Merge staging into main

.github/workflows/_reusable-tests.yml

@@ -95,27 +95,27 @@ jobs:
           COV_FLAG="-DWITH_CODE_COV=ON"
         fi
         cmake -B build -S . -DCMAKE_BUILD_TYPE=Release -DBUILD_TESTS=ON ${COV_FLAG}
-        cmake --build build
+        cmake --build build -j $(nproc)
 
     - name: Configure and compile MNE-CPP (MacOS)
       if: matrix.os == 'macos-26'
       run: |
         cmake -B build -S . -DCMAKE_BUILD_TYPE=Release -DBUILD_TESTS=ON
-        cmake --build build
+        cmake --build build -j $(sysctl -n hw.logicalcpu)
 
     - name: Configure and compile MNE-CPP (Windows)
       if: matrix.os == 'windows-2025'
       run: |
         cmd.exe /c "call `"C:\Program Files\Microsoft Visual Studio\2022\Enterprise\VC\Auxiliary\Build\vcvars64.bat`" && set > %temp%\vcvars.txt"
         Get-Content "$env:temp\vcvars.txt" | Foreach-Object { if ($_ -match "^(.*?)=(.*)$") { Set-Content "env:\$($matches[1])" $matches[2] } }
         cmake -B build -S . -DCMAKE_BUILD_TYPE=Release -DBUILD_TESTS=ON
-        cmake --build build --config Release
+        cmake --build build --config Release --parallel
 
     # ── Run tests ──────────────────────────────────────────────────────────
     - name: Run tests (Linux)
       if: matrix.os == 'ubuntu-24.04'
       env:
-        QTEST_FUNCTION_TIMEOUT: 900000
+        QTEST_FUNCTION_TIMEOUT: ${{ inputs.with_code_coverage && 1800000 || 900000 }}
         QT_QPA_PLATFORM: offscreen
         MNE_DATA: ~/mne_data
       run: |
@@ -150,26 +150,33 @@ jobs:
         token: ${{ secrets.CODECOV_TOKEN }}
 
     # ── Coverage: threshold & regression check (staging branch) ────────────
-    - name: Install lcov
+    - name: Install fastcov
       if: matrix.os == 'ubuntu-24.04' && inputs.with_code_coverage && !inputs.upload_codecov
-      run: sudo apt-get install -y -qq lcov
+      run: pip install fastcov
 
-    - name: Generate lcov report
+    - name: Generate coverage report (fastcov)
       id: lcov
       if: matrix.os == 'ubuntu-24.04' && inputs.with_code_coverage && !inputs.upload_codecov
       run: |
-        lcov --capture --directory build \
-             --output-file coverage.info \
-             --ignore-errors mismatch 2>/dev/null || true
-        # Remove external/test code from the report
-        lcov --remove coverage.info \
-             '*/src/external/*' '*/src/examples/*' '*/src/testframes/*' \
-             '/usr/*' '*/Qt/*' \
-             --output-file coverage_filtered.info \
-             --ignore-errors unused 2>/dev/null || true
-        # Extract total line coverage percentage
-        COVERAGE=$(lcov --summary coverage_filtered.info 2>&1 \
-                   | grep -oP 'lines\.*:\s*\K[0-9]+(\.[0-9]+)?' || echo "0")
+        echo "=== Coverage diagnostics ==="
+        echo "gcno files: $(find build -name '*.gcno' 2>/dev/null | wc -l)"
+        echo "gcda files: $(find build -name '*.gcda' 2>/dev/null | wc -l)"
+        # Collect coverage data with fastcov (10-100x faster than lcov)
+        fastcov -d build -o coverage.json
+        # Full report in lcov format
+        fastcov -C coverage.json --lcov -o coverage.info
+        # Filtered report: only MNE-CPP libraries (no apps, tests, examples, external, Qt, Eigen)
+        fastcov -C coverage.json --lcov -o coverage_filtered.info \
+             --include src/libraries/ \
+             --exclude /usr Qt eigen
+        # Extract total line coverage percentage from lcov format
+        TOTAL_LINES=$(grep -c "^DA:" coverage_filtered.info 2>/dev/null || echo "0")
+        HIT_LINES=$(grep "^DA:" coverage_filtered.info | awk -F, '$2 > 0' | wc -l 2>/dev/null || echo "0")
+        if [ "$TOTAL_LINES" -gt 0 ]; then
+          COVERAGE=$(awk "BEGIN {printf \"%.2f\", $HIT_LINES * 100.0 / $TOTAL_LINES}")
+        else
+          COVERAGE="0"
+        fi
         echo "Total line coverage: ${COVERAGE}%"
         echo "coverage=${COVERAGE}" >> "$GITHUB_OUTPUT"
 
