Merge branch 'SimVascular:master' into CRLVessel

Author: rjrios915

.github/workflows/test.yml

@@ -7,85 +7,39 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-22.04, ubuntu-latest, macos-13, macos-latest, windows-latest]
-        version: [13] # GCC version
+        os: [ubuntu-latest, macos-latest, windows-latest]
       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
+      - uses: actions/setup-python@v5
         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: Install dependencies to get correct version numbers (Ubuntu)
+      - name: Install ubuntu dependencies
         if: startsWith(matrix.os, 'ubuntu')
-        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 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
+        run: sudo apt update && sudo apt install build-essential cmake lcov graphviz
 
-      - name: Install POISX-like svZeroDSolver
+      - name: Install POSIX-like
         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 pip install networkx
+        run: python -m pip install -e ".[dev]"
 
       - name: Test the build
+        if: ${{!startsWith(matrix.os, 'windows')}}
         run: |
           cd tests
-          conda run pytest -v --durations=0 --ignore=test_dirgraph.py
+          python -m pytest -v --durations=0 --ignore=test_dirgraph.py
 
-      - name: Build using CMake for POISX-like Systems
+      - name: Build using CMake for POSIX-like Systems
         if: ${{!startsWith(matrix.os, 'windows')}}
         run: |
           mkdir Release
           cd Release
           cmake -DCMAKE_BUILD_TYPE=Release -DENABLE_DISTRIBUTION=ON ..
           make -j2
 
-      - 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
+      - name: Test interface POSIX-like Systems
         if: ${{!startsWith(matrix.os, 'windows')}}
         run: |
           cd tests/test_interface
@@ -98,67 +52,73 @@ jobs:
           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')
+        if: startsWith(matrix.os, 'ubuntu-latest')
         run: |
           cd Release
           cmake -DENABLE_COVERAGE=ON ..
           make -j2
           cd ../tests
-          conda run pytest -v --durations=0 --coverage --ignore=test_dirgraph.py
+          python -m pytest -v --durations=0 --coverage --ignore=test_dirgraph.py
           cd ../Release
           make coverage
 
       - name: Save coverage report
-        if: startsWith(matrix.os, 'ubuntu-22.04')
+        if: startsWith(matrix.os, 'ubuntu-latest')
         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')
+        if: startsWith(matrix.os, 'ubuntu-latest')
         uses: codecov/codecov-action@v4
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
-      - name: Build installer POISX-like Systems
+      - name: Build installer POSIX-like Systems
         if: ${{!startsWith(matrix.os, 'windows')}}
         run: |
           cd Release
           cpack
           cp distribution/svZeroDSolver_* ..
 
-      - name: Install NSIS
+      - name: Setup MSVC dev cmd
         if: startsWith(matrix.os, 'windows')
-        run: choco install nsis -y
+        uses: ilammy/msvc-dev-cmd@v1
 
-      - name: Build installer Windows Systems
+      - name: Install and test Windows
         if: startsWith(matrix.os, 'windows')
+        continue-on-error: true
         shell: pwsh
         run: |
-          # NSIS will be at C:\Program Files (x86)\NSIS\Bin
+          python -m pip install --upgrade cmake cmake-setuptools numpy ninja pytest pandas graphviz networkx pydot
+
+          # keep MinGW/Strawberry off PATH (so Eigen won't try Fortran)
+          $pattern = '^(C:\\mingw64\\bin|C:\\tools\\mingw64\\bin|C:\\Strawberry\\c\\bin|C:\\Strawberry\\perl\\site\\bin|C:\\Strawberry\\perl\\bin)$'
+
+          # one build dir for everything: executables + Python module
+          $build = Join-Path $env:GITHUB_WORKSPACE 'Release'
+          cmake -S . -B $build -G Ninja `
+            -DCMAKE_BUILD_TYPE=Release `
+            -DEIGEN_BUILD_BLAS=OFF `
+            -DEIGEN_BUILD_DOC=OFF -DEIGEN_TEST_FORTRAN=OFF -DEIGEN_TEST_CXX11=OFF -DEIGEN_TEST_NOQT=ON `
+            -DCMAKE_Fortran_COMPILER:FILEPATH="" `
+            -DENABLE_DISTRIBUTION=ON
+          cmake --build $build --parallel 2
+
+          # make the Python extension importable
+          $pydDir = Join-Path $build 'python'
+          $env:PYTHONPATH = "$pydDir;$env:PYTHONPATH"
+
+          # run integration tests
+          cd (Join-Path $env:GITHUB_WORKSPACE 'tests')
+          python -m pytest -v --durations=0 --ignore=test_dirgraph.py
+
+          # build installer
+          choco install nsis -y
           echo "C:\Program Files (x86)\NSIS\Bin" | Out-File -FilePath $env:GITHUB_PATH -Encoding utf8 -Append
-          cd Release
+          cd $build
           cpack -C Release
           Copy-Item distribution\svZeroDSolver_* -Destination ..\
 

