Setup

.JuliaFormatter.toml

@@ -0,0 +1 @@
+style = "blue"

.github/dependabot.yml

@@ -0,0 +1,7 @@
+# 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: "weekly"

.github/workflows/Documentation.yml

@@ -0,0 +1,29 @@
+name: Documentation
+
+on:
+  push:
+    branches:
+      - main # update to match your development branch (master, main, dev, trunk, ...)
+    tags: '*'
+  pull_request:
+
+jobs:
+  build:
+    permissions:
+      contents: write
+      pull-requests: read
+      statuses: write
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
+        with:
+          version: '1'
+      - uses: julia-actions/cache@v2
+      - 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/workflows/TagBot.yml

@@ -0,0 +1,33 @@
+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 }}
+          # Edit the following line to reflect the actual name of the GitHub Secret containing your private key
+          ssh: ${{ secrets.DOCUMENTER_KEY }}
+          # ssh: ${{ secrets.NAME_OF_MY_SSH_PRIVATE_KEY_SECRET }}

.github/workflows/Test.yml

@@ -0,0 +1,35 @@
+name: Test
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+
+# needed to allow julia-actions/cache to delete old caches that it has created
+permissions:
+  actions: write
+  contents: read
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        julia-version: ['1.6', '1']
+
+    steps:
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
+        with:
+          version: ${{ matrix.julia-version }}
+          arch: x64
+      - uses: julia-actions/cache@v2
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-runtest@v1
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v4
+        with:
+          files: lcov.info
+          token: ${{ secrets.CODECOV_TOKEN }}
+          fail_ci_if_error: false

.gitignore

@@ -16,6 +16,7 @@ deps/src/
 # Build artifacts for creating documentation generated by the Documenter package
 docs/build/
 docs/site/
+docs/src/index.md
 
 # File generated by Pkg, the package manager, based on a corresponding Project.toml
 # It records a fixed state of all packages used by the project. As such, it should not be

Project.toml

@@ -0,0 +1,13 @@
+name = "SparseMatrixColorings"
+uuid = "0a514795-09f3-496d-8182-132a7b665d35"
+authors = ["Guillaume Dalle <[email protected]>"]
+version = "0.1.0"
+
+[deps]
+Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
+
+[compat]
+Random = "1"
+SparseArrays = "1"
+julia = "1.6"

README.md

@@ -1,2 +1,27 @@
 # SparseMatrixColorings.jl
-Coloring algorithms for sparse Jacobian and Hessian matrices
+
+[![Build Status](https://github.com/gdalle/SparseMatrixColorings.jl/actions/workflows/Test.yml/badge.svg?branch=main)](https://github.com/gdalle/SparseMatrixColorings.jl/actions/workflows/Test.yml?query=branch%3Amain)
+[![Dev Documentation](https://img.shields.io/badge/docs-dev-blue.svg)](https://gdalle.github.io/SparseMatrixColorings.jl/dev/)
+[![Coverage](https://codecov.io/gh/gdalle/SparseMatrixColorings.jl/branch/main/graph/badge.svg)](https://app.codecov.io/gh/gdalle/SparseMatrixColorings.jl)
+[![Code Style: Blue](https://img.shields.io/badge/code%20style-blue-4495d1.svg)](https://github.com/JuliaDiff/BlueStyle)
+
+Coloring algorithms for sparse Jacobian and Hessian matrices.
+
+## Getting started
+
+To install this package, run the following in a Julia Pkg REPL:
+
+```julia
+pkg> add https://github.com/gdalle/SparseMatrixColorings.jl
+```
+
+## Background
+
+The algorithms implemented in this package are all taken from the following survey:
+
+> [_What Color Is Your Jacobian? Graph Coloring for Computing Derivatives_](https://epubs.siam.org/doi/10.1137/S0036144504444711), Gebremedhin et al. (2005)
+
+## Alternatives
+
+- [ColPack.jl](https://github.com/michel2323/ColPack.jl)
+- [SparseDiffTools.jl](https://github.com/JuliaDiff/SparseDiffTools.jl)

docs/Project.toml

@@ -0,0 +1,3 @@
+[deps]
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+SparseMatrixColorings = "0a514795-09f3-496d-8182-132a7b665d35"

docs/make.jl

@@ -0,0 +1,14 @@
+using Documenter
+using SparseMatrixColorings
+
+cp(joinpath(@__DIR__, "..", "README.md"), joinpath(@__DIR__, "src", "index.md"); force=true)
+
+makedocs(;
+    modules=[SparseMatrixColorings],
+    authors="Guillaume Dalle",
+    sitename="SparseMatrixColorings.jl",
+    format=Documenter.HTML(),
+    pages=["Home" => "index.md", "API reference" => "api.md"],
+)
+
+deploydocs(; repo="github.com/gdalle/SparseMatrixColorings.jl", devbranch="main")

docs/src/api.md

@@ -0,0 +1,19 @@
+# API reference
+
+```@meta
+CollapsedDocStrings = true
+```
+
+## Public
+
+```@autodocs
+Modules = [SparseMatrixColorings]
+Private = false
+```
+
+## Private
+
+```@autodocs
+Modules = [SparseMatrixColorings]
+Private = false
+```

src/SparseMatrixColorings.jl

@@ -0,0 +1,6 @@
+module SparseMatrixColorings
+
+using Random: AbstractRNG
+using SparseArrays: SparseMatrixCSC
+
+end

test/Project.toml

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+[deps]
+Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+JET = "c3a54625-cd67-489e-a8e7-0a5a0ff4e31b"
+JuliaFormatter = "98e50ef6-434e-11e9-1051-2b60c6c9e899"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

test/runtests.jl

@@ -0,0 +1,25 @@
+using Aqua
+using Documenter
+using JET
+using JuliaFormatter
+using SparseMatrixColorings
+using Test
+
+@testset verbose = true "SparseMatrixColorings" begin
+    @testset verbose = true "Code quality" begin
+        @testset "Aqua" begin
+            Aqua.test_all(SparseMatrixColorings)
+        end
+        @testset "JET" begin
+            JET.test_package(SparseMatrixColorings)
+        end
+        @testset "JuliaFormatter" begin
+            @test JuliaFormatter.format(
+                SparseMatrixColorings; verbose=false, overwrite=false
+            )
+        end
+    end
+    @testset "Doctests" begin
+        Documenter.doctest(SparseMatrixColorings)
+    end
+end