Merge pull request #18 from Shreyas-Ekanathan/upstream

Upstream

Author: Shreyas-Ekanathan

.github/workflows/CI.yml

@@ -34,6 +34,7 @@ jobs:
           - OrdinaryDiffEqExponentialRK
           - OrdinaryDiffEqExtrapolation
           - OrdinaryDiffEqFIRK
+          - OrdinaryDiffEqFIRKGenerator
           - OrdinaryDiffEqFeagin
           - OrdinaryDiffEqFunctionMap
           - OrdinaryDiffEqHighOrderRK

.github/workflows/CompatHelper.yml

@@ -23,4 +23,4 @@ jobs:
       - name: CompatHelper.main()
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        run: julia -e 'using CompatHelper; CompatHelper.main(;subdirs=["", "docs", "test/downstream"])'
+        run: julia -e 'using CompatHelper; CompatHelper.main(;subdirs=["", "docs", "test/downstream", "lib"])'

Project.toml

@@ -1,7 +1,7 @@
 name = "OrdinaryDiffEq"
 uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
 authors = ["Chris Rackauckas <accounts@chrisrackauckas.com>", "Yingbo Ma <mayingbo5@gmail.com>"]
-version = "6.89.0"
+version = "6.90.1"
 
 [deps]
 ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b"

lib/OrdinaryDiffEqCore/Project.toml

@@ -1,7 +1,7 @@
 name = "OrdinaryDiffEqCore"
 uuid = "bbf590c4-e513-4bbe-9b18-05decba2e5d8"
 authors = ["ParamThakkar123 <paramthakkar864@gmail.com>"]
-version = "1.10.0"
+version = "1.11.0"
 
 [deps]
 ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b"
@@ -49,7 +49,7 @@ Accessors = "0.1.36"
 Adapt = "3.0, 4"
 ArrayInterface = "7"
 DataStructures = "0.18"
-DiffEqBase = "6.157"
+DiffEqBase = "6.160"
 DiffEqDevTools = "2.44.4"
 DocStringExtensions = "0.9"
 EnumX = "1"
@@ -70,7 +70,7 @@ Random = "<0.0.1, 1"
 RecursiveArrayTools = "2.36, 3"
 Reexport = "1.0"
 SafeTestsets = "0.1.0"
-SciMLBase = "2.57.2"
+SciMLBase = "2.60"
 SciMLOperators = "0.3"
 SciMLStructures = "1"
 SimpleUnPack = "1"

lib/OrdinaryDiffEqCore/src/alg_utils.jl

@@ -17,6 +17,9 @@ end
 
 SciMLBase.forwarddiffs_model_time(alg::RosenbrockAlgorithm) = true
 
+SciMLBase.allows_late_binding_tstops(::OrdinaryDiffEqAlgorithm) = true
+SciMLBase.allows_late_binding_tstops(::DAEAlgorithm) = true
+
 # isadaptive is defined below.
 
 ## OrdinaryDiffEq Internal Traits

lib/OrdinaryDiffEqCore/src/initialize_dae.jl

@@ -169,7 +169,7 @@ function _initialize_dae!(integrator, prob::Union{ODEProblem, DAEProblem},
     end
 
     alg = default_nlsolve(alg.nlsolve, isinplace, initializeprob.u0, initializeprob, isAD)
-    nlsol = solve(initializeprob, alg)
+    nlsol = solve(initializeprob, alg, abstol = integrator.opts.abstol, reltol = integrator.opts.reltol)
     if isinplace === Val{true}()
         integrator.u .= prob.f.initializeprobmap(nlsol)
     elseif isinplace === Val{false}()

lib/OrdinaryDiffEqCore/src/solve.jl

@@ -242,6 +242,12 @@ function DiffEqBase.__init(
         resType = typeof(res_prototype)
     end
 
+    if tstops isa AbstractArray || tstops isa Tuple || tstops isa Number
+        _tstops = nothing
+    else
+        _tstops = tstops
+        tstops = ()
+    end
     tstops_internal = initialize_tstops(tType, tstops, d_discontinuities, tspan)
     saveat_internal = initialize_saveat(tType, saveat, tspan)
     d_discontinuities_internal = initialize_d_discontinuities(tType, d_discontinuities,
@@ -264,29 +270,7 @@ function DiffEqBase.__init(
     end
 