@@ -206,16 +213,23 @@ jobs:
           fi
         fi
 
-        # --- Regression check ---
+        # --- Regression check (allow up to 2% drop) ---
         if [ "$CHECK_REGRESSION" = "true" ] && [ -f .coverage-baseline ]; then
           PREVIOUS=$(cat .coverage-baseline)
           echo "  Previous coverage: ${PREVIOUS}%"
-          if (( $(echo "${CURRENT} < ${PREVIOUS}" | bc -l) )); then
+          ALLOWED_DROP="2.0"
+          LIMIT=$(echo "${PREVIOUS} - ${ALLOWED_DROP}" | bc -l)
+          if (( $(echo "${CURRENT} < ${LIMIT}" | bc -l) )); then
             DELTA=$(echo "${PREVIOUS} - ${CURRENT}" | bc -l)
-            echo "  ❌ FAIL: Coverage dropped by ${DELTA}% (${PREVIOUS}% → ${CURRENT}%)"
+            echo "  ❌ FAIL: Coverage dropped by ${DELTA}% (${PREVIOUS}% → ${CURRENT}%), exceeds ${ALLOWED_DROP}% tolerance"
             FAILED=true
           else
-            echo "  ✅ PASS: Coverage did not regress"
+            if (( $(echo "${CURRENT} < ${PREVIOUS}" | bc -l) )); then
+              DELTA=$(echo "${PREVIOUS} - ${CURRENT}" | bc -l)
+              echo "  ⚠️  WARN: Coverage dropped by ${DELTA}% (within ${ALLOWED_DROP}% tolerance)"
+            else
+              echo "  ✅ PASS: Coverage did not regress"
+            fi
           fi
         fi
 

.github/workflows/main.yml

@@ -22,7 +22,7 @@
 #
 # Branch model:  Feature → Staging → Main
 # ═══════════════════════════════════════════════════════════════════════════
-name: Main
+name: Release
 
 on:
   push:
@@ -84,13 +84,11 @@ jobs:
 
     - name: Deploy qch to GitHub Release
       if: startsWith(github.ref, 'refs/tags/')
-      uses: svenstaro/upload-release-action@v2
-      with:
-        repo_token: ${{ secrets.GH_PAT || secrets.GITHUB_TOKEN }}
-        file: doc/doxygen/qt-creator_doc/mne-cpp.qch
-        asset_name: mne-cpp-${{ github.ref_name }}-doc-qtcreator.qch
-        tag: ${{ github.ref }}
-        overwrite: true
+      env:
+        GH_TOKEN: ${{ secrets.GH_PAT || secrets.GITHUB_TOKEN }}
+      run: |
+        cp doc/doxygen/qt-creator_doc/mne-cpp.qch "mne-cpp-${{ github.ref_name }}-doc-qtcreator.qch"
+        gh release upload "${{ github.ref_name }}" "mne-cpp-${{ github.ref_name }}-doc-qtcreator.qch" --clobber
 
     - name: Deploy Doxygen to GitHub Pages (production)
       env:
@@ -294,13 +292,11 @@ jobs:
         tar cfz mne-cpp-wasm.tar.gz -C out/wasm .
 
     - name: Upload WASM to GitHub Release
-      uses: svenstaro/upload-release-action@v2
-      with:
-        repo_token: ${{ secrets.GH_PAT || secrets.GITHUB_TOKEN }}
-        file: mne-cpp-wasm.tar.gz
-        asset_name: mne-cpp-${{ github.ref_name }}-wasm.tar.gz
-        tag: ${{ github.ref }}
-        overwrite: true
+      env:
+        GH_TOKEN: ${{ secrets.GH_PAT || secrets.GITHUB_TOKEN }}
+      run: |
+        cp mne-cpp-wasm.tar.gz "mne-cpp-${{ github.ref_name }}-wasm.tar.gz"
+        gh release upload "${{ github.ref_name }}" "mne-cpp-${{ github.ref_name }}-wasm.tar.gz" --clobber
 
     - name: Deploy WASM to mne-cpp/wasm repository
       env:

