Automatic code formatting using pre-commit and clang-format

.clang-format

@@ -0,0 +1,223 @@
+---
+BasedOnStyle: Microsoft
+AccessModifierOffset: -4
+AlignAfterOpenBracket: Align
+AlignArrayOfStructures: None
+AlignConsecutiveAssignments:
+  Enabled: false
+  AcrossEmptyLines: false
+  AcrossComments: false
+  AlignCompound: false
+  PadOperators: true
+AlignConsecutiveBitFields:
+  Enabled: false
+  AcrossEmptyLines: false
+  AcrossComments: false
+  AlignCompound: false
+  PadOperators: false
+AlignConsecutiveDeclarations:
+  Enabled: false
+  AcrossEmptyLines: false
+  AcrossComments: false
+  AlignCompound: false
+  PadOperators: false
+AlignConsecutiveMacros:
+  Enabled: false
+  AcrossEmptyLines: false
+  AcrossComments: false
+  AlignCompound: false
+  PadOperators: false
+AlignEscapedNewlines: Right
+AlignOperands: Align
+AlignTrailingComments:
+  Kind: Always
+  OverEmptyLines: 0
+AllowAllArgumentsOnNextLine: true
+AllowAllParametersOfDeclarationOnNextLine: true
+AllowShortBlocksOnASingleLine: Never
+AllowShortCaseLabelsOnASingleLine: false
+AllowShortEnumsOnASingleLine: false
+AllowShortFunctionsOnASingleLine: None
+AllowShortIfStatementsOnASingleLine: Never
+AllowShortLambdasOnASingleLine: All
+AllowShortLoopsOnASingleLine: false
+AlwaysBreakAfterDefinitionReturnType: None
+AlwaysBreakAfterReturnType: None
+AlwaysBreakBeforeMultilineStrings: false
+AlwaysBreakTemplateDeclarations: MultiLine
+AttributeMacros:
+  - __capability
+BinPackArguments: true
+BinPackParameters: true
+BitFieldColonSpacing: Both
+BraceWrapping:
+  AfterCaseLabel: false
+  AfterClass: true
+  AfterControlStatement: Always
+  AfterEnum: true
+  AfterFunction: true
+  AfterNamespace: true
+  AfterObjCDeclaration: true
+  AfterStruct: true
+  AfterUnion: false
+  AfterExternBlock: true
+  BeforeCatch: true
+  BeforeElse: true
+  BeforeLambdaBody: false
+  BeforeWhile: false
+  IndentBraces: false
+  SplitEmptyFunction: true
+  SplitEmptyRecord: true
+  SplitEmptyNamespace: true
+BreakAfterAttributes: Never
+BreakAfterJavaFieldAnnotations: false
+BreakArrays: true
+BreakBeforeBinaryOperators: None
+BreakBeforeBraces: Custom
+BreakBeforeConceptDeclarations: Always
+BreakBeforeInlineASMColon: OnlyMultiline
+BreakBeforeTernaryOperators: true
+BreakConstructorInitializers: BeforeColon
+BreakInheritanceList: BeforeColon
+BreakStringLiterals: true
+ColumnLimit: 120
+CommentPragmas: "^ IWYU pragma:"
+CompactNamespaces: false
+ConstructorInitializerIndentWidth: 4
+ContinuationIndentWidth: 4
+Cpp11BracedListStyle: true
+DerivePointerAlignment: false
+DisableFormat: false
+EmptyLineAfterAccessModifier: Never
+EmptyLineBeforeAccessModifier: LogicalBlock
+ExperimentalAutoDetectBinPacking: false
+FixNamespaceComments: true
+ForEachMacros:
+  - foreach
+  - Q_FOREACH
+  - BOOST_FOREACH
+IfMacros:
+  - KJ_IF_MAYBE
+IncludeBlocks: Preserve
+IncludeCategories:
+  - Regex: ^"(llvm|llvm-c|clang|clang-c)/
+    Priority: 2
+    SortPriority: 0
+    CaseSensitive: false
+  - Regex: ^(<|"(gtest|gmock|isl|json)/)
+    Priority: 3
+    SortPriority: 0
+    CaseSensitive: false
+  - Regex: .*
+    Priority: 1
+    SortPriority: 0
+    CaseSensitive: false
+IncludeIsMainRegex: (Test)?$
+IncludeIsMainSourceRegex: ""
+IndentAccessModifiers: false
+IndentCaseBlocks: false
+IndentCaseLabels: false
+IndentExternBlock: AfterExternBlock
+IndentGotoLabels: true
+IndentPPDirectives: None
+IndentRequiresClause: true
+IndentWidth: 4
