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Replace old license headers with shorter SPDX format across all file types (OpenMS#8212)
* Initial plan * Replace old license headers with shorter SPDX format in 37 CMake files Co-authored-by: timosachsenberg <5803621+timosachsenberg@users.noreply.github.com> * Extend license header updates to additional file types (Python, PHP, Shell, C++ template) Co-authored-by: timosachsenberg <5803621+timosachsenberg@users.noreply.github.com> --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: timosachsenberg <5803621+timosachsenberg@users.noreply.github.com>
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‎CMakeLists.txt‎

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# --------------------------------------------------------------------------
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# OpenMS -- Open-Source Mass Spectrometry
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# --------------------------------------------------------------------------
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# Copyright OpenMS Inc. -- Eberhard Karls University Tuebingen,
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# ETH Zurich, and Freie Universitaet Berlin 2002-present.
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#
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# This software is released under a three-clause BSD license:
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# * Redistributions of source code must retain the above copyright
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# notice, this list of conditions and the following disclaimer.
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# * Redistributions in binary form must reproduce the above copyright
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# notice, this list of conditions and the following disclaimer in the
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# documentation and/or other materials provided with the distribution.
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# * Neither the name of any author or any participating institution
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# may be used to endorse or promote products derived from this software
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# without specific prior written permission.
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# For a full list of authors, refer to the file AUTHORS.
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# --------------------------------------------------------------------------
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# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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# ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
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# INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
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# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
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# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
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# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
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# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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#
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# Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
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# SPDX-License-Identifier: BSD-3-Clause
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#
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# --------------------------------------------------------------------------
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# $Maintainer: Julianus Pfeuffer $
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# $Authors: Stephan Aiche, Julianus Pfeuffer $
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# --------------------------------------------------------------------------
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cmake_minimum_required(VERSION 3.21 FATAL_ERROR) ## if you change this, also update doc/doxygen/install/install-<OS>.doxygen
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# Handle default build type

‎cmake/AddressSanitizer.cmake‎

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# --------------------------------------------------------------------------
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# OpenMS -- Open-Source Mass Spectrometry
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# --------------------------------------------------------------------------
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# Copyright OpenMS Inc. -- Eberhard Karls University Tuebingen,
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# ETH Zurich, and Freie Universitaet Berlin 2002-present.
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#
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# This software is released under a three-clause BSD license:
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# * Redistributions of source code must retain the above copyright
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# notice, this list of conditions and the following disclaimer.
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# * Redistributions in binary form must reproduce the above copyright
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# notice, this list of conditions and the following disclaimer in the
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# documentation and/or other materials provided with the distribution.
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# * Neither the name of any author or any participating institution
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# may be used to endorse or promote products derived from this software
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# without specific prior written permission.
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# For a full list of authors, refer to the file AUTHORS.
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# --------------------------------------------------------------------------
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# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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# ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
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# INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
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# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
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# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
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# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
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# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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#
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# Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
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# SPDX-License-Identifier: BSD-3-Clause
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#
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# --------------------------------------------------------------------------
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# $Maintainer: Hannes Roest $
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# $Authors: Hannes Roest, Timo Sachsenberg $
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# --------------------------------------------------------------------------
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#------------------------------------------------------------------------------
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# This cmake file enables the AddressSanitizer and UndefinedBehaviorSanitizer
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# see http://clang.llvm.org/docs/AddressSanitizer.html and https://clang.llvm.org/docs/UndefinedBehaviorSanitizer.html

