Rebase recent commits and update license (after resolving merge conflicts) (#180)

Co-authored-by: menon-karthik <[email protected]>
Co-authored-by: Martin Pfaller <[email protected]>
Co-authored-by: Nick Dorn <[email protected]>
Co-authored-by: Zachary Sexton <[email protected]>
Co-authored-by: Philip Cardiff <[email protected]>

Author: 5 people

.github/workflows/test.yml

@@ -7,48 +7,86 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-22.04, ubuntu-latest, macos-13, macos-latest]
+        os: [ubuntu-22.04, ubuntu-latest, macos-13, macos-latest, windows-latest]
         version: [13] # GCC version
       fail-fast: false
     env:
       GCC_V: ${{ matrix.version }}
+      CONDA_ENV: zerod
+      PYTHONPATH: ${{ github.workspace }}
     steps:
       - uses: actions/checkout@v4
       - uses: conda-incubator/setup-miniconda@v3
         with:
           auto-update-conda: true
+          activate-environment: ${{env.CONDA_ENV}}
+          python-version: "3.11.4"
       - name: Install ubuntu dependencies
         if: startsWith(matrix.os, 'ubuntu')
         run: sudo apt update && sudo apt install build-essential cmake lcov
-      - name: Create conda environment
-        run: |
-          #export PATH="/usr/share/miniconda/bin:$PATH"
-          #alias conda="$CONDA/bin/conda"
-          conda create -n zerod python=3.11.4
+
       - name: Install dependencies to get correct version numbers (Ubuntu)
         if: startsWith(matrix.os, 'ubuntu')
-        run: conda install -n zerod -c conda-forge libstdcxx-ng=${GCC_V} gcc=${GCC_V}
+        run: conda install -c conda-forge libstdcxx-ng=${GCC_V} gcc=${GCC_V}
+
       - name: Install dependencies to get correct version numbers (MacOS)
         if: startsWith(matrix.os, 'macos')
         run: |
           brew install gcc@${GCC_V}
           ln -s /usr/local/bin/gcc-${GCC_V} /usr/local/bin/gcc
-      - name: Install svZeroDSolver
-        run: conda run -n zerod pip install -e ".[dev]"
+
+      - name: Install dependencies for windows
+        if: startsWith(matrix.os, 'windows')
+        shell: pwsh
+        run: |
+          choco install mingw --no-progress
+          conda install -y -c conda-forge cmake graphviz python-graphviz pydot
+          pip install --upgrade cmake-setuptools
+
+      - name: Install POISX-like svZeroDSolver
+        if: ${{!startsWith(matrix.os, 'windows')}}
+        run: conda run pip install -e ".[dev]"
+
+      - name: Install Windows svZeroDSolver
+        if: startsWith(matrix.os, 'windows')
+        shell: pwsh
+        run: |
+          $Env:CMAKE_GENERATOR = 'MinGW Makefiles'
+          Write-Host "→ Using CMAKE_GENERATOR = $Env:CMAKE_GENERATOR"
+          pip install --no-build-isolation -v .[dev]
+          pip show pysvzerod
+
       - name: Install Networkx
         run: |
-            conda run -n zerod pip install networkx
+            conda run pip install networkx
+
       - name: Test the build
         run: |
           cd tests
-          conda run -n zerod pytest -v --durations=0 --ignore=test_dirgraph.py
-      - name: Build using CMake
+          conda run pytest -v --durations=0 --ignore=test_dirgraph.py
+
+      - name: Build using CMake for POISX-like Systems
+        if: ${{!startsWith(matrix.os, 'windows')}}
         run: |
           mkdir Release
           cd Release
           cmake -DCMAKE_BUILD_TYPE=Release -DENABLE_DISTRIBUTION=ON ..
           make -j2
-      - name: Test interface
+
+      - name: Build using CMake for Windows Systems
+        if: startsWith(matrix.os, 'windows')
+        shell: pwsh
+        run: |
+          mkdir Release
+          cd Release
+          cmake -G "MinGW Makefiles" `
+                -DCMAKE_BUILD_TYPE=Release `
+                -DENABLE_DISTRIBUTION=ON `
+                ..
+          cmake --build . --parallel 2
+
+      - name: Test interface POISX-like Systems
+        if: ${{!startsWith(matrix.os, 'windows')}}
         run: |
           cd tests/test_interface
           mkdir build_tests
@@ -59,32 +97,65 @@ jobs:
           ./svZeroD_interface_test01 ../../../../Release ../../test_01/svzerod_3Dcoupling.json
           cd ../test_02
           ./svZeroD_interface_test02 ../../../../Release ../../test_02/svzerod_tuned.json
+
+      - name: Test interface Windows Systems
+        if: startsWith(matrix.os, 'windows')
+        shell: pwsh
+        run: |
+          cd tests/test_interface
+          mkdir build_tests
+          cd build_tests
+          cmake -G "MinGW Makefiles" ..
+          cmake --build . --parallel 2
+          cd test_01
+          ./svZeroD_interface_test01.exe `
+            ../../../../Release `
+            ../../test_01/svzerod_3Dcoupling.json
+          
+          cd ../test_02
+          ./svZeroD_interface_test02 `
+            ../../../../Release `
+            ../../test_02/svzerod_tuned.json
+
       - name: Generate code coverage
         if: startsWith(matrix.os, 'ubuntu-22.04')
         run: |
           cd Release
           cmake -DENABLE_COVERAGE=ON ..
           make -j2
           cd ../tests
-          conda run -n zerod pytest -v --durations=0 --coverage --ignore=test_dirgraph.py
+          conda run pytest -v --durations=0 --coverage --ignore=test_dirgraph.py
           cd ../Release
           make coverage
+
       - name: Save coverage report
         if: startsWith(matrix.os, 'ubuntu-22.04')
         uses: actions/upload-artifact@v4
         with:
           name: coverage_report
           path: Release/coverage
+
       - name: Upload coverage reports to Codecov
         if: startsWith(matrix.os, 'ubuntu-22.04')
         uses: codecov/codecov-action@v4
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
-      - name: Build installer
+
+      - name: Build installer POISX-like Systems
+        if: ${{!startsWith(matrix.os, 'windows')}}
         run: |
           cd Release
           cpack
           cp distribution/svZeroDSolver_* ..
+
+      - name: Build installer Windows Systems
+        if: startsWith(matrix.os, 'windows')
+        shell: pwsh
+        run: |
+          cd Release
+          cpack
+          Copy-Item distribution\svZeroDSolver_* -Destination ..\
+
       - name: Upload installer
         uses: actions/upload-artifact@v4
         with:

