Merge remote-tracking branch 'upstream/main' into releases

Author: andiwand

.github/workflows/analysis.yml

@@ -95,6 +95,69 @@ jobs:
           name: coverage-build
           path: build
 
+  clang_tidy:
+    runs-on: ubuntu-latest
+    container: ghcr.io/acts-project/ubuntu2404_clang19:83
+
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+
+      - name: Mark workspace as safe
+        run: git config --global --add safe.directory /__w/acts/acts
+
+      - name: Fetch base branch
+        if: github.event_name == 'pull_request'
+        run: git fetch origin "${{ github.base_ref }}"
+
+      - uses: astral-sh/setup-uv@v5
+
+      - name: Install clang-tidy
+        run: |
+          apt-get update && apt-get install -y clang-tidy-19
+          ln -sf /usr/bin/clang-tidy-19 /usr/bin/clang-tidy
+          ln -sf /usr/bin/clang++-19 /usr/bin/clang++
+          ln -sf /usr/bin/clang-19 /usr/bin/clang
+
+      - name: Install dependencies
+        uses: ./.github/actions/dependencies
+        with:
+          compiler: clang++
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Configure
+        run: >
+          cmake -B build -S .
+          --preset=gitlab-ci-clangtidy
+
+      - name: Run codegen
+        run: cmake --build build --target ActsCodegen
+
+      - name: Analyze (PR - changed files only)
+        if: github.event_name == 'pull_request'
+        run: >
+          uv run CI/clang_tidy/run_clang_tidy_pr.py
+          analyze build fixes.yml --base-ref "origin/${{ github.base_ref }}"
+
+      - name: Analyze (push - all files)
+        if: github.event_name == 'push'
+        run: >
+          uv run CI/clang_tidy/run_clang_tidy_pr.py
+          analyze build fixes.yml --all
+
+      - name: Upload fixes
+        if: always()
+        uses: actions/upload-artifact@v6
+        with:
+          name: clang-tidy-fixes
+          path: fixes.yml
+
+      - name: Annotate
+        run: >
+          uv run CI/clang_tidy/run_clang_tidy_pr.py
+          annotate fixes.yml
+
   build_performance:
     runs-on: ubuntu-latest
     container: ghcr.io/acts-project/ubuntu2404:83

.github/workflows/builds.yml

@@ -409,7 +409,7 @@ jobs:
 
       - name: Build
         id: build
-        uses: addnab/docker-run-action@v3
+        uses: eic/docker-run-action@v3
         continue-on-error: true
         with:
           image: "ghcr.io/eic/eic_ci_without_acts:nightly"

.github/workflows/update-pip-requirements.yml

@@ -16,16 +16,19 @@ jobs:
       # This branch will receive updates each time the workflow runs
       # It doesn't matter if it's deleted when merged, it'll be re-created
       BRANCH_NAME: auto-dependency-upgrades
+      PYTHON_VERSION: "3.14"
     steps:
       - uses: actions/checkout@v6
 
       - name: Set up Python
         uses: actions/setup-python@v6
         with:
-          python-version: 3.14
+          python-version: ${{ env.PYTHON_VERSION }}
 
-      - name: Install pip-tools
-        run: pip install pip-tools
+      - name: Install uv
+        run: |
+          python -m pip install -U pip
+          python -m pip install -U uv
 
       - name: Compile all requirements.txt
         run: |
@@ -38,7 +41,8 @@ jobs:
             Examples/Scripts
           )
           for folder in "${folder_list[@]}"; do
-            pip-compile "${folder}/requirements.in" > "${folder}/requirements.txt"
+            rm "${folder}/requirements.txt"
+            uv pip compile --python-version "$PYTHON_VERSION" "${folder}/requirements.in" -o "${folder}/requirements.txt"
           done
 
       - name: Detect changes
@@ -68,7 +72,7 @@ jobs:
           PR=$(gh pr list --head $BRANCH_NAME --json number -q '.[0].number')
           if [ -z $PR ]; then
             gh pr create \
-            --head $BRANCH_NAME \
+            --head "$BRANCH_NAME" \
             --title "chore: automated python requirements upgrades" \
             --body "Full log: https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}"
           else

