fix(ci): fix build failures from CI run #283

- mne_inverse_pipeline: rewrite to use MnaProject::pipeline/MnaStep API
  instead of nonexistent MnaProject::graph; use qInstallMessageHandler
  instead of MNELogger::setupFromEnvironment
- annotationmodel.cpp: remove duplicate 'entries' variable redefinitions
  in saveAnnotationCsv and saveAnnotationTxt
- sliceobject.h: add Eigen/Geometry include for Vector3d::cross()
- Remove macOS Intel CI jobs (MacOSDynamicIntel, MacOSStaticIntel,
  macOSSDKIntel, MacOSInstallerIntel) — macos-13 runners deprecated

Author: chdinh

.github/workflows/release-installer.yml

@@ -236,156 +236,6 @@ jobs:
         cp MNE-CPP-*-Darwin.dmg "${{ steps.tag.outputs.asset_prefix }}-macos-installer-arm64.dmg"
         gh release upload "${{ steps.tag.outputs.tag }}" "${{ steps.tag.outputs.asset_prefix }}-macos-installer-arm64.dmg" --clobber
 
-  MacOSInstallerIntel:
-    runs-on: macos-13
-
-    steps:
-    - name: Clone repository
-      uses: actions/checkout@v5
-
-    - name: Install Qt Installer Framework
-      env:
-        GH_TOKEN: ${{ secrets.GH_PAT || secrets.GITHUB_TOKEN }}
-      run: |
-        ./scripts/ci/download_toolchain.sh \
-          --kind ifw \
-          --version "${{ env.QIF_VERSION }}" \
-          --output-dir "$RUNNER_TEMP/ifw"
-
-    - name: Determine release tag
-      id: tag
-      shell: bash
-      run: |
-        if [[ "$GITHUB_REF" == refs/tags/* ]]; then
-          TAG="${GITHUB_REF#refs/tags/}"
-          echo "tag=${TAG}" >> "$GITHUB_OUTPUT"
-          echo "asset_prefix=mne-cpp-${TAG#v}" >> "$GITHUB_OUTPUT"
-        elif [[ "$GITHUB_REF" == "refs/heads/main" ]]; then
-          echo "tag=latest" >> "$GITHUB_OUTPUT"
-          echo "asset_prefix=mne-cpp-latest" >> "$GITHUB_OUTPUT"
-        else
-          echo "tag=dev_build" >> "$GITHUB_OUTPUT"
-          echo "asset_prefix=mne-cpp-dev" >> "$GITHUB_OUTPUT"
-        fi
-
-    - name: Prepare installer payload
-      shell: bash
-      env:
-        GH_TOKEN: ${{ secrets.GH_PAT || secrets.GITHUB_TOKEN }}
-      run: |
-        ./scripts/deploy/prepare_bootstrap_installer.sh \
-          --release-tag "${{ steps.tag.outputs.tag }}" \
-          --asset-prefix "${{ steps.tag.outputs.asset_prefix }}" \
-          --platform macos \
-          --arch x86_64 \
-          --output-dir build_installer/staging
-
-    - name: Import Apple Developer ID certificate
-      if: env.APPLE_DEVELOPER_ID_P12 != ''
-      env:
-        APPLE_DEVELOPER_ID_P12: ${{ secrets.APPLE_DEVELOPER_ID_P12 }}
-        APPLE_DEVELOPER_ID_PASSWORD: ${{ secrets.APPLE_DEVELOPER_ID_PASSWORD }}
-      run: |
-        KEYCHAIN_PATH="$RUNNER_TEMP/signing.keychain-db"
-        KEYCHAIN_PASSWORD="$(openssl rand -hex 16)"
-
-        security create-keychain -p "$KEYCHAIN_PASSWORD" "$KEYCHAIN_PATH"
-        security set-keychain-settings -lut 21600 "$KEYCHAIN_PATH"
-        security unlock-keychain -p "$KEYCHAIN_PASSWORD" "$KEYCHAIN_PATH"
-
-        echo "$APPLE_DEVELOPER_ID_P12" | base64 --decode > "$RUNNER_TEMP/certificate.p12"
-        security import "$RUNNER_TEMP/certificate.p12" \
-          -k "$KEYCHAIN_PATH" \
-          -P "$APPLE_DEVELOPER_ID_PASSWORD" \
-          -T /usr/bin/codesign \
-          -T /usr/bin/productsign
-
-        security set-key-partition-list -S apple-tool:,apple:,codesign: \
-          -s -k "$KEYCHAIN_PASSWORD" "$KEYCHAIN_PATH"
-
