First release

.github/workflows/CompatHelper.yml

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+name: CompatHelper
+on:
+  schedule:
+    - cron: 0 0 * * *
+  workflow_dispatch:
+jobs:
+  CompatHelper:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Pkg.add("CompatHelper")
+        run: julia -e 'using Pkg; Pkg.add("CompatHelper")'
+      - name: CompatHelper.main()
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
+        run: julia -e 'using CompatHelper; CompatHelper.main()'

.github/workflows/Documentation.yml

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+name: Documentation
+
+on:
+  push:
+    branches:
+      - master # update to match your development branch (master, main, dev, trunk, ...)
+    tags: '*'
+  pull_request:
+
+jobs:
+  build:
+    permissions:
+      contents: write
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: '1.7'
+      - 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

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+name: TagBot
+on:
+  issue_comment:
+    types:
+      - created
+  workflow_dispatch:
+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/Test.yml

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+name: Run tests
+
+on:
+  push:
+    branches:
+      - master # update to match your development branch (master, main, dev, trunk, ...)
+    tags: '*'
+  pull_request:
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        julia-version: ['1.7', '1.8']
+        julia-arch: [x64]
+        os: [ubuntu-latest, windows-latest, macOS-latest]
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Setup Julia
+        uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.julia-version }}
+          arch: ${{ matrix.julia-arch }}
+      - name: Build package
+        uses: julia-actions/julia-buildpkg@v1
+      - name: Run unit tests
+        uses: julia-actions/julia-runtest@v1
+        with:
+          annotate: true

.gitignore

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+/Manifest.toml
+/docs/build/
+ssh_keys

LICENSE

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+MIT License
+
+Copyright (c) 2022 Abhinav Natarajan <[email protected]>
+
+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 = "RedClust"
+uuid = "bf1adee6-87fe-4679-8d23-51fe99940a25"
+authors = ["Abhinav Natarajan <[email protected]>"]
+version = "0.1.0"
+
+[deps]
+Clustering = "aaaa29a8-35af-508c-8bc3-b662a17a0fe5"
+Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7"
+Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+Match = "7eb4fadd-790c-5f42-8a69-bfa0b872bfbf"
+ProgressBars = "49802e3a-d2f1-5c88-81d8-b72133a6f568"
+RCall = "6f49c342-dc21-5d91-9882-a32aef131414"
+Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
+StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
+
+[compat]
+Clustering = "0.13.5, 0.14"
+Distances = "0.10.3"
+Distributions = "0.25.42"
+Match = "1.2"
+ProgressBars = "1.4"
+RCall = "0.13.8"
+SpecialFunctions = "1.8, 2"
+StatsBase = "0.33.8"
+julia = "1.7"

README.md

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+# RedClust
+
+[![Stable](https://img.shields.io/badge/docs-stable-blue?style=flat-square)](https://abhinavnatarajan.github.io/RedClust.jl/stable/)
+[![Dev](https://img.shields.io/badge/docs-dev-blue?style=flat-square)](https://abhinavnatarajan.github.io/RedClust.jl/dev/)
+![GitHub Workflow Status (branch)](https://img.shields.io/github/workflow/status/abhinavnatarajan/RedClust.jl/Run%20tests/master?style=flat-square)
+![GitHub](https://img.shields.io/github/license/abhinavnatarajan/RedClust.jl?style=flat-square)
+![GitHub tag (latest SemVer)](https://img.shields.io/github/v/tag/abhinavnatarajan/RedClust.jl?style=flat-square) 
+
+## Introduction
+
+[RedClust](https://github.com/abhinavnatarajan/RedClust.jl) is a [Julia](https://julialang.org/) package for Bayesian clustering of high-dimensional Euclidean data using pairwise dissimilarities instead of the raw observations. It uses an MCMC sampler to generate posterior samples from the space of all possible clustering structures on the data. 
+
+## Installation
+The package can be installed by typing `]add RedClust` into the Julia REPL or by the usual method:
+```julia
+using Pkg
+Pkg.add("RedClust")
+```
+RedClust also requires [`R`](https://www.r-project.org/) and the R package [`salso`](https://CRAN.R-project.org/package=salso). If R is already installed, make sure the `R_HOME` environment variable is set to the R home directory (you could run `R.home()` in R to determine the location of this directory). If R or `salso` are not found, they are automatically installed during package installation.   
+
+## Basic example
+```julia
+using RedClust
+# Generate data
+pnts, distM, clusts, probs, oracle_coclustering = 
+	generatemixture(N, K; α = 10, σ = data_σ, dim = data_dim)
+# Let RedClust choose the best prior hyperparameters
+params = fitprior(pnts, "k-means", false).params
+# Set the MCMC options
+options = MCMCOptionsList(numiters = 5000)
+data = MCMCData(D = distM)
+# Run the sampler
+result = runsampler(data, options, params)
+```
+
+## Citing this package
+If you want to use this package in your work, please cite it as:
+
+Natarajan, A., De Iorio, M., Heinecke, A., Mayer, E. and Glenn, S., 2022. ‘Cohesion and Repulsion in Bayesian Distance Clustering’, arXiv [2107.05414](https://arxiv.org/abs/2107.05414).

