Merge branch 'SimVascular:master' into master

.github/workflows/test_visualization.yml

@@ -6,7 +6,7 @@ jobs:
  test:
  strategy:
  matrix:
- os: [ubuntu-22.04, macos-13]
+ os: [ubuntu-latest, macos-latest]
  fail-fast: false
  runs-on: ${{ matrix.os }}
 

distribution/CMakeLists.txt

@@ -18,17 +18,19 @@ if(ENABLE_DISTRIBUTION)
  set(CPACK_PACKAGE_FILE_NAME "${CPACK_PACKAGE_NAME}_${CPACK_PACKAGE_VERSION}")
 
  # define install location
- set(CPACK_PACKAGING_INSTALL_PREFIX "/usr/local/sv/ZeroDSolver/${CPACK_PACKAGE_VERSION}")
+ set(CPACK_PACKAGING_INSTALL_PREFIX "/usr/local/sv/svZeroDSolver/${CPACK_PACKAGE_VERSION}")
 
  # define install target within build folder
  set(CPACK_OUTPUT_FILE_PREFIX ${CMAKE_BINARY_DIR}/distribution)
 
  if(APPLE)
  set(CPACK_GENERATOR "productbuild")
- elseif(LINUX)
+ endif()
+
+ if(${CMAKE_SYSTEM_NAME} MATCHES "Linux")
  set(CPACK_GENERATOR DEB)
  set(CPACK_DEBIAN_PACKAGE_DEPENDS "")
- endif(APPLE)
+ endif()
 
  # create the installer for both solver and calibrator
  install(TARGETS svzerodsolver svzerodcalibrator

docs/pages/developer_guide.md

@@ -10,9 +10,15 @@ in the `src` directory and a collection of different applications in the
 `applications` folder. Each application is written for a different use-case
 of svZeroDSolver, namely:
 
-* svZeroDCalibrator in `svzerodcalibrator.cpp`
 * svZerodSolver in `svzerodsolver.cpp`
 * Python API in `pysvzerod.cpp`
+* svZeroDCalibrator in `svzerodcalibrator.cpp`
+* svZeroDVisualization for visualizing 0D models and results
+* svZeroDGUI for creating new 0D models grahically.
+
+[Architecture for svZeroDVisualization](@ref visualization).
+
+[Architecture for svZeroDGUI](@ref GUI).
 
 
 # Build in debug mode

docs/pages/main.md

@@ -92,10 +92,10 @@ cmake --build .
  <summary>**Building on Sherlock**</summary>
 
 ```bash
-module load cmake/3.23.1 gcc/12.1.0 binutils/2.38
+module load cmake/3.23.1 gcc/14.2.0 binutils/2.38
 mkdir Release
 cd Release
-cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_COMPILER=/share/software/user/open/gcc/12.1.0/bin/g++ -DCMAKE_C_COMPILER=/share/software/user/open/gcc/12.1.0/bin/gcc ..
+cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_COMPILER=/share/software/user/open/gcc/14.2.0/bin/g++ -DCMAKE_C_COMPILER=/share/software/user/open/gcc/14.2.0/bin/gcc ..
 cmake --build .
 ```
 
@@ -334,7 +334,7 @@ Coronary outlet | OpenLoopCoronaryBC | `CORONARY`
 
 The above table describes the most commonly used boundary conditions. In addition, svZeroDSolver includes various closed-loop boundary conditions. Examples can be found in `svZeroDSolver/tests/cases`.
 
-Note that the `FLOW` and `PRESSURE` boundary conditions accept mathematical expressions in `bc_values`. For example, values of the boundary condition can be specified as a function of time as follow: 
+Values of the boundary condition can be specified as a function of time as follow: 
 ```python
 {
  "bc_name": "INFLOW", # Name of the boundary condition
@@ -347,21 +347,22 @@ Note that the `FLOW` and `PRESSURE` boundary conditions accept mathematical expr
 ```
 See `svZeroDSolver/tests/cases/pulsatileFlow_R_RCR.json` for an example.
 
-They can also be specified as a mathematica expression as follow: 
-```python
-{
- "bc_name": "INFLOW", # Name of the boundary condition
- "bc_type": "FLOW", # Type of the boundary condition
- "bc_values": {
- "fn": "2.0 * (4*atan(1.)) * cos(2.0 * (4*atan(1.)) * t)"
- }
-},
-```
-For an example with a mathematical expression for the boundary condition, see `svZeroDSolver/tests/cases/timeDep_Flow.json`. 
+<!--Uncomment below when the time-varying functionailty is merged-->
+<!--For `FLOW` and `PRESSURE` boundary conditions, they can also be specified as a mathematical expression as follow: -->
+<!--```python-->
+<!--{-->
+<!-- "bc_name": "INFLOW", # Name of the boundary condition-->
+<!-- "bc_type": "FLOW", # Type of the boundary condition-->
+<!-- "bc_values": {-->
+<!-- "fn": "2.0 * (4*atan(1.)) * cos(2.0 * (4*atan(1.)) * t)"-->
+<!-- }-->
+<!--},-->
+<!--```-->
+<!--For an example with a mathematical expression for the boundary condition, see `svZeroDSolver/tests/cases/timeDep_Flow.json`. -->
 
 ## Simulation Outputs
 
-The siumulation outputs will be saved in the specified CSV file (`<name_of_output_file>.csv`) when running `svZeroDSolver` from the command line as follows:
+The simulation outputs will be saved in the specified CSV file (`<name_of_output_file>.csv`) when running `svZeroDSolver` from the command line as follows:
 ```bash
 svzerodsolver <name_of_configuration_file>.json <name_of_output_file>.csv
 ```

tests/test_dirgraph.py

@@ -54,8 +54,30 @@ def test_directed_graph_generation(setup_files):
 
  generated_dot_file_path = tmp_path / (os.path.splitext(os.path.basename(input_file_path))[0] + "_directed_graph.dot")
 
- assert filecmp.cmp(generated_dot_file_path, expected_dot_file_path), \
- f"The generated dot file '{generated_dot_file_path}' does not match the expected dot file '{expected_dot_file_path}'."
+ # Open the expected and generated dot files to compare line-by-line
+ with open(generated_dot_file_path, 'r') as generated_dot_file:
+ with open(expected_dot_file_path, 'r') as expected_dot_file:
+ generated_lines = generated_dot_file.readlines()
+ expected_lines = expected_dot_file.readlines()
+ match = True
+ # Check if number of lines is equal in each file
+ if len(generated_lines) == len(expected_lines):
+ for line_num in range(len(generated_lines)):
+ # Remove spaces and other characters that should not be in the comparison
+ clean_generated_line = " ".join(generated_lines[line_num].split())
+ clean_expected_line = " ".join(expected_lines[line_num].split())
+ # Compare lines and print line that do not match
+ if clean_generated_line != clean_expected_line:
+ print("\nThe following line does not match:")
+ print("--- Generated dot file:", clean_generated_line) 
+ print("--- Expected dot file:", clean_expected_line)
+ match = False
+
+ else:
+ raise RuntimeError(f"ERROR: The generated dot file '{generated_dot_file_path}' and the expected dot file '{expected_dot_file_path}' do not have the same number of lines.")
+
+ if not match:
+ raise RuntimeError(f"The generated dot file '{generated_dot_file_path}' does not match the expected dot file '{expected_dot_file_path}'.")
 
 if __name__ == "__main__":
- pytest.main()
+ pytest.main()