Merge branch 'main' into vc/string2

EnzymeAD · Jan 17, 2025 · 75f18b7 · 75f18b7
2 parents f343d45 + b95c737
commit 75f18b7
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diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -0,0 +1,7 @@
+# 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"
diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -25,7 +25,7 @@ jobs:
           - '1.11'
           - 'nightly'
         os:
-          - ubuntu-20.04
+          - ubuntu-24.04
           - macOS-latest
           - windows-latest
         arch:
@@ -38,17 +38,17 @@ jobs:
             arch: x64
             libEnzyme: local
         include:
-          - os: ubuntu-20.04
+          - os: ubuntu-24.04
             arch: x86
             libEnzyme: packaged
             version: '1.10'
             assertions: false
-          - os: ubuntu-20.04
+          - os: ubuntu-24.04
             arch: x64
             libEnzyme: packaged
             version: '1.10'
             assertions: true
-          - os: ubuntu-20.04
+          - os: ubuntu-24.04
             arch: x64
             libEnzyme: packaged
             version: '1.11'
@@ -72,16 +72,7 @@ jobs:
           sed -i.bak 's/exit 2/exit 0/g' julia/deps/tools/jlchecksum
           make -C julia -j $(nproc) FORCE_ASSERTIONS=1 LLVM_ASSERTIONS=1 JULIA_PRECOMPILE=0
           echo $PWD/julia/usr/bin >> $GITHUB_PATH
-      - uses: actions/cache@v2
-        env:
-          cache-name: cache-artifacts
-        with:
-          path: ~/.julia/artifacts
-          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
-          restore-keys: |
-            ${{ runner.os }}-test-${{ env.cache-name }}-
-            ${{ runner.os }}-test-
-            ${{ runner.os }}-
+      - uses: julia-actions/cache@v2
       - name: add EnzymeCore
         shell: julia --color=yes --project=. {0}
         run: |
@@ -95,16 +86,16 @@ jobs:
         continue-on-error: ${{ matrix.version == 'nightly' }}
         id: build_libenzyme
         run: |
-          julia --project=deps -e 'using Pkg; Pkg.instantiate()'
-          julia --project=deps deps/build_local.jl
+          julia --color=yes --project=deps -e 'using Pkg; Pkg.instantiate()'
+          julia --color=yes --project=deps deps/build_local.jl
           cp LocalPreferences.toml test/
       - name: Build libEnzyme MacOS
         if: ${{ matrix.libEnzyme == 'local' && matrix.os == 'macOS-latest'}}
         continue-on-error: ${{ matrix.version == 'nightly' }}
         id: build_libenzyme_mac
         run: |
-          julia --project=deps -e 'using Pkg; Pkg.instantiate()'
-          SDKROOT=`xcrun --show-sdk-path` julia --project=deps deps/build_local.jl
+          julia --color=yes --project=deps -e 'using Pkg; Pkg.instantiate()'
+          SDKROOT=`xcrun --show-sdk-path` julia --color=yes --project=deps deps/build_local.jl
           cp LocalPreferences.toml test/
       - uses: julia-actions/julia-buildpkg@v1
         if: matrix.version != 'nightly' || steps.build_libenzyme.outcome == 'success' || steps.build_libenzyme_mac.outcome == 'success'
@@ -120,10 +111,10 @@ jobs:
           JULIA_PKG_SERVER_REGISTRY_PREFERENCE: eager
       - uses: julia-actions/julia-processcoverage@v1
         if: matrix.version != 'nightly' || steps.run_tests.outcome == 'success'
-      - uses: codecov/codecov-action@v4
+      - uses: codecov/codecov-action@v5
         if: matrix.version != 'nightly' || steps.run_tests.outcome == 'success'
         with:
-          file: lcov.info
+          files: lcov.info
           token: ${{ secrets.CODECOV_TOKEN }}
           fail_ci_if_error: false  # or true if you want CI to fail when Codecov fails
   enzymetestutils:
@@ -150,16 +141,7 @@ jobs:
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
-      - uses: actions/cache@v2
-        env:
-          cache-name: cache-artifacts
-        with:
-          path: ~/.julia/artifacts
-          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
-          restore-keys: |
-            ${{ runner.os }}-test-${{ env.cache-name }}-
-            ${{ runner.os }}-test-
-            ${{ runner.os }}-
+      - uses: julia-actions/cache@v2
       - name: setup EnzymeTestUtils
