Merge remote-tracking branch 'origin/master' into dev_classGUI

# Conflicts:
#	MatRad_Config.m
#	dicom/@matRad_DicomExporter/matRad_DicomExporter.m
#	dicom/matRad_scanDicomImportFolder.m
#	matRadGUI.m
#	matRad_showDVH.m
#	plotting/matRad_plotIsoDoseLines.m

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,31 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: "[BUG]"
+labels: bug
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Choose the following settings '...'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Desktop (please complete the following information):**
+ - OS: [e.g. Windows]
+ - Environment & Version [e.g. Matlab 2020b]
+ - matRad Version [e.g. 2.10.0] If developing with git, state the branch and commit ID, if possible
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: "[Feature Request] "
+labels: enhancement
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/ISSUE_TEMPLATE/i-am-contributing-to-matrad-but-need-help.md

@@ -0,0 +1,20 @@
+---
+name: I am contributing to matRad but need help
+about: If you want to contribute a piece of software to matRad but want assistance
+title: ''
+labels: enhancement, help wanted
+assignees: ''
+
+---
+
+**I want to implement and contribute the following feature to matRad:**
+Please describe what feature you want to contribute. Is it related to a question, bug report, feature request, Pull request? Please state here.
+
+**Current state of the contribution:**
+If you already have a branch, e.g., on a repository fork in your account, where you work on the contribution, please give a link here.
+
+**I have the following issues:**
+Please describe what hinders you in finalizing the contribution and where you would like to need help.
+
+**Further questions:**
+Some additional questions you might have (i.e. coding style, how to formulate the pull request, etc.).

.github/ISSUE_TEMPLATE/question-about-matrad-s-code.md

@@ -0,0 +1,17 @@
+---
+name: Question about matRad's Code
+about: How to formulate questions about matRad
+title: ''
+labels: question
+assignees: ''
+
+---
+
+**What is the question? Which file(s) does it concern?**
+A clear description of what you do not understand and which files / branch / part of matRad it concerns.
+
+**My question is related to the following inquiry:**
+Please state if your question is related to some issue (bug report, feature request, etc.) or pull request.
+
+**I have checked the following matRad Wiki pages and references:**
+A description of what you read to address your question. If you have nothing to write here, you should maybe think about reading up on some stuff before asking a question...

.github/PULL_REQUEST_TEMPLATE/bugfix_pull_request.md

@@ -0,0 +1,15 @@
+### Bug description
+Either describe the bug and how to reproduce it (see the corresponding issue template) or reference the respective issue.
+
+### Approach
+Describe why your approach fixes the described bug
+
+### Open Questions and/or Concerns
+Use a github checklists to adress any concerns like. e.g.
+- [ ] I wasn't sure about this or that variable and if I did the correct thing with it
+- [ ] I am not sure if this is compatible with the latest Matlab version
+- [ ] etc.
+This checklist then has to be checked before merge
+
+### References
+Any helpful external information (e.g. links to stackoverflow question, blogposts, etc.)

.github/PULL_REQUEST_TEMPLATE/feature_pull_request.md

@@ -0,0 +1,18 @@
+### Bug description
+Describe the new feature you want to contribute and reference respective issues if this specific enhancement was asked for.
+
+### Approach
+Describe how you implemented the feature:
+- How does my feature change matRad code?
+- Are there any new parameters associated with the feature that need to be documented? (maybe think about providing defaults in MatRad_Config)
+- Are there external dependencies (toolboxes, mex files, etc.)?
+
+### Open Questions and/or Concerns
+Use a github checklists to adress any concerns like. e.g.
+- [ ] I wasn't sure about this or that variable and if I did the correct thing with it
+- [ ] I am not sure if this is compatible with the latest Matlab version
+- [ ] etc.
+This self-defined checklist then has to be checked before merge by reviewers and yourself.
+
+### References
+Any helpful external information (e.g. links to stackoverflow question, blogposts, external software websites, etc.)

.github/PULL_REQUEST_TEMPLATE/release_checklist_pull_request.md

@@ -0,0 +1,17 @@
+### Release Version
+Version of new Release and Type (new major release, minor release, patch release)
+
+### Release Checklist
+
+- [ ] Version number changed in matRad_getVersion
+- [ ] Adapted Changelog.txt
+- [ ] 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
+
+### References
+Any references regarding new functionality etc.
+

