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‎.github/PULL_REQUEST_TEMPLATE.md

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<!-- Comment lines like this one will remain invisible -->
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<!-- Thank you for your contribution! Please fill in this template so that we
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can understand your intent and the proposed changes. If anything about this
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template is unclear, just mention it! -->
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**Summary**
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<!-- Summary of what & why - explain your motivation and/or link to any GitHub issues this relates to -->
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**Proposed changes**
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<!-- Large PRs should ideally be preceded by a design discussion on a separate issue! -->
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<!-- A clear and concise description of the contents of this pull request. -->
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* ...
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**What alternatives have you considered?**
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<!-- A clear and concise description of any alternative solutions or features you've considered. -->
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**Breaking changes**
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<!-- If this PR breaks backwards-compatibility, please start the PR title with `**BREAKING**`! -->
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<!-- In this section, describe any changes that are not backwards-compatible, -->
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<!-- why it is worth breaking backwards compatiblity, -->
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<!-- and how a user would have to address these changes in their downstream code. -->

‎.github/workflows/Cancel.yml

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‎.github/workflows/CompatHelper.yml

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CompatHelper:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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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 = "2"
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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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subdirs = ["", "test", "docs"]
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for f in readdir(joinpath(@__DIR__, "examples"); join=true)
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for f in readdir("examples"; join=true)
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if isdir(f)
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push!(subdirs, joinpath("examples", basename(f)))
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end
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end
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CompatHelper.main(; subdirs=subdirs)
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@info "CompatHelper directories" subdirs
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CompatHelper.main(; subdirs=subdirs, bump_version=true)
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shell: julia --color=yes {0}
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

‎.github/workflows/benchmark-comment.yml

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# Credit to @aviastek, where this code comes from in JET.jl
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# To workaroud https://github.com/actions/first-interaction/issues/10 in a secure way,
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# we take the following steps to generate and comment a performance benchmark result:
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# 1. first "performance tracking" workflow will generate the benchmark results in an unprivileged environment triggered on `pull_request` event
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# 2. then this "performance tracking (comment)" workflow will show the result to us as a PR comment in a privileged environment
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# Note that this workflow can only be modifed by getting checked-in to the default branch
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# and thus is secure even though this workflow is granted with write permissions, etc.
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# xref: https://securitylab.github.com/research/github-actions-preventing-pwn-requests/
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name: Post Benchmark Comments
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on:
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workflow_run:
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workflows:
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- performance tracking
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types:
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- completed
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jobs:
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comment:
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runs-on: ubuntu-latest
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if: >
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${{ github.event.workflow_run.event == 'pull_request' &&
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github.event.workflow_run.conclusion == 'success' }}
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steps:
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- uses: actions/checkout@v2
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# restore records from the artifacts
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- uses: dawidd6/action-download-artifact@v2
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with:
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workflow: benchmark.yml
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name: Benchmarking
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workflow_conclusion: success
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- name: output benchmark result
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id: output-result-markdown
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run: |
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echo ::set-output name=body::$(cat ./benchmark-result.artifact)
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- name: output pull request number
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id: output-pull-request-number
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run: |
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echo ::set-output name=body::$(cat ./pull-request-number.artifact)
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# check if the previous comment exists
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- name: find comment
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uses: peter-evans/find-comment@v1
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id: fc
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with:
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issue-number: ${{ steps.output-pull-request-number.outputs.body }}
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comment-author: 'github-actions[bot]'
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body-includes: Kernel Benchmark Result
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# create/update comment
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- name: create comment
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if: ${{ steps.fc.outputs.comment-id == 0 }}
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uses: peter-evans/create-or-update-comment@v1
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with:
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issue-number: ${{ steps.output-pull-request-number.outputs.body }}
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body: ${{ steps.output-result-markdown.outputs.body }}
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- name: update comment
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if: ${{ steps.fc.outputs.comment-id != 0 }}
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uses: peter-evans/create-or-update-comment@v1
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with:
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comment-id: ${{ steps.fc.outputs.comment-id }}
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body: ${{ steps.output-result-markdown.outputs.body }}