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)
@@ -58,6 +31,22 @@ if(ENABLE_COVERAGE)
     WORKING_DIRECTORY ${CMAKE_BINARY_DIR})
 endif()
 
+if (WIN32 AND MSVC)
+    # CMake ≥ 3.15 has a proper variable
+    if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15")
+        set(CMAKE_MSVC_RUNTIME_LIBRARY
+                "MultiThreaded$<$<CONFIG:Debug>:Debug>")
+    else()
+        # CMake < 3.15: manually swap /MD → /MT in all flags for static
+        # versions of the runtime libraries
+        foreach(_var
+                CMAKE_C_FLAGS CMAKE_C_FLAGS_DEBUG CMAKE_C_FLAGS_RELEASE
+                CMAKE_CXX_FLAGS CMAKE_CXX_FLAGS_DEBUG CMAKE_CXX_FLAGS_RELEASE
+                CMAKE_SHARED_LINKER_FLAGS)
+            string(REPLACE "/MD" "/MT" ${_var} "${${_var}}")
+        endforeach()
+    endif()
+endif()
 # -----------------------------------------------------------------------------
 # Set the location to store the binaries and libraries created by this project.
 # -----------------------------------------------------------------------------
@@ -159,7 +148,38 @@ add_executable(svzerodcalibrator applications/svzerodcalibrator.cpp
 # -----------------------------------------------------------------------------
 # Replace EXCLUDE_FROM_ALL with SHARED to test building the Python 
 # shared library.
-pybind11_add_module(pysvzerod EXCLUDE_FROM_ALL applications/pysvzerod.cpp)
+
+pybind11_add_module(pysvzerod applications/pysvzerod.cpp)
+if(WIN32 AND "${CMAKE_GENERATOR}" STREQUAL "MinGW Makefiles")
+    message(STATUS ">> Applying static‑link flags to pysvzerod")
+
+    include(CheckCXXCompilerFlag)
+    set(_static_flags
+            -static
+            -static-libgcc
+            -static-libstdc++
+    )
+    # test for winpthread support before adding
+    check_cxx_compiler_flag("-static-libwinpthread" HAVE_WINPTHREAD)
+    if(HAVE_WINPTHREAD)
+        list(APPEND _static_flags -static-libwinpthread)
+    else()
+        find_package(Threads REQUIRED)
+        target_link_libraries(pysvzerod PRIVATE Threads::Threads)
+    endif()
+    # apply to compile *and* link
+    foreach(_f IN LISTS _static_flags)
+        target_compile_options(pysvzerod PRIVATE ${_f})
+        # CMake ≥3.13:
+        target_link_options   (pysvzerod PRIVATE ${_f})
+    endforeach()
+
+    # verify in the configure log for static compilation:
+    get_target_property(_ccopts pysvzerod COMPILE_OPTIONS)
+    message(STATUS ">>> pysvzerod COMPILE_OPTIONS = ${_ccopts}")
+    get_target_property(_lnkopts pysvzerod LINK_OPTIONS)
+    message(STATUS ">>> pysvzerod LINK_OPTIONS   = ${_lnkopts}")
+endif()
 
 # -----------------------------------------------------------------------------
 # Add source sub-directories.
@@ -232,3 +252,22 @@ add_custom_target(codeformat
 # check code format
 add_custom_target(codecheck
   COMMAND find ${SDIR}/*.h ${SDIR}/*.cpp | xargs clang-format -style=file:${PROJECT_SOURCE_DIR}/.clang-format --dry-run --Werror)
+
+set_target_properties(pysvzerod PROPERTIES
+        LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/python
+)
+
+# standard install target locations
+install(TARGETS pysvzerod
+        LIBRARY DESTINATION "${CMAKE_INSTALL_LIBDIR}"
+        ARCHIVE DESTINATION "${CMAKE_INSTALL_LIBDIR}"
+        RUNTIME DESTINATION "${CMAKE_INSTALL_LIBDIR}"
+)
+
+# append correct suffix for windows python runtime files
+if (WIN32)
+    set_target_properties(pysvzerod PROPERTIES
+            PREFIX ""
+            SUFFIX ".pyd"
+    )
+endif()

LICENSE.txt

@@ -1,7 +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.
 
-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: 
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
 
-The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
 
-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.
+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.
+
+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 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