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Rohith Krishna
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‎.clang-format‎

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---
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Language: Cpp
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# BasedOnStyle: LLVM
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AccessModifierOffset: -2
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AlignAfterOpenBracket: Align
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AlignArrayOfStructures: None
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AlignConsecutiveMacros: None
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AlignConsecutiveAssignments: None
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AlignConsecutiveBitFields: None
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AlignConsecutiveDeclarations: None
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AlignEscapedNewlines: Right
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AlignOperands: Align
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AlignTrailingComments: true
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AllowAllArgumentsOnNextLine: true
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AllowAllParametersOfDeclarationOnNextLine: true
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AllowShortEnumsOnASingleLine: true
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AllowShortBlocksOnASingleLine: Never
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AllowShortCaseLabelsOnASingleLine: false
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AllowShortFunctionsOnASingleLine: All
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AllowShortLambdasOnASingleLine: All
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AllowShortIfStatementsOnASingleLine: true
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AllowShortLoopsOnASingleLine: false
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AlwaysBreakAfterDefinitionReturnType: None
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AlwaysBreakAfterReturnType: None
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AlwaysBreakBeforeMultilineStrings: false
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AlwaysBreakTemplateDeclarations: MultiLine
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AttributeMacros:
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- __capability
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BinPackArguments: true
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BinPackParameters: false
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BraceWrapping:
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AfterCaseLabel: false
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AfterClass: false
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AfterControlStatement: Never
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AfterEnum: false
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AfterFunction: false
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AfterNamespace: false
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AfterObjCDeclaration: false
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AfterStruct: false
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AfterUnion: false
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AfterExternBlock: false
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BeforeCatch: false
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BeforeElse: false
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BeforeLambdaBody: false
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BeforeWhile: false
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IndentBraces: false
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SplitEmptyFunction: true
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SplitEmptyRecord: true
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SplitEmptyNamespace: true
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BreakBeforeBinaryOperators: None
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BreakBeforeConceptDeclarations: true
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BreakBeforeBraces: Attach
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BreakBeforeInheritanceComma: false
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BreakInheritanceList: BeforeColon
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BreakBeforeTernaryOperators: true
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BreakConstructorInitializersBeforeComma: false
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BreakConstructorInitializers: BeforeColon
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BreakAfterJavaFieldAnnotations: false
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BreakStringLiterals: true
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ColumnLimit: 111
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CommentPragmas: '^ IWYU pragma:'
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QualifierAlignment: Leave
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CompactNamespaces: false
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ConstructorInitializerIndentWidth: 4
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ContinuationIndentWidth: 4
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Cpp11BracedListStyle: true
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DeriveLineEnding: true
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DerivePointerAlignment: false
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DisableFormat: false
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EmptyLineAfterAccessModifier: Never
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EmptyLineBeforeAccessModifier: LogicalBlock
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ExperimentalAutoDetectBinPacking: false
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PackConstructorInitializers: BinPack
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BasedOnStyle: ''
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ConstructorInitializerAllOnOneLineOrOnePerLine: false
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AllowAllConstructorInitializersOnNextLine: true
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FixNamespaceComments: true
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ForEachMacros:
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- foreach
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- Q_FOREACH
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- BOOST_FOREACH
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IfMacros:
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- KJ_IF_MAYBE
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IncludeBlocks: Preserve
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IncludeCategories:
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- Regex: '^"(llvm|llvm-c|clang|clang-c)/'
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Priority: 2
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SortPriority: 0
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CaseSensitive: false
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- Regex: '^(<|"(gtest|gmock|isl|json)/)'
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Priority: 3
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SortPriority: 0
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CaseSensitive: false
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- Regex: '.*'
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Priority: 1
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SortPriority: 0
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CaseSensitive: false
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IncludeIsMainRegex: '(Test)?$'
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IncludeIsMainSourceRegex: ''
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IndentAccessModifiers: false
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IndentCaseLabels: false
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IndentCaseBlocks: false
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IndentGotoLabels: true
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IndentPPDirectives: None
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IndentExternBlock: AfterExternBlock
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IndentRequires: false
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IndentWidth: 2
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IndentWrappedFunctionNames: false
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InsertTrailingCommas: None
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JavaScriptQuotes: Leave
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JavaScriptWrapImports: true
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KeepEmptyLinesAtTheStartOfBlocks: true
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LambdaBodyIndentation: Signature
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MacroBlockBegin: ''
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MacroBlockEnd: ''
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MaxEmptyLinesToKeep: 1
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NamespaceIndentation: None
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ObjCBinPackProtocolList: Auto
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ObjCBlockIndentWidth: 2
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ObjCBreakBeforeNestedBlockParam: true
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ObjCSpaceAfterProperty: false
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ObjCSpaceBeforeProtocolList: true
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PenaltyBreakAssignment: 2
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PenaltyBreakBeforeFirstCallParameter: 19
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PenaltyBreakComment: 300
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PenaltyBreakFirstLessLess: 120
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PenaltyBreakOpenParenthesis: 0
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PenaltyBreakString: 1000
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PenaltyBreakTemplateDeclaration: 10
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PenaltyExcessCharacter: 1000000
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PenaltyReturnTypeOnItsOwnLine: 60
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PenaltyIndentedWhitespace: 0
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PointerAlignment: Right
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PPIndentWidth: -1
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ReferenceAlignment: Pointer
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ReflowComments: true
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RemoveBracesLLVM: false
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SeparateDefinitionBlocks: Leave
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ShortNamespaceLines: 1
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SortIncludes: CaseSensitive
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SortJavaStaticImport: Before
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SortUsingDeclarations: true
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SpaceAfterCStyleCast: false
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SpaceAfterLogicalNot: false
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SpaceAfterTemplateKeyword: true
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SpaceBeforeAssignmentOperators: true
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SpaceBeforeCaseColon: false
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SpaceBeforeCpp11BracedList: false
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SpaceBeforeCtorInitializerColon: true
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SpaceBeforeInheritanceColon: true
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SpaceBeforeParens: ControlStatements
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SpaceBeforeParensOptions:
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AfterControlStatements: true
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AfterForeachMacros: true
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AfterFunctionDefinitionName: false
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AfterFunctionDeclarationName: false
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AfterIfMacros: true
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AfterOverloadedOperator: false
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BeforeNonEmptyParentheses: false
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SpaceAroundPointerQualifiers: Default
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SpaceBeforeRangeBasedForLoopColon: true
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SpaceInEmptyBlock: false
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SpaceInEmptyParentheses: false
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SpacesBeforeTrailingComments: 1
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SpacesInAngles: Never
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SpacesInConditionalStatement: false
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SpacesInContainerLiterals: true
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SpacesInCStyleCastParentheses: false
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SpacesInLineCommentPrefix:
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Minimum: 1
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Maximum: -1
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SpacesInParentheses: false
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SpacesInSquareBrackets: false
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SpaceBeforeSquareBrackets: false
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BitFieldColonSpacing: Both
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Standard: Latest
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StatementAttributeLikeMacros:
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- Q_EMIT
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StatementMacros:
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- Q_UNUSED
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- QT_REQUIRE_VERSION
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TabWidth: 8
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UseCRLF: false
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UseTab: Never
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WhitespaceSensitiveMacros:
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- STRINGIZE
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- PP_STRINGIZE
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- BOOST_PP_STRINGIZE
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- NS_SWIFT_NAME
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- CF_SWIFT_NAME
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...
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‎.gitignore‎

