Initial Commit

.JuliaFormatter.toml

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+# Use SciML style: https://github.com/SciML/SciMLStyle
+style = "sciml"
+
+# Python style alignment. See https://github.com/domluna/JuliaFormatter.jl/pull/732.
+yas_style_nesting = true
+
+# Align struct fields for better readability of large struct definitions
+align_struct_field = true
+
+# Allow Dict definitions to be aligned like arrays. See https://github.com/domluna/JuliaFormatter.jl/pull/676
+variable_call_indent = ["Dict"]

.codecov.yml

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+# xref: https://docs.codecov.io/docs/codecovyml-reference
+
+# Disable annotations (annoying!)
+github_checks:
+  annotations: false

.github/dependabot.yml

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+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "monthly"

.github/workflows/CompatHelper.yml

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+name: CompatHelper
+on:
+  schedule:
+    - cron: 0 0 * * *
+  workflow_dispatch:
+permissions:
+  contents: write
+  pull-requests: write
+jobs:
+  CompatHelper:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check if Julia is already available in the PATH
+        id: julia_in_path
+        run: which julia
+        continue-on-error: true
+      - name: Install Julia, but only if it is not already available in the PATH
+        uses: julia-actions/setup-julia@v2
+        with:
+          version: '1'
+          arch: ${{ runner.arch }}
+        if: steps.julia_in_path.outcome != 'success'
+      - name: "Add the General registry via Git"
+        run: |
+          import Pkg
+          ENV["JULIA_PKG_SERVER"] = ""
+          Pkg.Registry.add("General")
+        shell: julia --color=yes {0}
+      - name: "Install CompatHelper"
+        run: |
+          import Pkg
+          name = "CompatHelper"
+          uuid = "aa819f21-2bde-4658-8897-bab36330d9b7"
+          version = "3"
+          Pkg.add(; name, uuid, version)
+        shell: julia --color=yes {0}
+      - name: "Run CompatHelper"
+        run: |
+          import CompatHelper
+          CompatHelper.main(; subdirs=["", "test", "docs"])
+        shell: julia --color=yes {0}
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
+          # COMPATHELPER_PRIV: ${{ secrets.COMPATHELPER_PRIV }}

.github/workflows/Documenter.yml

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+name: Documentation
+
+on:
+  push:
+    branches:
+      - 'main'
+    tags: '*'
+    paths-ignore:
+      - '.github/workflows/ci.yml'
+      - '.github/workflows/CompatHelper.yml'
+      - '.github/workflows/TagBot.yml'
+  pull_request:
+    paths-ignore:
+      - '.github/workflows/ci.yml'
+      - '.github/workflows/CompatHelper.yml'
+      - '.github/workflows/TagBot.yml'
+  workflow_dispatch:
+
+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:
+  build-docs:
+    name: Build and Deploy Documentation
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out project
+        uses: actions/checkout@v4
+      - name: Set up Julia
+        uses: julia-actions/setup-julia@v2
+        with:
+          version: '1'
+          show-versioninfo: true
+      - uses: julia-actions/cache@v1
+      - name: Build package
+        uses: julia-actions/julia-buildpkg@v1
+      - 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 }}
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # For authentication with SSH deploy key
+        run: julia --project=docs --color=yes docs/make.jl

.github/workflows/FormatCheck.yml

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+name: Format Check
+
+on:
+  push:
+    branches:
+      - 'main'
+    tags: '*'
+  pull_request:
+
+jobs:
+  check-format:
+    name: Check format with JuliaFormatter.jl
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out project
+        uses: actions/checkout@v4
+      - name: Set up Julia
+        uses: julia-actions/setup-julia@v2
+        with:
+          version: '1'
+      - run: julia -e 'using InteractiveUtils; versioninfo(verbose=true)'
+      - uses: julia-actions/cache@v1
+      - name: Install JuliaFormatter and format
+        # This will use the latest version by default but you can set the version like so:
+        #
+        # julia  -e 'using Pkg; Pkg.add(PackageSpec(name = "JuliaFormatter", version = "0.13.0"))'
+        run: |
+          julia  -e 'using Pkg; Pkg.add(PackageSpec(name = "JuliaFormatter", version="1.0.45"))'
+          julia  -e 'using JuliaFormatter; format(".")'
+      - name: Format check
+        run: |
+          julia -e '
+          out = Cmd(`git diff --name-only`) |> read |> String
+          if out == ""
+              exit(0)
+          else
+              @error "Some files have not been formatted !!!"
+              write(stdout, out)
+              exit(1)
+          end'

