v2.0: remove almost all solver, preconditioner infrastructure in favor of LinearSolve

CHANGELOG.md

@@ -1,12 +1,14 @@
 # Changelog
 
-## [2.0.0] - Planned
+## [2.0.0] - 2026-01-06
 
-### Breaking
-- remove solver + precon API which is not based on precs or directly overloading `\`.
+- Remove solver + precon API which is not based on precs or directly overloading `\`.
   Fully rely on LinearSolve (besides `\`)
-- Move AMGBuilder, ILUZeroBuilder etc. to the corresponding packages (depending on the PRs)
-- remove "old" SparseMatrixLNK (need to benchmark before)
+- Move AMGBuilder etc to corresponding packages (depending on the PRs)
+- Keep ILUZeroPreconBuilder, JacobiPreconBuilder
+- ExtendableSparseMatrix is now GenericExtendableSparseMatrix{SparseMatrixLNK}
+- Changes should be non-breaking if only ExtendableSparseMatrix was used, and no solvers or preconditioners
+  For those, see LinearSolve.jl.
 
 ## [1.7.0] - 2025-02-06
 - Bump Pardiso to 1.0 and LinearSolve to 3.0

Project.toml

@@ -1,33 +1,55 @@
 name = "ExtendableSparse"
 uuid = "95c220a8-a1cf-11e9-0c77-dbfce5f500b3"
+version = "2.0.0"
 authors = ["Juergen Fuhrmann <juergen.fuhrmann@wias-berlin.de>", "Daniel Runge"]
-version = "1.7.1"
 
 [deps]
 DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
 ILUZero = "88f59080-6952-5380-9ea5-54057fb9a43f"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
+SciMLPublic = "431bcebd-1456-4ced-9d72-93c2757fff0b"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 Sparspak = "e56a9233-b9d6-4f03-8d0f-1825330902ac"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
-SuiteSparse = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9"
-Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [weakdeps]
-AMGCLWrap = "4f76b812-4ba5-496d-b042-d70715554288"
-AlgebraicMultigrid = "2169fc97-5a83-5252-b627-83903c6c433c"
 IncompleteLU = "40713840-3770-5561-ab4c-a76e7d0d7895"
 LinearSolve = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae"
-Pardiso = "46dd5b70-b6fb-5a00-ae2d-e8fea33afaf2"
 
 [extensions]
-ExtendableSparseAMGCLWrapExt = "AMGCLWrap"
-ExtendableSparseAlgebraicMultigridExt = "AlgebraicMultigrid"
 ExtendableSparseIncompleteLUExt = "IncompleteLU"
-ExtendableSparsePardisoExt = "Pardiso"
 ExtendableSparseLinearSolveExt = "LinearSolve"
 