CMakeLists.txt

@@ -1,14 +1,27 @@
 # 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)
+set(CMAKE_POLICY_VERSION_MINIMUM 3.18)
+cmake_minimum_required(VERSION 3.18)
+cmake_policy(SET CMP0077 NEW)
+
 set(CMAKE_CXX_STANDARD 17)
 set(CMAKE_CXX_STANDARD_REQUIRED True)
 
-project(svZeroDSolver)
+project(svZeroDSolver LANGUAGES C CXX)
+
+set(CMAKE_POSITION_INDEPENDENT_CODE ON)
+
+# Force Eigen & superprojects to skip docs/tests/fortran no matter what
+set(BUILD_TESTING OFF CACHE BOOL "" FORCE)
+set(EIGEN_BUILD_DOC OFF CACHE BOOL "" FORCE)
+set(EIGEN_TEST_FORTRAN OFF CACHE BOOL "" FORCE)
+set(EIGEN_BUILD_BLAS OFF CACHE BOOL "" FORCE)
 
 include(FetchContent)
+set(PYBIND11_FINDPYTHON NEW CACHE STRING "" FORCE)
+find_package(Python COMPONENTS Interpreter Development REQUIRED)
+message(STATUS "Using Python: ${Python_EXECUTABLE} (${Python_VERSION})")
 
 # Enable code coverage
 # -----------------------------------------------------------------------------
@@ -33,18 +46,13 @@ endif()
 
 if (WIN32 AND MSVC)
     # CMake ≥ 3.15 has a proper variable
+    # Use dynamic CRT (/MD or /MDd) so EXE and DLL share the same heap.
+    # This is required when passing STL containers across DLL boundaries.
     if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.15")
         set(CMAKE_MSVC_RUNTIME_LIBRARY
-                "MultiThreaded$<$<CONFIG:Debug>:Debug>")
+                "MultiThreaded$<$<CONFIG:Debug>:Debug>DLL")
     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()
+        # CMake < 3.15: /MD is the default, so no changes needed
     endif()
 endif()
 # -----------------------------------------------------------------------------
@@ -75,7 +83,6 @@ FetchContent_Declare(
 set(EIGEN_BUILD_DOC OFF)
 set(BUILD_TESTING OFF)
 set(EIGEN_BUILD_PKGCONFIG OFF)
-set( OFF)
 
 FetchContent_MakeAvailable(Eigen)
 
@@ -84,7 +91,6 @@ FetchContent_MakeAvailable(Eigen)
 # -----------------------------------------------------------------------------
 # pybind11 is a library used to create Python bindings of existing C++ code.
 #
-set(PYBIND11_PYTHON_VERSION 3.8 CACHE STRING "")
 FetchContent_Declare(
     pybind11
     GIT_REPOSITORY https://github.com/pybind/pybind11

applications/svZeroDVisualization/visualize_simulation.py

@@ -388,9 +388,11 @@ def normalize_names(name):
         figure={
             'data': [edge_trace, vessel_trace, chamber_trace, valve_trace, junction_trace, bc_trace],
             'layout': go.Layout(
-                title='Network Graph',
-                titlefont_size=30,
-                title_x=0.5,
+                title={
+                    'text': 'Network Graph',
+                    'x': 0.5,
+                    'font': {'size': 30}
+                },
                 showlegend=True,
                 hovermode='closest',
                 margin=dict(b=20, l=0, r=0, t=50),
@@ -469,9 +471,11 @@ def update_graphs(clickData):
     fig = go.Figure(
         data=[edge_trace, vessel_trace, chamber_trace, valve_trace, junction_trace, bc_trace],
         layout=go.Layout(
-            title='Network Graph',
-            titlefont_size=30,
-            title_x=0.5,
+            title={
+                'text': 'Network Graph',
+                'x': 0.5,
+                'font': {'size': 30}
+            },
             showlegend=True,
             hovermode='closest',
             margin=dict(b=20, l=0, r=0, t=50),
@@ -651,4 +655,4 @@ def update_graphs(clickData):
 
 
 if __name__ == '__main__':
-    app.run_server(debug=True)
+    app.run(debug=True)

docs/pages/developer_guide.md

@@ -46,12 +46,20 @@ This is useful when continuously running the integration tests during developmen
 