-        security list-keychains -d user -s "$KEYCHAIN_PATH" $(security list-keychains -d user | tr -d '"')
-
-        IDENTITY=$(security find-identity -v -p codesigning "$KEYCHAIN_PATH" | head -1 | awk -F'"' '{print $2}')
-        echo "CODESIGN_IDENTITY=$IDENTITY" >> $GITHUB_ENV
-        echo "KEYCHAIN_PATH=$KEYCHAIN_PATH" >> $GITHUB_ENV
-        echo "Signing identity: $IDENTITY"
-
-    - name: Build installer with binarycreator
-      run: |
-        binarycreator \
-          -c build_installer/staging/config/config.xml \
-          -p build_installer/staging/packages \
-          MNE-CPP-${{ env.MNE_CPP_VERSION }}-Darwin
-
-    - name: Codesign installer app
-      if: env.CODESIGN_IDENTITY != ''
-      run: |
-        codesign --force --deep --options runtime --timestamp \
-          --sign "$CODESIGN_IDENTITY" \
-          "MNE-CPP-${{ env.MNE_CPP_VERSION }}-Darwin.app"
-        codesign --verify --verbose "MNE-CPP-${{ env.MNE_CPP_VERSION }}-Darwin.app"
-
-    - name: Free up disk space before DMG creation
-      run: |
-        echo "=== Disk usage before cleanup ==="
-        df -h
-        sudo rm -rf /usr/local/share/gtk-doc /usr/local/Cellar \
-          /usr/local/lib/node_modules /usr/share/dotnet \
-          /opt/hostedtoolcache /Users/runner/Library/Caches/* 2>/dev/null || true
-        echo "=== Disk usage after cleanup ==="
-        df -h
-
-    - name: Create DMG
-      run: |
-        hdiutil create \
-          -volname "MNE-CPP ${{ env.MNE_CPP_VERSION }}" \
-          -srcfolder "MNE-CPP-${{ env.MNE_CPP_VERSION }}-Darwin.app" \
-          -ov -format UDZO \
-          "MNE-CPP-${{ env.MNE_CPP_VERSION }}-Darwin.dmg"
-        ls -lh MNE-CPP-*-Darwin.dmg
-
-    - name: Codesign DMG
-      if: env.CODESIGN_IDENTITY != ''
-      run: |
-        codesign --force --timestamp \
-          --sign "$CODESIGN_IDENTITY" \
-          "MNE-CPP-${{ env.MNE_CPP_VERSION }}-Darwin.dmg"
-        codesign --verify --verbose "MNE-CPP-${{ env.MNE_CPP_VERSION }}-Darwin.dmg"
-
-    - name: Notarize DMG
-      if: env.CODESIGN_IDENTITY != ''
-      env:
-        APPLE_ID: ${{ secrets.APPLE_ID }}
-        APPLE_APP_PASSWORD: ${{ secrets.APPLE_APP_PASSWORD }}
-        APPLE_TEAM_ID: ${{ secrets.APPLE_TEAM_ID }}
-      run: |
-        xcrun notarytool submit \
-          "MNE-CPP-${{ env.MNE_CPP_VERSION }}-Darwin.dmg" \
-          --apple-id "$APPLE_ID" \
-          --password "$APPLE_APP_PASSWORD" \
-          --team-id "$APPLE_TEAM_ID" \
-          --wait \
-          --timeout 30m
-
-        xcrun stapler staple "MNE-CPP-${{ env.MNE_CPP_VERSION }}-Darwin.dmg"
-
-        spctl --assess --type open --context context:primary-signature \
-          "MNE-CPP-${{ env.MNE_CPP_VERSION }}-Darwin.dmg" \
-          && echo "Notarization verified successfully" \
-          || echo "Warning: spctl check returned non-zero (may be expected on CI)"
-
-    - name: Cleanup keychain
-      if: always() && env.KEYCHAIN_PATH != ''
-      run: |
-        security delete-keychain "$KEYCHAIN_PATH" 2>/dev/null || true
-
-    - name: Upload installer
-      env:
-        GH_TOKEN: ${{ secrets.GH_PAT || secrets.GITHUB_TOKEN }}
-      run: |
-        cp MNE-CPP-*-Darwin.dmg "${{ steps.tag.outputs.asset_prefix }}-macos-installer-x86_64.dmg"
-        gh release upload "${{ steps.tag.outputs.tag }}" "${{ steps.tag.outputs.asset_prefix }}-macos-installer-x86_64.dmg" --clobber
-
   WindowsInstaller:
     runs-on: windows-2025
 