+IndentWrappedFunctionNames: false
+InsertBraces: false
+InsertNewlineAtEOF: true
+InsertTrailingCommas: None
+IntegerLiteralSeparator:
+  Binary: 0
+  BinaryMinDigits: 0
+  Decimal: 0
+  DecimalMinDigits: 0
+  Hex: 0
+  HexMinDigits: 0
+JavaScriptQuotes: Leave
+JavaScriptWrapImports: true
+KeepEmptyLinesAtTheStartOfBlocks: true
+LambdaBodyIndentation: Signature
+Language: Cpp
+LineEnding: DeriveLF
+MacroBlockBegin: ""
+MacroBlockEnd: ""
+MaxEmptyLinesToKeep: 1
+NamespaceIndentation: None
+ObjCBinPackProtocolList: Auto
+ObjCBlockIndentWidth: 2
+ObjCBreakBeforeNestedBlockParam: true
+ObjCSpaceAfterProperty: false
+ObjCSpaceBeforeProtocolList: true
+PPIndentWidth: -1
+PackConstructorInitializers: BinPack
+PenaltyBreakAssignment: 2
+PenaltyBreakBeforeFirstCallParameter: 19
+PenaltyBreakComment: 300
+PenaltyBreakFirstLessLess: 120
+PenaltyBreakOpenParenthesis: 0
+PenaltyBreakString: 1000
+PenaltyBreakTemplateDeclaration: 10
+PenaltyExcessCharacter: 1000000
+PenaltyIndentedWhitespace: 0
+PenaltyReturnTypeOnItsOwnLine: 1000
+PointerAlignment: Left
+QualifierAlignment: Leave
+ReferenceAlignment: Pointer
+ReflowComments: true
+RemoveBracesLLVM: false
+RemoveSemicolon: false
+RequiresClausePosition: OwnLine
+RequiresExpressionIndentation: OuterScope
+SeparateDefinitionBlocks: Leave
+ShortNamespaceLines: 1
+SortIncludes: Never
+SortJavaStaticImport: Before
+SortUsingDeclarations: LexicographicNumeric
+SpaceAfterCStyleCast: false
+SpaceAfterLogicalNot: false
+SpaceAfterTemplateKeyword: true
+SpaceAroundPointerQualifiers: Default
+SpaceBeforeAssignmentOperators: true
+SpaceBeforeCaseColon: false
+SpaceBeforeCpp11BracedList: false
+SpaceBeforeCtorInitializerColon: true
+SpaceBeforeInheritanceColon: true
+SpaceBeforeParens: ControlStatements
+SpaceBeforeParensOptions:
+  AfterControlStatements: true
+  AfterForeachMacros: true
+  AfterFunctionDeclarationName: false
+  AfterFunctionDefinitionName: false
+  AfterIfMacros: true
+  AfterOverloadedOperator: false
+  AfterRequiresInClause: false
+  AfterRequiresInExpression: false
+  BeforeNonEmptyParentheses: false
+SpaceBeforeRangeBasedForLoopColon: true
+SpaceBeforeSquareBrackets: false
+SpaceInEmptyBlock: true
+SpaceInEmptyParentheses: false
+SpacesBeforeTrailingComments: 1
+SpacesInAngles: Never
+SpacesInCStyleCastParentheses: false
+SpacesInConditionalStatement: false
+SpacesInContainerLiterals: false
+SpacesInLineCommentPrefix:
+  Minimum: 1
+  Maximum: -1
+SpacesInParentheses: false
+SpacesInSquareBrackets: false
+Standard: Latest
+StatementAttributeLikeMacros:
+  - Q_EMIT
+StatementMacros:
+  - Q_UNUSED
+  - QT_REQUIRE_VERSION
+TabWidth: 4
+UseTab: ForContinuationAndIndentation
+WhitespaceSensitiveMacros:
+  - BOOST_PP_STRINGIZE
+  - CF_SWIFT_NAME
+  - NS_SWIFT_NAME
+  - PP_STRINGIZE
+  - STRINGIZE

.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
-

.gitignore

@@ -75,6 +75,8 @@ doc/tex/docs/*.aux
 ### Ignore IDE files ###
 .vs/
 .idea/
+.vscode/
+.clangd/
 *.iws
 *.kdev4
 .kdev4/

.pre-commit-config.yaml

@@ -0,0 +1,16 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.2.0
+    hooks:
+    -   id: trailing-whitespace
+        args: [--markdown-linebreak-ext=md]
+    -   id: end-of-file-fixer
+    -   id: check-yaml
+- repo: https://github.com/pre-commit/mirrors-clang-format
+  rev: v18.1.8
+  hooks:
+  - id: clang-format
+    types_or: [c++, c]
+exclude: ^ThirdParty/

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.
-