.gitlab-ci.yml

@@ -43,62 +43,6 @@ variables:
     - rm -rf spack/.git spack/opt spack/var/spack/cache
     - find spack -type f -name "*.pyc" -delete || true
 
-clang_tidy:
-  stage: build
-  image: registry.cern.ch/ghcr.io/acts-project/ubuntu2404:83
-  tags:
-    - large
-  artifacts:
-    paths:
-      - src/clang-tidy/
-    when: always
-    expire_in: 1 week
-
-  cache:
-   - !reference [.spack_cache, cache]
-
-  script:
-    - git clone $CLONE_URL src
-    - cd src
-    - git checkout $HEAD_SHA
-    - >
-        apt-get update
-        && apt-get install -y clang-tidy-18
-        && ln -sf /usr/bin/clang++-18 /usr/bin/clang++
-        && ln -sf /usr/bin/clang-18 /usr/bin/clang
-        && ln -sf /usr/bin/clang-tidy-18 /usr/bin/clang-tidy
-
-    - |
-      CI/dependencies/setup.sh -c clang++ -e .env
-      source .env
-
-    - >
-        cmake -B build -S .
-        --preset=gitlab-ci-clangtidy
-        -DCMAKE_CXX_COMPILER=clang++
-        -DCMAKE_C_COMPILER=clang
-
-    # Main clang-tidy run during cmake compilation
-    - CI/clang_tidy/run_clang_tidy.sh clang-tidy build
-
-    # Install dependencies for processing scripts
-    - python3 -m pip install -r CI/clang_tidy/requirements.txt
-
-    # Parse the main clang-tidy run
-    - >
-        CI/clang_tidy/parse_clang_tidy.py
-        clang-tidy/clang-tidy.log
-        clang-tidy/clang-tidy.json
-        --exclude "*thirdparty*"
-        --exclude "*ActsPodioEdm*"
-        --exclude "*build/_deps/*"
-
-    # Check the combined report against the defined limits
-    - CI/clang_tidy/check_clang_tidy.py --report clang-tidy/clang-tidy.json --config CI/clang_tidy/limits.yml
-
-  after_script:
-   - !reference [.spack_cleanup, after_script]
-
 build_gnn_cpu:
   stage: build
   image: registry.cern.ch/ghcr.io/acts-project/ubuntu2404_gnn:83

Alignment/include/ActsAlignment/Kernel/Alignment.hpp

@@ -94,14 +94,14 @@ struct AlignmentOptions {
 ///
 struct AlignmentResult {
   // The change of alignment parameters
-  Acts::ActsDynamicVector deltaAlignmentParameters;
+  Acts::DynamicVector deltaAlignmentParameters;
 
   // The aligned parameters for detector elements
   std::unordered_map<Acts::SurfacePlacementBase*, Acts::Transform3>
       alignedParameters;
 
   // The covariance of alignment parameters
-  Acts::ActsDynamicMatrix alignmentCovariance;
+  Acts::DynamicMatrix alignmentCovariance;
 
   // The average chi2/ndf (ndf is the measurement dim)
   double averageChi2ONdf = std::numeric_limits<double>::max();