.github/workflows/release-macos.yml

@@ -204,173 +204,3 @@ jobs:
       run: |
         cp mne-cpp-macos-static-arm64.tar.gz "${{ steps.release-info.outputs.prefix }}-macos-static-arm64.tar.gz"
         gh release upload "${{ steps.release-info.outputs.tag }}" "${{ steps.release-info.outputs.prefix }}-macos-static-arm64.tar.gz" --clobber
-
-
-  MacOSDynamicIntel:
-    runs-on: macos-13
-
-    steps:
-    - name: Clone repository
-      uses: actions/checkout@v5
-
-    - name: Determine release info
-      id: release-info
-      run: |
-        if [[ "$GITHUB_REF" == refs/tags/* ]]; then
-          TAG="${GITHUB_REF#refs/tags/}"
-          echo "tag=${TAG}" >> "$GITHUB_OUTPUT"
-          echo "prefix=mne-cpp-${TAG#v}" >> "$GITHUB_OUTPUT"
-          echo "should_upload=true" >> "$GITHUB_OUTPUT"
-        elif [[ "$GITHUB_REF" == "refs/heads/main" ]]; then
-          echo "tag=latest" >> "$GITHUB_OUTPUT"
-          echo "prefix=mne-cpp-latest" >> "$GITHUB_OUTPUT"
-          echo "should_upload=true" >> "$GITHUB_OUTPUT"
-        elif [[ "$GITHUB_REF" == "refs/heads/staging" ]]; then
-          echo "tag=dev_build" >> "$GITHUB_OUTPUT"
-          echo "prefix=mne-cpp-dev" >> "$GITHUB_OUTPUT"
-          echo "should_upload=true" >> "$GITHUB_OUTPUT"
-        else
-          echo "tag=none" >> "$GITHUB_OUTPUT"
-          echo "prefix=mne-cpp-local" >> "$GITHUB_OUTPUT"
-          echo "should_upload=false" >> "$GITHUB_OUTPUT"
-        fi
-    - name: Install Python 3.10 version
-      uses: actions/setup-python@v6
-      with:
-        python-version: '3.10'
-        architecture: 'x64'
-    - name: Download Qt toolchain
-      env:
-        GH_TOKEN: ${{ secrets.GH_PAT || secrets.GITHUB_TOKEN }}
-      run: |
-        ./scripts/ci/download_toolchain.sh \
-          --kind qt \
-          --version "6.11.0" \
-          --linkage dynamic \
-          --output-dir "$RUNNER_TEMP/qt"
-    - name: Download Eigen package
-      env:
-        GH_TOKEN: ${{ secrets.GH_PAT || secrets.GITHUB_TOKEN }}
-      run: |
-        ./scripts/ci/download_toolchain.sh \
-          --kind eigen \
-          --version "5.0.1" \
-          --output-dir "$GITHUB_WORKSPACE/src/external/eigen"
-    - name: Download ONNX Runtime
-      env:
-        GH_TOKEN: ${{ secrets.GH_PAT || secrets.GITHUB_TOKEN }}
-      run: |
-        ./scripts/ci/download_toolchain.sh \
-          --kind onnxruntime \
-          --version "1.21.0" \
-          --output-dir "$GITHUB_WORKSPACE/src/external/onnxruntime"
-    - name: Configure and compile MNE-CPP
-      run: |
-        ./scripts/build/build_project.sh -- -DUSE_ONNXRUNTIME=ON
-    - name: Deploy binaries (MacOS)
-      run: |
-        ./scripts/deploy/deploy.bat dynamic pack
-    - name: Upload release binaries
-      if: steps.release-info.outputs.should_upload == 'true'
-      env:
-        GH_TOKEN: ${{ secrets.GH_PAT || secrets.GITHUB_TOKEN }}
-      run: |
-        cp mne-cpp-macos-dynamic-x86_64.tar.gz "${{ steps.release-info.outputs.prefix }}-macos-dynamic-x86_64.tar.gz"
-        gh release upload "${{ steps.release-info.outputs.tag }}" "${{ steps.release-info.outputs.prefix }}-macos-dynamic-x86_64.tar.gz" --clobber
-
-
-  MacOSStaticIntel:
-    runs-on: macos-13
-
-    steps:
-    - name: Clone repository
-      uses: actions/checkout@v5
-
-    - name: Determine release info
-      id: release-info
-      run: |
-        if [[ "$GITHUB_REF" == refs/tags/* ]]; then
-          TAG="${GITHUB_REF#refs/tags/}"
-          echo "tag=${TAG}" >> "$GITHUB_OUTPUT"
-          echo "prefix=mne-cpp-${TAG#v}" >> "$GITHUB_OUTPUT"