+[compat]
+AMGCLWrap = "2"
+AlgebraicMultigrid = "0.4, 0.5, 0.6, 1"
+Aqua = "0.8"
+BenchmarkTools = "1"
+ChunkSplitters = "2, 3"
+DocStringExtensions = "0.8, 0.9"
+ExplicitImports = "1"
+ExtendableGrids = "1.9"
+ForwardDiff = "0.10, 1"
+ILUZero = "0.2"
+IncompleteLU = "^0.2.1"
+InteractiveUtils = "1.11.0"
+IterativeSolvers = "0.9"
+LinearAlgebra = "1.9"
+LinearSolve = "2.36.0, 3.7.1"
+Metis = "1"
+MultiFloats = "1, 2"
+OhMyThreads = "0.6, 0.7, 0.8"
+Printf = "1.9"
+Random = "1.9"
+RecursiveFactorization = "0.2"
+SciMLPublic = "1.0.1"
+SparseArrays = "1.9"
+Sparspak = "0.3.6"
+StaticArrays = "1"
+Test = "1.9"
+julia = "1.9"
+
 [extras]
 AMGCLWrap = "4f76b812-4ba5-496d-b042-d70715554288"
 AlgebraicMultigrid = "2169fc97-5a83-5252-b627-83903c6c433c"
@@ -38,48 +60,15 @@ ExplicitImports = "7d51a73a-1435-4ff3-83d9-f097790105c7"
 ExtendableGrids = "cfc395e8-590f-11e8-1f13-43a2532b2fa8"
 ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
 IncompleteLU = "40713840-3770-5561-ab4c-a76e7d0d7895"
+InteractiveUtils = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
 IterativeSolvers = "42fd0dbc-a981-5370-80f2-aaf504508153"
 LinearSolve = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae"
 Metis = "2679e427-3c69-5b7f-982b-ece356f1e94b"
 MultiFloats = "bdf0d083-296b-4888-a5b6-7498122e68a5"
 OhMyThreads = "67456a42-1dca-4109-a031-0a68de7e3ad5"
-Pardiso = "46dd5b70-b6fb-5a00-ae2d-e8fea33afaf2"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 RecursiveFactorization = "f2c3362d-daeb-58d1-803e-2bc74f2840b4"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
-[compat]
-AMGCLWrap = "2"
-AlgebraicMultigrid = "0.4, 0.5, 0.6, 1"
-DocStringExtensions = "0.8, 0.9"
-ExtendableGrids = "1.9"
-ILUZero = "0.2"
-IncompleteLU = "^0.2.1"
-IterativeSolvers = "0.9"
-LinearSolve = "2.36.0, 3.7.1"
-Pardiso = "0.5.1, 1"
-Sparspak = "0.3.6"
-StaticArrays = "1.5.24"
-julia = "1.9"
-
 [targets]
-test = [
-    "AMGCLWrap",
-    "AlgebraicMultigrid",
-    "Aqua",
-    "BenchmarkTools",
-    "ChunkSplitters",
-    "ExplicitImports",
-    "ExtendableGrids",
-    "ForwardDiff",
-    "IncompleteLU",
-    "IterativeSolvers",
-    "LinearSolve",
-    "Metis",
-    "MultiFloats", 
-    "OhMyThreads",
-    "Pardiso",
-    "Random",
-    "RecursiveFactorization",
-    "Test",
-]
+test = ["AMGCLWrap", "AlgebraicMultigrid", "Aqua", "BenchmarkTools", "ChunkSplitters", "ExplicitImports", "ExtendableGrids", "ForwardDiff", "IncompleteLU", "IterativeSolvers", "LinearSolve", "Metis", "MultiFloats", "OhMyThreads", "Random", "RecursiveFactorization", "Test"]

README.md

@@ -3,6 +3,7 @@
 [![Build status](https://github.com/WIAS-PDELib/ExtendableSparse.jl/actions/workflows/ci.yml/badge.svg?branch=master)](https://github.com/WIAS-PDELib/ExtendableSparse.jl/actions/workflows/ci.yml?query=branch%3Amaster)
 [![](https://img.shields.io/badge/docs-stable-blue.svg)](https://WIAS-PDELib.github.io/ExtendableSparse.jl/stable)
 [![](https://img.shields.io/badge/docs-dev-blue.svg)](https://WIAS-PDELib.github.io/ExtendableSparse.jl/dev)
+[![Aqua QA](https://raw.githubusercontent.com/JuliaTesting/Aqua.jl/master/badge.svg)](https://github.com/JuliaTesting/Aqua.jl)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3530554.svg)](https://doi.org/10.5281/zenodo.3530554)
 [![code style: runic](https://img.shields.io/badge/code_style-%E1%9A%B1%E1%9A%A2%E1%9A%BE%E1%9B%81%E1%9A%B2-black)](https://github.com/fredrikekre/Runic.jl)
 
@@ -42,7 +43,7 @@ With the help of [Sparspak.jl](https://github.com/PetrKryslUCSD/Sparspak.jl), th
 `sparse(A)` creates a standard `SparseMatrixCSC` from a filled `ExtendableSparseMatrix` which can be used e.g. to create preconditioners. So one can instead perform e.g.
 
 ```
-LinearSolve.solve(p, KrylovJL_CG(); Pl = ILUZero.ilu0(sparse(A)))
+LinearSolve.solve(p, KrylovJL_CG(; precs=ILUZeroPreconBuilder()))
 ```
 
 ## Rationale
@@ -94,27 +95,6 @@ triggering two index searches, one for `getindex!` and another one for `setindex
 
 See [Julia issue #15630](https://github.com/JuliaLang/julia/issues/15630) for a discussion on this.
 