         shell: julia --color=yes {0}
         id: setup_testutils
@@ -182,7 +164,7 @@ jobs:
         if: matrix.version != 'nightly' || steps.run_tests.outcome == 'success'
         with:
           directories: lib/EnzymeTestUtils/src
-      - uses: codecov/codecov-action@v4
+      - uses: codecov/codecov-action@v5
         if: matrix.version != 'nightly' || steps.run_tests.outcome == 'success'
         with:
           files: lcov.info
@@ -212,16 +194,7 @@ jobs:
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
-      - uses: actions/cache@v2
-        env:
-          cache-name: cache-artifacts
-        with:
-          path: ~/.julia/artifacts
-          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
-          restore-keys: |
-            ${{ runner.os }}-test-${{ env.cache-name }}-
-            ${{ runner.os }}-test-
-            ${{ runner.os }}-
+      - uses: julia-actions/cache@v2
       - name: setup EnzymeCore
         shell: julia --color=yes {0}
         id: setup_testutils
@@ -244,7 +217,7 @@ jobs:
         if: matrix.version != 'nightly' || steps.run_tests.outcome == 'success'
         with:
           directories: lib/EnzymeCore/src
-      - uses: codecov/codecov-action@v4
+      - uses: codecov/codecov-action@v5
         if: matrix.version != 'nightly' || steps.run_tests.outcome == 'success'
         with:
           files: lcov.info
@@ -287,19 +260,18 @@ jobs:
           version: '1'
       - uses: julia-actions/cache@v2
       - run: |
-          julia --project=docs -e '
+          julia --color=yes --project=docs -e '
             using Pkg
-            Pkg.develop([PackageSpec(path="lib/EnzymeCore"), PackageSpec(path="lib/EnzymeTestUtils"), PackageSpec(path=pwd())])
             Pkg.instantiate()'
         env:
           JULIA_PKG_SERVER_REGISTRY_PREFERENCE: eager
       - run: |
-          julia --project=docs -e '
+          julia --color=yes --project=docs -e '
             using Documenter: DocMeta, doctest
             using Enzyme
             DocMeta.setdocmeta!(Enzyme, :DocTestSetup, :(using Enzyme); recursive=true)
             doctest(Enzyme)'
-      - run: julia --project=docs docs/make.jl
+      - run: julia --color=yes --project=docs docs/make.jl
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
diff --git a/.github/workflows/Format.yml b/.github/workflows/Format.yml
@@ -0,0 +1,55 @@
+name: 'Format'
+
+on:
+  pull_request_target:
+    paths: ['**/*.jl']
+    types: [opened, synchronize, reopened, ready_for_review]
+
+permissions:
+  contents: read
+
+  # needed for julia-actions/cache to delete old caches
+  actions: write
+
+  # needed for googleapis/code-suggester
+  pull-requests: write
+
+jobs:
+  runic:
+    runs-on: ubuntu-latest
+    if: github.event.pull_request.draft == false
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          ref: ${{github.event.pull_request.head.ref}}
+          repository: ${{github.event.pull_request.head.repo.full_name}}
+          fetch-depth: 0
+
+      - name: Setup Julia
+        uses: julia-actions/setup-julia@v2
+        with:
+          version: '1'
+          arch: 'x64'
+      - uses: julia-actions/cache@v2
+
+      - name: Install Runic
+        run: |
+          julia --project=@runic -e 'using Pkg; Pkg.add("Runic")'
+          curl -o git-runic https://raw.githubusercontent.com/fredrikekre/Runic.jl/master/bin/git-runic
+          chmod +x git-runic
+          sudo mv git-runic /usr/local/bin
+
+      - name: Run Runic
+        run: |
+          set +e
+          git runic origin/master
+          [ $? -eq 2 ] && exit 1 || exit 0
+
+      - name: Suggest changes
+        uses: googleapis/code-suggester@v2
+        env:
+          ACCESS_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          command: review
+          pull_number: ${{ github.event.pull_request.number }}
+          git_dir: '.'
diff --git a/.github/workflows/PreviewCleanup.yml b/.github/workflows/PreviewCleanup.yml
@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout gh-pages branch
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           ref: gh-pages
       - name: Delete preview and history + push changes

