Update license

CMakeLists.txt

@@ -1,32 +1,5 @@
-# Copyright (c) Stanford University, The Regents of the University of
-#               California, and others.
-#
-# All Rights Reserved.
-#
-# See Copyright-SimVascular.txt for additional details.
-#
-# Permission is hereby granted, free of charge, to any person obtaining
-# a copy of this software and associated documentation files (the
-# "Software"), to deal in the Software without restriction, including
-# without limitation the rights to use, copy, modify, merge, publish,
-# distribute, sublicense, and/or sell copies of the Software, and to
-# permit persons to whom the Software is furnished to do so, subject
-# to the following conditions:
-#
-# The above copyright notice and this permission notice shall be included
-# in all copies or substantial portions of the Software.
-#
-# 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 THE COPYRIGHT OWNER
-# OR CONTRIBUTORS 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.
+# SPDX-FileCopyrightText: Copyright (c) Stanford University, The Regents of the University of California, and others.
+# SPDX-License-Identifier: BSD-3-Clause
 
 set(CMAKE_POLICY_VERSION_MINIMUM 3.5)
 cmake_minimum_required(VERSION 3.5)
@@ -297,4 +270,4 @@ if (WIN32)
             PREFIX ""
             SUFFIX ".pyd"
     )
-endif()
+endif()

LICENSE.txt

@@ -1,11 +1,11 @@
-Copyright (c) Stanford University, The Regents of the University of California, and others.
+Copyright 2016-2025 Stanford University, The Regents of the University of California, and others.
 
-All Rights Reserved.
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
 
-See Copyright-SimVascular.txt for additional details.
+1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
 
-Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: 
+2. 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.
 
-The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
 
-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 THE COPYRIGHT OWNER OR CONTRIBUTORS 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.
+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 THE COPYRIGHT HOLDER OR CONTRIBUTORS 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.

applications/pysvzerod.cpp

@@ -1,32 +1,5 @@
-// Copyright (c) Stanford University, The Regents of the University of
-//               California, and others.
-//
-// All Rights Reserved.
-//
-// See Copyright-SimVascular.txt for additional details.
-//
-// Permission is hereby granted, free of charge, to any person obtaining
-// a copy of this software and associated documentation files (the
-// "Software"), to deal in the Software without restriction, including
-// without limitation the rights to use, copy, modify, merge, publish,
-// distribute, sublicense, and/or sell copies of the Software, and to
-// permit persons to whom the Software is furnished to do so, subject
-// to the following conditions:
-//
-// The above copyright notice and this permission notice shall be included
-// in all copies or substantial portions of the Software.
-//
-// 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 THE COPYRIGHT OWNER
-// OR CONTRIBUTORS 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.
+// SPDX-FileCopyrightText: Copyright (c) Stanford University, The Regents of the University of California, and others.
+// SPDX-License-Identifier: BSD-3-Clause
 /**
  * @file pysvzerod.cpp
  * @brief Python interface for svZeroDSolver

applications/svZeroDGUI/static/js/app.js

@@ -1,3 +1,5 @@
+// SPDX-FileCopyrightText: Copyright (c) Stanford University, The Regents of the University of California, and others.
+// SPDX-License-Identifier: BSD-3-Clause
 /**
  * app.js
  *

applications/svZeroDGUI/static/js/cytoscape-edgehandles.js

@@ -1,3 +1,5 @@
+// SPDX-FileCopyrightText: Copyright (c) Stanford University, The Regents of the University of California, and others.
+// SPDX-License-Identifier: BSD-3-Clause
 /**
  * cytoscape-edgehandles.js
  *
@@ -1168,4 +1170,4 @@ module.exports = __WEBPACK_EXTERNAL_MODULE_14__;
 
 /***/ })
 /******/ ]);
-});
+});

applications/svZeroDVisualization/dirgraph_connections.py

@@ -1,34 +1,7 @@
 # coding=utf-8
 
-# Copyright (c) Stanford University, The Regents of the University of
-#               California, and others.
-#
-# All Rights Reserved.
-#
-# See Copyright-SimVascular.txt for additional details.
-#
-# Permission is hereby granted, free of charge, to any person obtaining
-# a copy of this software and associated documentation files (the
-# "Software"), to deal in the Software without restriction, including
-# without limitation the rights to use, copy, modify, merge, publish,
-# distribute, sublicense, and/or sell copies of the Software, and to
-# permit persons to whom the Software is furnished to do so, subject
-# to the following conditions:
-#
-# The above copyright notice and this permission notice shall be included
-# in all copies or substantial portions of the Software.
-#
-# 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 THE COPYRIGHT OWNER
-# OR CONTRIBUTORS 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.
+# SPDX-FileCopyrightText: Copyright (c) Stanford University, The Regents of the University of California, and others.
+# SPDX-License-Identifier: BSD-3-Clause
 
 import numpy as np
 from dirgraph_wire import wire

applications/svZeroDVisualization/dirgraph_steady_bc.py

@@ -1,33 +1,5 @@
-# Copyright (c) Stanford University, The Regents of the University of
-#               California, and others.
-#
-# All Rights Reserved.
-#
-# See Copyright-SimVascular.txt for additional details.
-#
-# Permission is hereby granted, free of charge, to any person obtaining
-# a copy of this software and associated documentation files (the
-# "Software"), to deal in the Software without restriction, including
-# without limitation the rights to use, copy, modify, merge, publish,
-# distribute, sublicense, and/or sell copies of the Software, and to
-# permit persons to whom the Software is furnished to do so, subject
-# to the following conditions:
-#
-# The above copyright notice and this permission notice shall be included
-# in all copies or substantial portions of the Software.
-#
-# 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 THE COPYRIGHT OWNER
-# OR CONTRIBUTORS 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.
-
+# SPDX-FileCopyrightText: Copyright (c) Stanford University, The Regents of the University of California, and others.
+# SPDX-License-Identifier: BSD-3-Clause
 import copy
 import numpy as np
 

