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Create monorepo (#136)
* Move everything * More moving around * More moving * Try out tests * Try with docs * Rename * Fix codecov * De-toggle tests * Remove Manifests * Remove all Manifests * License symlinks * Remove index * Rm test true * Semicolons * Interpolation * Dev both at once * Fix parse * Unique * Ahem * Bracket * Add Licenses, untoggle tests * Tag prefix * Manual buildpkg * Clean up * Fix
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‎.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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tags: ['*']
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pull_request:
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workflow_dispatch:
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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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name: Test - ${{ matrix.pkg.name }} - Julia ${{ matrix.version }}
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runs-on: ${{ matrix.os }}
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timeout-minutes: 60
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permissions: # needed to allow julia-actions/cache to proactively delete old caches that it has created
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strategy:
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fail-fast: false
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matrix:
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pkg:
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- name: DifferentiationInterface
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dir: './DifferentiationInterface'
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- name: DifferentiationInterfaceTest
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dir: './DifferentiationInterfaceTest'
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version:
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- '1.10'
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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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steps:
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- uses: actions/checkout@v4
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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: ${{ matrix.arch }}
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- uses: julia-actions/cache@v1
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- uses: julia-actions/julia-buildpkg@v1
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- name: Install dependencies (replaces buildpkg)
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run: julia --project=${{ matrix.pkg.dir}}/ -e '
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using Pkg;
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if "${{ matrix.pkg.name}}" == "DifferentiationInterfaceTest";
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Pkg.develop(PackageSpec(path="./DifferentiationInterface"));
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end;
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Pkg.instantiate();'
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- uses: julia-actions/julia-runtest@v1
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with:
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project: ${{ matrix.pkg.dir }}
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- uses: julia-actions/julia-processcoverage@v1
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with:
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directories: src,ext,lib
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directories: ${{ matrix.pkg.dir }}/src,${{ matrix.pkg.dir }}/ext
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- uses: codecov/codecov-action@v4
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with:
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files: lcov.info
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token: ${{ secrets.CODECOV_TOKEN }}
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fail_ci_if_error: true
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docs:
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name: Documentation
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name: Docs - ${{ matrix.pkg.name }}
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runs-on: ubuntu-latest
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permissions:
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actions: write # needed to allow julia-actions/cache to proactively delete old caches that it has created
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contents: write
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statuses: write
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strategy:
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fail-fast: false
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matrix:
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pkg:
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- name: DifferentiationInterface
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dir: './DifferentiationInterface'
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- name: DifferentiationInterfaceTest
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dir: './DifferentiationInterfaceTest'
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steps:
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- uses: actions/checkout@v4
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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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- name: Configure doc environment
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shell: julia --project=docs --color=yes {0}
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run: |
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using Pkg
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Pkg.Registry.update() # TODO: remove? useful for fresh releases
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Pkg.develop(PackageSpec(path=pwd()))
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Pkg.develop(PackageSpec(path=joinpath(pwd(), "lib", "DifferentiationInterfaceTest")))
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Pkg.instantiate()
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- uses: julia-actions/julia-buildpkg@v1
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- uses: julia-actions/julia-docdeploy@v1
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- name: Install dependencies
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run: julia --project=${{ matrix.pkg.dir}}/docs/ -e '
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using Pkg;
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if "${{ matrix.pkg.name}}" == "DifferentiationInterface";
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Pkg.develop(PackageSpec(path="./DifferentiationInterface"));
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else;
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Pkg.develop([PackageSpec(path="./DifferentiationInterface"), PackageSpec(path="${{ matrix.pkg.dir}}")]);
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end;
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Pkg.instantiate();'
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- name: Build and deploy
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
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- name: Run doctests
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shell: julia --project=docs --color=yes {0}
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run: |
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using Documenter: DocMeta, doctest
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using DifferentiationInterface
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DocMeta.setdocmeta!(DifferentiationInterface, :DocTestSetup, :(using DifferentiationInterface); recursive=true)
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doctest(DifferentiationInterface)
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # If authenticating with GitHub Actions token
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DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # If authenticating with SSH deploy key
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run: julia --project=${{ matrix.pkg.dir}}/docs/ ${{ matrix.pkg.dir}}/docs/make.jl

‎.github/workflows/CompatHelper.yml‎

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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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run: julia -e 'using CompatHelper; CompatHelper.main()'
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run: julia -e 'using CompatHelper; CompatHelper.main(subdirs=["DifferentiationInterface", "DifferentiationInterfaceTest"])'

‎.github/workflows/DocPreviewCleanup.yml‎

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name: Doc Preview Cleanup
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on:
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pull_request:
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types: [closed]
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# Ensure that only one "Doc Preview Cleanup" workflow is force pushing at a time
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concurrency:
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group: doc-preview-cleanup
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cancel-in-progress: false
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jobs:
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doc-preview-cleanup:
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runs-on: ubuntu-latest
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permissions:
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contents: write
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steps:
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- name: Checkout gh-pages branch
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uses: actions/checkout@v4
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with:
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ref: gh-pages
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- name: Delete preview and history + push changes
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run: |
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if [ -d "${preview_dir}" ]; then
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git config user.name "Documenter.jl"
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git config user.email "documenter@juliadocs.github.io"
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git rm -rf "${preview_dir}"
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git commit -m "delete preview"
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git branch gh-pages-new $(echo "delete history" | git commit-tree HEAD^{tree})
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git push --force origin gh-pages-new:gh-pages
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fi
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env:
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preview_dir: previews/PR${{ github.event.number }}

‎.github/workflows/TagBot.yml‎

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‎.gitignore‎

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*.jl.cov
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*.jl.mem
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/.benchmarkci
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/benchmark/*.json
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**/docs/build/
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**/docs/src/index.md
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/docs/build/
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/docs/src/index.md
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Manifest.toml
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**/Manifest.toml
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**/docs/Manifest.toml
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*.csv

‎DifferentiationInterface/LICENSE‎

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MIT License
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Copyright (c) 2024 Guillaume Dalle, Adrian Hill
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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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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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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.

Project.toml renamed to DifferentiationInterface/Project.toml

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[extensions]
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DifferentiationInterfaceChainRulesCoreExt = "ChainRulesCore"
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DifferentiationInterfaceDiffractorExt = ["AbstractDifferentiation", "Diffractor"]
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DifferentiationInterfaceDiffractorExt = [
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"AbstractDifferentiation",
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"Diffractor",
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]
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DifferentiationInterfaceEnzymeExt = "Enzyme"
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DifferentiationInterfaceFastDifferentiationExt = "FastDifferentiation"
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DifferentiationInterfaceFiniteDiffExt = "FiniteDiff"
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[extras]
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ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b"
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Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
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Chairmarks = "0ca39b1e-fe0b-4e98-acfc-b1656634c4de"
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DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
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Diffractor = "9f5e2b26-1114-432f-b630-d3fe2085c51c"
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Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
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Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9"
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Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
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[targets]
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test = ["ADTypes", "Aqua", "Chairmarks", "DataFrames", "Diffractor", "Documenter", "Enzyme", "FastDifferentiation", "FiniteDiff", "FiniteDifferences", "ForwardDiff", "JET", "JuliaFormatter", "Pkg", "PolyesterForwardDiff", "ReverseDiff", "SparseArrays", "SparseDiffTools", "Symbolics", "Tapir", "Test", "Tracker", "Zygote"]
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test = [
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"ADTypes",
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"Aqua",
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"Diffractor",
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"Documenter",
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"Enzyme",
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"FastDifferentiation",
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"FiniteDiff",
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"FiniteDifferences",
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"ForwardDiff",
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"JET",
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"JuliaFormatter",
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"Pkg",
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"PolyesterForwardDiff",
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"ReverseDiff",
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"SparseArrays",
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"SparseDiffTools",
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"Symbolics",
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"Tapir",
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"Test",
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"Tracker",
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"Zygote",
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]