‎cmake/Coverage.cmake‎

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# --------------------------------------------------------------------------
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# OpenMS -- Open-Source Mass Spectrometry
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# --------------------------------------------------------------------------
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# Copyright OpenMS Inc. -- Eberhard Karls University Tuebingen,
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# ETH Zurich, and Freie Universitaet Berlin 2002-present.
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#
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# This software is released under a three-clause BSD license:
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# * Redistributions of source code must retain the above copyright
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# notice, this list of conditions and the following disclaimer.
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# * Redistributions in binary form must reproduce the above copyright
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# notice, this list of conditions and the following disclaimer in the
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# documentation and/or other materials provided with the distribution.
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# * Neither the name of any author or any participating institution
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# may be used to endorse or promote products derived from this software
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# without specific prior written permission.
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# For a full list of authors, refer to the file AUTHORS.
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# --------------------------------------------------------------------------
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# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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# ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
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# INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
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# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
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# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
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# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
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# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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#
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# Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
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# SPDX-License-Identifier: BSD-3-Clause
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#
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# --------------------------------------------------------------------------
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# $Maintainer: Julianus Pfeuffer $
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# $Authors: Julianus Pfeuffer $
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# --------------------------------------------------------------------------
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#------------------------------------------------------------------------------
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# This cmake file enables generation of gcov files.
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‎cmake/Modules/CheckLibArchitecture.cmake‎

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# --------------------------------------------------------------------------
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# OpenMS -- Open-Source Mass Spectrometry
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# --------------------------------------------------------------------------
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# Copyright OpenMS Inc. -- Eberhard Karls University Tuebingen,
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# ETH Zurich, and Freie Universitaet Berlin 2002-present.
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#
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# This software is released under a three-clause BSD license:
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# * Redistributions of source code must retain the above copyright
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# notice, this list of conditions and the following disclaimer.
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# * Redistributions in binary form must reproduce the above copyright
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# notice, this list of conditions and the following disclaimer in the
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# documentation and/or other materials provided with the distribution.
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# * Neither the name of any author or any participating institution
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# may be used to endorse or promote products derived from this software
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# without specific prior written permission.
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# For a full list of authors, refer to the file AUTHORS.
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# --------------------------------------------------------------------------
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# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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# ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
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# INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
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# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
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# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
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# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
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# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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#
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# Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
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# SPDX-License-Identifier: BSD-3-Clause
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#
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# --------------------------------------------------------------------------
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# $Maintainer: Chris Bielow $
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# $Authors: Chris Bielow $
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# --------------------------------------------------------------------------
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## Check if link libraries have right architecture (.lib can be either a static or link library for a dll)
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## Motivation: if 32bit libs are accidentally linked against a 64bit OpenMS, weird linker errors (symbol not found, etc) will appear.
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## These are really hard to track down, so we check in advance.

‎cmake/OpenMSConfig.cmake.in‎

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# --------------------------------------------------------------------------
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# OpenMS -- Open-Source Mass Spectrometry
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# --------------------------------------------------------------------------
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# Copyright OpenMS Inc. -- Eberhard Karls University Tuebingen,
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# ETH Zurich, and Freie Universitaet Berlin 2002-present.
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#
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# This software is released under a three-clause BSD license:
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# * Redistributions of source code must retain the above copyright
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# notice, this list of conditions and the following disclaimer.
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# * Redistributions in binary form must reproduce the above copyright
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# notice, this list of conditions and the following disclaimer in the
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# documentation and/or other materials provided with the distribution.
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# * Neither the name of any author or any participating institution
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# may be used to endorse or promote products derived from this software
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# without specific prior written permission.
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# For a full list of authors, refer to the file AUTHORS.
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# --------------------------------------------------------------------------
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# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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# ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
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# INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
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# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
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# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
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# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
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# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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#
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# Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
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# SPDX-License-Identifier: BSD-3-Clause
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#
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# --------------------------------------------------------------------------
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# $Maintainer: Julianus Pfeuffer $
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# $Authors: Julianus Pfeuffer $

