
 SimpleNonlinearSolve = "1"
 SimpleUnPack = "1"
-SparseArrays = "1.9"
-SparseDiffTools = "2.3"
+SparseDiffTools = "2"
 Static = "0.8, 1"
 StaticArrayInterface = "1.2"
 StaticArrays = "1.0"

diff --git a/docs/make.jl b/docs/make.jl
@@ -7,7 +7,21 @@ makedocs(sitename = "OrdinaryDiffEq.jl",
     authors = "Chris Rackauckas et al.",
     clean = true,
     doctest = false,
-    modules = [OrdinaryDiffEq],
+    modules = [OrdinaryDiffEq,
+        OrdinaryDiffEq.OrdinaryDiffEqExtrapolation,
+        OrdinaryDiffEq.OrdinaryDiffEqStabilizedRK,
+        OrdinaryDiffEq.OrdinaryDiffEqStabilizedIRK,
+        OrdinaryDiffEq.OrdinaryDiffEqLowStorageRK,
+        OrdinaryDiffEq.OrdinaryDiffEqSSPRK,
+        OrdinaryDiffEq.OrdinaryDiffEqFeagin,
+        OrdinaryDiffEq.OrdinaryDiffEqSymplecticRK,
+        OrdinaryDiffEq.OrdinaryDiffEqRKN,
+        OrdinaryDiffEq.OrdinaryDiffEqVerner,
+        OrdinaryDiffEq.OrdinaryDiffEqSDIRK,
+        OrdinaryDiffEq.OrdinaryDiffEqBDF,
+        OrdinaryDiffEq.OrdinaryDiffEqDefault,
+        OrdinaryDiffEq.OrdinaryDiffEqFIRK],
+    warnonly = [:docs_block, :missing_docs, :eval_block],
     format = Documenter.HTML(analytics = "UA-90474609-3",
         assets = ["assets/favicon.ico"],
         canonical = "https://ordinarydiffeq.sciml.ai/stable/"),

diff --git a/lib/OrdinaryDiffEqAdamsBashforthMoulton/LICENSE.md b/lib/OrdinaryDiffEqAdamsBashforthMoulton/LICENSE.md
@@ -0,0 +1,24 @@
+The OrdinaryDiffEq.jl package is licensed under the MIT "Expat" License:
+
+> Copyright (c) 2016-2020: ChrisRackauckas, Yingbo Ma, Julia Computing Inc, and
+> other contributors:
+> 
+> https://github.com/SciML/OrdinaryDiffEq.jl/graphs/contributors
+> 
+> Permission is hereby granted, free of charge, to any person obtaining a copy
+> of this software and associated documentation files (the "Software"), to deal
+> in the Software without restriction, including without limitation the rights
+> to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+> copies of the Software, and to permit persons to whom the Software is
+> furnished to do so, subject to the following conditions:
+> 
+> The above copyright notice and this permission notice shall be included in all
+> copies or substantial portions of the Software.
+> 
+> THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+> IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+> FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+> AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+> LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+> OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+> SOFTWARE.
diff --git a/lib/OrdinaryDiffEqAdamsBashforthMoulton/Project.toml b/lib/OrdinaryDiffEqAdamsBashforthMoulton/Project.toml
@@ -0,0 +1,30 @@
+name = "OrdinaryDiffEqAdamsBashforthMoulton"
+uuid = "89bda076-bce5-4f1c-845f-551c83cdda9a"
+authors = ["ParamThakkar123 <[email protected]>"]
+version = "1.0.0"
+
+[deps]
+FastBroadcast = "7034ab61-46d4-4ed7-9d0f-46aef9175898"
+MuladdMacro = "46d2c3a1-f734-5fdb-9937-b9b9aeba4221"
+OrdinaryDiffEqCore = "bbf590c4-e513-4bbe-9b18-05decba2e5d8"
+OrdinaryDiffEqLowOrderRK = "1344f307-1e59-4825-a18e-ace9aa3fa4c6"
+Polyester = "f517fe37-dbe3-4b94-8317-1923a5111588"
+RecursiveArrayTools = "731186ca-8d62-57ce-b412-fbd966d074cd"
+Static = "aedffcd0-7271-4cad-89d0-dc628f76c6d3"
+ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b"
+DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e"
+Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
+
+[compat]
+julia = "1.10"
+
+[extras]
+DiffEqDevTools = "f3b72e0c-5b89-59e1-b016-84e28bfd966d"
+ODEProblemLibrary = "fdc4e326-1af4-4b90-96e7-779fcce2daa5"
+Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+SafeTestsets = "1bc83da4-3b8d-516f-aca4-4fe02f6d838f"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e"
+
+[targets]
+test = ["DiffEqDevTools", "ODEProblemLibrary", "Random", "SafeTestsets", "Test", "DiffEqBase"]
diff --git a/lib/OrdinaryDiffEqAdamsBashforthMoulton/src/OrdinaryDiffEqAdamsBashforthMoulton.jl b/lib/OrdinaryDiffEqAdamsBashforthMoulton/src/OrdinaryDiffEqAdamsBashforthMoulton.jl
@@ -0,0 +1,30 @@
+module OrdinaryDiffEqAdamsBashforthMoulton
+
+import OrdinaryDiffEqCore: OrdinaryDiffEqMutableCache, OrdinaryDiffEqConstantCache, @cache,
+                           alg_cache,
+                           initialize!, @unpack, perform_step!, alg_order, isstandard,
+                           OrdinaryDiffEqAlgorithm,
+                           OrdinaryDiffEqAdaptiveAlgorithm,
+                           OrdinaryDiffEqAdamsVarOrderVarStepAlgorithm,
+                           constvalue, calculate_residuals, calculate_residuals!,
+                           trivial_limiter!,
+                           full_cache
+import OrdinaryDiffEqLowOrderRK: BS3ConstantCache, BS3Cache, RK4ConstantCache, RK4Cache
+import RecursiveArrayTools: recursivefill!
+using MuladdMacro, FastBroadcast
+import Static: False
+import ADTypes: AutoForwardDiff
+
+using Reexport
+@reexport using DiffEqBase
+
+include("algorithms.jl")
+include("alg_utils.jl")
+include("adams_bashforth_moulton_caches.jl")
+include("adams_utils.jl")
+include("adams_bashforth_moulton_perform_step.jl")
+
+export AB3, AB4, AB5, ABM32, ABM43, ABM54, VCAB3,
+       VCAB4, VCAB5, VCABM3, VCABM4, VCABM5, VCABM
+
+end