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Merge pull request #783 from e0404/rc/v3
Update to release v3 "Cleve"
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‎.github/PULL_REQUEST_TEMPLATE/release_checklist_pull_request.md‎

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

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

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

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

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

‎.github/before_install_linux.sh‎

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

‎.github/codecov.yml‎

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coverage:
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range: 50...75

‎.github/runtests.bat‎

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

‎.github/runtests.sh‎

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

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

‎.github/workflows/test-results.yml‎

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

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

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