more license changes

cmake/MacOSX/sign_bins_and_libs.rb

@@ -1,34 +1,7 @@
 #!/usr/bin/ruby
 
-# --------------------------------------------------------------------------
-#                   OpenMS -- Open-Source Mass Spectrometry
-# --------------------------------------------------------------------------
-# Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
-# ETH Zurich, and Freie Universitaet Berlin 2002-2023.
-#
-# This software is released under a three-clause BSD license:
-#  * Redistributions of source code must retain the above copyright
-#    notice, this list of conditions and the following disclaimer.
-#  * Redistributions in binary form must reproduce the above copyright
-#    notice, this list of conditions and the following disclaimer in the
-#    documentation and/or other materials provided with the distribution.
-#  * Neither the name of any author or any participating institution
-#    may be used to endorse or promote products derived from this software
-#    without specific prior written permission.
-# For a full list of authors, refer to the file AUTHORS.
-# --------------------------------------------------------------------------
-# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-# ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
-# INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
-# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
-# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
-# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
-# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
-# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
-# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-#
+# Copyright (c) 2002-present, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
+# SPDX-License-Identifier: BSD-3-Clause
 # --------------------------------------------------------------------------
 # $Maintainer: Stephan Aiche $
 # $Authors: Stephan Aiche $

cmake/OpenMSConfigVersion.cmake.in

@@ -1,32 +1,5 @@
-# --------------------------------------------------------------------------
-#                   OpenMS -- Open-Source Mass Spectrometry
-# --------------------------------------------------------------------------
-# Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
-# ETH Zurich, and Freie Universitaet Berlin 2002-2023.
-#
-# This software is released under a three-clause BSD license:
-#  * Redistributions of source code must retain the above copyright
-#    notice, this list of conditions and the following disclaimer.
-#  * Redistributions in binary form must reproduce the above copyright
-#    notice, this list of conditions and the following disclaimer in the
-#    documentation and/or other materials provided with the distribution.
-#  * Neither the name of any author or any participating institution
-#    may be used to endorse or promote products derived from this software
-#    without specific prior written permission.
-# For a full list of authors, refer to the file AUTHORS.
-# --------------------------------------------------------------------------
-# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-# ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
-# INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
-# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
-# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
-# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
-# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
-# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
-# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-#
+# Copyright (c) 2002-present, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
+# SPDX-License-Identifier: BSD-3-Clause#
 # --------------------------------------------------------------------------
 # $Maintainer: Julianus Pfeuffer $
 # $Authors: Julianus Pfeuffer $

cmake/knime/TPCOPYRIGHT

@@ -1,6 +1,6 @@
 For the plugin infrastructure and the adapter code, the
 copyright belongs to The OpenMS Team -- Eberhard Karls University Tuebingen,
-ETH Zurich, and Freie Universitaet Berlin 2002-2023.
+ETH Zurich, and Freie Universitaet Berlin 2002-present.
 
 For the underlying thirdparty executables, please see the description of
 the individual nodes.

doc/doxygen/public/PyOpenMS.doxygen

@@ -1,4 +1,4 @@
-// Copyright (c) 2002-2023, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
+// Copyright (c) 2002-present, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
 // SPDX-License-Identifier: BSD-3-Clause
 // 
 // --------------------------------------------------------------------------

doc/doxygen/public/TOPP.doxygen

@@ -1,4 +1,4 @@
-// Copyright (c) 2002-2023, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
+// Copyright (c) 2002-present, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
 // SPDX-License-Identifier: BSD-3-Clause
 //
 // --------------------------------------------------------------------------

src/pyOpenMS/doCythonCompileOnly.py

@@ -1,35 +1,8 @@
 #!/usr/bin/env python
 # -*- coding: utf-8  -*-
 """
---------------------------------------------------------------------------
-                  OpenMS -- Open-Source Mass Spectrometry
---------------------------------------------------------------------------
-Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
-ETH Zurich, and Freie Universitaet Berlin 2002-2023.
-
-This software is released under a three-clause BSD license:
- * Redistributions of source code must retain the above copyright
-   notice, this list of conditions and the following disclaimer.
- * Redistributions in binary form must reproduce the above copyright
-   notice, this list of conditions and the following disclaimer in the
-   documentation and/or other materials provided with the distribution.
- * Neither the name of any author or any participating institution
-   may be used to endorse or promote products derived from this software
-   without specific prior written permission.
-For a full list of authors, refer to the file AUTHORS.
---------------------------------------------------------------------------
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
-INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
-EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
-PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
-OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
-WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
-OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
-ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
+Copyright (c) 2002-present, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
+SPDX-License-Identifier: BSD-3-Clause
 --------------------------------------------------------------------------
 $Maintainer: Hannes Roest $
 $Authors: Hannes Roest $

src/topp/CMakeLists.txt

@@ -1,4 +1,4 @@
-# Copyright (c) 2002-2023, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
+# Copyright (c) 2002-present, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
 # SPDX-License-Identifier: BSD-3-Clause
 # --------------------------------------------------------------------------
 # $Maintainer: Stephan Aiche, Chris Bielow $

tools/SPDX.txt

@@ -1,2 +1,2 @@
-// Copyright (c) 2002-2023, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
+// Copyright (c) 2002-present, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
 // SPDX-License-Identifier: BSD-3-Clause

