Dev

.JuliaFormatter.toml

@@ -1,6 +1,5 @@
 # See https://domluna.github.io/JuliaFormatter.jl/stable/ for a list of options
 style = "blue"
-
 margin = 92
 
 align_assignment = true
@@ -15,4 +14,4 @@ format_docstrings = true
 conditional_to_if = true
 indent_submodule = true
 
-always_for_in=true
+always_for_in = true

.github/codecov.yml

@@ -0,0 +1,12 @@
+coverage:
+  status:
+    project:
+      default:
+        informational: true
+    patch:
+      default:
+        informational: true
+
+comment:
+  layout: "reach, diff, flags, files"
+  require_changes: true

.github/dependabot.yml

@@ -0,0 +1,12 @@
+version: 2
+
+updates:
+  - package-ecosystem: "julia"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"

.github/workflows/AutoMerge.yml

@@ -0,0 +1,23 @@
+name: Auto-merge dependency PRs
+
+on: pull_request_target
+
+permissions:
+  contents: write
+  pull-requests: write
+
+jobs:
+  dependabot:
+    name: Dependabot
+    runs-on: ubuntu-latest
+    if: github.actor == 'dependabot[bot]'
+    steps:
+      - name: Fetch Dependabot metadata
+        uses: dependabot/fetch-metadata@v3
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+      - name: Enable auto-merge
+        run: gh pr merge --auto --squash "$PR_URL"
+        env:
+          PR_URL: ${{ github.event.pull_request.html_url }}
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/CI.yml

@@ -1,41 +1,64 @@
 name: CI
+
+env:
+  JULIA_PKG_SERVER_REGISTRY_PREFERENCE: conservative
+
 on:
   push:
     branches:
-      - 'master'
-      - 'dev'
-    tags: '*'
+      - main
+      - dev
+    tags: "*"
   pull_request:
     branches:
-      - 'master'
+      - main
+      - dev
   release:
     types: [published]
 
+permissions:
+  actions: write
+  contents: read
+
 jobs:
   test:
-    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
+    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
         version:
-          - '1.10'
+          - "1.10"
+          - "1"
         os:
           - ubuntu-latest
         arch:
           - x64
     steps:
-      - uses: actions/checkout@v4
-      - uses: julia-actions/setup-julia@v1
+      - uses: actions/checkout@v6
+      - uses: julia-actions/setup-julia@v3
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
-      - uses: julia-actions/cache@v1
+      - uses: julia-actions/cache@v3
+      - name: Ensure General registry
+        run: |
+          julia -e '
+            using Pkg
+            if isempty(Pkg.Registry.reachable_registries())
+              try
+                Pkg.Registry.add()
+              catch
+                ENV["JULIA_PKG_SERVER"] = ""
+                Pkg.Registry.add(Pkg.RegistrySpec(
+                  url="https://github.com/JuliaRegistries/General.git",
+                ))
+              end
+            end'
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1
       - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v4
+      - uses: codecov/codecov-action@v6
         with:
           files: lcov.info
-        env:
-          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+          token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/Documentation.yml

@@ -1,30 +1,49 @@
 name: Documentation
 
+env:
+  JULIA_PKG_SERVER_REGISTRY_PREFERENCE: conservative
+
 on:
   push:
     branches:
-      - 'master'
-      - 'dev'
-    tags: '*'
+      - main
+      - dev
+    tags: "*"
   pull_request:
   release:
     types: [published]
 
 jobs:
   build:
+    name: Documentation
     permissions:
       contents: write
       statuses: write
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
-      - uses: julia-actions/setup-julia@v1
+      - uses: actions/checkout@v6
+      - uses: julia-actions/setup-julia@v3
         with:
-          version: '1'
+          version: "1"
+      - uses: julia-actions/cache@v3
+      - name: Ensure General registry
+        run: |
+          julia -e '
+            using Pkg
+            if isempty(Pkg.Registry.reachable_registries())
+              try
+                Pkg.Registry.add()
+              catch
+                ENV["JULIA_PKG_SERVER"] = ""
+                Pkg.Registry.add(Pkg.RegistrySpec(
+                  url="https://github.com/JuliaRegistries/General.git",
+                ))
+              end
+            end'
       - 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 }} # If authenticating with GitHub Actions token
-          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # If authenticating with SSH deploy key
-        run: julia --project=docs/ docs/make.jl
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
+        run: julia --project=docs/ docs/make.jl