diff --git a/.github/workflows/benchmark_pr.yml b/.github/workflows/benchmark_pr.yml
@@ -6,16 +6,22 @@ on:
 permissions:
   pull-requests: write
 
+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:
     generate_plots:
         runs-on: ubuntu-latest
 
         steps:
-            - uses: actions/checkout@v2
-            - uses: julia-actions/setup-julia@v1
+            - uses: actions/checkout@v4
+            - uses: julia-actions/setup-julia@v2
               with:
                 version: "1"
-            - uses: julia-actions/cache@v1
+            - uses: julia-actions/cache@v2
             - name: Extract Package Name from Project.toml
               id: extract-package-name
               run: |
@@ -26,8 +32,8 @@ jobs:
                 JULIA_NUM_THREADS: 2
               run: |
                 # Lightweight build step, as sometimes the runner runs out of memory:
-                julia -e 'ENV["JULIA_PKG_PRECOMPILE_AUTO"]=0; import Pkg; Pkg.add("AirspeedVelocity")'
-                julia -e 'ENV["JULIA_PKG_PRECOMPILE_AUTO"]=0; import Pkg; Pkg.build("AirspeedVelocity")'
+                julia --color=yes -e 'ENV["JULIA_PKG_PRECOMPILE_AUTO"]=0; import Pkg; Pkg.add("AirspeedVelocity")'
+                julia --color=yes -e 'ENV["JULIA_PKG_PRECOMPILE_AUTO"]=0; import Pkg; Pkg.build("AirspeedVelocity")'
             - name: Add ~/.julia/bin to PATH
               run: |
                 echo "$HOME/.julia/bin" >> $GITHUB_PATH
@@ -60,15 +66,15 @@ jobs:
                 echo 'Go to "Actions"->"Benchmark a pull request"->[the most recent run]->"Artifacts" (at the bottom).' >> body.md
 
             - name: Find Comment
-              uses: peter-evans/find-comment@v2
+              uses: peter-evans/find-comment@v3
               id: fcbenchmark
               with:
                 issue-number: ${{ github.event.pull_request.number }}
                 comment-author: 'github-actions[bot]'
                 body-includes: Benchmark Results
 
             - name: Comment on PR
-              uses: peter-evans/create-or-update-comment@v3
+              uses: peter-evans/create-or-update-comment@v4
               with:
                 comment-id: ${{ steps.fcbenchmark.outputs.comment-id }}
                 issue-number: ${{ github.event.pull_request.number }}

diff --git a/.github/workflows/scripts_deploy.yml b/.github/workflows/scripts_deploy.yml
@@ -9,23 +9,23 @@ on:
 