 * The changes should be implemented in a feature branch of the developer's fork of svZeroDSolver. 
 * Once the changes are implemented, the developer should make sure the build, documentation, and code format tests are passing on the user's feature branch. 
-  * The tests are automatically run when pushing changes to the developer's remote branch on Github. 
-  * Alternatively, the developer can run the tests locally. 
-    * The build tests can be run using the `pip` install and `pytest`. 
-    * The tests for the C++ interface require the `CMake` install and can be run by building the tests in `svZeroDSolver/tests/test_interface`. 
-    * Code formatting can be performed following the instructions in the Formatting section below. 
-    * The documentation can be built following the instructions in the Documentation section below. 
+
+# Testing code changes
+* Tests are automatically run as Github workflows when pushing changes to the developer's remote branch on Github. These tests are defined in the `.github/workflows` directory.
+* It may be helpful and more efficient to run the build tests locally with each incremental change the developer makes. This can be done by following these steps:
+  1. If you do not have `pytest` installed in your virtual environment, install it with `pip install pytest`
+  2. We first need to build the svZeroDSolver project. This can be done by running `pip install -e .` from the svZeroDSolver directory
+  3. From the main svZeroDSolver directory, `cd tests`.
+  4. Now that you are in the `tests` directory, run `pytest`. The terminal output will show which tests are passing.
+    * To run a specific subset of tests matching a certain pattern, e.g., only the calibrator, you can use `pytest -k calibrator`. 
+    * To see all simulation output, run `pytest -sv`.
+    * If you want to run the tests using the binaries in the `Release` directory instead of the python module, you can call `pytest --coverage`
+* The tests for the C++ interface require the `CMake` install and can be run by building the tests in `svZeroDSolver/tests/test_interface`.
+* Code formatting can be performed following the instructions in the [Formatting](#formatting) section. 
+* The documentation can be built following the instructions in the [Documentation](#documentation) section. 
 * Once all the tests are passing, the developer should open a pull request from the feature branch and link the relevant issue.
 
 # Adding new blocks
@@ -66,7 +74,7 @@ Steps required to visualize a new block with svZeroDSolver Visualization applica
 
 We follow the [Google C++ Style Guide](https://google.github.io/styleguide/cppguide.html).
 
-## Formatting
+## Formatting {#formatting}
 
 We use [clang-format](https://clang.llvm.org/docs/ClangFormat.html) to automatically 
 format our code accoring to the [Google Style](https://google.github.io/styleguide/cppguide.html), 
@@ -78,7 +86,11 @@ There are tools for your favorite IDE to automatically format your code. Example
 - [vim](https://github.com/rhysd/vim-clang-format)
 - [and many more](https://clang.llvm.org/docs/ClangFormat.html)
 
-Before committing any changes, you can run the following
+Before formatting the code with clang-format, ensure that you have latest clang-format version by running `clang-format --version`. To upgrade `clang-format` use the following commands
+  * on MacOS: `brew upgrade clang-format`
+  * on Ubuntu: `sudo apt upgrade clang-format`
+
+Before committing any changes, run the following
 command **from your build folder** to format all your files:
 
 ```bash
@@ -105,7 +117,7 @@ requirements.
 
 On Sherlock at Stanford, clang-format is included in the `llvm` module.
 
-# Documentation
+# Documentation {#documentation}
 
 We use [Doxygen](https://doxygen.nl) to automatically build an html documentation
 from source code. Please have at Doxygen's [Documentation Guide](https://www.doxygen.nl/manual/docblocks.html)

setup.cfg

@@ -15,6 +15,9 @@ install_requires =
 [options.extras_require]
 dev = 
     pytest
+    graphviz
+    networkx
+    pydot
 
 [options.entry_points]
 console_scripts =

src/algebra/Integrator.cpp

@@ -83,7 +83,8 @@ State Integrator::step(const State& old_state, double time) {
     // Abort if maximum number of non-linear iterations is reached
     else if (i == max_iter - 1) {
       throw std::runtime_error(
-          "Maximum number of non-linear iterations reached.");
+          "Maximum number of non-linear iterations reached at time " +
+          std::to_string(time));
     }
 
     // Evaluate Jacobian