tools/checker.php

@@ -1,33 +1,6 @@
 <?php
-# --------------------------------------------------------------------------
-#                   OpenMS -- Open-Source Mass Spectrometry
-# --------------------------------------------------------------------------
-# Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
-# ETH Zurich, and Freie Universitaet Berlin 2002-2023.
-#
-# This software is released under a three-clause BSD license:
-#  * Redistributions of source code must retain the above copyright
-#    notice, this list of conditions and the following disclaimer.
-#  * Redistributions in binary form must reproduce the above copyright
-#    notice, this list of conditions and the following disclaimer in the
-#    documentation and/or other materials provided with the distribution.
-#  * Neither the name of any author or any participating institution
-#    may be used to endorse or promote products derived from this software
-#    without specific prior written permission.
-# For a full list of authors, refer to the file AUTHORS.
-# --------------------------------------------------------------------------
-# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-# ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
-# INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
-# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
-# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
-# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
-# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
-# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
-# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-#
+# Copyright (c) 2002-present, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
+# SPDX-License-Identifier: BSD-3-Clause
 # --------------------------------------------------------------------------
 # $Maintainer:$
 # $Authors: Marc Sturm $

tools/create_class.rb

@@ -1,33 +1,7 @@
 #!/usr/bin/env ruby
 
-# --------------------------------------------------------------------------
-#                   OpenMS -- Open-Source Mass Spectrometry
-# --------------------------------------------------------------------------
-# Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
-# ETH Zurich, and Freie Universitaet Berlin 2002-2023.
-#
-# This software is released under a three-clause BSD license:
-#  * Redistributions of source code must retain the above copyright
-#    notice, this list of conditions and the following disclaimer.
-#  * Redistributions in binary form must reproduce the above copyright
-#    notice, this list of conditions and the following disclaimer in the
-#    documentation and/or other materials provided with the distribution.
-#  * Neither the name of any author or any participating institution
-#    may be used to endorse or promote products derived from this software
-#    without specific prior written permission.
-# For a full list of authors, refer to the file AUTHORS.
-# --------------------------------------------------------------------------
-# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-# ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
-# INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
-# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
-# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
-# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
-# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
-# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
-# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+# Copyright (c) 2002-present, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
+# SPDX-License-Identifier: BSD-3-Clause
 #
 # --------------------------------------------------------------------------
 # $Maintainer: Stephan Aiche $

tools/rest_server_update_helper.sh

@@ -1,32 +1,6 @@
 #!/bin/bash
-# --------------------------------------------------------------------------
-#                   OpenMS -- Open-Source Mass Spectrometry
-# --------------------------------------------------------------------------
-# Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
-# ETH Zurich, and Freie Universitaet Berlin 2002-2023.
-#
-# This software is released under a three-clause BSD license:
-#  * Redistributions of source code must retain the above copyright
-#    notice, this list of conditions and the following disclaimer.
-#  * Redistributions in binary form must reproduce the above copyright
-#    notice, this list of conditions and the following disclaimer in the
-#    documentation and/or other materials provided with the distribution.
-#  * Neither the name of any author or any participating institution
-#    may be used to endorse or promote products derived from this software
-#    without specific prior written permission.
-# For a full list of authors, refer to the file AUTHORS.
-# --------------------------------------------------------------------------
-# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-# ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
-# INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
-# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
-# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
-# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
-# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
-# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
-# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+# Copyright (c) 2002-present, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
+# SPDX-License-Identifier: BSD-3-Clause
 #
 # --------------------------------------------------------------------------
 # $Maintainer: Timo Sachsenberg $

tools/scripts/create_im_with_swathIm.py

@@ -1,35 +1,8 @@
 #!/usr/bin/env python
 # -*- coding: utf-8  -*-
 """
---------------------------------------------------------------------------
-                  OpenMS -- Open-Source Mass Spectrometry
---------------------------------------------------------------------------
-Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
-ETH Zurich, and Freie Universitaet Berlin 2002-2023.
-
-This software is released under a three-clause BSD license:
- * Redistributions of source code must retain the above copyright
-   notice, this list of conditions and the following disclaimer.
- * Redistributions in binary form must reproduce the above copyright
-   notice, this list of conditions and the following disclaimer in the
-   documentation and/or other materials provided with the distribution.
- * Neither the name of any author or any participating institution
-   may be used to endorse or promote products derived from this software
-   without specific prior written permission.
-For a full list of authors, refer to the file AUTHORS.
---------------------------------------------------------------------------
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
-INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
-EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
-PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
-OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
-WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
-OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
-ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
+Copyright (c) 2002-present, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
+SPDX-License-Identifier: BSD-3-Clause
 --------------------------------------------------------------------------
 $Maintainer: Hannes Roest, Joshua Charkow $
 $Authors: Hannes Roest, Joshua Charkow $

tools/scripts/create_sonar.py

@@ -1,34 +1,8 @@
 #!/usr/bin/env python
 # -*- coding: utf-8  -*-
 """
---------------------------------------------------------------------------
-                  OpenMS -- Open-Source Mass Spectrometry
---------------------------------------------------------------------------
-Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
-ETH Zurich, and Freie Universitaet Berlin 2002-2023.
-
-This software is released under a three-clause BSD license:
- * Redistributions of source code must retain the above copyright
-   notice, this list of conditions and the following disclaimer.
- * Redistributions in binary form must reproduce the above copyright
-   notice, this list of conditions and the following disclaimer in the
-   documentation and/or other materials provided with the distribution.
- * Neither the name of any author or any participating institution
-   may be used to endorse or promote products derived from this software
-   without specific prior written permission.
-For a full list of authors, refer to the file AUTHORS.
---------------------------------------------------------------------------
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
-INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
-EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
-PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
-OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
-WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
-OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
-ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+Copyright (c) 2002-present, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
+SPDX-License-Identifier: BSD-3-Clause
 
 --------------------------------------------------------------------------
 $Maintainer: Hannes Roest $