.github/stale.yml

@@ -0,0 +1,26 @@
+# Number of days of inactivity before an issue becomes stale
+daysUntilStale: 14
+# Number of days of inactivity before a stale issue is closed
+daysUntilClose: 28
+# Issues with these labels will never be considered stale
+exemptLabels:
+  - Hotfix needed
+  - bug
+  - enhancement
+  - help wanted
+# Label to use when marking an issue as stale
+staleLabel: stale
+# Comment to post when marking an issue as stale. Set to `false` to disable
+markComment: >
+  This issue has been automatically marked as stale because it has not had
+  recent activity. It will be closed if no further activity occurs. Thank you
+  for your contributions. 
+# Comment to post when closing a stale issue. Set to `false` to disable
+closeComment: >
+  This issue has been automatically closed because it has not seen any 
+  activity in four weeks. This happens usually when the issue has already
+  been solved or it is no longer relevant. If that's not the case,
+  feel free to reopen the issue.
+
+#Only use on issues for now
+only: issues

.travis.yml

@@ -1,65 +1,102 @@
-language: cpp
-group: travis_latest
-
-matrix:
+jobs:
   include:
     # works on Precise and Trusty
-    - os: linux
+    - name: "Ubuntu Octave"
+      os: linux
+      language: cpp
+      dist: focal # 20.04 -> Octave 5.2
+      services: 
+        - xvfb
       addons:
         apt:
-          sources:
-            - ubuntu-toolchain-r-test
+          update: true
           packages:
-            - g++-7
-      env:
-        - MATRIX_EVAL="CC=gcc-7 && CXX=g++-7"
-    - os: osx
-    - os: windows
+            - gdb
+            - gfortran
+            - fonts-freefont-otf
+            - gnuplot-x11
+            - libgdcm-dev
+            - octave
+            - liboctave-dev      
+    - name: "Ubuntu Matlab"
+      os: linux
+      language: matlab
+      dist: focal
+    - name: "OSX Octave"
+      os: osx
+      language: cpp
+      addons:
+        homebrew:
+          update: true
+          packages: 
+            - llvm
+            - libomp
+            - gdcm
+            - octave
+      cache:
+        directories:
+          - $HOME/Library/Caches/Homebrew
+    - name: "Windows Octave"
+      os: windows
+      language: cpp
+      cache:
+        directories:
+          - $HOME/AppData/Local/Temp/chocolatey
+          - /C/ProgramData/chocolatey/
   allow_failures:
     - os: windows
     - os: osx
 
 before_install:
   # Linux setup
-  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then echo "Testing matRad on linux..." ; fi
-  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then eval "${MATRIX_EVAL}" ; fi
-  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo chmod +x before_install_linux.sh ; fi
-  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo ./before_install_linux.sh; fi
+  - if [[ "$TRAVIS_JOB_NAME" == "Ubuntu Octave" ]]; then echo "Testing matRad on linux with Octave..." ; fi
+  - if [[ "$TRAVIS_JOB_NAME" == "Ubuntu Octave" ]]; then sudo chmod +x .travis/before_install_linux.sh ; fi
+  - if [[ "$TRAVIS_JOB_NAME" == "Ubuntu Octave" ]]; then sudo .travis/before_install_linux.sh; fi
+
+  # Linux Matlab Setup
+  - if [[ "$TRAVIS_JOB_NAME" == "Ubuntu Matlab" ]]; then echo "Testing matRad on linux with Matlab..." ; fi
+  - if [[ "$TRAVIS_JOB_NAME" == "Ubuntu Matlab" ]]; then sudo chmod +x .travis/runtests.sh ; fi
+  - if [[ "$TRAVIS_JOB_NAME" == "Ubuntu Matlab" ]]; then sudo chmod +x MCsquare/bin/MCsquare_linux ; fi
 
   # OSX setup
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then echo "Testing matRad on Mac OSX..." ; fi
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install octave  > /dev/null ; fi
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install llvm > /dev/null ; fi
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install libomp > /dev/null ; fi
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then sudo chmod +x before_install_osx.sh ; fi
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then sudo ./before_install_osx.sh; fi
+  - if [[ "$TRAVIS_JOB_NAME" == "OSX Octave" ]]; then echo "Testing matRad on Mac OSX..." ; fi
+  - if [[ "$TRAVIS_JOB_NAME" == "OSX Octave" ]]; then sudo chmod +x .travis/before_install_osx.sh ; fi
+  - if [[ "$TRAVIS_JOB_NAME" == "OSX Octave" ]]; then sudo .travis/before_install_osx.sh; fi
 