.github/workflows/TagBot.yml

@@ -1,9 +1,14 @@
 name: TagBot
+
 on:
   issue_comment:
     types:
       - created
   workflow_dispatch:
+
+permissions:
+  contents: write
+
 jobs:
   TagBot:
     if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'

.gitignore

@@ -1,8 +1,12 @@
+.vscode/
+*.dat
+*.jld2
 *.jl.*.cov
 *.jl.cov
 *.jl.mem
+*.mem
+lcov.info
 /Manifest.toml
 /docs/Manifest.toml
 /docs/build/
-lcov.info
-*.vscode
+/docs/site/

CITATION.cff

@@ -0,0 +1,12 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it using the metadata below."
+title: "CorrectionFactorMatrixMethod.jl"
+type: software
+authors:
+  - family-names: Tetzner
+    given-names: Joshua
+repository-code: "https://github.com/JoshuaTetzner/CorrectionFactorMatrixMethod.jl"
+url: "https://JoshuaTetzner.github.io/CorrectionFactorMatrixMethod.jl/"
+license: MIT
+version: 0.1.0
+# doi: "Add the Zenodo DOI after the first archived release."

Project.toml

@@ -1,7 +1,7 @@
 name = "CorrectionFactorMatrixMethod"
 uuid = "1b32fdd5-07c8-465a-bf7d-415ac82a78be"
 version = "0.1.0"
-authors = ["""Joshua <joshua.tetzner@uni-rostock.de\n>"""]
+authors = ["Joshua Tetzner <joshua.tetzner@uni-rostock.de>"]
 
 [deps]
 BlockSparseMatrices = "1ef78180-cc57-4e70-b6ec-c3e471307147"
@@ -22,8 +22,47 @@ CFMMBEAST = ["BEAST", "CompScienceMeshes"]
 CFMMExaFMMt = ["ExaFMMt", "BEAST"]
 
 [compat]
-BlockSparseMatrices = "0.3.0"
-CompScienceMeshes = "0.12"
-MKL = "0.6.3"
-OhMyThreads = "0.8.4"
-SparseArrays = "1.12.0"
+Aqua = "0.8"
+BEAST = "2"
+BlockSparseMatrices = "0.3"
+CompScienceMeshes = "0.11, 0.12"
+ExaFMMt = "0.1"
+ExplicitImports = "1"
+H2Trees = "0.3"
+JET = "0.9, 0.10, 0.11"
+JuliaFormatter = "2"
+LinearAlgebra = "1.10"
+LinearMaps = "3"
+MKL = "0.9"
+OhMyThreads = "0.8"
+SparseArrays = "1.10"
+StaticArrays = "1"
+Test = "1.10"
+TestItemRunner = "1"
+TestItems = "1"
+julia = "1.10"
+
+[extras]
+Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
+ExplicitImports = "7d51a73a-1435-4ff3-83d9-f097790105c7"
+JET = "c3a54625-cd67-489e-a8e7-0a5a0ff4e31b"
+JuliaFormatter = "98e50ef6-434e-11e9-1051-2b60c6c9e899"
+StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+TestItemRunner = "f8b46487-2199-4994-9208-9a1283c18c0a"
+TestItems = "1c621080-faea-4a02-84b6-bbd5e436b8fe"
+
+[targets]
+test = [
+    "Aqua",
+    "BEAST",
+    "CompScienceMeshes",
+    "ExaFMMt",
+    "ExplicitImports",
+    "JET",
+    "JuliaFormatter",
+    "StaticArrays",
+    "Test",
+    "TestItemRunner",
+    "TestItems",
+]

