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Add .mailmap file and pre-commit hooks
The hooks check for source code formatting (using clang-format) and the presence of the license header.
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‎.clang-format‎

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AccessModifierOffset: -2
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AlignAfterOpenBracket: true
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AlignEscapedNewlinesLeft: false
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AlignOperands: true
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AlignTrailingComments: true
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AllowAllParametersOfDeclarationOnNextLine: false
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AllowShortBlocksOnASingleLine: false
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AllowShortCaseLabelsOnASingleLine: false
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AllowShortFunctionsOnASingleLine: All
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AllowShortIfStatementsOnASingleLine: false
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AllowShortLoopsOnASingleLine: false
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AlwaysBreakAfterDefinitionReturnType: false
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AlwaysBreakBeforeMultilineStrings: false
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AlwaysBreakTemplateDeclarations: false
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BinPackArguments: true
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BinPackParameters: true
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BreakBeforeBinaryOperators: None
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BreakBeforeBraces: Attach
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BreakBeforeTernaryOperators: true
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BreakConstructorInitializersBeforeComma: false
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ColumnLimit: 85
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CommentPragmas: '^ IWYU pragma:'
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ConstructorInitializerAllOnOneLineOrOnePerLine: true
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ConstructorInitializerIndentWidth: 4
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ContinuationIndentWidth: 4
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Cpp11BracedListStyle: true
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DerivePointerAlignment: false
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DisableFormat: false
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ExperimentalAutoDetectBinPacking: false
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IndentCaseLabels: true
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IndentWidth: 2
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IndentWrappedFunctionNames: false
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KeepEmptyLinesAtTheStartOfBlocks: true
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Language: Cpp
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MaxEmptyLinesToKeep: 1
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NamespaceIndentation: None
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ObjCBlockIndentWidth: 2
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ObjCSpaceAfterProperty: true
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ObjCSpaceBeforeProtocolList: false
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PenaltyBreakBeforeFirstCallParameter: 19
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PenaltyBreakComment: 300
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PenaltyBreakFirstLessLess: 120
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PenaltyBreakString: 1000
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PenaltyExcessCharacter: 1000000
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PenaltyReturnTypeOnItsOwnLine: 200
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PointerAlignment: Middle
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SpaceAfterCStyleCast: false
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SpaceBeforeAssignmentOperators: true
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SpaceBeforeParens: ControlStatements
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SpaceInEmptyParentheses: false
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SpacesBeforeTrailingComments: 1
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SpacesInAngles: false
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SpacesInCStyleCastParentheses: false
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SpacesInContainerLiterals: true
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SpacesInParentheses: false
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SpacesInSquareBrackets: false
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Standard: Cpp11
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TabWidth: 8
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UseTab: Never

