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Initial package implementation
Co-authored-by: Scott Hayashi <[email protected]> Co-authored-by: jlrestrepol <[email protected]>
1 parent 8716435 commit 1c5a6eb

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‎.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
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version: 2
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updates:
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- package-ecosystem: "github-actions"
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directory: "/" # Location of package manifests
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schedule:
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interval: "weekly"

‎.github/workflows/CompatHelper.yml

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name: CompatHelper
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on:
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schedule:
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- cron: 0 0 * * *
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workflow_dispatch:
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permissions:
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contents: write
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pull-requests: write
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jobs:
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CompatHelper:
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runs-on: ubuntu-latest
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steps:
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- name: Check if Julia is already available in the PATH
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id: julia_in_path
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run: which julia
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continue-on-error: true
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- name: Install Julia, but only if it is not already available in the PATH
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uses: julia-actions/setup-julia@v1
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with:
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version: '1'
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arch: ${{ runner.arch }}
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if: steps.julia_in_path.outcome != 'success'
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- name: "Add the General registry via Git"
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run: |
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import Pkg
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ENV["JULIA_PKG_SERVER"] = ""
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Pkg.Registry.add("General")
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shell: julia --color=yes {0}
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- name: "Install CompatHelper"
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run: |
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import Pkg
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name = "CompatHelper"
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uuid = "aa819f21-2bde-4658-8897-bab36330d9b7"
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version = "3"
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Pkg.add(; name, uuid, version)
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shell: julia --color=yes {0}
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- name: "Run CompatHelper"
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run: |
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import CompatHelper
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CompatHelper.main()
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shell: julia --color=yes {0}
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
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# COMPATHELPER_PRIV: ${{ secrets.COMPATHELPER_PRIV }}

‎.github/workflows/TagBot.yml

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name: TagBot
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on:
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issue_comment:
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types:
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- created
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workflow_dispatch:
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inputs:
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lookback:
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default: 3
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permissions:
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actions: read
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checks: read
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contents: write
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deployments: read
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issues: read
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discussions: read
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packages: read
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pages: read
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pull-requests: read
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repository-projects: read
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security-events: read
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statuses: read
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jobs:
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TagBot:
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if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
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runs-on: ubuntu-latest
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steps:
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- uses: JuliaRegistries/TagBot@v1
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with:
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token: ${{ secrets.GITHUB_TOKEN }}
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# Edit the following line to reflect the actual name of the GitHub Secret containing your private key
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ssh: ${{ secrets.DOCUMENTER_KEY }}
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# ssh: ${{ secrets.NAME_OF_MY_SSH_PRIVATE_KEY_SECRET }}

‎.github/workflows/ci.yml

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name: CI
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on:
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push:
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branches:
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- main
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- dev
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- 'releases/**'
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tags: '*'
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pull_request:
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release:
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concurrency:
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# Skip intermediate builds: always.
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# Cancel intermediate builds: only if it is a pull request build.
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
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jobs:
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test:
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name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
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runs-on: ${{ matrix.os }}
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continue-on-error: ${{ matrix.version == 'nightly' }}
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strategy:
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fail-fast: false
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matrix:
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version:
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- '1.6'
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- '1'
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- 'nightly'
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os:
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- ubuntu-latest
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arch:
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- x64
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include:
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- version: 1
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os: ubuntu-latest
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arch: x86
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- version: 1
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os: macOS-latest
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arch: x64
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- version: 1
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os: windows-latest
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arch: x64
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steps:
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- uses: actions/checkout@v3
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- uses: julia-actions/setup-julia@v1
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with:
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version: ${{ matrix.version }}
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arch: ${{ matrix.arch }}
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- uses: julia-actions/cache@v1
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- uses: julia-actions/julia-buildpkg@v1
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env:
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PYTHON: 'Conda'
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- uses: julia-actions/julia-runtest@v1
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with:
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coverage: ${{ matrix.version == '1' && matrix.os == 'ubuntu-latest' && matrix.arch == 'x64' }}
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- uses: julia-actions/julia-processcoverage@v1
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if: matrix.version == '1' && matrix.os == 'ubuntu-latest' && matrix.arch == 'x64'
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- uses: codecov/codecov-action@v3
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if: matrix.version == '1' && matrix.os == 'ubuntu-latest' && matrix.arch == 'x64'
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with:
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file: lcov.info
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docs:
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name: Documentation
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- uses: julia-actions/setup-julia@v1
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with:
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version: '1'
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- uses: julia-actions/cache@v1
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- uses: julia-actions/julia-buildpkg@v1
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env:
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PYTHON: 'Conda'
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- uses: julia-actions/julia-docdeploy@v1
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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# Needed due to https://github.com/JuliaDocs/Documenter.jl/issues/1177
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DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
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GKSwstype: 'nul'

‎.gitignore

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

‎LICENSE.md

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The BATTestCases.jl package is licensed under the MIT "Expat" License:
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> Copyright (c) 2020:
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>
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> Oliver Schulz <[email protected]> and contributors
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>
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> Permission is hereby granted, free of charge, to any person obtaining a copy
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> of this software and associated documentation files (the "Software"), to deal
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> in the Software without restriction, including without limitation the rights
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> to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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> copies of the Software, and to permit persons to whom the Software is
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> furnished to do so, subject to the following conditions:
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>
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> The above copyright notice and this permission notice shall be included in all
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> copies or substantial portions of the Software.
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>
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> THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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> IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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> FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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> AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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> LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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> OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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> SOFTWARE.
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>

‎Project.toml

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

‎README.md

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

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build/
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site/

‎docs/Project.toml

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

‎docs/make.jl

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

‎docs/src/LICENSE.md

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

‎docs/src/api.md

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

‎docs/src/index.md

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# BATTestCases.jl
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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).
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"""
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BATTestCases
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A collection of test cases for BAT.jl.
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"""
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module BATTestCases
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using LinearAlgebra
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using Random
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using Statistics
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using ArraysOfArrays: nestedview
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using ArgCheck: @argcheck
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using Distributions
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using DocStringExtensions
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using QuadGK: quadgk
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using Random123: Philox4x
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using SpecialFunctions: gamma
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using StatsBase
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import AdaptiveRejectionSampling
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include("rng.jl")
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include("funnel.jl")
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include("gaussian_shell.jl")
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include("multimodal_student_t.jl")
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end # module

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