-          echo "should_upload=true" >> "$GITHUB_OUTPUT"
-        elif [[ "$GITHUB_REF" == "refs/heads/main" ]]; then
-          echo "tag=latest" >> "$GITHUB_OUTPUT"
-          echo "prefix=mne-cpp-latest" >> "$GITHUB_OUTPUT"
-          echo "should_upload=true" >> "$GITHUB_OUTPUT"
-        elif [[ "$GITHUB_REF" == "refs/heads/staging" ]]; then
-          echo "tag=dev_build" >> "$GITHUB_OUTPUT"
-          echo "prefix=mne-cpp-dev" >> "$GITHUB_OUTPUT"
-          echo "should_upload=true" >> "$GITHUB_OUTPUT"
-        else
-          echo "tag=none" >> "$GITHUB_OUTPUT"
-          echo "prefix=mne-cpp-local" >> "$GITHUB_OUTPUT"
-          echo "should_upload=false" >> "$GITHUB_OUTPUT"
-        fi
-    - name: Install Python 3.10 version
-      uses: actions/setup-python@v6
-      with:
-        python-version: '3.10'
-        architecture: 'x64'
-    - name: Install dependencies
-      run: |
-        brew list ninja >/dev/null 2>&1 || brew install ninja
-    - name: Download Eigen package
-      env:
-        GH_TOKEN: ${{ secrets.GH_PAT || secrets.GITHUB_TOKEN }}
-      run: |
-        ./scripts/ci/download_toolchain.sh \
-          --kind eigen \
-          --version "5.0.1" \
-          --output-dir "$GITHUB_WORKSPACE/src/external/eigen"
-    - name: Download ONNX Runtime
-      env:
-        GH_TOKEN: ${{ secrets.GH_PAT || secrets.GITHUB_TOKEN }}
-      run: |
-        ./scripts/ci/download_toolchain.sh \
-          --kind onnxruntime \
-          --version "1.21.0" \
-          --output-dir "$GITHUB_WORKSPACE/src/external/onnxruntime"
-    - name: Cache static Qt binaries
-      id: cache-qt-static
-      uses: actions/cache@v5
-      with:
-        path: Qt6_static
-        key: qt-6.11.0-static-macos-x86_64
-    - name: Download pre-built static Qt
-      id: download-qt-static
-      if: steps.cache-qt-static.outputs.cache-hit != 'true'
-      continue-on-error: true
-      env:
-        GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      run: |
-        gh release download qt_binaries -p "qt6_6110_static_binaries_macos.tar.gz" -D /tmp
-        mkdir -p Qt6_static
-        tar xfz /tmp/qt6_6110_static_binaries_macos.tar.gz -C Qt6_static
-    - name: Build static Qt from source
-      if: steps.cache-qt-static.outputs.cache-hit != 'true' && steps.download-qt-static.outcome != 'success'
-      run: |
-        cd ..
-        git clone https://code.qt.io/qt/qt5.git -b v6.11.0
-        cd qt5
-        ./init-repository -f --module-subset=qtbase,qtsvg,qtshadertools
-        cd ..
-        mkdir qt6_shadow
-        cd qt6_shadow
-        ../qt5/configure -static -release -prefix "$GITHUB_WORKSPACE/Qt6_static" -skip webengine -nomake tests -nomake examples -no-dbus -no-ssl -no-pch -opensource -confirm-license -- -DCMAKE_BUILD_TYPE=Release
-        cmake --build . --parallel $(sysctl -n hw.ncpu)
-        cmake --install .
-    - name: Configure and compile MNE-CPP (static)
-      run: |
-        export CMAKE_PREFIX_PATH=$GITHUB_WORKSPACE/Qt6_static
-        ./scripts/build/build_project.sh static -- -DUSE_ONNXRUNTIME=ON
-    - name: Deploy binaries (MacOS)
-      run: |
-        ./scripts/deploy/deploy.bat static pack
-    - name: Upload release binaries
-      if: steps.release-info.outputs.should_upload == 'true'
-      env:
-        GH_TOKEN: ${{ secrets.GH_PAT || secrets.GITHUB_TOKEN }}
-      run: |
-        cp mne-cpp-macos-static-x86_64.tar.gz "${{ steps.release-info.outputs.prefix }}-macos-static-x86_64.tar.gz"
-        gh release upload "${{ steps.release-info.outputs.tag }}" "${{ steps.release-info.outputs.prefix }}-macos-static-x86_64.tar.gz" --clobber