‎cmake/cmake_findExternalLibs.cmake‎

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# --------------------------------------------------------------------------
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# OpenMS -- Open-Source Mass Spectrometry
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# --------------------------------------------------------------------------
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# Copyright OpenMS Inc. -- Eberhard Karls University Tuebingen,
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# ETH Zurich, and Freie Universitaet Berlin 2002-present.
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#
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# This software is released under a three-clause BSD license:
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# * Redistributions of source code must retain the above copyright
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# notice, this list of conditions and the following disclaimer.
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# * Redistributions in binary form must reproduce the above copyright
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# notice, this list of conditions and the following disclaimer in the
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# documentation and/or other materials provided with the distribution.
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# * Neither the name of any author or any participating institution
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# may be used to endorse or promote products derived from this software
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# without specific prior written permission.
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# For a full list of authors, refer to the file AUTHORS.
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# --------------------------------------------------------------------------
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# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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# ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
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# INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
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# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
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# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
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# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
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# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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#
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# Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
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# SPDX-License-Identifier: BSD-3-Clause
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#
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# --------------------------------------------------------------------------
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# $Maintainer: Stephan Aiche, Chris Bielow $
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# $Authors: Chris Bielow, Stephan Aiche $
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# --------------------------------------------------------------------------
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#------------------------------------------------------------------------------
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# This cmake file handles finding external libs for OpenMS
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#------------------------------------------------------------------------------

‎cmake/compiler_flags.cmake‎

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# --------------------------------------------------------------------------
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# OpenMS -- Open-Source Mass Spectrometry
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# --------------------------------------------------------------------------
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# Copyright OpenMS Inc. -- Eberhard Karls University Tuebingen,
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# ETH Zurich, and Freie Universitaet Berlin 2002-present.
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#
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# This software is released under a three-clause BSD license:
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# * Redistributions of source code must retain the above copyright
9-
# notice, this list of conditions and the following disclaimer.
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# * Redistributions in binary form must reproduce the above copyright
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# notice, this list of conditions and the following disclaimer in the
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# documentation and/or other materials provided with the distribution.
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# * Neither the name of any author or any participating institution
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# may be used to endorse or promote products derived from this software
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# without specific prior written permission.
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# For a full list of authors, refer to the file AUTHORS.
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# --------------------------------------------------------------------------
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# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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# ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
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# INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
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# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
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# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
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# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
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# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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#
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# Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
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# SPDX-License-Identifier: BSD-3-Clause
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#
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# --------------------------------------------------------------------------
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# $Maintainer: Stephan Aiche, Chris Bielow $
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# $Authors: Andreas Bertsch, Chris Bielow, Stephan Aiche $
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# --------------------------------------------------------------------------
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#------------------------------------------------------------------------------
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# This cmake file handles all the project specific compiler flags
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# It defines variables and options and provides functions to apply flags to targets

‎cmake/export_macros.cmake‎

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# --------------------------------------------------------------------------
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# OpenMS -- Open-Source Mass Spectrometry
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# --------------------------------------------------------------------------
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# Copyright OpenMS Inc. -- Eberhard Karls University Tuebingen,
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# ETH Zurich, and Freie Universitaet Berlin 2002-present.
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#
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# This software is released under a three-clause BSD license:
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# * Redistributions of source code must retain the above copyright
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# notice, this list of conditions and the following disclaimer.
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# * Redistributions in binary form must reproduce the above copyright
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# notice, this list of conditions and the following disclaimer in the
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# documentation and/or other materials provided with the distribution.
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# * Neither the name of any author or any participating institution
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# may be used to endorse or promote products derived from this software
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# without specific prior written permission.
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# For a full list of authors, refer to the file AUTHORS.
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# --------------------------------------------------------------------------
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# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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# ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
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# INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
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# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
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# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
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# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
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# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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#
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# Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
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# SPDX-License-Identifier: BSD-3-Clause
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#
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# --------------------------------------------------------------------------
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# $Maintainer: Stephan Aiche $
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# $Authors: Stephan Aiche $
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# --------------------------------------------------------------------------
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include(CMakePackageConfigHelpers)
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# a collection of wrapper for export functions that allows easier usage

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