Initial package implementation

Co-authored-by: Scott Hayashi <[email protected]>
Co-authored-by: jlrestrepol <[email protected]>

.codecov.yml

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+# comment: 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: "weekly"

.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@v1
+        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()
+        shell: julia --color=yes {0}
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
+          # COMPATHELPER_PRIV: ${{ secrets.COMPATHELPER_PRIV }}

.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 }}
+          # 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/ci.yml

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+name: CI
+
+on:
+  push:
+    branches:
+      - main
+      - dev
+      - 'releases/**'
+    tags: '*'
+  pull_request:
+  release:
+
+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:
+  test:
+    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
+    runs-on: ${{ matrix.os }}
+    continue-on-error: ${{ matrix.version == 'nightly' }}
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+          - '1.6'
+          - '1'
+          - 'nightly'
+        os:
+          - ubuntu-latest
+        arch:
+          - x64
+        include:
+          - version: 1
+            os: ubuntu-latest
+            arch: x86
+          - version: 1
+            os: macOS-latest
+            arch: x64
+          - version: 1
+            os: windows-latest
+            arch: x64
+    steps:
+      - uses: actions/checkout@v3
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+      - uses: julia-actions/cache@v1
+      - uses: julia-actions/julia-buildpkg@v1
+        env:
+          PYTHON: 'Conda'
+      - uses: julia-actions/julia-runtest@v1
+        with:
+          coverage: ${{ matrix.version == '1' && matrix.os == 'ubuntu-latest' && matrix.arch == 'x64' }}
+      - uses: julia-actions/julia-processcoverage@v1
+        if: matrix.version == '1' && matrix.os == 'ubuntu-latest' && matrix.arch == 'x64'
+      - uses: codecov/codecov-action@v3
+        if: matrix.version == '1' && matrix.os == 'ubuntu-latest' && matrix.arch == 'x64'
+        with:
+          file: lcov.info
+  docs:
+    name: Documentation
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: '1'
+      - uses: julia-actions/cache@v1
+      - uses: julia-actions/julia-buildpkg@v1
+        env:
+          PYTHON: 'Conda'
+      - uses: julia-actions/julia-docdeploy@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          # Needed due to https://github.com/JuliaDocs/Documenter.jl/issues/1177
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
+          GKSwstype: 'nul'

.gitignore

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+.DS_Store
+*.jl.cov
+*.jl.*.cov
+*.jl.mem
+.ipynb_checkpoints
+.vscode
+Manifest.toml

LICENSE.md

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+The BATTestCases.jl package is licensed under the MIT "Expat" License:
+
+> Copyright (c) 2020:
+>
+>    Oliver Schulz <[email protected]> and contributors
+> 
+> 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 = "BATTestCases"
+uuid = "91d0e2c9-dbaa-453b-b50b-030d574b201f"
+version = "0.1.0"
+
+[deps]
+AdaptiveRejectionSampling = "c75e803d-635f-53bd-ab7d-544e482d8c75"
+ArgCheck = "dce04be8-c92d-5529-be00-80e4d2c0e197"
+ArraysOfArrays = "65a8f2f4-9b39-5baf-92e2-a9cc46fdf018"
+Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
+DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+QuadGK = "1fd47b50-473d-5c70-9696-f719f8f3bcdc"
+Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+Random123 = "74087812-796a-5b5d-8853-05524746bad3"
+SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
+Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
+StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
+
+[compat]
+AdaptiveRejectionSampling = "0.1.1"
+ArgCheck = "1, 2"
+ArraysOfArrays = "0.4, 0.5, 0.6"
+Distributions = "0.25"
+DocStringExtensions = "0.8, 0.9"
+QuadGK = "2"
+Random123 = "1.2"
+SpecialFunctions = "0.10, 1, 2"
+StatsBase = "0.32, 0.33, 0.34"
+julia = "1.6"