.github/workflows/SpellCheck.yml

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+name: Spell Check
+
+on: [pull_request, workflow_dispatch]
+
+jobs:
+  typos-check:
+    name: Spell Check with Typos
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout Actions Repository
+        uses: actions/checkout@v4
+      - name: Check spelling
+        uses: crate-ci/typos@v1.21.0

.github/workflows/TagBot.yml

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+name: TagBot
+on:
+  issue_comment:
+    types:
+      - created
+  workflow_dispatch:
+    inputs:
+      lookback:
+        default: 3
+permissions:
+  actions: read
+  checks: read
+  contents: write
+  deployments: read
+  issues: read
+  discussions: read
+  packages: read
+  pages: read
+  pull-requests: read
+  repository-projects: read
+  security-events: read
+  statuses: read
+jobs:
+  TagBot:
+    if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: JuliaRegistries/TagBot@v1
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          ssh: ${{ secrets.DOCUMENTER_KEY }}

.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches:
+      - main
+    tags: ['*']
+    paths-ignore:
+      - 'CITATION.bib'
+      - 'LICENSE.md'
+      - 'README.md'
+      - '.zenodo.json'
+      - '.github/workflows/CompatHelper.yml'
+      - '.github/workflows/SpellCheck.yml'
+      - '.github/workflows/TagBot.yml'
+      - 'docs/**'
+  pull_request:
+    paths-ignore:
+      - 'CITATION.bib'
+      - 'LICENSE.md'
+      - 'README.md'
+      - '.zenodo.json'
+      - '.github/workflows/CompatHelper.yml'
+      - '.github/workflows/SpellCheck.yml'
+      - '.github/workflows/TagBot.yml'
+      - 'docs/**'
+  workflow_dispatch:
+
+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:
+  build:
+    name: Run Tests (Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }})
+    runs-on: ubuntu-latest
+    strategy:
+      # Don't cancel all running jobs when one job fails
+      fail-fast: false
+      matrix:
+        version:
+          - '1.9'
+          - '1'
+        os:
+          - ubuntu-latest
+        arch:
+          - x64
+        include:
+          # Also run tests on Windows and macOS-ARM, but only with the latest Julia version
+          - version: '1'
+            os: windows-latest
+            arch: x64
+          - version: '1'
+            os: macos-14
+            arch: arm64
+
+    steps:
+      - name: Check out project
+        uses: actions/checkout@v4
+      - name: Set up Julia
+        uses: julia-actions/setup-julia@v2
+        with:
+          version: ${{ matrix.version }}
+      - run: julia -e 'using InteractiveUtils; versioninfo(verbose=true)'
+      - uses: julia-actions/cache@v1
+      - name: Build package
+        uses: julia-actions/julia-buildpkg@v1
+      - name: Run tests
+        uses: julia-actions/julia-runtest@v1
+        with:
+          annotate: true
+          # Only run coverage in one Job (Ubuntu and latest Julia version)
+          coverage: ${{ matrix.os == 'ubuntu-latest' && matrix.version == '1' }}
+      - name: Process coverage results
+        # Only run coverage in one Job (Ubuntu and latest Julia version)
+        if: matrix.os == 'ubuntu-latest' && matrix.version == '1'
+        uses: julia-actions/julia-processcoverage@v1
+        with:
+          directories: src,test
+      - name: Upload coverage report to Codecov
+        # Only run coverage in one Job (Ubuntu and latest Julia version)
+        if: matrix.os == 'ubuntu-latest' && matrix.version == '1'
+        uses: codecov/codecov-action@v4
+        with:
+          files: lcov.info
+          fail_ci_if_error: true
+          flags: unit
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.gitignore