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lib/chai_weights/
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lib/chai_cache/
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servers/
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valid_remapped
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lig_test
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dataset.pkl
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run_digs.sh
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# *.pdb
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.vscode
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slurm_logs/
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**/output/
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**/outputs/
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*/notebooks/
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*/models/
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__pycache__/
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*/run_scripts/
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unit_tests/
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ruff.toml
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*/scratch/
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*/wandb/
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rf2aa/dataset_20240318.pkl
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*.csv
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*.err
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*.log
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*.sublime-workspace
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/*.pdb
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/rf_diffusion/*.pdb
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/rf_diffusion/samples/
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/doc/build
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/doc/source/api
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pytest*.log
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slurm_logs_*
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.vscode
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.env
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*.ipynb
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data/run.sh
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.cache
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.hypothesis
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_pytest_tmp_*
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rf_diffusion/tmp
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rf_diffusion/debug
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doc/build
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doc/source/api/
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doc/source/rf_diffusion.conditions.rst
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doc/source/rf_diffusion.inference.rst
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doc/source/rf_diffusion.observer.rst
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doc/source/rf_diffusion.rst
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doc/source/rf_diffusion.sym.rst
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doc/source/rf_diffusion.test_seq_diff.rst
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doc/source/rf_diffusion.viz.rst
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.envrc
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*.egg-info
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_*_tests
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_notes
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unidealized
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.yapf_hash
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jobs.list*
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\#*
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*\#
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rf_diffusion/open_source_tests/
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rf_diffusion/test_outputs/

‎.sourcery.yaml‎

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# 🪄 This is your project's Sourcery configuration file.
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# You can use it to get Sourcery working in the way you want, such as
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# ignoring specific refactorings, skipping directories in your project,
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# or writing custom rules.
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# 📚 For a complete reference to this file, see the documentation at
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# https://docs.sourcery.ai/Configuration/Project-Settings/
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# This file was auto-generated by Sourcery on 2024-07-18 at 19:42.
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version: '1' # The schema version of this config file
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ignore: # A list of paths or files which Sourcery will ignore.
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- .git
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- env
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- .env
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- .tox
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- node_modules
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- vendor
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- venv
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- .venv
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- ~/.pyenv
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- ~/.rye
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- ~/.vscode
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- .vscode
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- ~/.cache
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- ~/.config
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- ~/.local
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rule_settings:
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enable:
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- default
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disable: [] # A list of rule IDs Sourcery will never suggest.
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rule_types:
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- refactoring
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- suggestion
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- comment
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python_version: '3.10' # A string specifying the lowest Python version your project supports. Sourcery will not suggest refactorings requiring a higher Python version.
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# rules: # A list of custom rules Sourcery will include in its analysis.
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# - id: no-print-statements
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# description: Do not use print statements in the test directory.
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# pattern: print(...)
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# language: python
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# replacement:
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# condition:
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# explanation:
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# paths:
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# include:
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# - test
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# exclude:
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# - conftest.py
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# tests: []
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# tags: []
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# rule_tags: {} # Additional rule tags.
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# metrics:
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# quality_threshold: 25.0
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# github:
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# labels: []
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# ignore_labels:
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# - sourcery-ignore
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# request_review: author
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# sourcery_branch: sourcery/{base_branch}
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# clone_detection:
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# min_lines: 3
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# min_duplicates: 2
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# identical_clones_only: false
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# proxy:
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# url:
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# ssl_certs_file:
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# no_ssl_verify: false
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# coding_assistant:
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# project_description: ''
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# enabled:

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