deps/build.jl

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+script = 
+`Rscript -e 'dir.create(Sys.getenv("R_LIBS_USER"), recursive = TRUE)
+if (!require("salso")) {
+    install.packages("salso", lib = Sys.getenv("R_LIBS_USER"), repos = "http://cran.us.r-project.org")
+}'`
+run(script)

docs/Manifest.toml

@@ -0,0 +1,103 @@
+# This file is machine-generated - editing it directly is not advised
+
+julia_version = "1.8.1"
+manifest_format = "2.0"
+project_hash = "f7d6d28d478dfcb10e5302531e2f35d5341ef21b"
+
+[[deps.ANSIColoredPrinters]]
+git-tree-sha1 = "574baf8110975760d391c710b6341da1afa48d8c"
+uuid = "a4c015fc-c6ff-483c-b24f-f7ea428134e9"
+version = "0.0.1"
+
+[[deps.Base64]]
+uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
+
+[[deps.Dates]]
+deps = ["Printf"]
+uuid = "ade2ca70-3891-5945-98fb-dc099432e06a"
+
+[[deps.DocStringExtensions]]
+deps = ["LibGit2"]
+git-tree-sha1 = "5158c2b41018c5f7eb1470d558127ac274eca0c9"
+uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
+version = "0.9.1"
+
+[[deps.Documenter]]
+deps = ["ANSIColoredPrinters", "Base64", "Dates", "DocStringExtensions", "IOCapture", "InteractiveUtils", "JSON", "LibGit2", "Logging", "Markdown", "REPL", "Test", "Unicode"]
+git-tree-sha1 = "6030186b00a38e9d0434518627426570aac2ef95"
+uuid = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+version = "0.27.23"
+
+[[deps.IOCapture]]
+deps = ["Logging", "Random"]
+git-tree-sha1 = "f7be53659ab06ddc986428d3a9dcc95f6fa6705a"
+uuid = "b5f81e59-6552-4d32-b1f0-c071b021bf89"
+version = "0.2.2"
+
+[[deps.InteractiveUtils]]
+deps = ["Markdown"]
+uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
+
+[[deps.JSON]]
+deps = ["Dates", "Mmap", "Parsers", "Unicode"]
+git-tree-sha1 = "3c837543ddb02250ef42f4738347454f95079d4e"
+uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
+version = "0.21.3"
+
+[[deps.LibGit2]]
+deps = ["Base64", "NetworkOptions", "Printf", "SHA"]
+uuid = "76f85450-5226-5b5a-8eaa-529ad045b433"
+
+[[deps.Logging]]
+uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"
+
+[[deps.Markdown]]
+deps = ["Base64"]
+uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"
+
+[[deps.Mmap]]
+uuid = "a63ad114-7e13-5084-954f-fe012c677804"
+
+[[deps.NetworkOptions]]
+uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908"
+version = "1.2.0"
+
+[[deps.Parsers]]
+deps = ["Dates"]
+git-tree-sha1 = "3d5bf43e3e8b412656404ed9466f1dcbf7c50269"
+uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
+version = "2.4.0"
+
+[[deps.Printf]]
+deps = ["Unicode"]
+uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7"
+
+[[deps.REPL]]
+deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"]
+uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
+
+[[deps.Random]]
+deps = ["SHA", "Serialization"]
+uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+
+[[deps.RedClust]]
+path = ".."
+uuid = "bf1adee6-87fe-4679-8d23-51fe99940a25"
+version = "0.1.0"
+
+[[deps.SHA]]
+uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
+version = "0.7.0"
+
+[[deps.Serialization]]
+uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
+
+[[deps.Sockets]]
+uuid = "6462fe0b-24de-5631-8697-dd941f90decc"
+
+[[deps.Test]]
+deps = ["InteractiveUtils", "Logging", "Random", "Serialization"]
+uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[[deps.Unicode]]
+uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"

docs/Project.toml

@@ -0,0 +1,3 @@
+[deps]
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+RedClust = "bf1adee6-87fe-4679-8d23-51fe99940a25"

docs/make.jl

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+using RedClust
+using Documenter
+
+DocMeta.setdocmeta!(RedClust, :DocTestSetup, :(using RedClust); recursive=true)
+
+makedocs(;
+    modules=[RedClust],
+    authors="Abhinav Natarajan <[email protected]>",
+    repo="https://github.com/abhinavnatarajan/RedClust.jl/blob/{commit}{path}#{line}",
+    sitename="RedClust.jl",
+    format=Documenter.HTML(;
+        prettyurls=get(ENV, "CI", "false") == "true",
+        canonical="https://abhinavnatarajan.github.io/RedClust.jl",
+        edit_link="main",
+        assets=String[],
+    ),
+    pages=[
+    "Introduction" => "index.md",
+    "Reference" => "reference.md"
+    ]
+)
+
+deploydocs(;
+    repo="github.com/abhinavnatarajan/RedClust.jl",
+    devbranch="master"
+)