Merge pull request #783 from e0404/rc/v3

Update to release v3 "Cleve"

.github/PULL_REQUEST_TEMPLATE/release_checklist_pull_request.md

@@ -3,14 +3,14 @@ Version of new Release and Type (new major release, minor release, patch release
 
 ### Release Checklist
 
-- [ ] Version number changed in matRad_getVersion
-- [ ] Adapted Changelog.txt
+- [ ] Adapted Changelog.md
 - [ ] All required mex files compiled
 - [ ] Third Party libraries / scripts up to date
 - [ ] Standalone(s) generated and tested
 - [ ] Wiki adapted
 - [ ] Optional changes to README.md
 - [ ] Check license information
+- [ ] Version number changed in matRad_getVersion
 
 ### References
 Any references regarding new functionality etc.

.github/actions/test-matlab/action.yml

@@ -0,0 +1,42 @@
+name: 'Matlab Test'
+author: 'e0404'
+description: 'Runs a Matlab Test for a given version'
+
+inputs:
+  matlab-version:
+    description: Matlab Version, e.g. R2022b
+    required: true
+
+runs:
+  using: 'composite'
+  steps:       
+    # Install MATLAB
+    - name: Install MATLAB
+      uses: matlab-actions/setup-matlab@v2
+      with:
+        release: ${{ inputs.matlab-version }}
+        products: Image_Processing_Toolbox Parallel_Computing_Toolbox Optimization_Toolbox
+
+    # Runs test command
+    - name: Run Tests
+      uses: matlab-actions/run-command@v2
+      with:
+        command: matRad_runTests('test',true);
+
+    - name: Upload Test Results
+      if: always()
+      uses: actions/upload-artifact@v4
+      with:
+        name: test-results-matlab-${{ inputs.matlab-version }}
+        path: |
+          testresults.xml
+          coverage.xml
+          coverage.json
+
+    
+    - name: Publish Test Results
+      uses: test-summary/action@v2
+      if: success() || failure()
+      with:
+        paths: testresults.xml
+        # check_name: "${{ github.job }}"

.github/actions/test-octave/action.yml

@@ -0,0 +1,39 @@
+name: 'Octave Test'
+author: 'e0404'
+description: 'Runs an Octave test. Uses the version in the respective Ubuntu-OS'
+
+runs:
+  using: 'composite'
+  steps:
+    - name: Install OCTAVE
+      shell: bash
+      run: | 
+        sudo apt update
+        sudo apt-get install -y gdb gfortran fonts-freefont-otf gnuplot-x11 libgdcm-dev octave liboctave-dev
+    - name: Prepare Test Environment
+      shell: bash
+      run: |
+        sudo chmod +x .github/before_install_linux.sh
+        sudo .github/before_install_linux.sh
+    - name: Run Tests
+      shell: bash 
+      run: xvfb-run -a .github/runtests.sh octave-cli
+      # uses: GabrielBB/xvfb-action@v1 #For Headless tests
+      # with:
+      #   run: .github/runtests.sh octave-cli
+    - name: Upload Test Results
+      if: always()
+      uses: actions/upload-artifact@v4
+      with:
+        name: test-results-octave
+        path: testresults.xml
+
+    - name: Publish Test Results
+      # uses: EnricoMi/publish-unit-test-result-action@v2
+      uses: test-summary/action@v2
+      if: success() || failure()
+      with:
+        # files: |
+        #   testresults.xml
+        paths: testresults.xml
+        # check_name: "${{ github.job }}"

.github/before_install_linux.sh

@@ -1,9 +1,10 @@
 #!/usr/bin/env bash
 
 sudo chmod +x .github/runtests.sh
-sudo chmod +x MCsquare/bin/MCsquare_linux
+sudo chmod +x thirdParty/MCsquare/bin/MCsquare_linux
 
-mv optimization/optimizer/ipopt.m optimization/optimizer/ipopt.m.bak
+mv matRad/optimization/optimizer/ipopt.m optimization/optimizer/ipopt.m.bak
 
 octave --no-gui --eval "pkg install -forge dicom"
 octave --no-gui --eval "pkg install -forge nan"
+octave --no-gui --eval "pkg install -forge image"