‎.gitattributes‎

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# API files
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/api/*.h licensefile=.githooks/license-maintainer/LICENSE-C
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/api/*.F90 licensefile=.githooks/license-maintainer/LICENSE-Fortran
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# include directory
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/include/*.hpp licensefile=.githooks/license-maintainer/LICENSE-C++
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/include/Config.hpp.in licensefile=.githooks/license-maintainer/LICENSE-C++
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# bin
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/src/bin/*.cpp licensefile=.githooks/license-maintainer/LICENSE-C++
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# bi_operators
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/src/bi_operators/*.hpp licensefile=.githooks/license-maintainer/LICENSE-C++
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# cavity
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/src/cavity/*.cpp licensefile=.githooks/license-maintainer/LICENSE-C++
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/src/cavity/*.hpp licensefile=.githooks/license-maintainer/LICENSE-C++
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# green
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/src/green/*.hpp licensefile=.githooks/license-maintainer/LICENSE-C++
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/src/green/dielectric_profile/*.hpp licensefile=.githooks/license-maintainer/LICENSE-C++
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# interface
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/src/interface/*.cpp licensefile=.githooks/license-maintainer/LICENSE-C++
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/src/interface/*.hpp licensefile=.githooks/license-maintainer/LICENSE-C++
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# metal
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/src/metal/*.F90 licensefile=.githooks/license-maintainer/LICENSE-Fortran
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# pedra
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/src/pedra/*.inc licensefile=.githooks/license-maintainer/LICENSE-Fortran
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pedra/pedra_cavity.F90 licensefile=.githooks/license-maintainer/LICENSE-Fortran
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pedra/pedra_cavity_derivatives.F90 licensefile=.githooks/license-maintainer/LICENSE-Fortran
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pedra/pedra_cavity_interface.F90 licensefile=.githooks/license-maintainer/LICENSE-Fortran
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pedra/pedra_dblas.F90 licensefile=.githooks/license-maintainer/LICENSE-Fortran
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pedra/pedra_precision.F90 licensefile=.githooks/license-maintainer/LICENSE-Fortran
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pedra/pedra_print.F90 licensefile=.githooks/license-maintainer/LICENSE-Fortran
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pedra/pedra_symmetry.F90 licensefile=.githooks/license-maintainer/LICENSE-Fortran
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pedra/pedra_utils.F90 licensefile=.githooks/license-maintainer/LICENSE-Fortran
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# solver
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/src/solver/*.cpp licensefile=.githooks/license-maintainer/LICENSE-C++
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/src/solver/*.hpp licensefile=.githooks/license-maintainer/LICENSE-C++
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# utils
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/src/utils/*.cpp licensefile=.githooks/license-maintainer/LICENSE-C++
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/src/utils/*.hpp licensefile=.githooks/license-maintainer/LICENSE-C++
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# tests
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/tests/unit_tests.cpp licensefile=.githooks/license-maintainer/LICENSE-C++
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/tests/TestingMolecules.hpp licensefile=.githooks/license-maintainer/LICENSE-C++
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/tests/Fortran_host/*.F90 licensefile=.githooks/license-maintainer/LICENSE-Fortran
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/tests/C_host/*.h licensefile=.githooks/license-maintainer/LICENSE-C
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/tests/C_host/*.c licensefile=.githooks/license-maintainer/LICENSE-C
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/tests/bi_operators/*.cpp licensefile=.githooks/license-maintainer/LICENSE-C++
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/tests/cpcm/*.cpp licensefile=.githooks/license-maintainer/LICENSE-C++
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/tests/dielectric_profile/*.cpp licensefile=.githooks/license-maintainer/LICENSE-C++
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/tests/gepol/*.cpp licensefile=.githooks/license-maintainer/LICENSE-C++
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/tests/green/*.hpp licensefile=.githooks/license-maintainer/LICENSE-C++
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/tests/green/*.cpp licensefile=.githooks/license-maintainer/LICENSE-C++
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/tests/iefpcm/*.cpp licensefile=.githooks/license-maintainer/LICENSE-C++
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/tests/input/*.cpp licensefile=.githooks/license-maintainer/LICENSE-C++
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/tests/numerical_quadrature/*.cpp licensefile=.githooks/license-maintainer/LICENSE-C++
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# tools
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/src/make_cmake_files.py licensefile=.githooks/license-maintainer/LICENSE-Python
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/tools/pcmsolver.py.in licensefile=.githooks/license-maintainer/LICENSE-Python
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/tests/make_cmake_files.py licensefile=.githooks/license-maintainer/LICENSE-Python

