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Merge branch 'dev' of https://github.com/e0404/matRad into dev_BEDpro…
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amitantony committed Feb 8, 2024
2 parents 14a50ab + c8caf34 commit 44082de
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#!/usr/bin/env bash

sudo chmod +x .travis/runtests.sh
sudo chmod +x .github/runtests.sh
sudo chmod +x MCsquare/bin/MCsquare_linux

mv optimization/optimizer/ipopt.m optimization/optimizer/ipopt.m.bak
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3 changes: 2 additions & 1 deletion .travis/runtests.sh → .github/runtests.sh
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## Make sure some failures are detected by the CI runners
function exitIfError {
# pass "$?" as argument: i.e. the exit status of the last call
if [ "$1" -ne 0 ]; then
# currently octave 6 can finish with a segfault when the program is closed due to some bug, for now we try to ignore it
if [ "$1" -ne 0 ] && [ "$1" -ne 139 ]; then
exit $1;
fi
}
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51 changes: 34 additions & 17 deletions .github/workflows/tests.yml
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# This is a basic workflow to help you get started with Actions
name: Testing
name: Tests
# Controls when the action will run.
on: [push, pull_request, workflow_dispatch]
jobs:
test-matlab: #Matlab test Job
test-matlab-stable: #Matlab test Job for supported Release
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2 # Checks-out repository under $GITHUB_WORKSPACE
- uses: actions/checkout@v3 # Checks-out repository under $GITHUB_WORKSPACE
# Install MATLAB
- name: Install MATLAB
uses: matlab-actions/setup-matlab@v1
uses: matlab-actions/setup-matlab@v1
with:
release: R2022b
# Runs test command
- name: Run Tests
uses: matlab-actions/run-command@v1
with:
command: cd unitTest; matRad_runTests
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
with:
release: latest
# Runs test command
- name: Run Tests
uses: matlab-actions/run-command@v1
with:
command: cd unitTest; matRad_runTests
test-octave: #Octave test Job
runs-on: ubuntu-20.04 # We use Ubuntu-20.04 because it has Octave 5.2
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@v2 # Checks-out repository under $GITHUB_WORKSPACE
- uses: actions/checkout@v3 # Checks-out repository under $GITHUB_WORKSPACE
- name: Install OCTAVE
run: |
sudo apt-get update
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 .travis/before_install_linux.sh
sudo .travis/before_install_linux.sh
- name: Run Tests
uses: GabrielBB/xvfb-action@v1 #For Headless tests
with:
run: .travis/runtests.sh octave-cli
- name: Upload Logs if failure
uses: actions/upload-artifact@v2
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()
with:
name: Test Log
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5 changes: 4 additions & 1 deletion AUTHORS.txt
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List of all matRad developers that contributed code (alphabetical)

* Nelly Abbani
* Nabe Al-Hasnawi
* Mark Bangert
* Amit Ben Antony Bennan
* Lucas Burigo
Expand All @@ -14,6 +16,7 @@ List of all matRad developers that contributed code (alphabetical)
* Cindy Hermann
* Noa Homolka
* Fabian Jäger
* Fernando Hueso-González
* Navid Khaledi
* Thomas Klinge
* Jeremias Kunz
Expand All @@ -31,4 +34,4 @@ List of all matRad developers that contributed code (alphabetical)
* Jona Welsch
* Hans-Peter Wieser
* Johanna Winter
* Tong Xu
* Tong Xu
123 changes: 123 additions & 0 deletions CITATION.cff
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cff-version: 1.2.0
message: "If you use matRad, consider citing it and the corresponding research paper"
authors:
- family-names: "Ackermann"
given-names: "Benjamin"
- family-names: "Bangert"
given-names: "Mark"
- family-names: "Bennan"
given-names: "Amit Ben Antony"
- family-names: "Burigo"
given-names: "Lucas"
- family-names: "Cabal"
given-names: "Gonzalo"
- family-names: "Cisternas"
given-names: "Eduardo"
- family-names: "Charton"
given-names: "Louis"
- family-names: "Christiansen"
given-names: "Eric"
- family-names: "Ecker"
given-names: "Swantje"
- family-names: "Ellerbrock"
given-names: "Malte"
- family-names: "Gabryś"
given-names: "Hubert"
- family-names: "Handrack"
given-names: "Josefine"
- family-names: "Heath"
given-names: "Emily"
- family-names: "Hermann"
given-names: "Cindy"
- family-names: "Homolka"
given-names: "Noa"
- family-names: "Jäkel"
given-names: "Oliver"
- family-names: "Klinge"
given-names: "Thomas"
- family-names: "Mairani"
given-names: "Andrea"
- family-names: "Mescher"
given-names: "Hennig"
- family-names: "Müller"
given-names: "Lucas-Raphael"
- family-names: "Neishabouri"
given-names: "Ahmad"
- family-names: "Palkowitsch"
given-names: "Martina"
- family-names: "Parodi"
given-names: "Katia"
- family-names: "Pezzano"
given-names: "Giuseppe"
- family-names: "Ramirez"
given-names: "Daniel"
- family-names: "Stadler"
given-names: "Alexander"
- family-names: "Ulrich"
given-names: "Silke"
- family-names: "Wahl"
given-names: "Niklas"
orcid: "https://orcid.org/0000-0002-1451-223X"
- family-names: "Welsch"
given-names: "Jona"
- family-names: "Wieser"
given-names: "Hans-Peter"
- family-names: "Winter"
given-names: "Johanna"
- family-names: "Xu"
given-names: "Tong"

title: "matRad"
version: 2.10.1
doi: 10.5281/zenodo.3879616
date-released: 2020-06-05
url: "http://www.matRad.org"
location: "Heidelberg"
organization: "Deutsches Krebsforschungszentrum"
preferred-citation:
type: article
authors:
- family-names: "Wieser"
given-names: "Hans-Peter"
- family-names: "Cisternas"
given-names: "Eduardo"
- family-names: "Wahl"
given-names: "Niklas"
orcid: "https://orcid.org/0000-0002-1451-223X"
- family-names: "Ulrich"
given-names: "Silke"
- family-names: "Stadler"
given-names: "Alexander"
- family-names: "Mescher"
given-names: "Hennig"
- family-names: "Müller"
given-names: "Lucas-Raphael"
- family-names: "Klinge"
given-names: "Thomas"
- family-names: "Gabryś"
given-names: "Hubert"
- family-names: "Burigo"
given-names: "Lucas"
- family-names: "Mairani"
given-names: "Andrea"
- family-names: "Ecker"
given-names: "Swantje"
- family-names: "Ackermann"
given-names: "Benjamin"
- family-names: "Ellerbrock"
given-names: "Malte"
- family-names: "Parodi"
given-names: "Katia"
- family-names: "Jäkel"
given-names: "Oliver"
- family-names: "Bangert"
given-names: "Mark"

doi: 10.1002/mp.12251
journal: "Medical Physics"
start: 2556
end: 2568
title: "Development of the open-source dose calculation and optimization toolkit matRad"
issue: 6
volume: 46
year: 2017
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