.github/workflows/release-installer.yml

@@ -205,14 +205,11 @@ jobs:
         ls -lh MNE-CPP-*.run
 
     - name: Upload installer
-      uses: svenstaro/upload-release-action@v2
-      with:
-        repo_token: ${{ secrets.GH_PAT || secrets.GITHUB_TOKEN }}
-        file: MNE-CPP-*-Linux.run
-        file_glob: true
-        asset_name: ${{ steps.tag.outputs.asset_prefix }}-linux-installer-x86_64.run
-        tag: ${{ steps.tag.outputs.tag }}
-        overwrite: true
+      env:
+        GH_TOKEN: ${{ secrets.GH_PAT || secrets.GITHUB_TOKEN }}
+      run: |
+        cp MNE-CPP-*-Linux.run "${{ steps.tag.outputs.asset_prefix }}-linux-installer-x86_64.run"
+        gh release upload "${{ steps.tag.outputs.tag }}" "${{ steps.tag.outputs.asset_prefix }}-linux-installer-x86_64.run" --clobber
 
   # =========================================================================
   # macOS Installer  (.dmg)
@@ -540,14 +537,11 @@ jobs:
         security delete-keychain "$KEYCHAIN_PATH" 2>/dev/null || true
 
     - name: Upload installer
-      uses: svenstaro/upload-release-action@v2
-      with:
-        repo_token: ${{ secrets.GH_PAT || secrets.GITHUB_TOKEN }}
-        file: MNE-CPP-*-Darwin.dmg
-        file_glob: true
-        asset_name: ${{ steps.tag.outputs.asset_prefix }}-macos-installer-arm64.dmg
-        tag: ${{ steps.tag.outputs.tag }}
-        overwrite: true
+      env:
+        GH_TOKEN: ${{ secrets.GH_PAT || secrets.GITHUB_TOKEN }}
+      run: |
+        cp MNE-CPP-*-Darwin.dmg "${{ 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
 
   # =========================================================================
   # Windows Installer  (.exe)
@@ -734,11 +728,9 @@ jobs:
         Get-ChildItem MNE-CPP-*-win64.exe
 
     - name: Upload installer
-      uses: svenstaro/upload-release-action@v2
-      with:
-        repo_token: ${{ secrets.GH_PAT || secrets.GITHUB_TOKEN }}
-        file: MNE-CPP-*-win64.exe
-        file_glob: true
-        asset_name: ${{ steps.tag.outputs.asset_prefix }}-windows-installer-x86_64.exe
-        tag: ${{ steps.tag.outputs.tag }}
-        overwrite: true
+      shell: bash
+      env:
+        GH_TOKEN: ${{ secrets.GH_PAT || secrets.GITHUB_TOKEN }}
+      run: |
+        cp MNE-CPP-*-win64.exe "${{ steps.tag.outputs.asset_prefix }}-windows-installer-x86_64.exe"
+        gh release upload "${{ steps.tag.outputs.tag }}" "${{ steps.tag.outputs.asset_prefix }}-windows-installer-x86_64.exe" --clobber

.github/workflows/release-linux.yml

@@ -58,13 +58,11 @@ jobs:
         ./tools/deploy.bat dynamic pack
     - name: Upload release binaries
       if: steps.release-info.outputs.should_upload == 'true'
-      uses: svenstaro/upload-release-action@v2
-      with:
-        repo_token: ${{ secrets.GH_PAT || secrets.GITHUB_TOKEN }}
-        file: mne-cpp-linux-dynamic-x86_64.tar.gz
-        asset_name: ${{ steps.release-info.outputs.prefix }}-linux-dynamic-x86_64.tar.gz
-        tag: ${{ steps.release-info.outputs.tag }}
-        overwrite: true
+      env:
+        GH_TOKEN: ${{ secrets.GH_PAT || secrets.GITHUB_TOKEN }}
+      run: |
+        cp mne-cpp-linux-dynamic-x86_64.tar.gz "${{ steps.release-info.outputs.prefix }}-linux-dynamic-x86_64.tar.gz"
+        gh release upload "${{ steps.release-info.outputs.tag }}" "${{ steps.release-info.outputs.prefix }}-linux-dynamic-x86_64.tar.gz" --clobber
 
