Format all code with clang

Author: ronald-jaepel

.github/ISSUE_TEMPLATE/feature_request.md

@@ -20,4 +20,4 @@ A clear and concise description of any alternative solutions or features you've
 Add any other context or screenshots about the feature request here.
 
 **Internal**
-For CADET Team members: Please assign a label, an assignee, and a topic in the project. 
+For CADET Team members: Please assign a label, an assignee, and a topic in the project.

.github/workflows/ci.yml

@@ -203,4 +203,3 @@ jobs:
           ${INSTALL_PREFIX}/bin/cadet-cli --version || true
           ${INSTALL_PREFIX}/bin/createLWE
           ${INSTALL_PREFIX}/bin/cadet-cli LWE.h5 || true
-

BUILD-OSX.md

@@ -31,7 +31,7 @@ brew install eigen
 
 ### LAPACK
 
-You can either use the native LAPACK implementation provided by Mac OS X (vecLib, Accelerate) 
+You can either use the native LAPACK implementation provided by Mac OS X (vecLib, Accelerate)
 or install the freely available [Intel MKL](https://software.intel.com/sites/campaigns/nest/) which is very fast and probably faster than Accelerate.
 
 ## Build CADET
@@ -41,10 +41,9 @@ or install the freely available [Intel MKL](https://software.intel.com/sites/cam
 
 * If using Intel MKL, execute `export MKLROOT=/opt/intel/mkl`
 * Using standard LAPACK: Execute `cmake -DCMAKE_INSTALL_PREFIX="<ROOT>/install" ../`
- 
+
     Using MKL (sequential): Execute `cmake -DCMAKE_INSTALL_PREFIX="<ROOT>/install" -DBLA_VENDOR=Intel10_64lp_seq ../`
- 
+
     Using MKL (parallel): Execute `cmake -DCMAKE_INSTALL_PREFIX="<ROOT>/install" -DBLA_VENDOR=Intel10_64lp ../`
 * Execute `make`
 * Execute `make install`
-

BUILD-WINDOWS.md

@@ -5,10 +5,10 @@
 * Optional: Git
 * Optional but not generally recommended*: Intel OneAPI TBB
 
-*For most use-cases it is more efficient to parallelize by running multiple CADET simulations instead 
+*For most use-cases it is more efficient to parallelize by running multiple CADET simulations instead
 of parallelizing within one CADET simulation. Including the parallelization code in CADET can lead to performance
-losses, even if parallelization within CADET is not used. 
-Therefore, we recommend not including the parallelization library TBB 
+losses, even if parallelization within CADET is not used.
+Therefore, we recommend not including the parallelization library TBB
 unless you know your simulations are large enough to benefit from it.
 
 Assumed directory structure:
@@ -46,7 +46,7 @@ We are using Visual Studio because it is the easiest way to install all required
 
 ## Prepare CADET code
 
-- Clone the CADET source code into a `CADET` folder: 
+- Clone the CADET source code into a `CADET` folder:
   - `git clone https://github.com/modsim/CADET.git CADET`
 - Create the directories `CADET\build` and `CADET\install`
 
