From 539a5137256d2ecc567165e025ec2b272a5623d4 Mon Sep 17 00:00:00 2001
From: Daljit Singh <129752264+daljit46@users.noreply.github.com>
Date: Wed, 24 Jan 2024 15:13:50 +0000
Subject: [PATCH 1/2] Add coverage workflow

---
 .github/workflows/coverage.yml | 76 ++++++++++++++++++++++++++++++++++
 1 file changed, 76 insertions(+)
 create mode 100644 .github/workflows/coverage.yml

diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml
new file mode 100644
index 0000000000..7d971cbf14
--- /dev/null
+++ b/.github/workflows/coverage.yml
@@ -0,0 +1,76 @@
+
+name: Weekly Coverage Analysis
+
+on:
+  workflow_dispatch:
+  # Run this every Sunday at midnight
+  schedule:
+    - cron: "0 0 * * 0"
+
+jobs:
+  linux-clang-build:
+    runs-on: ubuntu-latest
+
+    env:
+      SCCACHE_GHA_ENABLED: "true"
+      SCCACHE_CACHE_SIZE: "2G"
+
+    steps:
+    - uses: actions/checkout@v1
+      with:
+        submodules: true
+        ref: dev
+
+    - name: install dependencies
+      run: |
+         sudo apt-get update
+         sudo apt-get install gcovr libqt5opengl5-dev libqt5svg5-dev libglvnd-dev libeigen3-dev zlib1g-dev libfftw3-dev ninja-build
+    - name: Run sccache-cache
+      uses: mozilla-actions/sccache-action@v0.0.3
+
+    - name: Get CMake
+      uses: lukka/get-cmake@latest
+      with:
+        cmakeVersion: '3.16.3'
+
+    - name: Print CMake version
+      run: cmake --version
+
+    - name: configure
+      run: >
+        cmake
+        -B build
+        -G Ninja
+        -D CMAKE_BUILD_TYPE=Debug
+        -D MRTRIX_BUILD_TESTS=ON
+        -D CMAKE_CXX_FLAGS="--coverage"
+
+    - name: build
+      run: cmake --build build
+
+    - name: Unit tests
+      run: cd build && ctest -R unit --output-on-failure
+
+    - name: Binary tests
+      run: cd build && ctest -R bin --output-on-failure
+
+    - name: Report coverage
+      run: >
+        gcovr ${{ github.workspace }}/build
+        --root ${{ github.workspace }}
+        --exclude ${{ github.workspace }}/build
+    
+    - name: Generate html report
+      run: >
+        mkdir report &&
+        gcovr ${{ github.workspace }}/build
+        --root ${{ github.workspace }}
+        --exclude ${{ github.workspace }}/build
+        --html --html-details
+        -o report/coverage.html
+    
+    - name: Upload html report
+      uses: actions/upload-artifact@v2
+      with:
+        name: mrtrix3-coverage-report
+        path: ${{ github.workspace }}/report
\ No newline at end of file

From 4a0e77d3fc781ae7b29cb4c5c7c458d9139c82a8 Mon Sep 17 00:00:00 2001
From: Daljit Singh <129752264+daljit46@users.noreply.github.com>
Date: Thu, 25 Jan 2024 13:53:08 +0000
Subject: [PATCH 2/2] REMOVE BEFORE MERGE: trigger on pull request

---
 .github/workflows/coverage.yml | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml
index 7d971cbf14..c32705be38 100644
--- a/.github/workflows/coverage.yml
+++ b/.github/workflows/coverage.yml
@@ -6,7 +6,9 @@ on:
   # Run this every Sunday at midnight
   schedule:
     - cron: "0 0 * * 0"
-
+  # IMPORTANT: remove this before merging
+  pull_request:
+    
 jobs:
   linux-clang-build:
     runs-on: ubuntu-latest
@@ -24,7 +26,8 @@ jobs:
     - name: install dependencies
       run: |
          sudo apt-get update
-         sudo apt-get install gcovr libqt5opengl5-dev libqt5svg5-dev libglvnd-dev libeigen3-dev zlib1g-dev libfftw3-dev ninja-build
+         sudo apt-get install gcovr qt6-base-dev libglvnd-dev libeigen3-dev zlib1g-dev libfftw3-dev ninja-build
+
     - name: Run sccache-cache
       uses: mozilla-actions/sccache-action@v0.0.3
 
@@ -73,4 +76,4 @@ jobs:
       uses: actions/upload-artifact@v2
       with:
         name: mrtrix3-coverage-report
-        path: ${{ github.workspace }}/report
\ No newline at end of file
+        path: ${{ github.workspace }}/report