README.md

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+# BATTestCases.jl
+
+[![Documentation for stable version](https://img.shields.io/badge/docs-stable-blue.svg)](https://bat.github.io/BATTestCases.jl/stable)
+[![Documentation for development version](https://img.shields.io/badge/docs-dev-blue.svg)](https://bat.github.io/BATTestCases.jl/dev)
+[![License](http://img.shields.io/badge/license-MIT-brightgreen.svg?style=flat)](LICENSE.md)
+[![Build Status](https://github.com/bat/BATTestCases.jl/workflows/CI/badge.svg?branch=main)](https://github.com/bat/BATTestCases.jl/actions?query=workflow%3ACI)
+[![Codecov](https://codecov.io/gh/bat/BATTestCases.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/bat/BATTestCases.jl)
+
+
+## Documentation
+
+* [Documentation for stable version](https://bat.github.io/BATTestCases.jl/stable)
+* [Documentation for development version](https://bat.github.io/BATTestCases.jl/dev)
+
+BATTestCases.jl provides a collection of test cases for
+[BAT.jl](https://github.com/bat/BAT.jl) and should be useful for tesing
+other bayesian Julia software (MCMC samplers, etc.) as well.
+

docs/.gitignore

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+build/
+site/

docs/Project.toml

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+[deps]
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+Markdown = "d6f4376e-aef5-505a-96c1-9c027394607a"
+
+[compat]
+Documenter = "~0.27"

docs/make.jl

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+# Use
+#
+#     DOCUMENTER_DEBUG=true julia --color=yes make.jl local [nonstrict] [fixdoctests]
+#
+# for local builds.
+
+using Documenter
+using BATTestCases
+
+# Doctest setup
+DocMeta.setdocmeta!(
+    BATTestCases,
+    :DocTestSetup,
+    :(using BATTestCases);
+    recursive=true,
+)
+
+makedocs(
+    sitename = "BATTestCases",
+    modules = [BATTestCases],
+    format = Documenter.HTML(
+        prettyurls = !("local" in ARGS),
+        canonical = "https://bat.github.io/BATTestCases.jl/stable/"
+    ),
+    pages = [
+        "Home" => "index.md",
+        "API" => "api.md",
+        "LICENSE" => "LICENSE.md",
+    ],
+    doctest = ("fixdoctests" in ARGS) ? :fix : true,
+    linkcheck = !("nonstrict" in ARGS),
+    strict = !("nonstrict" in ARGS),
+)
+
+deploydocs(
+    repo = "github.com/bat/BATTestCases.jl.git",
+    forcepush = true,
+    push_preview = true,
+)

docs/src/LICENSE.md

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+# LICENSE
+
+```@eval
+using Markdown
+Markdown.parse_file(joinpath(@__DIR__, "..", "..", "LICENSE.md"))
+```

docs/src/api.md

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+# API
+
+## Modules
+
+```@index
+Order = [:module]
+```
+
+## Types and constants
+
+```@index
+Order = [:type, :constant]
+```
+
+## Functions and macros
+
+```@index
+Order = [:macro, :function]
+```
+
+# Documentation
+
+```@autodocs
+Modules = [BATTestCases]
+Order = [:module, :type, :constant, :macro, :function]
+```

docs/src/index.md

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+# BATTestCases.jl
+
+BATTestCases.jl provides a collection of test cases for [BAT.jl](https://github.com/bat/BAT.jl) and should be useful for tesing other Bayesian Julia software (MCMC samplers, etc.) as well.

src/BATTestCases.jl

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+# This file is a part of BATTestCases.jl, licensed under the MIT License (MIT).
+
+"""
+    BATTestCases
+
+A collection of test cases for BAT.jl.
+"""
+module BATTestCases
+
+using LinearAlgebra
+using Random
+using Statistics
+using ArraysOfArrays: nestedview
+using ArgCheck: @argcheck
+using Distributions
+using DocStringExtensions
+using QuadGK: quadgk
+using Random123: Philox4x
+using SpecialFunctions: gamma
+using StatsBase
+
+import AdaptiveRejectionSampling
+
+
+include("rng.jl")
+include("funnel.jl")
+include("gaussian_shell.jl")
+include("multimodal_student_t.jl")
+
+end # module