 
   LinuxStatic:
@@ -141,10 +139,8 @@ jobs:
         ./tools/deploy.bat static pack
     - name: Upload release binaries
       if: steps.release-info.outputs.should_upload == 'true'
-      uses: svenstaro/upload-release-action@v2
-      with:
-        repo_token: ${{ secrets.GH_PAT || secrets.GITHUB_TOKEN }}
-        file: mne-cpp-linux-static-x86_64.tar.gz
-        asset_name: ${{ steps.release-info.outputs.prefix }}-linux-static-x86_64.tar.gz
-        tag: ${{ steps.release-info.outputs.tag }}
-        overwrite: true
+      env:
+        GH_TOKEN: ${{ secrets.GH_PAT || secrets.GITHUB_TOKEN }}
+      run: |
+        cp mne-cpp-linux-static-x86_64.tar.gz "${{ steps.release-info.outputs.prefix }}-linux-static-x86_64.tar.gz"
+        gh release upload "${{ steps.release-info.outputs.tag }}" "${{ steps.release-info.outputs.prefix }}-linux-static-x86_64.tar.gz" --clobber

.github/workflows/release-macos.yml

@@ -77,13 +77,11 @@ jobs:
         fi
     - name: Upload release binaries
       if: steps.release-info.outputs.should_upload == 'true'
-      uses: svenstaro/upload-release-action@v2
-      with:
-        repo_token: ${{ secrets.GH_PAT || secrets.GITHUB_TOKEN }}
-        file: mne-cpp-macos-dynamic-arm64.tar.gz
-        asset_name: ${{ steps.release-info.outputs.prefix }}-macos-dynamic-arm64.tar.gz
-        tag: ${{ steps.release-info.outputs.tag }}
-        overwrite: true
+      env:
+        GH_TOKEN: ${{ secrets.GH_PAT || secrets.GITHUB_TOKEN }}
+      run: |
+        cp mne-cpp-macos-dynamic-arm64.tar.gz "${{ steps.release-info.outputs.prefix }}-macos-dynamic-arm64.tar.gz"
+        gh release upload "${{ steps.release-info.outputs.tag }}" "${{ steps.release-info.outputs.prefix }}-macos-dynamic-arm64.tar.gz" --clobber
 
 
   MacOSStatic:
@@ -159,10 +157,8 @@ jobs:
         ./tools/deploy.bat static pack
     - name: Upload release binaries
       if: steps.release-info.outputs.should_upload == 'true'
-      uses: svenstaro/upload-release-action@v2
-      with:
-        repo_token: ${{ secrets.GH_PAT || secrets.GITHUB_TOKEN }}
-        file: mne-cpp-macos-static-arm64.tar.gz
-        asset_name: ${{ steps.release-info.outputs.prefix }}-macos-static-arm64.tar.gz
-        tag: ${{ steps.release-info.outputs.tag }}
-        overwrite: true
+      env:
+        GH_TOKEN: ${{ secrets.GH_PAT || secrets.GITHUB_TOKEN }}
+      run: |
+        cp mne-cpp-macos-static-arm64.tar.gz "${{ 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

.github/workflows/release-windows.yml

@@ -72,13 +72,12 @@ jobs:
         }
     - name: Upload release binaries
       if: steps.release-info.outputs.should_upload == 'true'
-      uses: svenstaro/upload-release-action@v2
-      with:
-        repo_token: ${{ secrets.GH_PAT || secrets.GITHUB_TOKEN }}
-        file: mne-cpp-windows-dynamic-x86_64.zip
-        asset_name: ${{ steps.release-info.outputs.prefix }}-windows-dynamic-x86_64.zip
-        tag: ${{ steps.release-info.outputs.tag }}
-        overwrite: true
+      shell: bash
+      env:
+        GH_TOKEN: ${{ secrets.GH_PAT || secrets.GITHUB_TOKEN }}
+      run: |
+        cp mne-cpp-windows-dynamic-x86_64.zip "${{ steps.release-info.outputs.prefix }}-windows-dynamic-x86_64.zip"
+        gh release upload "${{ steps.release-info.outputs.tag }}" "${{ steps.release-info.outputs.prefix }}-windows-dynamic-x86_64.zip" --clobber
 
 
   WinStatic:
@@ -156,10 +155,9 @@ jobs:
         ./tools/deploy.bat static pack
     - name: Upload release binaries
       if: steps.release-info.outputs.should_upload == 'true'
-      uses: svenstaro/upload-release-action@v2
-      with:
-        repo_token: ${{ secrets.GH_PAT || secrets.GITHUB_TOKEN }}
-        file: mne-cpp-windows-static-x86_64.zip
-        asset_name: ${{ steps.release-info.outputs.prefix }}-windows-static-x86_64.zip
-        tag: ${{ steps.release-info.outputs.tag }}
-        overwrite: true
+      shell: bash
+      env:
+        GH_TOKEN: ${{ secrets.GH_PAT || secrets.GITHUB_TOKEN }}
+      run: |
+        cp mne-cpp-windows-static-x86_64.zip "${{ steps.release-info.outputs.prefix }}-windows-static-x86_64.zip"
+        gh release upload "${{ steps.release-info.outputs.tag }}" "${{ steps.release-info.outputs.prefix }}-windows-static-x86_64.zip" --clobber