 jobs:
   docs:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - uses: julia-actions/setup-julia@v1
+      - uses: julia-actions/setup-julia@v2
         with:
           version: '1'
-      - uses: julia-actions/cache@v1
+      - uses: julia-actions/cache@v2
       - run: |
-          julia --project=docs -e '
+          julia --color=yes --project=docs -e '
             using Pkg
             Pkg.develop([PackageSpec(path="lib/EnzymeCore"), PackageSpec(path=pwd()), PackageSpec(path="lib/EnzymeTestUtils")])
             Pkg.instantiate()'
         env:
           JULIA_PKG_SERVER_REGISTRY_PREFERENCE: eager
       - run: |
-          julia --project=docs -e '
+          julia --color=yes --project=docs -e '
             using Documenter: DocMeta, doctest
             using Enzyme
             DocMeta.setdocmeta!(Enzyme, :DocTestSetup, :(using Enzyme); recursive=true)

diff --git a/.gitignore b/.gitignore
@@ -7,5 +7,6 @@ lib/EnzymeCore/Manifest.toml
 /test/Manifest.toml
 /docs/Manifest.toml
 /docs/build/
+/docs/src/generated/
 
 .vscode
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,5 @@
+repos:
+  - repo: https://github.com/fredrikekre/runic-pre-commit
+    rev: v1.0.0
+    hooks:
+      - id: runic
diff --git a/docs/Project.toml b/docs/Project.toml
@@ -1,9 +1,16 @@
 [deps]
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9"
+EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869"
+EnzymeTestUtils = "12d8515a-0907-448a-8884-5fe00fdf1c5a"
 Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [compat]
 Documenter = "1"
 Literate = "2"
+
+[sources]
+Enzyme = {path = ".."}
+EnzymeCore = {path = "../lib/EnzymeCore"}
+EnzymeTestUtils = {path = "../lib/EnzymeTestUtils"}
diff --git a/docs/make.jl b/docs/make.jl
@@ -1,6 +1,3 @@
-pushfirst!(LOAD_PATH, joinpath(@__DIR__, "..")) # add Enzyme to environment stack
-pushfirst!(LOAD_PATH, joinpath(@__DIR__, "..", "lib")) # add EnzymeCore to environment stack
-
 using Enzyme
 using EnzymeCore
 using EnzymeTestUtils

diff --git a/docs/src/index.md b/docs/src/index.md
@@ -227,7 +227,7 @@ Enzyme provides convenience functions for second-order derivative computations,
 
 Unlike [`autodiff`](@ref) and [`gradient`](@ref), a mode is not specified. Here, Enzyme will choose to perform forward over reverse mode (generally the fastest for this type of operation).
 
-```jldoctest hvp; filter = r"([0-9]+\\.[0-9]{8})[0-9]+" => s"\\1***"
+```jldoctest hvp; filter = r"([0-9]+\.[0-9]{8})[0-9]+" => s"\1***"
 julia> f(x) = sin(x[1] * x[2]);
 
 julia> hvp(f, [2.0, 3.0], [5.0, 2.7])
@@ -238,7 +238,7 @@ julia> hvp(f, [2.0, 3.0], [5.0, 2.7])
 
 Enzyme also provides an in-place variant which will store the hessian vector product in a pre-allocated array (this will, however, still allocate another array for storing an intermediate gradient).
 
-```jldoctest hvp2; filter = r"([0-9]+\\.[0-9]{8})[0-9]+" => s"\\1***"
+```jldoctest hvp2; filter = r"([0-9]+\.[0-9]{8})[0-9]+" => s"\1***"
 julia> f(x) = sin(x[1] * x[2])
 f (generic function with 1 method)
 
@@ -254,7 +254,7 @@ julia> res
 
 Finally. Enzyme provides a second in-place variant which simultaneously computes both the hessian vector product, and the gradient. This function uses no additional allocation, and is much more efficient than separately computing the hvp and the gradient.
 
-```jldoctest hvp3; filter = r"([0-9]+\\.[0-9]{8})[0-9]+" => s"\\1***"
+```jldoctest hvp3; filter = r"([0-9]+\.[0-9]{8})[0-9]+" => s"\1***"
 julia> f(x) = sin(x[1] * x[2]);
 
 julia> res = Vector{Float64}(undef, 2);