‎.githooks/canonicalize_filename.sh‎

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#!/bin/sh
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#
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# PCMSolver, an API for the Polarizable Continuum Model
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# Copyright (C) 2016 Roberto Di Remigio, Luca Frediani and collaborators
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#
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# This file is part of PCMSolver.
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#
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# PCMSolver is free software: you can redistribute it and/or modify
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# it under the terms of the GNU Lesser General Public License as published by
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# the Free Software Foundation, either version 3 of the License, or
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# (at your option) any later version.
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#
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# PCMSolver is distributed in the hope that it will be useful,
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# but WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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# GNU Lesser General Public License for more details.
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#
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# You should have received a copy of the GNU Lesser General Public License
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# along with PCMSolver. If not, see <http://www.gnu.org/licenses/>.
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#
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# For information on the complete list of contributors to the
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# PCMSolver API, see: <http://pcmsolver.readthedocs.io/>
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#
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# Provide the canonicalize filename (physical filename with out any symlinks)
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# like the GNU version readlink with the -f option regardless of the version of
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# readlink (GNU or BSD).
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# This file is part of a set of unofficial pre-commit hooks available
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# at github.
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# Link: https://github.com/githubbrowser/Pre-commit-hooks
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# Contact: David Martin, [email protected]
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###########################################################
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# There should be no need to change anything below this line.
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# Canonicalize by recursively following every symlink in every component of the
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# specified filename. This should reproduce the results of the GNU version of
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# readlink with the -f option.
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#
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# Reference: http://stackoverflow.com/questions/1055671/how-can-i-get-the-behavior-of-gnus-readlink-f-on-a-mac
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canonicalize_filename () {
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local target_file="$1"
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local physical_directory=""
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local result=""
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# Need to restore the working directory after work.
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local working_dir="`pwd`"
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cd -- "$(dirname -- "$target_file")"
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target_file="$(basename -- "$target_file")"
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# Iterate down a (possible) chain of symlinks
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while [ -L "$target_file" ]
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do
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target_file="$(readlink -- "$target_file")"
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cd -- "$(dirname -- "$target_file")"
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target_file="$(basename -- "$target_file")"
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done
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# Compute the canonicalized name by finding the physical path
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# for the directory we're in and appending the target file.
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physical_directory="`pwd -P`"
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result="$physical_directory/$target_file"
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# restore the working directory after work.
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cd -- "$working_dir"
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echo "$result"
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}