.github/codecov.yml

@@ -0,0 +1,2 @@
+coverage:
+  range: 50...75

.github/runtests.bat

@@ -33,7 +33,7 @@ set CONTINUOUS_INTEGRATION=true
 set CI=true
 
 REM Actually run the test suite
-cd unitTest
+cd test
 set TESTDIR="%cd%"
 REM also CD in MATLAB/Octave to make sure that startup files
 REM cannot play any role in setting the path

.github/runtests.sh

@@ -39,11 +39,8 @@ export CONTINUOUS_INTEGRATION=true
 export CI=true
 
 ## Actually run the test suite
-cd unitTest
-TESTDIR=`pwd`
 # also CD in MATLAB/Octave to make sure that startup files
 # cannot play any role in setting the path
-${Runner} ${Switches} "cd('${TESTDIR}'); matRad_runTests" > ../runtests.log #2> ../runtests.err put stdout to log, but let it print error messages
+${Runner} ${Switches} "matRad_runTests('test');" > ../runtests.log #2> ../runtests.err put stdout to log, but let it print error messages
 exitIfError $?
-cd ..
 

.github/workflows/coverage-report.yml

@@ -0,0 +1,66 @@
+name: Coverage Report
+
+permissions:
+    checks: write
+    pull-requests: write
+    actions: read
+    contents: read
+
+
+on:
+    workflow_call:
+
+jobs:
+    coverage_report:
+        runs-on: ubuntu-latest
+
+        steps:
+
+            - name: Download Coverage Artifact
+              uses: actions/download-artifact@v4
+              with:
+                  name: test-results-matlab-R2022b
+                  path: coverage
+
+            - name: Upload to Coveralls
+              uses: coverallsapp/github-action@v2
+              with:
+                  github-token: ${{ secrets.GITHUB_TOKEN }}
+                  file: coverage/coverage.json
+                  format: coveralls
+
+            - name: Upload to Codecov
+              uses: codecov/codecov-action@v4
+              with:
+                  token: ${{ secrets.CODECOV_TOKEN }}
+                  file: coverage/coverage.xml
+                  fail_ci_if_error: false
+
+            - name: Publish Coverage Report
+              uses: irongut/[email protected]
+              with:
+                  filename: coverage/coverage.xml
+                  badge: true
+                  fail_below_min: false
+                  format: markdown
+                  hide_branch_rate: true
+                  hide_complexity: true
+                  indicators: true
+                  output: both
+                  thresholds: '50 70'
+
+            - name: Attach Job Summary
+              uses: actions/github-script@v7
+              with:
+                script: |
+                  const fs = require('fs');
+                  const markdownContent = fs.readFileSync('code-coverage-results.md', 'utf8');
+                  core.summary.addRaw(markdownContent);
+                  core.summary.write();
+                        
+            - name: Add Coverage PR Comment
+              uses: marocchino/sticky-pull-request-comment@v2
+              if: github.event_name == 'pull_request'
+              with:
+                  recreate: true
+                  path: code-coverage-results.md

.github/workflows/test-results.yml

@@ -0,0 +1,40 @@
+name: Test Report
+
+permissions:
+    checks: write
+    pull-requests: write
+
+on:
+    workflow_call:
+
+jobs:
+    test_report:
+        runs-on: ubuntu-latest
+
+        steps:
+
+            - name: Download Results for Matlab R2022b
+              uses: actions/download-artifact@v4
+              with:
+                  name: test-results-matlab-R2022b
+                  path: test-results/matlab-R2022b
+
+            - name: Download Results for Matlab Latest
+              uses: actions/download-artifact@v4
+              with:
+                  name: test-results-matlab-latest
+                  path: test-results/matlab-latest
+
+            - name: Download Results for Octave
+              uses: actions/download-artifact@v4
+              with:
+                  name: test-results-octave
+                  path: test-results/octave
+
+            - name: Publish Test Results
+              uses: EnricoMi/publish-unit-test-result-action@v2
+              with:
+                  files: |
+                      test-results/*/testresults.xml
+
+            