‎.github/workflows/benchmark.yml

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name: Run benchmarks
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on:
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pull_request:
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types: [opened, synchronize, reopened, labeled]
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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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Benchmarking:
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runs-on: ubuntu-latest
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if: contains(github.event.pull_request.labels.*.name, 'performance critical')
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steps:
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# setup
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- uses: actions/checkout@v2
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- uses: julia-actions/setup-julia@latest
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with:
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version: '1.7'
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- uses: julia-actions/julia-buildpkg@latest
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- name: install dependencies
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run: julia -e 'using Pkg; pkg"add PkgBenchmark [email protected]"'
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# run the benchmark suite
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- name: run benchmarks
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run: |
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using BenchmarkCI
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BenchmarkCI.judge()
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BenchmarkCI.displayjudgement()
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shell: julia --color=yes {0}
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# generate and record the benchmark result as markdown
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- name: generate benchmark result
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run: |
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using BenchmarkCI
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judgement = BenchmarkCI._loadjudge(BenchmarkCI.DEFAULT_WORKSPACE)
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title = "Kernel Benchmark Result"
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ciresult = BenchmarkCI.CIResult(; judgement, title)
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comment = sprint() do io
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return BenchmarkCI.printcommentmd(io, ciresult)
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end
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comment = replace(comment, "%" => "%25", "\\n" => "%0A", "\\r" => "%0D")
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write("benchmark-result.artifact", comment)
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shell: julia --color=yes {0}
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# record the pull request number
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- name: record pull request number
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run: echo ${{ github.event.pull_request.number }} > ./pull-request-number.artifact
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# save as artifacts (performance tracking (comment) workflow will use it)
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- uses: actions/upload-artifact@v2
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with:
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name: Benchmarking
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path: ./*.artifact

‎.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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- master
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pull_request:
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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.group }}
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GROUP: ${{ matrix.group }}
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- uses: julia-actions/julia-processcoverage@v1
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if: matrix.version == '1' && matrix.os == 'ubuntu-latest'
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- name: Coveralls parallel
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- name: Send coverage to CodeCov
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if: matrix.version == '1' && matrix.os == 'ubuntu-latest'
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uses: coverallsapp/github-action@master
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uses: codecov/codecov-action@v2
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with:
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github-token: ${{ secrets.GITHUB_TOKEN }}
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path-to-lcov: ./lcov.info
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flag-name: run-${{ matrix.group }}
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parallel: true
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finish:
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needs: test
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runs-on: ubuntu-latest
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steps:
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- name: Send coverage
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uses: coverallsapp/github-action@master
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with:
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github-token: ${{ secrets.github_token }}
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parallel-finished: true
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file: lcov.info

‎.github/workflows/docs.yml

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tags: '*'
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pull_request:
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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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‎.github/workflows/format.yml

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on:
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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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format:

‎.gitignore

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/test/Manifest.toml
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coverage/
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.DS_store
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benchmark/Manifest.toml

‎Project.toml

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name = "KernelFunctions"
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uuid = "ec8451be-7e33-11e9-00cf-bbf324bd1392"
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version = "0.10.6"
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version = "0.10.33"
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[deps]
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ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
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Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7"
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FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b"
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Functors = "d9f16b24-f501-4c13-a1f2-28368ffc5196"
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IrrationalConstants = "92d709cd-6900-40b7-9082-c6be49f344b6"
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LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
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LogExpFunctions = "2ab3a3ac-af41-5b50-aa03-7779005ae688"
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Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
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Requires = "ae029012-a4dd-5104-9daa-d747884805df"
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SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
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StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
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StatsFuns = "4c63d2b9-4356-54db-8cca-17b64c39e42c"
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TensorCore = "62fd8b95-f654-4bbd-a8a5-9c27f68ccd50"
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Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
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ZygoteRules = "700de1a5-db45-46bc-99cf-38207098b444"
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[compat]
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ChainRulesCore = "0.9.44, 0.10"
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ChainRulesCore = "1"
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Compat = "3.7"
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CompositionsBase = "0.1"
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Distances = "0.10"
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FillArrays = "0.10, 0.11"
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FillArrays = "0.10, 0.11, 0.12, 0.13"
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Functors = "0.1, 0.2"
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IrrationalConstants = "0.1"
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LogExpFunctions = "0.2.1, 0.3"
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Requires = "1.0.1"
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SpecialFunctions = "0.8, 0.9, 0.10, 1"
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SpecialFunctions = "0.8, 0.9, 0.10, 1, 2"
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StatsBase = "0.32, 0.33"
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StatsFuns = "0.8, 0.9"
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ZygoteRules = "0.2"
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julia = "1.3"