applications/svZeroDVisualization/dirgraph_utils.py

@@ -1,5 +1,7 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
+# SPDX-FileCopyrightText: Copyright (c) Stanford University, The Regents of the University of California, and others.
+# SPDX-License-Identifier: BSD-3-Clause
 """
 This code will create a directed graph by reading a .json file.
 """
@@ -710,4 +712,4 @@ def set_up_0d_network(zero_d_solver_input_file_path: object, output_dir, name_ty
         zero_d_solver_input_file_path,
         d,
         draw_directed_graph=draw_directed_graph, output_dir=output_dir
-    )
+    )

applications/svZeroDVisualization/dirgraph_wire.py

@@ -1,34 +1,7 @@
 # coding=utf-8
 
-# Copyright (c) Stanford University, The Regents of the University of
-#               California, and others.
-#
-# All Rights Reserved.
-#
-# See Copyright-SimVascular.txt for additional details.
-#
-# Permission is hereby granted, free of charge, to any person obtaining
-# a copy of this software and associated documentation files (the
-# "Software"), to deal in the Software without restriction, including
-# without limitation the rights to use, copy, modify, merge, publish,
-# distribute, sublicense, and/or sell copies of the Software, and to
-# permit persons to whom the Software is furnished to do so, subject
-# to the following conditions:
-#
-# The above copyright notice and this permission notice shall be included
-# in all copies or substantial portions of the Software.
-#
-# 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 THE COPYRIGHT OWNER
-# OR CONTRIBUTORS 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.
+# SPDX-FileCopyrightText: Copyright (c) Stanford University, The Regents of the University of California, and others.
+# SPDX-License-Identifier: BSD-3-Clause
 
 import numpy as np
 

applications/svZeroDVisualization/visualize_simulation.py

@@ -1,3 +1,6 @@
+# SPDX-FileCopyrightText: Copyright (c) Stanford University, The Regents of the University of California, and others.
+# SPDX-License-Identifier: BSD-3-Clause
+
 import sys
 import argparse
 import pysvzerod
@@ -648,4 +651,4 @@ def update_graphs(clickData):
 
 
 if __name__ == '__main__':
-    app.run_server(debug=True)
+    app.run_server(debug=True)

applications/svzerodcalibrator.cpp

@@ -1,32 +1,5 @@
-// Copyright (c) Stanford University, The Regents of the University of
-//               California, and others.
-//
-// All Rights Reserved.
-//
-// See Copyright-SimVascular.txt for additional details.
-//
-// Permission is hereby granted, free of charge, to any person obtaining
-// a copy of this software and associated documentation files (the
-// "Software"), to deal in the Software without restriction, including
-// without limitation the rights to use, copy, modify, merge, publish,
-// distribute, sublicense, and/or sell copies of the Software, and to
-// permit persons to whom the Software is furnished to do so, subject
-// to the following conditions:
-//
-// The above copyright notice and this permission notice shall be included
-// in all copies or substantial portions of the Software.
-//
-// 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 THE COPYRIGHT OWNER
-// OR CONTRIBUTORS 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.
+// SPDX-FileCopyrightText: Copyright (c) Stanford University, The Regents of the University of California, and others.
+// SPDX-License-Identifier: BSD-3-Clause
 /**
  * @file svzerodcalibrator.cpp
  * @brief Main routine for svZeroDCalibrator

applications/svzerodsolver.cpp

@@ -1,32 +1,5 @@
-// Copyright (c) Stanford University, The Regents of the University of
-//               California, and others.
-//
-// All Rights Reserved.
-//
-// See Copyright-SimVascular.txt for additional details.
-//
-// Permission is hereby granted, free of charge, to any person obtaining
-// a copy of this software and associated documentation files (the
-// "Software"), to deal in the Software without restriction, including
-// without limitation the rights to use, copy, modify, merge, publish,
-// distribute, sublicense, and/or sell copies of the Software, and to
-// permit persons to whom the Software is furnished to do so, subject
-// to the following conditions:
-//
-// The above copyright notice and this permission notice shall be included
-// in all copies or substantial portions of the Software.
-//
-// 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 THE COPYRIGHT OWNER
-// OR CONTRIBUTORS 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.
+// SPDX-FileCopyrightText: Copyright (c) Stanford University, The Regents of the University of California, and others.
+// SPDX-License-Identifier: BSD-3-Clause
 /**
  * @file svzerodsolver.cpp
  * @brief Main routine of svZeroDSolver

src/algebra/CMakeLists.txt

@@ -1,32 +1,5 @@
-# Copyright (c) Stanford University, The Regents of the University of
-#               California, and others.
-#
-# All Rights Reserved.
-#
-# See Copyright-SimVascular.txt for additional details.
-#
-# Permission is hereby granted, free of charge, to any person obtaining
-# a copy of this software and associated documentation files (the
-# "Software"), to deal in the Software without restriction, including
-# without limitation the rights to use, copy, modify, merge, publish,
-# distribute, sublicense, and/or sell copies of the Software, and to
-# permit persons to whom the Software is furnished to do so, subject
-# to the following conditions:
-#
-# The above copyright notice and this permission notice shall be included
-# in all copies or substantial portions of the Software.
-#
-# 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 THE COPYRIGHT OWNER
-# OR CONTRIBUTORS 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.
+# SPDX-FileCopyrightText: Copyright (c) Stanford University, The Regents of the University of California, and others.
+# SPDX-License-Identifier: BSD-3-Clause
 
 # Build the algebra object files.