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+Manifest.toml
+docs/build
+docs/src/index.md
+docs/src/authors.md
+docs/src/license.md
+public/
+coverage/
+coverage_report/
+*.jl.*.cov
+.vscode/
+run
+
+.DS_Store
+
+LocalPreferences.toml

AUTHORS.md

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+# Authors
+
+This package is maintained by the authors of
+[TrixiParticles.jl](https://github.com/trixi-framework/TrixiParticles.jl).
+For a full list of authors, see
+[AUTHORS.md](https://github.com/trixi-framework/TrixiParticles.jl/blob/main/AUTHORS.md)
+in the TrixiParticles.jl repository.
+These authors form "The TrixiParticles.jl Authors", as mentioned in the [LICENSE.md](LICENSE.md) file.

LICENSE.md

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+MIT License
+
+Copyright (c) 2023-present The TrixiParticles.jl Authors (see [AUTHORS.md](AUTHORS.md)) \
+Copyright (c) 2023-present Helmholtz-Zentrum hereon GmbH, Institute of Surface Science \
+ \
+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.

Project.toml

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+name = "TrixiNeighborhoodSearch"
+uuid = "1c4d5385-0a27-49de-8e2c-43b175c8985c"
+authors = ["Erik Faulhaber <44124897+efaulhaber@users.noreply.github.com>"]
+version = "0.1.0-pre"
+
+[compat]
+julia = "1.9"

README.md

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+# TrixiNeighborhoodSearch.jl
+
+[![Docs-stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://trixi-framework.github.io/TrixiNeighborhoodSearch.jl/stable)
+[![Docs-dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://trixi-framework.github.io/TrixiNeighborhoodSearch.jl/dev)
+[![Build Status](https://github.com/trixi-framework/TrixiNeighborhoodSearch.jl/workflows/CI/badge.svg)](https://github.com/trixi-framework/TrixiNeighborhoodSearch.jl/actions?query=workflow%3ACI)
+[![Coveralls](https://coveralls.io/repos/github/trixi-framework/TrixiNeighborhoodSearch.jl/badge.svg)](https://coveralls.io/github/trixi-framework/TrixiNeighborhoodSearch.jl)
+[![Codecov](https://codecov.io/gh/trixi-framework/TrixiNeighborhoodSearch.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/trixi-framework/TrixiNeighborhoodSearch.jl)
+[![License: MIT](https://img.shields.io/badge/License-MIT-success.svg)](https://opensource.org/license/mit/)

SECURITY.md

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+# Security Policy
+
+The Trixi.jl development team takes security issues seriously. We appreciate
+all efforts to responsibly disclose any security issues and will make every
+effort to acknowledge contributions.
+
+
+## Supported Versions
+
+The current stable release following the interpretation of
+[semantic versioning (SemVer)](https://julialang.github.io/Pkg.jl/dev/compatibility/#Version-specifier-format-1)
+used in the Julia ecosystem is supported with security updates.
+
+
+## Reporting a Vulnerability
+
+To report a security issue, please use the GitHub Security Advisory
+["Report a Vulnerability"](https://github.com/trixi-framework/TrixiNeighborhoodSearch.jl/security/advisories/new)
+tab.
+
+We will send a response indicating the next steps in handling your report.
+After the initial reply to your report, we will keep you informed of the
+progress towards a fix and full announcement, and may ask for additional
+information or guidance.
+
+Please report security bugs in third-party modules directly to the person
+or team maintaining the module.
+
+Public notifications of vulnerabilities will be shared in community channels
+such as Slack.

docs/Project.toml

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+[deps]
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+
+[compat]
+Documenter = "1"