.github/workflows/tests.yml

@@ -1,57 +1,52 @@
 # This is a basic workflow to help you get started with Actions
 name: Tests
+
+permissions:
+  checks: write
+  pull-requests: write
+  actions: read
+  contents: read
+
 # Controls when the action will run. 
 on: [push, pull_request, workflow_dispatch]  
 jobs:
   test-matlab-stable: #Matlab test Job for supported Release
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3 # Checks-out repository under $GITHUB_WORKSPACE
-      # Install MATLAB
-      - name: Install MATLAB
-        uses: matlab-actions/setup-matlab@v1
+      - uses: actions/checkout@v4 # Checks-out repository under $GITHUB_WORKSPACE
         with:
-          release: R2022b
-      # Runs test command
-      - name: Run Tests
-        uses: matlab-actions/run-command@v1
+          submodules: 'true'
+      - name: Run Test
+        uses: ./.github/actions/test-matlab
         with:
-          command: cd unitTest; matRad_runTests
+          matlab-version: R2022b
+
   test-matlab-latest: #Matlab test Job for latest Matlab release
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3 # Checks-out repository under $GITHUB_WORKSPACE
-      # Install MATLAB
-      - name: Install MATLAB
-        uses: matlab-actions/setup-matlab@v1
+      - uses: actions/checkout@v4 # Checks-out repository under $GITHUB_WORKSPACE
         with:
-          release: latest
-      # Runs test command
-      - name: Run Tests
-        uses: matlab-actions/run-command@v1
+          submodules: 'true'
+      - uses: ./.github/actions/test-matlab
         with:
-          command: cd unitTest; matRad_runTests
+          matlab-version: latest
+
   test-octave-6: #Octave test Job
     runs-on: ubuntu-22.04 # We use Ubuntu-22.04 because it has Octave 6.4
     steps:
-      - uses: actions/checkout@v3 # Checks-out repository under $GITHUB_WORKSPACE
-      - name: Install OCTAVE
-        run: | 
-          sudo apt update
-          sudo apt-get install -y gdb gfortran fonts-freefont-otf gnuplot-x11 libgdcm-dev octave liboctave-dev
-      - name: Prepare Test Environment
-        run: |
-          sudo chmod +x .github/before_install_linux.sh
-          sudo .github/before_install_linux.sh
-      - name: Run Tests 
-        run: xvfb-run -a .github/runtests.sh octave-cli
-        # uses: GabrielBB/xvfb-action@v1 #For Headless tests
-        # with:
-        #   run: .github/runtests.sh octave-cli
-      - name: Upload logs if test fails
-        uses: actions/upload-artifact@v3
-        if: failure()
+      - uses: actions/checkout@v4 # Checks-out repository under $GITHUB_WORKSPACE
         with:
-          name: Test Log
-          path: runtests.log
-
+          submodules: 'true'
+      - uses: ./.github/actions/test-octave
+
+  test-report:
+    name: Collect Test Results
+    needs: [test-matlab-stable, test-matlab-latest, test-octave-6]
+    uses: ./.github/workflows/test-results.yml
+    secrets: inherit
+
+  coverage-report:
+    name: Collect Coverage Report
+    needs: [test-matlab-stable]
+    uses: ./.github/workflows/coverage-report.yml
+    secrets: inherit

.gitignore

@@ -1 +1,7 @@
-MCsquare/bin/Materials/
+thirdParty/MCsquare/bin/Materials/
+userdata/*
+testresults.xml
+coverage.xml
+coverage.json
+*.asv
+build/

.gitmodules

@@ -1,7 +1,23 @@
+[submodule "submodules/matlab2tikz"]
+	path = submodules/matlab2tikz
+	url = https://github.com/e0404/matlab2tikz.git
+	branch = dev
+[submodule "submodules/latexTable"]
+	path = submodules/latexTable
+	url = https://github.com/e0404/latexTable.git
+	branch = dev
 [submodule "submodules/MCsquare"]
 	path = submodules/MCsquare
 	url = https://github.com/e0404/MCsquare.git
 [submodule "submodules/ompMC"]
 	path = submodules/ompMC
 	url = https://github.com/e0404/ompMC
 	branch = dev_parallel
+[submodule "submodules/MOxUnit"]
+	path = submodules/MOxUnit
+    url = https://github.com/e0404/MOxUnit
+    branch = matRad
+[submodule "submodules/MOcov"]
+	path = submodules/MOcov
+	url = https://github.com/e0404/MOcov
+	branch = matRad