Alignment/include/ActsAlignment/Kernel/Alignment.ipp

@@ -78,11 +78,10 @@ void ActsAlignment::Alignment<fitter_t>::calculateAlignmentParameters(
   alignResult.alignmentDof =
       alignResult.idxedAlignSurfaces.size() * Acts::eAlignmentSize;
   // Initialize derivative of chi2 w.r.t. alignment parameters for all tracks
-  Acts::ActsDynamicVector sumChi2Derivative =
-      Acts::ActsDynamicVector::Zero(alignResult.alignmentDof);
-  Acts::ActsDynamicMatrix sumChi2SecondDerivative =
-      Acts::ActsDynamicMatrix::Zero(alignResult.alignmentDof,
-                                    alignResult.alignmentDof);
+  Acts::DynamicVector sumChi2Derivative =
+      Acts::DynamicVector::Zero(alignResult.alignmentDof);
+  Acts::DynamicMatrix sumChi2SecondDerivative = Acts::DynamicMatrix::Zero(
+      alignResult.alignmentDof, alignResult.alignmentDof);
   // Copy the fit options
   fit_options_t fitOptionsWithRefSurface = fitOptions;
   // Calculate contribution to chi2 derivatives from all input trajectories
@@ -134,18 +133,17 @@ void ActsAlignment::Alignment<fitter_t>::calculateAlignmentParameters(
   // calculate the covariance of the alignment parameters)
   // @TODO: use more stable method for solving the inverse
   std::size_t alignDof = alignResult.alignmentDof;
-  Acts::ActsDynamicMatrix sumChi2SecondDerivativeInverse =
-      Acts::ActsDynamicMatrix::Zero(alignDof, alignDof);
+  Acts::DynamicMatrix sumChi2SecondDerivativeInverse =
+      Acts::DynamicMatrix::Zero(alignDof, alignDof);
   sumChi2SecondDerivativeInverse = sumChi2SecondDerivative.inverse();
   if (sumChi2SecondDerivativeInverse.hasNaN()) {
     ACTS_DEBUG("Chi2 second derivative inverse has NaN");
   }
 
   // Initialize the alignment results
-  alignResult.deltaAlignmentParameters =
-      Acts::ActsDynamicVector::Zero(alignDof);
+  alignResult.deltaAlignmentParameters = Acts::DynamicVector::Zero(alignDof);
   alignResult.alignmentCovariance =
-      Acts::ActsDynamicMatrix::Zero(alignDof, alignDof);
+      Acts::DynamicMatrix::Zero(alignDof, alignDof);
   // Solve the linear equation to get alignment parameters change
   alignResult.deltaAlignmentParameters =
       -sumChi2SecondDerivative.fullPivLu().solve(sumChi2Derivative);

Alignment/include/ActsAlignment/Kernel/detail/AlignmentEngine.hpp

@@ -35,31 +35,31 @@ struct TrackAlignmentState {
   std::size_t alignmentDof = 0;
 
   // The measurements covariance
-  Acts::ActsDynamicMatrix measurementCovariance;
+  Acts::DynamicMatrix measurementCovariance;
 
   // The track parameters covariance
-  Acts::ActsDynamicMatrix trackParametersCovariance;
+  Acts::DynamicMatrix trackParametersCovariance;
 
   // The projection matrix
-  Acts::ActsDynamicMatrix projectionMatrix;
+  Acts::DynamicMatrix projectionMatrix;
 
   // The residual
-  Acts::ActsDynamicVector residual;
+  Acts::DynamicVector residual;
 
   // The covariance of residual
-  Acts::ActsDynamicMatrix residualCovariance;
+  Acts::DynamicMatrix residualCovariance;
 
   // The chi2
   double chi2 = 0;
 
   // The derivative of residual w.r.t. alignment parameters
-  Acts::ActsDynamicMatrix alignmentToResidualDerivative;
+  Acts::DynamicMatrix alignmentToResidualDerivative;
 
   // The derivative of chi2 w.r.t. alignment parameters
-  Acts::ActsDynamicVector alignmentToChi2Derivative;
+  Acts::DynamicVector alignmentToChi2Derivative;
 
   // The second derivative of chi2 w.r.t. alignment parameters
-  Acts::ActsDynamicMatrix alignmentToChi2SecondDerivative;
+  Acts::DynamicMatrix alignmentToChi2SecondDerivative;
 
