Merge branch 'main' into features/1243-Refactoring_of_communication_s…

…eparate_mpi4py_-wrappers_from_DNDarrays
helmholtz-analytics · Jan 22, 2024 · abe3d20 · abe3d20
2 parents 47a4d25 + 983e12d
commit abe3d20
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Showing 34 changed files with 1,782 additions and 111 deletions.
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -0,0 +1,16 @@
+version: 2
+updates:
+  - package-ecosystem: github-actions
+    directory: /
+    schedule:
+      interval: daily
+
+  - package-ecosystem: pip
+    directory: /doc
+    schedule:
+      interval: daily
+
+  - package-ecosystem: docker
+    directory: /heat/core/tests
+    schedule:
+      interval: daily
diff --git a/.github/workflows/CIBase.yml b/.github/workflows/CIBase.yml
@@ -7,10 +7,18 @@ on:
       - 'release/**'
       - 'support/**'
 
+permissions:
+  contents: read
+
 jobs:
   starter:
     runs-on: ubuntu-latest
     steps:
+      - name: Harden Runner
+        uses: step-security/harden-runner@eb238b55efaa70779f274895e782ed17c84f2895 # v2.6.1
+        with:
+          egress-policy: audit
+
       - name: 'start test'
         run: |
          curl -s -X POST \

diff --git a/.github/workflows/CommentPR.yml b/.github/workflows/CommentPR.yml
@@ -15,8 +15,13 @@ jobs:
     outputs:
       PR_NR: ${{ steps.step1.outputs.test }}
     steps:
+      - name: Harden Runner
+        uses: step-security/harden-runner@eb238b55efaa70779f274895e782ed17c84f2895 # v2.6.1
+        with:
+          egress-policy: audit
+
       - name: 'Download artifact'
-        uses: actions/github-script@v6
+        uses: actions/github-script@d7906e4ad0b1822421a7e6a35d5ca353c962f410 # v6.4.1
         with:
           script: |
             let allArtifacts = await github.rest.actions.listWorkflowRunArtifacts({
@@ -40,7 +45,7 @@ jobs:
         run: unzip pr_number.zip
 
       - name: 'Comment on PR'
-        uses: actions/github-script@v6
+        uses: actions/github-script@d7906e4ad0b1822421a7e6a35d5ca353c962f410 # v6.4.1
         with:
           github-token: ${{ secrets.GITHUB_TOKEN }}
           script: |
@@ -59,7 +64,12 @@ jobs:
     needs: upload
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - name: Harden Runner
+        uses: step-security/harden-runner@eb238b55efaa70779f274895e782ed17c84f2895 # v2.6.1
+        with:
+          egress-policy: audit
+
+      - uses: actions/checkout@f43a0e5ff2bd294095638e18286ca9a3d1956744 # v3.6.0
 
       - name: 'Trigger Workflow'
         run: |

diff --git a/.github/workflows/ReceivePR.yml b/.github/workflows/ReceivePR.yml
@@ -11,16 +11,21 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - name: Harden Runner
+        uses: step-security/harden-runner@eb238b55efaa70779f274895e782ed17c84f2895 # v2.6.1
+        with:
+          egress-policy: audit
+
+      - uses: actions/checkout@f43a0e5ff2bd294095638e18286ca9a3d1956744 # v3.6.0
 
       - name: Use Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@65d7f2d534ac1bc67fcd62888c5f4f3d2cb2b236 # v4.7.1
         with:
           python-version: 3.8
           architecture: x64
 
       - name: Setup MPI
-        uses: mpi4py/setup-mpi@v1
+        uses: mpi4py/setup-mpi@40c19a60792debf8ca403a3e6ee5f84c4e76555d # v1.2.1
         with:
           mpi: openmpi
 
@@ -36,7 +41,7 @@ jobs:
         run: |
           mkdir -p ./pr
           echo $PR_NUMBER > ./pr/pr_number
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@a8a3f3ad30e3422c9c7b888a15615d19a852ae32 # v3.1.3
         with:
           name: pr_number
           path: pr/
diff --git a/.github/workflows/bench_report.yml b/.github/workflows/bench_report.yml
@@ -16,8 +16,13 @@ jobs:
     name: Benchmark report
     runs-on: ubuntu-latest
     steps:
+      - name: Harden Runner
+        uses: step-security/harden-runner@eb238b55efaa70779f274895e782ed17c84f2895 # v2.6.1
+        with:
+          egress-policy: audit
+
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
       - name: "Collect Gitlab Benchmarks"
         run: |
           curl --location \
@@ -33,7 +38,7 @@ jobs:
           cat report.txt >> $GITHUB_STEP_SUMMARY
       - name: Compare and Save Benchmark Results
         id: action_bench
-        uses: benchmark-action/github-action-benchmark@v1
+        uses: benchmark-action/github-action-benchmark@70405016b032d44f409e4b1b451c40215cbe2393 # v1.18.0
         with:
           github-token: ${{secrets.GITHUB_TOKEN}}
           # Benchmark action input and output