README.md

@@ -1 +1,80 @@
 # CorrectionFactorMatrixMethod.jl
+
+[![Docs-stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://JoshuaTetzner.github.io/CorrectionFactorMatrixMethod.jl/stable/)
+[![Docs-dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://JoshuaTetzner.github.io/CorrectionFactorMatrixMethod.jl/dev/)
+[![MIT license](https://img.shields.io/badge/License-MIT-blue.svg)](https://github.com/JoshuaTetzner/CorrectionFactorMatrixMethod.jl/blob/main/LICENSE)
+[![CI](https://github.com/JoshuaTetzner/CorrectionFactorMatrixMethod.jl/actions/workflows/CI.yml/badge.svg)](https://github.com/JoshuaTetzner/CorrectionFactorMatrixMethod.jl/actions/workflows/CI.yml)
+[![codecov](https://codecov.io/gh/JoshuaTetzner/CorrectionFactorMatrixMethod.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/JoshuaTetzner/CorrectionFactorMatrixMethod.jl)
+
+## Introduction
+
+This package builds matrix-free boundary-element operators that combine a fast
+multipole approximation of the far interactions with directly assembled
+near-field corrections. The result behaves like the dense boundary-element
+matrix under matrix-vector products, but is never assembled explicitly, so it
+can be used directly inside an iterative solver such as `Krylov.gmres`.
+
+The generic correction and linear-map machinery lives in the core package.
+Support for concrete operators and spaces is provided through package
+extensions for
+[BEAST.jl](https://github.com/krcools/BEAST.jl),
+[CompScienceMeshes.jl](https://github.com/krcools/CompScienceMeshes.jl), and
+[ExaFMMt.jl](https://github.com/JoshuaTetzner/ExaFMMt.jl), which are loaded
+automatically once these packages are available.
+
+## Correction-Factor Matrix Method
+
+For a boundary-element matrix $A$, the far field is approximated by an
+FMM-backed map $A_\mathrm{FMM}$. The near interactions are evaluated with the
+boundary-element quadrature and corrected for the part already represented by
+the FMM:
+
+$$Ax \approx A_\mathrm{FMM}\,x + \left(A_\mathrm{near} - A_\mathrm{FMM,near}\right)x.$$
+
+The sparse correction blocks are selected from an
+[H2Trees.jl](https://github.com/djukic14/H2Trees.jl) tree. A matrix-vector
+product evaluates the FMM map first and then adds the sparse near correction.
+Transpose and adjoint products follow the corresponding `LinearMaps.jl`
+interfaces. Further details are given in the
+[documentation](https://JoshuaTetzner.github.io/CorrectionFactorMatrixMethod.jl/dev/details/method/).
+
+## Installation
+
+Installing CorrectionFactorMatrixMethod is done by entering the package manager
+(enter `]` at the Julia REPL) and issuing:
+
+```
+pkg> add https://github.com/JoshuaTetzner/CorrectionFactorMatrixMethod.jl.git
+```
+
+The supported boundary-element integration requires Julia 1.10 or later.
+
+## First steps
+
+Load the optional BEAST, CompScienceMeshes, and ExaFMMt packages, build a
+boundary-element operator with its test and trial spaces, and assemble the
+correction-factor operator:
+
+```julia
+using BEAST, CompScienceMeshes, ExaFMMt
+using CorrectionFactorMatrixMethod
+
+mesh = meshsphere(1.0, 0.4)
+space = raviartthomas(mesh)
+operator = Maxwell3D.singlelayer(; wavenumber=1.0)
+
+matrix = CFMM.assemble(operator, space)
+result = matrix * rand(scalartype(operator), numfunctions(space))
+```
+
+[`CFMM.assemble`](https://JoshuaTetzner.github.io/CorrectionFactorMatrixMethod.jl/dev/manual/manual/)
+constructs an optimized tree automatically. Existing trees and all lower-level
+FMM, quadrature, and scheduler options can be supplied as keywords. The
+returned operator implements the `LinearMaps.jl` interface, so it can be passed
+straight to an iterative solver. Runnable EFIE and MFIE examples are in the
+[`examples/`](examples) directory and in the
+[documentation](https://JoshuaTetzner.github.io/CorrectionFactorMatrixMethod.jl/dev/).
+
+## References
+
+- [1] Adelman, Ross, Nail A. Gumerov, and Ramani Duraiswami. *FMM/GPU-Accelerated Boundary Element Method for Computational Magnetics and Electrostatics.* IEEE Transactions on Magnetics 53, no. 12 (December 2017): 1–11. [https://doi.org/10.1109/TMAG.2017.2725951](https://doi.org/10.1109/TMAG.2017.2725951).

docs/Project.toml

@@ -0,0 +1,8 @@
+[deps]
+CorrectionFactorMatrixMethod = "1b32fdd5-07c8-465a-bf7d-415ac82a78be"
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+
+[compat]
+CorrectionFactorMatrixMethod = "0.1"
+Documenter = "1"
+julia = "1.10"