-## Factorizations and Preconditioners
-
-The package provides a common API for factorizations and preconditioners supporting
-series of solutions of similar problem as they occur during nonlinear and transient solves.
-For details, see the [corresponding documentation](https://WIAS-PDELib.github.io/ExtendableSparse.jl/stable/iter/).
-
-With the advent of LinearSolve.jl, this functionality probably will be reduced to some core cases.
-
-### Interfaces to other packages
-
-The package directly provides interfaces to other sparse matrix solvers and preconditioners. Dependencies on these
-packages are handled via [Requires.jl](https://github.com/JuliaPackaging/Requires.jl).
-Currently, support includes:
-
-  - [Pardiso.jl](https://github.com/JuliaSparse/Pardiso.jl) (both ["project Pardiso"](https://pardiso-project.org)
-    and [MKL Pardiso](https://software.intel.com/content/www/us/en/develop/documentation/onemkl-developer-reference-fortran/top/sparse-solver-routines/onemkl-pardiso-parallel-direct-sparse-solver-interface.html))
-  - [IncompleteLU.jl](https://github.com/haampie/IncompleteLU.jl)
-  - [AlgebraicMultigrid.jl](https://github.com/JuliaLinearAlgebra/AlgebraicMultigrid.jl) (Ruge-Stüben AMG)
-
-For a similar approach, see [Preconditioners.jl](https://github.com/mohamed82008/Preconditioners.jl)
-
 ## Alternatives
 
 You may also evaluate alternatives to this package:

docs/Project.toml

@@ -7,12 +7,9 @@ DocumenterTools = "35a29f4d-8980-5a13-9543-d66fff28ecb8"
 ExtendableSparse = "95c220a8-a1cf-11e9-0c77-dbfce5f500b3"
 ILUZero = "88f59080-6952-5380-9ea5-54057fb9a43f"
 IncompleteLU = "40713840-3770-5561-ab4c-a76e7d0d7895"
+InteractiveUtils = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
 IterativeSolvers = "42fd0dbc-a981-5370-80f2-aaf504508153"
 LinearSolve = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae"
 MultiFloats = "bdf0d083-296b-4888-a5b6-7498122e68a5"
+SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 Sparspak = "e56a9233-b9d6-4f03-8d0f-1825330902ac"
-
-[compat]
-Documenter = "1.0"
-IterativeSolvers = "0.9"
-LinearSolve = "2.36.0"

docs/make.jl

@@ -1,4 +1,4 @@
-using Documenter, ExtendableSparse, AlgebraicMultigrid, IncompleteLU, Sparspak, LinearAlgebra
+using Documenter, ExtendableSparse, AlgebraicMultigrid, IncompleteLU, Sparspak, LinearAlgebra, SparseArrays, Base, InteractiveUtils
 
 function mkdocs()
     return makedocs(;
@@ -10,13 +10,13 @@ function mkdocs()
         authors = "J. Fuhrmann",
         repo = "https://github.com/WIAS-PDELib/ExtendableSparse.jl",
         pages = [
-            "Home" => "index.md",
+            "Home" => "home.md",
             "example.md",
             "extsparse.md",
+            "extensions.md",
             "linearsolve.md",
-            "internal.md",
-            "iter.md",
-            "changes.md",
+            "misc.md",
+            "index.md",
         ]
     )
 end

docs/src/extensions.md

@@ -0,0 +1,26 @@
+# Matrix extensions
+
+## AbstractSparseMatrixExtension
+```@docs
+ExtendableSparse.AbstractSparseMatrixExtension
+```
+
+## SparseMatrixLNK
+
+```@autodocs 
+Modules = [ExtendableSparse]
+Pages = ["sparsematrixlnk.jl"]
+```
+
+## SparseMatrixDILNKC
+
+```@autodocs 
+Modules = [ExtendableSparse]
+Pages = ["sparsematrixdilnkc.jl"]
+```
+
+## SparseMatrixDict
+```@autodocs 
+Modules = [ExtendableSparse]
+Pages = ["sparsematrixdict.jl"]
+```

docs/src/extsparse.md

@@ -1,20 +1,79 @@
-# Sparse matrix handling
+# Extendable matrices
+The type hierarchy of extendable matrices in this package is as follows:
 