   // The alignable surfaces on the track and their indices in both the global
   // alignable surfaces pool and those relevant with this track
@@ -104,7 +104,7 @@ template <typename traj_t, typename parameters_t = Acts::BoundTrackParameters>
 TrackAlignmentState trackAlignmentState(
     const Acts::GeometryContext& gctx, const traj_t& multiTraj,
     Acts::TrackIndexType entryIndex,
-    const std::pair<Acts::ActsDynamicMatrix,
+    const std::pair<Acts::DynamicMatrix,
                     std::unordered_map<std::size_t, std::size_t>>&
         globalTrackParamsCov,
     const std::unordered_map<const Acts::Surface*, std::size_t>&
@@ -170,20 +170,19 @@ TrackAlignmentState trackAlignmentState(
   // Initialize the alignment matrices with components from the measurement
   // states
   // The measurement covariance
-  alignState.measurementCovariance = Acts::ActsDynamicMatrix::Zero(
+  alignState.measurementCovariance = Acts::DynamicMatrix::Zero(
       alignState.measurementDim, alignState.measurementDim);
   // The bound parameters to measurement projection matrix
-  alignState.projectionMatrix = Acts::ActsDynamicMatrix::Zero(
+  alignState.projectionMatrix = Acts::DynamicMatrix::Zero(
       alignState.measurementDim, alignState.trackParametersDim);
   // The derivative of residual w.r.t. alignment parameters
-  alignState.alignmentToResidualDerivative = Acts::ActsDynamicMatrix::Zero(
+  alignState.alignmentToResidualDerivative = Acts::DynamicMatrix::Zero(
       alignState.measurementDim, alignState.alignmentDof);
   // The track parameters covariance
-  alignState.trackParametersCovariance = Acts::ActsDynamicMatrix::Zero(
+  alignState.trackParametersCovariance = Acts::DynamicMatrix::Zero(
       alignState.trackParametersDim, alignState.trackParametersDim);
   // The residual
-  alignState.residual =
-      Acts::ActsDynamicVector::Zero(alignState.measurementDim);
+  alignState.residual = Acts::DynamicVector::Zero(alignState.measurementDim);
 
   // Unpack global track parameters covariance and the starting row/column for
   // all smoothed states.
@@ -203,13 +202,13 @@ TrackAlignmentState trackAlignmentState(
     iMeasurement -= measdim;
     iParams -= Acts::eBoundSize;
     // (a) Get and fill the measurement covariance matrix
-    const Acts::ActsDynamicMatrix measCovariance =
+    const Acts::DynamicMatrix measCovariance =
         state.effectiveCalibratedCovariance();
     alignState.measurementCovariance.block(iMeasurement, iMeasurement, measdim,
                                            measdim) = measCovariance;
 
     // (b) Get and fill the bound parameters to measurement projection matrix
-    const Acts::ActsDynamicMatrix H =
+    const Acts::DynamicMatrix H =
         state.projectorSubspaceHelper().fullProjector().topLeftCorner(
             measdim, Acts::eBoundSize);
     alignState.projectionMatrix.block(iMeasurement, iParams, measdim,
@@ -277,11 +276,11 @@ TrackAlignmentState trackAlignmentState(
                     alignState.measurementCovariance.inverse() *
                     alignState.residual;
   alignState.alignmentToChi2Derivative =
-      Acts::ActsDynamicVector::Zero(alignState.alignmentDof);
-  alignState.alignmentToChi2SecondDerivative = Acts::ActsDynamicMatrix::Zero(
+      Acts::DynamicVector::Zero(alignState.alignmentDof);
+  alignState.alignmentToChi2SecondDerivative = Acts::DynamicMatrix::Zero(
       alignState.alignmentDof, alignState.alignmentDof);
   // The covariance of residual
-  alignState.residualCovariance = Acts::ActsDynamicMatrix::Zero(
+  alignState.residualCovariance = Acts::DynamicMatrix::Zero(
       alignState.measurementDim, alignState.measurementDim);
   alignState.residualCovariance = alignState.measurementCovariance -
                                   alignState.projectionMatrix *

CI/clang_tidy/filter.yml

@@ -0,0 +1,27 @@
+# Exclusion filters for CI/clang_tidy/annotate.py
+#
+# Diagnostics whose file path matches any of these regexes are dropped
+# and do NOT gate the job or produce annotations.
+
+exclude_path_regexes:
+  # Third-party / vendored code
+  - (^|/)thirdparty/
+  - (^|/)third_party/
+
+  # Generated PODIO EDM
+  - ActsPodioEdm
+  - EDM4hep/generated
+
+  # Generated ROOT dictionaries
+  - Dict.cxx$
+
+  # Build-tree dependencies fetched by CMake
+  - (^|/)build/_deps/
+
+  # System / external headers that may leak into diagnostics
+  - ^/usr/
+  - ^/opt/
+  - ^/cvmfs/
+
+# Severity for GitHub annotations ("error" or "warning")
+severity: error