‎README.md

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# KernelFunctions.jl
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![CI](https://github.com/JuliaGaussianProcesses/KernelFunctions.jl/workflows/CI/badge.svg?branch=master)
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[![Coverage Status](https://coveralls.io/repos/github/JuliaGaussianProcesses/KernelFunctions.jl/badge.svg?branch=master)](https://coveralls.io/github/JuliaGaussianProcesses/KernelFunctions.jl?branch=master)
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[![codecov](https://codecov.io/gh/JuliaGaussianProcesses/KernelFunctions.jl/branch/master/graph/badge.svg?token=rmDh3gb7hN)](https://codecov.io/gh/JuliaGaussianProcesses/KernelFunctions.jl)
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[![Documentation (stable)](https://img.shields.io/badge/docs-stable-blue.svg)](https://juliagaussianprocesses.github.io/KernelFunctions.jl/stable)
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[![Documentation (latest)](https://img.shields.io/badge/docs-dev-blue.svg)](https://juliagaussianprocesses.github.io/KernelFunctions.jl/dev)
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[![ColPrac: Contributor's Guide on Collaborative Practices for Community Packages](https://img.shields.io/badge/ColPrac-Contributor's%20Guide-blueviolet)](https://github.com/SciML/ColPrac)
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[![Code Style: Blue](https://img.shields.io/badge/code%20style-blue-4495d1.svg)](https://github.com/invenia/BlueStyle)
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[![DOI](https://zenodo.org/badge/188430419.svg)](https://zenodo.org/badge/latestdoi/188430419)
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## Kernel functions for machine learning
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KernelFunctions.jl provide a flexible and complete framework for kernel functions, pretransforming the input data.
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KernelFunctions.jl provides a flexible framework for defining kernel functions, and an extensive collection of implementations.
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The aim is to make the API as model-agnostic as possible while still being user-friendly, and to interoperate well with generic packages for handling parameters like [ParameterHandling.jl](https://github.com/invenia/ParameterHandling.jl/) and FluxML's [Functors.jl](https://github.com/FluxML/Functors.jl/).
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The aim is to make the API as model-agnostic as possible while still being user-friendly.
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Where appropriate, kernels are AD-compatible.
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## Examples
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</p>
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## Packages goals (by priority)
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- Ensure AD Compatibility (already the case for Zygote, ForwardDiff)
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- Toeplitz Matrices compatibility
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## Related Work
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Directly inspired by the [MLKernels](https://github.com/trthatcher/MLKernels.jl) package.
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See the JuliaGaussianProcesses [Github organisation](https://github.com/JuliaGaussianProcesses) and [website](https://juliagaussianprocesses.github.io/) for more related packages.
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## Issues/Contributing
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If you notice a problem or would like to contribute by adding more kernel functions or features please [submit an issue](https://github.com/JuliaGaussianProcesses/KernelFunctions.jl/issues), or open a PR (please see the [ColPrac](https://github.com/SciML/ColPrac) contribution guidelines).

‎benchmark/MLKernels.jl

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‎benchmark/Project.toml

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[deps]
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BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
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KernelFunctions = "ec8451be-7e33-11e9-00cf-bbf324bd1392"

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