@@ -78,15 +78,15 @@ We are using Visual Studio because it is the easiest way to install all required
           execute `set TBBROOT="C:/Program Files (x86)/Intel/oneAPI/tbb/latest"` and
         - `cmake -DCMAKE_INSTALL_PREFIX=..\out\install\aRELEASE -G "Visual Studio 17 2022" -A x64 -DCMAKE_BUILD_TYPE=Release -DCMAKE_TOOLCHAIN_FILE="%VCPKG_ROOT%/scripts/buildsystems/vcpkg.cmake" -DVCPKG_TARGET_TRIPLET=x64-windows-static -DENABLE_STATIC_LINK_LAPACK=ON -DENABLE_STATIC_LINK_DEPS=ON -DBLA_VENDOR=Intel10_64lp --fresh ../`
     - `msbuild.exe INSTALL.vcxproj /p:Configuration=Release;Platform=x64`
-  
+
 - For PowerShell:
     - `cd CADET\build`
     - `vcpkg integrate install` (this only needs to be run _once_ and will require admin privileges)
     - `$ENV:MKLROOT = "C:\Program Files (x86)\Intel\oneAPI\mkl\latest"`
     - `cmake -DCMAKE_INSTALL_PREFIX="..\out\install\aRELEASE" -G "Visual Studio 17 2022" -A x64 -DCMAKE_BUILD_TYPE=Release -DCMAKE_TOOLCHAIN_FILE="$ENV:VCPKG_ROOT/scripts/buildsystems/vcpkg.cmake" -DVCPKG_TARGET_TRIPLET=x64-windows-static -DENABLE_STATIC_LINK_LAPACK=ON -DENABLE_STATIC_LINK_DEPS=ON -DBLA_VENDOR=Intel10_64lp_seq "../" --fresh`
       - If you want to use parallelization and have installed TBB, instead
            execute `$ENV:TBBROOT = "C:\Program Files (x86)\Intel\oneAPI\tbb\latest"`
-      and 
+      and
       - `cmake -DCMAKE_INSTALL_PREFIX="..\out\install\aRELEASE" -G "Visual Studio 17 2022" -A x64 -DCMAKE_BUILD_TYPE=Release -DCMAKE_TOOLCHAIN_FILE="$ENV:VCPKG_ROOT/scripts/buildsystems/vcpkg.cmake" -DVCPKG_TARGET_TRIPLET=x64-windows-static -DENABLE_STATIC_LINK_LAPACK=ON -DENABLE_STATIC_LINK_DEPS=ON -DBLA_VENDOR=Intel10_64lp "../" --fresh`
     - `msbuild.exe INSTALL.vcxproj /p:Configuration="Release;Platform=x64"`
 - The binaries will be located in `CADET\out\install\aRELEASE\bin`
@@ -99,4 +99,4 @@ We are using Visual Studio because it is the easiest way to install all required
   - `cadet-cli.exe LWE.h5`
 - And confirm the output of the LWE.h5 by opening it in HDF5view or loading it in CADET-Process.
 - If you get no printed return from the first command, run cadet-cli.exe by double-clicking it in the file explorer.
-This raises error messages that are not raised from a cmd or PowerShell window.
+This raises error messages that are not raised from a cmd or PowerShell window.

CMakeLists.txt

@@ -1,15 +1,15 @@
 # =============================================================================
 #  CADET
-#  
+#
 #  Copyright © The CADET Authors
 #            Please see the CONTRIBUTORS.md file.
-#  
+#
 #  All rights reserved. This program and the accompanying materials
 #  are made available under the terms of the GNU Public License v3.0 (or, at
 #  your option, any later version) which accompanies this distribution, and
 #  is available at http://www.gnu.org/licenses/gpl.html
 # =============================================================================
- 
+
 # Require a fairly new cmake version
 cmake_minimum_required(VERSION 3.12)
 
@@ -308,7 +308,7 @@ if (ENABLE_CADET_TOOLS OR ENABLE_CADET_CLI)
 				set(HDF5_SUPPORT_LIBRARIES ${HDF5_C_LIBRARIES})
 				list(REMOVE_AT HDF5_SUPPORT_LIBRARIES 0)
 			else()
-				set(HDF5_MAIN_LIBRARY ${HDF5_C_LIBRARIES}) 
+				set(HDF5_MAIN_LIBRARY ${HDF5_C_LIBRARIES})
 				set(HDF5_SUPPORT_LIBRARIES)
 			endif()
 
@@ -546,7 +546,7 @@ set(CPACK_SOURCE_IGNORE_FILES
 
 message("")
 message("--------------------------- Feature Summary ---------------------------")
-         
+
 feature_summary(WHAT ALL)
 
 # Summary

CMakeSettings.json

@@ -189,4 +189,4 @@
       ]
     }
   ]
-}
+}

CONTRIBUTORS.md

@@ -22,4 +22,3 @@ Salah Azzouzi (Forschungszentrum Juelich GmbH, IBG-1: Biotechnology, Juelich, Ge
 * Johannes Schmölder has received support from the IMI2/ EU/EFPIA joint undertaking Inno4Vac (grant no. 101007799).
 
 Follow the lead, become a contributor by sending a pull request or a patch.
-