‎DifferentiationInterface/README.md‎

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# DifferentiationInterface
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[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://gdalle.github.io/DifferentiationInterface.jl/DifferentiationInterface/dev/)
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[![Build Status](https://github.com/gdalle/DifferentiationInterface.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/gdalle/DifferentiationInterface.jl/actions/workflows/CI.yml?query=branch%3Amain)
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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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An interface to various automatic differentiation (AD) backends in Julia.
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## Goal
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This package provides a backend-agnostic syntax to differentiate functions of the following types:
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- _allocating_: `f(x) = y`
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- _mutating_: `f!(y, x) = nothing`
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## Features
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- First and second order operators
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- In-place and out-of-place differentiation
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- Preparation mechanism (e.g. to create a config or tape)
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- Thorough validation on standard inputs and outputs (scalars, vectors, matrices)
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- Testing and benchmarking utilities accessible to users with [DifferentiationInterfaceTest](https://gdalle.github.io/DifferentiationInterface.jl/DifferentiationInterfaceTest/)
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## Compatibility
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We support most of the backends defined by [ADTypes.jl](https://github.com/SciML/ADTypes.jl):
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| backend | object |
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| :------------------------------------------------------------------------------ | :--------------------------------------------------------- |
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| [ChainRulesCore.jl](https://github.com/JuliaDiff/ChainRulesCore.jl) | `AutoChainRules(ruleconfig)` |
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| [Diffractor.jl](https://github.com/JuliaDiff/Diffractor.jl) | `AutoDiffractor()` |
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| [Enzyme.jl](https://github.com/EnzymeAD/Enzyme.jl) | `AutoEnzyme(Enzyme.Forward)`, `AutoEnzyme(Enzyme.Reverse)` |
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| [FiniteDiff.jl](https://github.com/JuliaDiff/FiniteDiff.jl) | `AutoFiniteDiff()` |
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| [FiniteDifferences.jl](https://github.com/JuliaDiff/FiniteDifferences.jl) | `AutoFiniteDifferences(fdm)` |
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| [ForwardDiff.jl](https://github.com/JuliaDiff/ForwardDiff.jl) | `AutoForwardDiff()` |
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| [PolyesterForwardDiff.jl](https://github.com/JuliaDiff/PolyesterForwardDiff.jl) | `AutoPolyesterForwardDiff(; chunksize)` |
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| [ReverseDiff.jl](https://github.com/JuliaDiff/ReverseDiff.jl) | `AutoReverseDiff()` |
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| [SparseDiffTools.jl](https://github.com/JuliaDiff/SparseDiffTools.jl) | `AutoSparseForwardDiff()`, `AutoSparseFiniteDiff()` |
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| [Tracker.jl](https://github.com/FluxML/Tracker.jl) | `AutoTracker()` |
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| [Zygote.jl](https://github.com/FluxML/Zygote.jl) | `AutoZygote()` |
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We also provide some experimental backends ourselves:
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| backend | object |
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| :------------------------------------------------------------------------------- | :------------------------------------------------------------- |
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| [FastDifferentiation.jl](https://github.com/brianguenter/FastDifferentiation.jl) | `AutoFastDifferentiation()`, `AutoSparseFastDifferentiation()` |
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| [Tapir.jl](https://github.com/withbayes/Tapir.jl) | `AutoTapir()` |
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## Example
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```jldoctest readme
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julia> import ForwardDiff
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julia> using DifferentiationInterface
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julia> backend = AutoForwardDiff();
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julia> f(x) = sum(abs2, x);
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julia> value_and_gradient(f, backend, [1., 2., 3.])
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(14.0, [2.0, 4.0, 6.0])
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```
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## Related packages
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- [AbstractDifferentiation.jl](https://github.com/JuliaDiff/AbstractDifferentiation.jl) is the original inspiration for DifferentiationInterface.jl.
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- [AutoDiffOperators.jl](https://github.com/oschulz/AutoDiffOperators.jl) is an attempt to bridge ADTypes.jl with AbstractDifferentiation.jl.

docs/Project.toml renamed to DifferentiationInterface/docs/Project.toml

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ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b"
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BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
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ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
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Chairmarks = "0ca39b1e-fe0b-4e98-acfc-b1656634c4de"
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DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
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DifferentiationInterface = "a0c0ee7d-e4b9-4e03-894e-1c5f64a51d63"
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Diffractor = "9f5e2b26-1114-432f-b630-d3fe2085c51c"
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Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
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Markdown = "d6f4376e-aef5-505a-96c1-9c027394607a"
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PolyesterForwardDiff = "98d1487c-24ca-40b6-b7ab-df2af84e126b"
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PrettyTables = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d"
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Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
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ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267"
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SparseDiffTools = "47a9eef4-7e08-11e9-0b38-333d64bd3804"
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Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7"
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Tapir = "07d77754-e150-4737-8c94-cd238a1fb45b"
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Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
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Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c"
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Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
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