-## Matrix creation and update API
+[`ExtendableSparse.AbstractExtendableSparseMatrixCSC`](@ref) `<: SparseArrays.AbstractSparseMatrixCSC <: SparseArrays.AbstractSparseMatrix <: AbstractMatrix`
 
+The package defines two [subtypes](#Subtypes-of-AbstractExtendableSparseMatrixCSC) of [`ExtendableSparse.AbstractExtendableSparseMatrixCSC`](@ref) which are parametrized by types of [extension matrices](/extensions/#Matrix-extensions):
+- [`ExtendableSparse.GenericExtendableSparseMatrixCSC`](@ref) for single threaded assembly
+- [`ExtendableSparse.GenericMTExtendableSparseMatrixCSC`](@ref) for multithreaded assembly
+
+User facing defaults are defined by [type aliases](#Type-aliases):
+- `const MTExtendableSparseMatrixCSC = GenericMTExtendableSparseMatrixCSC{SparseMatrixDILNKC}`
+- `const STExtendableSparseMatrixCSC = GenericExtendableSparseMatrixCSC{SparseMatrixLNK}`
+- `const ExtendableSparseMatrixCSC = STExtendableSparseMatrixCSC`
+- `const ExtendableSparseMatrix = ExtendableSparseMatrixCSC`
+
+## Abstract type
+```@docs
+ExtendableSparse.AbstractExtendableSparseMatrixCSC
+```
+## Subtypes of AbstractExtendableSparseMatrixCSC
 ```@docs
+ExtendableSparse.GenericExtendableSparseMatrixCSC
+ExtendableSparse.GenericMTExtendableSparseMatrixCSC
+```
+
+## Type aliases
+```@docs
+MTExtendableSparseMatrixCSC
+STExtendableSparseMatrixCSC
+ExtendableSparseMatrixCSC
 ExtendableSparseMatrix
 ```
 
-```@autodocs
-Modules = [ExtendableSparse]
-Pages = ["extendable.jl"]
+
+## Required methods
+```@docs
+SparseArrays.sparse
+ExtendableSparse.rawupdateindex!
+ExtendableSparse.flush!
+ExtendableSparse.reset!
 ```
 
+## AbstractSparseMatrixCSC interface
+See [SparseArrways#395](https://github.com/JuliaSparse/SparseArrays.jl/pull/395)  for a discussion.
+
+
 ```@docs
-ExtendableSparse.lu
-LinearAlgebra.lu!
+SparseArrays.nnz
+SparseArrays.nonzeros
+SparseArrays.rowvals
+SparseArrays.findnz
+SparseArrays.dropzeros!
+SparseArrays.getcolptr
+SparseArrays.SparseMatrixCSC
+Base.size
+Base.eltype
+Base.show
+```
+
+## Linear Algebra
+```@docs
+Base.:\
 LinearAlgebra.ldiv!
+LinearAlgebra.mul!
+LinearAlgebra.norm
+LinearAlgebra.opnorm
+LinearAlgebra.cond
+LinearAlgebra.issymmetric
+```
+
+## Algebraic operations
+```@docs
+Base.:+
+Base.:-
+Base.:*
+
 ```
 
 ## Handling of homogeneous Dirichlet BC
@@ -23,10 +82,3 @@ mark_dirichlet
 eliminate_dirichlet!
 eliminate_dirichlet
 ```
-
-## Test matrix creation
-
-```@autodocs
-Modules = [ExtendableSparse]
-Pages = ["sprand.jl"]
-```

docs/src/home.md

@@ -0,0 +1,3 @@
+```@docs
+ExtendableSparse
+```

docs/src/index.md

@@ -1,11 +1,3 @@
-````@eval
-using Markdown
-Markdown.parse("""
-$(read("../../README.md",String))
-""")
-````
-
-
-## Index
+# Index
 ```@index
 ```