.github/workflows/staging.yml

@@ -33,9 +33,9 @@ concurrency:
   cancel-in-progress: true
 
 env:
-  # Minimum acceptable line coverage percentage.
+  # Minimum acceptable line coverage percentage (libraries only).
   # The pipeline will FAIL if coverage drops below this.
-  COVERAGE_THRESHOLD: 50
+  COVERAGE_THRESHOLD: 35
 
 jobs:
 
@@ -100,13 +100,15 @@ jobs:
       qt_version: '6.10.2'
 
   # ── Tests with coverage threshold & regression checks ────────────────────
+  # Add [skip-coverage] to your commit message to skip coverage analysis.
+  # Coverage is only collected on Ubuntu; macOS/Windows always run without it.
   Tests:
     uses: ./.github/workflows/_reusable-tests.yml
     with:
-      with_code_coverage: true
+      with_code_coverage: ${{ !contains(github.event.head_commit.message, '[skip-coverage]') }}
       upload_codecov: false
-      coverage_threshold: 50
-      fail_on_coverage_regression: true
+      coverage_threshold: ${{ contains(github.event.head_commit.message, '[skip-coverage]') && 0 || 35 }}
+      fail_on_coverage_regression: ${{ !contains(github.event.head_commit.message, '[skip-coverage]') }}
 
   # ── Doxygen API documentation (dev) ──────────────────────────────────────
   Doxygen:
@@ -131,13 +133,11 @@ jobs:
         doxygen mne-cpp_doxyfile
 
     - name: Deploy qch to dev_build release
-      uses: svenstaro/upload-release-action@v2
-      with:
-        repo_token: ${{ secrets.GH_PAT || secrets.GITHUB_TOKEN }}
-        file: doc/doxygen/qt-creator_doc/mne-cpp.qch
-        asset_name: mne-cpp-dev-doc-qtcreator.qch
-        tag: dev_build
-        overwrite: true
+      env:
+        GH_TOKEN: ${{ secrets.GH_PAT || secrets.GITHUB_TOKEN }}
+      run: |
+        cp doc/doxygen/qt-creator_doc/mne-cpp.qch mne-cpp-dev-doc-qtcreator.qch
+        gh release upload dev_build mne-cpp-dev-doc-qtcreator.qch --clobber
 
     - name: Deploy Doxygen to GitHub Pages (dev subdirectory)
       env:
@@ -262,10 +262,8 @@ jobs:
         tar cfz mne-cpp-wasm.tar.gz -C out/wasm .
 
     - name: Upload WASM to dev_build release
-      uses: svenstaro/upload-release-action@v2
-      with:
-        repo_token: ${{ secrets.GH_PAT || secrets.GITHUB_TOKEN }}
-        file: mne-cpp-wasm.tar.gz
-        asset_name: mne-cpp-dev-wasm.tar.gz
-        tag: dev_build
-        overwrite: true
+      env:
+        GH_TOKEN: ${{ secrets.GH_PAT || secrets.GITHUB_TOKEN }}
+      run: |
+        cp mne-cpp-wasm.tar.gz mne-cpp-dev-wasm.tar.gz
+        gh release upload dev_build mne-cpp-dev-wasm.tar.gz --clobber

README.md

@@ -3,7 +3,7 @@
 </p>
 <p align="center">
 <a href="https://github.com/mne-tools/mne-cpp/actions/workflows/main.yml" target="_blank">
-    <img src="https://github.com/mne-tools/mne-cpp/actions/workflows/main.yml/badge.svg?branch=main" alt="Main">
+    <img src="https://github.com/mne-tools/mne-cpp/actions/workflows/main.yml/badge.svg?branch=main" alt="Release">
 </a>
 <a href="https://github.com/mne-tools/mne-cpp/actions/workflows/staging.yml" target="_blank">
     <img src="https://github.com/mne-tools/mne-cpp/actions/workflows/staging.yml/badge.svg?branch=staging" alt="Staging">