diff --git a/.github/workflows/bench_trigger.yml b/.github/workflows/bench_trigger.yml
@@ -11,8 +11,13 @@ jobs:
     name: Trigger Benchmarks
     runs-on: ubuntu-latest
     steps:
+      - name: Harden Runner
+        uses: step-security/harden-runner@eb238b55efaa70779f274895e782ed17c84f2895 # v2.6.1
+        with:
+          egress-policy: audit
+
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
       - name: Trigger benchmarks (PR)
         id: setup_pr
         if: contains(github.event.pull_request.labels.*.name, 'benchmark PR')

diff --git a/.github/workflows/changelog-updater.yml b/.github/workflows/changelog-updater.yml
@@ -4,12 +4,22 @@ on:
   release:
     types: [released]
 
+permissions:
+  contents: read
+
 jobs:
   update:
+    permissions:
+      contents: write  # for stefanzweifel/git-auto-commit-action to push code in repo
     runs-on: ubuntu-latest
     steps:
+      - name: Harden Runner
+        uses: step-security/harden-runner@eb238b55efaa70779f274895e782ed17c84f2895 # v2.6.1
+        with:
+          egress-policy: audit
+
       - name: Checkout code
-        uses: actions/checkout@v3
+        uses: actions/checkout@f43a0e5ff2bd294095638e18286ca9a3d1956744 # v3.6.0
         with:
           repository: helmholtz-analytics/heat
           ref: ${{ github.event.release.target_commitish }}
@@ -25,7 +35,7 @@ jobs:
           rm newline.txt
           cat CHANGELOG.md
       - name: Commit updated CHANGELOG
-        uses: stefanzweifel/git-auto-commit-action@v4
+        uses: stefanzweifel/git-auto-commit-action@3ea6ae190baf489ba007f7c92608f33ce20ef04a # v4.16.0
         with:
           branch: ${{ github.event.release.target_commitish }}
           commit_message: Update CHANGELOG

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -36,14 +36,19 @@ jobs:
 
     name: Python ${{ matrix.py-version }} with ${{ matrix.pytorch-version }}; options ${{ matrix.install-options }}
     steps:
+      - name: Harden Runner
+        uses: step-security/harden-runner@eb238b55efaa70779f274895e782ed17c84f2895 # v2.6.1
+        with:
+          egress-policy: audit
+
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Setup MPI
-        uses: mpi4py/setup-mpi@v1
+        uses: mpi4py/setup-mpi@v1.2.0
         with:
           mpi: ${{ matrix.mpi }}
       - name: Use Python ${{ matrix.py-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@65d7f2d534ac1bc67fcd62888c5f4f3d2cb2b236 # v4.7.1
         with:
           python-version: ${{ matrix.py-version }}
           architecture: x64

diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml
@@ -0,0 +1,78 @@
+# For most projects, this workflow file will not need changing; you simply need
+# to commit it to your repository.
+#
+# You may wish to alter this file to override the set of languages analyzed,
+# or to provide custom queries or build logic.
+#
+# ******** NOTE ********
+# We have attempted to detect the languages in your repository. Please check
+# the `language` matrix defined below to confirm you have the correct set of
+# supported CodeQL languages.
+#
+name: "CodeQL"
+
+on:
+  push:
+    branches: ["main"]
+  pull_request:
+    # The branches below must be a subset of the branches above
+    branches: ["main"]
+  schedule:
+    - cron: "0 0 * * 1"
+
+permissions:
+  contents: read
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: ["python"]
+        # CodeQL supports [ $supported-codeql-languages ]
+        # Learn more about CodeQL language support at https://aka.ms/codeql-docs/language-support
+
+    steps:
+      - name: Harden Runner
+        uses: step-security/harden-runner@eb238b55efaa70779f274895e782ed17c84f2895 # v2.6.1
+        with:
+          egress-policy: audit
+
+      - name: Checkout repository
+        uses: actions/checkout@f43a0e5ff2bd294095638e18286ca9a3d1956744 # v3.6.0
+
+      # Initializes the CodeQL tools for scanning.
+      - name: Initialize CodeQL
+        uses: github/codeql-action/init@305f6546310b9203e892c28c1484e82977f4f63d # v2.22.10
+        with:
+          languages: ${{ matrix.language }}
+          # If you wish to specify custom queries, you can do so here or in a config file.
+          # By default, queries listed here will override any specified in a config file.
+          # Prefix the list here with "+" to use these queries and those in the config file.
+
+      # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
+      # If this step fails, then you should remove it and run the build manually (see below)
+      - name: Autobuild
+        uses: github/codeql-action/autobuild@305f6546310b9203e892c28c1484e82977f4f63d # v2.22.10
+
+      # ℹ️ Command-line programs to run using the OS shell.
+      # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
+
+      #   If the Autobuild fails above, remove it and uncomment the following three lines.
+      #   modify them (or add more) to build your code if your project, please refer to the EXAMPLE below for guidance.
+
+      # - run: |
+      #   echo "Run, Build Application using script"
+      #   ./location_of_script_within_repo/buildscript.sh
+
+      - name: Perform CodeQL Analysis
+        uses: github/codeql-action/analyze@305f6546310b9203e892c28c1484e82977f4f63d # v2.22.10
+        with:
+          category: "/language:${{matrix.language}}"
diff --git a/.github/workflows/codesee-arch-diagram.yml b/.github/workflows/codesee-arch-diagram.yml
@@ -17,6 +17,11 @@ jobs:
     continue-on-error: true
     name: Analyze the repo with CodeSee
     steps:
-      - uses: Codesee-io/codesee-action@v2
+      - name: Harden Runner
+        uses: step-security/harden-runner@eb238b55efaa70779f274895e782ed17c84f2895 # v2.6.1
+        with:
+          egress-policy: audit
+
+      - uses: Codesee-io/codesee-action@4f66933f195ad209dab16bcdd12cbacfff7f8707 # v2
         with:
           codesee-token: ${{ secrets.CODESEE_ARCH_DIAG_API_TOKEN }}
diff --git a/.github/workflows/create-branch-on-assignment.yml b/.github/workflows/create-branch-on-assignment.yml
@@ -10,7 +10,12 @@ jobs:
   create_issue_branch_job:
     runs-on: ubuntu-latest
     steps:
+      - name: Harden Runner
+        uses: step-security/harden-runner@eb238b55efaa70779f274895e782ed17c84f2895 # v2.6.1
+        with:
+          egress-policy: audit
+
       - name: Create Issue Branch
-        uses: robvanderleek/create-issue-branch@main
+        uses: robvanderleek/create-issue-branch@4b7c39bf18d2a2684800508051ee9910e405e193 # main
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/dependency-review.yml b/.github/workflows/dependency-review.yml
@@ -0,0 +1,27 @@
+# Dependency Review Action
+#
+# This Action will scan dependency manifest files that change as part of a Pull Request,
+# surfacing known-vulnerable versions of the packages declared or updated in the PR.
+# Once installed, if the workflow run is marked as required,
+# PRs introducing known-vulnerable packages will be blocked from merging.
+#
+# Source repository: https://github.com/actions/dependency-review-action
+name: 'Dependency Review'
+on: [pull_request]
+
+permissions:
+  contents: read
+
+jobs:
+  dependency-review:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Harden Runner
+        uses: step-security/harden-runner@eb238b55efaa70779f274895e782ed17c84f2895 # v2.6.1
+        with:
+          egress-policy: audit
+
+      - name: 'Checkout Repository'
+        uses: actions/checkout@f43a0e5ff2bd294095638e18286ca9a3d1956744 # v3.6.0
+      - name: 'Dependency Review'
+        uses: actions/dependency-review-action@0efb1d1d84fc9633afcdaad14c485cbbc90ef46c # v2.5.1
diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
@@ -17,31 +17,39 @@ on:
                 required: true
                 default: 'heat:1.3.0_torch2.0.0_cu12.1'
                 type: string
+permissions:
+  contents: read
+
 jobs:
     build-and-push-img:
         runs-on: ubuntu-latest
         steps:
+            - name: Harden Runner
+              uses: step-security/harden-runner@eb238b55efaa70779f274895e782ed17c84f2895 # v2.6.1
+              with:
+                egress-policy: audit
+
             -
               name: Checkout
-              uses: actions/checkout@v3
+              uses: actions/checkout@f43a0e5ff2bd294095638e18286ca9a3d1956744 # v3.6.0
             -
               name: Set up QEMU
-              uses: docker/setup-qemu-action@v2
+              uses: docker/setup-qemu-action@2b82ce82d56a2a04d2637cd93a637ae1b359c0a7 # v2.2.0
             -
               name: Set up Docker Buildx
-              uses: docker/setup-buildx-action@v2
+              uses: docker/setup-buildx-action@885d1462b80bc1c1c7f0b00334ad271f09369c55 # v2.10.0
               with:
                 driver: docker
             -
               name: Login to GitHub Container Registry
-              uses: docker/login-action@v2
+              uses: docker/login-action@465a07811f14bebb1938fbed4728c6a1ff8901fc # v2.2.0
               with:
                 registry: ghcr.io
                 username: ${{ github.repository_owner }}
                 password: ${{ secrets.GITHUB_TOKEN }}
             -
               name: Build
-              uses: docker/build-push-action@v4
+              uses: docker/build-push-action@0a97817b6ade9f46837855d676c4cca3a2471fc9 # v4.2.1
               with:
                 file: docker/Dockerfile.release
                 build-args: |
@@ -57,7 +65,7 @@ jobs:
                 docker run -v `pwd`:`pwd` -w `pwd` --rm test_${{ inputs.name }} pytest
             -
               name: Build and push
-              uses: docker/build-push-action@v4
+              uses: docker/build-push-action@0a97817b6ade9f46837855d676c4cca3a2471fc9 # v4.2.1
               with:
                 file: docker/Dockerfile.release
                 build-args: |