     ### Algorithm-specific defaults ###
-    if save_idxs === nothing
-        saved_subsystem = nothing
-    else
-        if !(save_idxs isa AbstractArray) || symbolic_type(save_idxs) != NotSymbolic()
-            _save_idxs = [save_idxs]
-        else
-            _save_idxs = save_idxs
-        end
-        saved_subsystem = SciMLBase.SavedSubsystem(prob, parameter_values(prob), _save_idxs)
-        if saved_subsystem !== nothing
-            _save_idxs = SciMLBase.get_saved_state_idxs(saved_subsystem)
-            if isempty(_save_idxs)
-                # no states to save
-                save_idxs = Int[]
-            elseif !(save_idxs isa AbstractArray) || symbolic_type(save_idxs) != NotSymbolic()
-                # only a single state to save, and save it as a scalar timeseries instead of
-                # single-element array
-                save_idxs = only(_save_idxs)
-            else
-                save_idxs = _save_idxs
-            end
-        end
-    end
+    save_idxs, saved_subsystem = SciMLBase.get_save_idxs_and_saved_subsystem(prob, save_idxs)
 
     if save_idxs === nothing
         ksEltype = Vector{rateType}
@@ -564,6 +548,13 @@ function DiffEqBase.__init(
         end
     end
 
+    if _tstops !== nothing
+        tstops = _tstops(parameter_values(integrator), prob.tspan)
+        for tstop in tstops
+            add_tstop!(integrator, tstop)
+        end
+    end
+
     handle_dt!(integrator)
     integrator
 end

lib/OrdinaryDiffEqDifferentiation/Project.toml

@@ -1,7 +1,7 @@
 name = "OrdinaryDiffEqDifferentiation"
 uuid = "4302a76b-040a-498a-8c04-15b101fed76b"
 authors = ["Chris Rackauckas <accounts@chrisrackauckas.com>", "Yingbo Ma <mayingbo5@gmail.com>"]
-version = "1.1.0"
+version = "1.2.0"
 
 [deps]
 ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b"

lib/OrdinaryDiffEqFIRK/Project.toml

@@ -1,49 +1,39 @@
 name = "OrdinaryDiffEqFIRK"
 uuid = "5960d6e9-dd7a-4743-88e7-cf307b64f125"
 authors = ["ParamThakkar123 <paramthakkar864@gmail.com>"]
-version = "1.2.0"
+version = "1.4.0"
 
 [deps]
 DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e"
 FastBroadcast = "7034ab61-46d4-4ed7-9d0f-46aef9175898"
 FastPower = "a4df4552-cc26-4903-aec0-212e50a0e84b"
-GenericLinearAlgebra = "14197337-ba66-59df-a3e3-ca00e7dcff7a"
-GenericSchur = "c145ed77-6b09-5dd9-b285-bf645a82121e"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 LinearSolve = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae"
 MuladdMacro = "46d2c3a1-f734-5fdb-9937-b9b9aeba4221"
 OrdinaryDiffEqCore = "bbf590c4-e513-4bbe-9b18-05decba2e5d8"
 OrdinaryDiffEqDifferentiation = "4302a76b-040a-498a-8c04-15b101fed76b"
 OrdinaryDiffEqNonlinearSolve = "127b3ac7-2247-4354-8eb6-78cf4e7c58e8"
-Polynomials = "f27b6e38-b328-58d1-80ce-0feddd5e7a45"
 RecursiveArrayTools = "731186ca-8d62-57ce-b412-fbd966d074cd"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
-RootedTrees = "47965b36-3f3e-11e9-0dcf-4570dfd42a8c"
 SciMLOperators = "c0aeaf25-5076-4817-a8d5-81caf7dfa961"
-Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7"
 
 [compat]
 DiffEqBase = "6.152.2"
 DiffEqDevTools = "2.44.4"
 FastBroadcast = "0.3.5"
 FastPower = "1"
-GenericLinearAlgebra = "0.3.13"
-GenericSchur = "0.5.4"
 LinearAlgebra = "<0.0.1, 1"
 LinearSolve = "2.32.0"
 MuladdMacro = "0.2.4"
 ODEProblemLibrary = "0.1.8"
 OrdinaryDiffEqCore = "1.1"
 OrdinaryDiffEqDifferentiation = "<0.0.1, 1"
 OrdinaryDiffEqNonlinearSolve = "<0.0.1, 1"
-Polynomials = "4.0.11"
 Random = "<0.0.1, 1"
 RecursiveArrayTools = "3.27.0"
 Reexport = "1.2.2"
-RootedTrees = "2.23.1"
 SafeTestsets = "0.1.0"
 SciMLOperators = "0.3.9"
-Symbolics = "6.15.3"
 Test = "<0.0.1, 1"
 julia = "1.10"
 

lib/OrdinaryDiffEqFIRK/src/OrdinaryDiffEqFIRK.jl

@@ -18,7 +18,6 @@ import OrdinaryDiffEqCore: alg_order, calculate_residuals!,
                            get_current_adaptive_order, get_fsalfirstlast,
                            isfirk, generic_solver_docstring
 using MuladdMacro, DiffEqBase, RecursiveArrayTools
-using Polynomials, GenericLinearAlgebra, GenericSchur
 using SciMLOperators: AbstractSciMLOperator
 using LinearAlgebra: I, UniformScaling, mul!, lu
 import LinearSolve