   # Windows Setup
-  - if [[ "$TRAVIS_OS_NAME" == "windows" ]]; then echo "Testing matRad on Windows..." ; fi
-  - if [[ "$TRAVIS_OS_NAME" == "windows" ]]; then choco install octave.portable ; fi  
-  - if [[ "$TRAVIS_OS_NAME" == "windows" ]]; then choco install cmake --installargs 'ADD_CMAKE_TO_PATH=System' ; fi
-  - if [[ "$TRAVIS_OS_NAME" == "windows" ]]; then bash ./before_install_win_gitbash.sh ; fi
+  - if [[ "$TRAVIS_JOB_NAME" == "Windows Octave" ]]; then echo "Testing matRad on Windows..." ; fi
+  - if [[ "$TRAVIS_JOB_NAME" == "Windows Octave" ]]; then choco install octave.portable ; fi  
+  - if [[ "$TRAVIS_JOB_NAME" == "Windows Octave" ]]; then bash .travis/before_install_win_gitbash.sh ; fi
 
 
 before_script:
-  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then ulimit -c unlimited -S ; fi
+  - if [[ "$TRAVIS_JOB_NAME" == "Ubuntu Octave" ]]; then ulimit -c unlimited -S ; fi
 
 
 after_failure:
   ## Linux stack trace
   # find core file
-  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then COREFILE=$(find . -maxdepth 1 -name "core*" | head -n 1) ; fi 
+  - if [[ "$TRAVIS_JOB_NAME" == "Ubuntu Octave" ]]; then COREFILE=$(find . -maxdepth 1 -name "core*" | head -n 1) ; fi 
   # print stack trace
-  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then gdb -c "$COREFILE" -ex "thread apply all bt" -ex "set pagination 0" -batch /usr/bin/octave-cli ; fi
-  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then tail runtests.log ; fi
+  - if [[ "$TRAVIS_JOB_NAME" == "Ubuntu Octave" ]]; then gdb -c "$COREFILE" -ex "thread apply all bt" -ex "set pagination 0" -batch /usr/bin/octave-cli ; fi
+  - if [[ "$TRAVIS_JOB_NAME" == "Ubuntu Octave" ]]; then tail runtests.log ; fi
 
 script:
-  # Linux script
-  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then travis_wait 45 ./runtests.sh octave-cli ; fi
+  # Linux Octave script
+  - if [[ "$TRAVIS_JOB_NAME" == "Ubuntu Octave" ]]; then travis_wait 45 .travis/runtests.sh octave-cli ; fi
+  # Linux Matlab script
+  - if [[ "$TRAVIS_JOB_NAME" == "Ubuntu Matlab" ]]; then travis_wait 45 .travis/runtests.sh matlab; fi
   # OSX script
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then travis_wait 45 ./runtests.sh octave-cli ; fi
+  - if [[ "$TRAVIS_JOB_NAME" == "OSX Octave" ]]; then travis_wait 45 .travis/runtests.sh octave-cli ; fi
   # Windows script
-  - if [[ "$TRAVIS_OS_NAME" == "windows" ]]; then travis_wait 45 ./runtests.sh octave-cli ; fi
+  - if [[ "$TRAVIS_JOB_NAME" == "Windows Octave" ]]; then travis_wait 45 "cmd.exe //C RefreshEnv.cmd & .travis/runtests.sh octave-cli" ; fi
+
+before_cache:
+  - if [[ "$TRAVIS_JOB_NAME" == "OSX Octave" ]]; then brew cleanup; fi
 
 notifications:
-    slack: e0404:u5tBXbO6D1mEwzJuFZV0MmqJ
+  slack: 
+    if: repo = e0404/matRad 
+    rooms:
+      - e0404:u5tBXbO6D1mEwzJuFZV0MmqJ
+

.travis/before_install_linux.sh

@@ -0,0 +1,9 @@
+#!/usr/bin/env bash
+
+sudo chmod +x .travis/runtests.sh
+sudo chmod +x MCsquare/bin/MCsquare_linux
+
+mv 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"

.travis/before_install_osx.sh

@@ -0,0 +1,9 @@
+#!/usr/bin/env bash
+
+sudo chmod +x .travis/runtests.sh
+sudo chmod +x MCsquare/bin/MCsquare_mac
+
+mv 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"

.travis/before_install_win_gitbash.sh

@@ -0,0 +1,11 @@
+#!/usr/bin/env bash
+
+sudo chmod +x .travis/runtests.sh
+#sudo chmod +x MCsquare/MCsquare_windows.exe
+
+#mv 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"
+
+cmd.exe //C RefreshEnv.cmd

runtests.sh → .travis/runtests.sh

@@ -18,7 +18,7 @@ fi
 if [ -z "$Switches" ] ; then
 	case "$Runner" in
 		*matlab* )
-			Switches="-nodesktop -r"
+			Switches="-batch"
 			;;
 
 		*octave* )

AUTHORS.txt

@@ -19,6 +19,7 @@ List of all matRad developers that contributed code (alphabetical)
 * Henning Mescher
 * Lucas-Raphael M�ller
 * Ahmad Neishabouri
+* Martina Palkowitsch
 * Giuseppe Pezzano
 * Daniel Ramirez
 * Carsten Scholz