‎.githooks/license-maintainer/LICENSE‎

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GNU LESSER GENERAL PUBLIC LICENSE
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Version 3, 29 June 2007
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Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
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Everyone is permitted to copy and distribute verbatim copies
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of this license document, but changing it is not allowed.
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This version of the GNU Lesser General Public License incorporates
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the terms and conditions of version 3 of the GNU General Public
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License, supplemented by the additional permissions listed below.
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0. Additional Definitions.
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As used herein, "this License" refers to version 3 of the GNU Lesser
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General Public License, and the "GNU GPL" refers to version 3 of the GNU
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General Public License.
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"The Library" refers to a covered work governed by this License,
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other than an Application or a Combined Work as defined below.
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An "Application" is any work that makes use of an interface provided
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by the Library, but which is not otherwise based on the Library.
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Defining a subclass of a class defined by the Library is deemed a mode
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of using an interface provided by the Library.
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A "Combined Work" is a work produced by combining or linking an
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Application with the Library. The particular version of the Library
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with which the Combined Work was made is also called the "Linked
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Version".
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The "Minimal Corresponding Source" for a Combined Work means the
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Corresponding Source for the Combined Work, excluding any source code
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for portions of the Combined Work that, considered in isolation, are
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based on the Application, and not on the Linked Version.
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The "Corresponding Application Code" for a Combined Work means the
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object code and/or source code for the Application, including any data
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and utility programs needed for reproducing the Combined Work from the
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Application, but excluding the System Libraries of the Combined Work.
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1. Exception to Section 3 of the GNU GPL.
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You may convey a covered work under sections 3 and 4 of this License
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without being bound by section 3 of the GNU GPL.
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2. Conveying Modified Versions.
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If you modify a copy of the Library, and, in your modifications, a
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facility refers to a function or data to be supplied by an Application
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that uses the facility (other than as an argument passed when the
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facility is invoked), then you may convey a copy of the modified
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version:
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a) under this License, provided that you make a good faith effort to
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ensure that, in the event an Application does not supply the
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function or data, the facility still operates, and performs
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whatever part of its purpose remains meaningful, or
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b) under the GNU GPL, with none of the additional permissions of
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this License applicable to that copy.
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3. Object Code Incorporating Material from Library Header Files.
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The object code form of an Application may incorporate material from
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a header file that is part of the Library. You may convey such object
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code under terms of your choice, provided that, if the incorporated
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material is not limited to numerical parameters, data structure
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layouts and accessors, or small macros, inline functions and templates
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(ten or fewer lines in length), you do both of the following:
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a) Give prominent notice with each copy of the object code that the
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Library is used in it and that the Library and its use are
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covered by this License.
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b) Accompany the object code with a copy of the GNU GPL and this license
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document.
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4. Combined Works.
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You may convey a Combined Work under terms of your choice that,
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taken together, effectively do not restrict modification of the
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portions of the Library contained in the Combined Work and reverse
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engineering for debugging such modifications, if you also do each of
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the following:
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a) Give prominent notice with each copy of the Combined Work that
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the Library is used in it and that the Library and its use are
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covered by this License.
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b) Accompany the Combined Work with a copy of the GNU GPL and this license
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document.
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c) For a Combined Work that displays copyright notices during
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copies of the GNU GPL and this license document.
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d) Do one of the following:
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0) Convey the Minimal Corresponding Source under the terms of this
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License, and the Corresponding Application Code in a form
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suitable for, and under terms that permit, the user to
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recombine or relink the Application with a modified version of
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the Linked Version to produce a modified Combined Work, in the
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manner specified by section 6 of the GNU GPL for conveying
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Corresponding Source.
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1) Use a suitable shared library mechanism for linking with the
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Library. A suitable mechanism is one that (a) uses at run time
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system, and (b) will operate properly with a modified version
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of the Library that is interface-compatible with the Linked
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Version.
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e) Provide Installation Information, but only if you would otherwise
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be required to provide such information under section 6 of the
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GNU GPL, and only to the extent that such information is
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necessary to install and execute a modified version of the
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Combined Work produced by recombining or relinking the
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Application with a modified version of the Linked Version. (If
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you use option 4d0, the Installation Information must accompany
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the Minimal Corresponding Source and Corresponding Application
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Code. If you use option 4d1, you must provide the Installation
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Information in the manner specified by section 6 of the GNU GPL
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for conveying Corresponding Source.)
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5. Combined Libraries.
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facilities that are not Applications and are not covered by this
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License, and convey such a combined library under terms of your
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choice, if you do both of the following:
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a) Accompany the combined library with a copy of the same work based
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on the Library, uncombined with any other library facilities,
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conveyed under the terms of this License.
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b) Give prominent notice with the combined library that part of it
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is a work based on the Library, and explaining where to find the
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accompanying uncombined form of the same work.
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6. Revised Versions of the GNU Lesser General Public License.
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The Free Software Foundation may publish revised and/or new versions
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of the GNU Lesser General Public License from time to time. Such new
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versions will be similar in spirit to the present version, but may
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differ in detail to address new problems or concerns.
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Each version is given a distinguishing version number. If the
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Library as you received it specifies that a certain numbered version
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of the GNU Lesser General Public License "or any later version"
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applies to it, you have the option of following the terms and
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conditions either of that published version or of any later version
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published by the Free Software Foundation. If the Library as you
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received it does not specify a version number of the GNU Lesser
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General Public License, you may choose any version of the GNU Lesser
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General Public License ever published by the Free Software Foundation.
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whether future versions of the GNU Lesser General Public License shall
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apply, that proxy's public statement of acceptance of any version is
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permanent authorization for you to choose that version for the
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Library.

‎.githooks/license-maintainer/LICENSE-C‎

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/**
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* PCMSolver, an API for the Polarizable Continuum Model
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* Copyright (C) YEAR AUTHORS
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*
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* This file is part of PCMSolver.
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*
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* PCMSolver is free software: you can redistribute it and/or modify
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* it under the terms of the GNU Lesser General Public License as published by
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* the Free Software Foundation, either version 3 of the License, or
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* (at your option) any later version.
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*
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* PCMSolver is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU Lesser General Public License for more details.
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*
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* You should have received a copy of the GNU Lesser General Public License
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* along with PCMSolver. If not, see <http://www.gnu.org/licenses/>.
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*
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* For information on the complete list of contributors to the
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* PCMSolver API, see: <http://pcmsolver.readthedocs.io/>
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*/
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