.github/workflows/release-sdk.yml

@@ -139,65 +139,6 @@ jobs:
         name: mne-cpp-sdk-macos-arm64
         path: ${{ runner.temp }}/mne-cpp-sdk-${{ env.MNE_CPP_VERSION }}-macos-arm64.tar.gz
 
-  macOSSDKIntel:
-    runs-on: macos-13
-    steps:
-    - name: Clone repository
-      uses: actions/checkout@v5
-
-    - name: Install Python 3.10
-      uses: actions/setup-python@v6
-      with:
-        python-version: '3.10'
-
-    - name: Download Qt toolchain
-      env:
-        GH_TOKEN: ${{ secrets.GH_PAT || secrets.GITHUB_TOKEN }}
-      run: |
-        ./scripts/ci/download_toolchain.sh \
-          --kind qt \
-          --version "6.11.0" \
-          --linkage dynamic \
-          --output-dir "$RUNNER_TEMP/qt"
-
-    - name: Download Eigen package
-      env:
-        GH_TOKEN: ${{ secrets.GH_PAT || secrets.GITHUB_TOKEN }}
-      run: |
-        ./scripts/ci/download_toolchain.sh \
-          --kind eigen \
-          --output-dir "$RUNNER_TEMP/eigen"
-
-    - name: Configure
-      run: |
-        cmake -S . -B build \
-          -DCMAKE_PREFIX_PATH="$RUNNER_TEMP/qt" \
-          -DCMAKE_INSTALL_PREFIX="$RUNNER_TEMP/sdk" \
-          -DEIGEN3_DIR="$RUNNER_TEMP/eigen" \
-          -DCMAKE_BUILD_TYPE=Release
-
-    - name: Build
-      run: cmake --build build --parallel $(sysctl -n hw.ncpu)
-
-    - name: Install SDK
-      run: cmake --install build --component sdk
-
-    - name: Copy examples
-      run: |
-        mkdir -p "$RUNNER_TEMP/sdk/share/mne-cpp/examples"
-        cp -r resources/examples/*.mna "$RUNNER_TEMP/sdk/share/mne-cpp/examples/" 2>/dev/null || true
-
-    - name: Package
-      run: |
-        cd "$RUNNER_TEMP"
-        tar czf "mne-cpp-sdk-${MNE_CPP_VERSION}-macos-x86_64.tar.gz" sdk/
-
-    - name: Upload artifact
-      uses: actions/upload-artifact@v4
-      with:
-        name: mne-cpp-sdk-macos-x86_64
-        path: ${{ runner.temp }}/mne-cpp-sdk-${{ env.MNE_CPP_VERSION }}-macos-x86_64.tar.gz
-
   WindowsSDK:
     runs-on: windows-2025
     steps: