Rename svZeroDPlus to svZeroDSolver (SimVascular#91)

Co-authored-by: Karthik Menon <[email protected]>

.github/workflows/documentation.yml

@@ -1,4 +1,4 @@
-# This workflow builds and deploys the html documentation for svZeroDPlus.
+# This workflow builds and deploys the html documentation for svZeroDSolver.
 name: Documentation
 on: [push, pull_request]
 permissions:

.github/workflows/test.yml

@@ -1,4 +1,4 @@
-# This workflow builds and tests svZeroDPlus. It is built and tested on
+# This workflow builds and tests svZeroDSolver. It is built and tested on
 # different versions of ubuntu and macOS.
 name: Build and test
 on: [push, pull_request]
@@ -14,7 +14,7 @@ jobs:
       - name: Install ubuntu dependencies
         if: startsWith(matrix.os, 'ubuntu')
         run: sudo apt update && sudo apt install build-essential cmake lcov
-      - name: Install svZeroDPlus
+      - name: Install svZeroDSolver
         run: |
           conda create -n zerod python=3.11.4
           conda run -n zerod pip install -e ".[dev]"
@@ -59,10 +59,10 @@ jobs:
         run: |
           cd Release
           cpack
-          cp distribution/svZeroDPlus_* ..
+          cp distribution/svZeroDSolver_* ..
       - name: Upload installer
         uses: actions/upload-artifact@v3
         with:
           name: ${{ matrix.os }} installer
-          path: svZeroDPlus_*
-          if-no-files-found: error
+          path: svZeroDSolver_*
+          if-no-files-found: error

CMakeLists.txt

@@ -153,11 +153,11 @@ add_executable(svzerodcalibrator applications/svzerodcalibrator.cpp
 )
 
 # -----------------------------------------------------------------------------
-# Setup building of the svzerodplus Python extension module.
+# Setup building of the pysvzerod Python extension module.
 # -----------------------------------------------------------------------------
 # Replace EXCLUDE_FROM_ALL with SHARED to test building the Python 
 # shared library.
-pybind11_add_module(svzerodplus EXCLUDE_FROM_ALL applications/svzerodplus.cpp)
+pybind11_add_module(pysvzerod EXCLUDE_FROM_ALL applications/pysvzerod.cpp)
 
 # -----------------------------------------------------------------------------
 # Add source sub-directories.
@@ -185,7 +185,7 @@ target_include_directories(svzerodcalibrator PUBLIC
   ${CMAKE_SOURCE_DIR}/src/solve 
 )
 
-target_include_directories(svzerodplus PUBLIC 
+target_include_directories(pysvzerod PUBLIC 
   ${CMAKE_SOURCE_DIR}/src/algebra
   ${CMAKE_SOURCE_DIR}/src/model 
   ${CMAKE_SOURCE_DIR}/src/optimize
@@ -203,13 +203,13 @@ target_link_libraries(svzerodsolver PRIVATE nlohmann_json::nlohmann_json)
 target_link_libraries(svzerodcalibrator PRIVATE Eigen3::Eigen)
 target_link_libraries(svzerodcalibrator PRIVATE nlohmann_json::nlohmann_json)
 
-target_link_libraries(svzerodplus PRIVATE Eigen3::Eigen)
-target_link_libraries(svzerodplus PRIVATE nlohmann_json::nlohmann_json)
-target_link_libraries(svzerodplus PRIVATE pybind11_json)
-target_link_libraries(svzerodplus PRIVATE svzero_algebra_library)
-target_link_libraries(svzerodplus PRIVATE svzero_model_library)
-target_link_libraries(svzerodplus PRIVATE svzero_optimize_library)
-target_link_libraries(svzerodplus PRIVATE svzero_solve_library)
+target_link_libraries(pysvzerod PRIVATE Eigen3::Eigen)
+target_link_libraries(pysvzerod PRIVATE nlohmann_json::nlohmann_json)
+target_link_libraries(pysvzerod PRIVATE pybind11_json)
+target_link_libraries(pysvzerod PRIVATE svzero_algebra_library)
+target_link_libraries(pysvzerod PRIVATE svzero_model_library)
+target_link_libraries(pysvzerod PRIVATE svzero_optimize_library)
+target_link_libraries(pysvzerod PRIVATE svzero_solve_library)
 
 
 # Create distribution

applications/svzerodplus.cpp → applications/pysvzerod.cpp

@@ -28,7 +28,7 @@
 // NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 /**
- * @file svzerodplus.cpp
+ * @file pysvzerod.cpp
  * @brief Python interface for svZeroDSolver
  */
 #include <pybind11/eigen.h>
@@ -42,7 +42,7 @@
 
 namespace py = pybind11;
 
-PYBIND11_MODULE(svzerodplus, m) {
+PYBIND11_MODULE(pysvzerod, m) {
   using Solver = Solver;
   py::class_<Solver>(m, "Solver")
       .def(py::init([](py::dict& config) {

container/profiling/Dockerfile

@@ -20,13 +20,13 @@ RUN apt-get -q update && \
     && apt-get clean \
     && rm -rf /var/lib/apt/lists/*
 
-COPY . /opt/svzerodplus
+COPY . /opt/pysvzerod
 
-RUN mkdir -p /opt/svzerodplus-build/relwithdebinfo && \
-    cd /opt/svzerodplus-build/relwithdebinfo && \
-    cmake -DCMAKE_BUILD_TYPE=RelWithDebInfo /opt/svzerodplus && \
+RUN mkdir -p /opt/pysvzerod-build/relwithdebinfo && \
+    cd /opt/pysvzerod-build/relwithdebinfo && \
+    cmake -DCMAKE_BUILD_TYPE=RelWithDebInfo /opt/pysvzerod && \
     cmake --build . --target svzerodsolver
 
 WORKDIR /opt/data
-RUN chmod +x /opt/svzerodplus/container/profiling/entrypoint.sh
-ENTRYPOINT ["/opt/svzerodplus/container/profiling/entrypoint.sh"]
+RUN chmod +x /opt/pysvzerod/container/profiling/entrypoint.sh
+ENTRYPOINT ["/opt/pysvzerod/container/profiling/entrypoint.sh"]

container/profiling/entrypoint.sh

@@ -1,5 +1,5 @@
 #! /bin/bash
 
 export LIBPROFILER=$(find /usr/lib -name "libprofiler.so")
-LD_PRELOAD=$LIBPROFILER CPUPROFILE=/opt/main.prof CPUPROFILE_FREQUENCY=100000 /opt/svzerodplus-build/relwithdebinfo/svzerodsolver $@ /opt/output.csv
-google-pprof --pdf /opt/svzerodplus-build/relwithdebinfo/svzerodsolver /opt/main.prof > profiling_report.pdf
+LD_PRELOAD=$LIBPROFILER CPUPROFILE=/opt/main.prof CPUPROFILE_FREQUENCY=100000 /opt/pysvzerod-build/relwithdebinfo/svzerodsolver $@ /opt/output.csv
+google-pprof --pdf /opt/pysvzerod-build/relwithdebinfo/svzerodsolver /opt/main.prof > profiling_report.pdf

distribution/CMakeLists.txt

@@ -7,10 +7,10 @@ if(ENABLE_DISTRIBUTION)
 
   # add description (shown in installer)
   set(CPACK_PACKAGE_VERSION "${TODAY}")
-  set(CPACK_PACKAGE_NAME "svZeroDPlus")
+  set(CPACK_PACKAGE_NAME "svZeroDSolver")
   set(CPACK_PACKAGE_VENDOR "SimVascular.org")
   set(CPACK_PACKAGE_CONTACT "SimVascular <[email protected]>")
-  set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "svZeroDPlus is a fast lumped-parameter solver for blood flow and pressure in hemodynamic networks")
+  set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "svZeroDSolver is a fast lumped-parameter solver for blood flow and pressure in hemodynamic networks")
   set(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_CURRENT_SOURCE_DIR}/../LICENSE.txt")
   set(CPACK_RESOURCE_FILE_README "${CMAKE_CURRENT_SOURCE_DIR}/readme.txt")
 
@@ -48,4 +48,4 @@ if(ENABLE_DISTRIBUTION)
   set(CPACK_COMPONENTS_ALL applications libraries headers)
 
   include(CPack)
-endif()
+endif()

distribution/readme.txt

@@ -1 +1 @@
-svZeroDPlus is a fast lumped-parameter solver for blood flow and pressure in hemodynamic networks.
+svZeroDSolver is a fast lumped-parameter solver for blood flow and pressure in hemodynamic networks.

docs/Doxyfile

@@ -4,7 +4,7 @@
 # Project related configuration options
 #---------------------------------------------------------------------------
 DOXYFILE_ENCODING      = UTF-8
-PROJECT_NAME           = svZeroDPlus
+PROJECT_NAME           = svZeroDSolver
 PROJECT_NUMBER         = 
 PROJECT_BRIEF          = 
 PROJECT_LOGO           =

docs/pages/developer_guide.md

@@ -4,15 +4,15 @@
 
 # Architecture
 
-svZeroDPlus is written in a highly modular manner to enable reuse of code
+svZeroDSolver is written in a highly modular manner to enable reuse of code
 for many different applications. It is divided into a header based library
 in the `src` directory and a collection of different applications in the
 `applications` folder. Each application is written for a different use-case
-of svZeroDPlus, namely:
+of svZeroDSolver, namely:
 
 * svZeroDCalibrator in `svzerodcalibrator.cpp`
 * svZerodSolver in `svzerodsolver.cpp`
-* Python API in `svzerodplus.cpp`
+* Python API in `pysvzerod.cpp`
 
 The header-based library in the `src` folder contains classes and functions that are collectively used by
 all applications. A good overview over the general architecture can be found in the
@@ -21,7 +21,7 @@ all applications. A good overview over the general architecture can be found in
 
 ## Build in debug mode
 
-For debug purposes it is recommended to build svZeroDPlus in Debug mode.
+For debug purposes it is recommended to build svZeroDSolver in Debug mode.
 
 ```bash
 mkdir Debug
@@ -69,7 +69,7 @@ make codecheck
 ```
 
 If the above commands do not work on your platform (it does not work on Sherlock at Stanford)
-you can run the following command **from the svZeroDPlus folder** to format all your files:
+you can run the following command **from the svZeroDSolver folder** to format all your files:
 
 ```bash
 find src/**/*.h src/**/*.cpp | xargs clang-format -style=Google -i
@@ -142,8 +142,8 @@ to create a profiling report. The generation of profiling reports requires
 [Docker](https://docs.docker.com/get-docker/) to be installed on your machine.
 
 ```docker
-docker build -t profile_svzerodplus -f container/profiling/Dockerfile .
-docker run -it -v $(PWD):/opt/data --rm profile_svzerodplus path/to/simulation_config.json
+docker build -t profile_svzerodsolver -f container/profiling/Dockerfile .
+docker run -it -v $(PWD):/opt/data --rm profile_svzerodsolver path/to/simulation_config.json
 ```
 
 This will generate a file called `profiling_report.pdf` in your current working directory.

docs/pages/main.md

@@ -1,20 +1,20 @@
-@mainpage svZeroDPlus
+@mainpage svZeroDSolver
 
 [TOC]
 
-svZeroDPlus is an application for performing simulations with 0D/lumped-parameter
+svZeroDSolver is an application for performing simulations with 0D/lumped-parameter
 computer models for cardiovascular flows. 
 
-Some noteworthy features of svZeroDPlus are:
+Some noteworthy features of svZeroDSolver are:
 * It is completely modular. Users can create custom flow models by arranging 
 blocks corresponding to blood vessels, junctions, different types of 
 boundary conditions, etc. 
 * It is written in C++ to enable high-performance applications.
-* svZeroDPlus offers both a Python API and a C++ shared library to interface with other 
+* svZeroDSolver offers both a Python API and a C++ shared library to interface with other 
 Python or C++-based applications. This allows it to be used in a fully coupled manner 
 with other multi-physics solvers, and for parameter estimation, uncertainty 
 quantification, etc.
-* The svZeroDCalibrator application, which is included in svZeroDPlus, optimizes 0D
+* The svZeroDCalibrator application, which is included in svZeroDSolver, optimizes 0D
 blood vessel parameters to recapitulate given time-varying flow and pressure measurements 
 (for example, from a high-fidelity 3D simulation). This allows users to build accurate 
 0D models that reflect observed hemodynamics.
@@ -44,13 +44,13 @@ You can find more details about governing equations in individual blocks, for ex
 - BloodVesselJunction
 - WindkesselBC
 
-For implementation details, have a look at the [source code](https://github.com/StanfordCBCL/svZeroDPlus).
+For implementation details, have a look at the [source code](https://github.com/simvascular/svZeroDSolver).
 
 [About SimVascular](https://simvascular.github.io)
 
 # Installation
 
-svZeroDPlus can be installed in two different ways. For using the Python
+svZeroDSolver can be installed in two different ways. For using the Python
 API, an installation via pip is recommended.
 
 ## Using pip
@@ -59,12 +59,12 @@ For a pip installation, simply run the following command
 (cloning of the repository is not required):
 
 ```bash
-pip install git+https://github.com/StanfordCBCL/svZeroDPlus.git
+pip install git+https://github.com/simvascular/svZeroDSolver.git
 ```
 
 ## Using CMake
 
-If you want to build svZeroDPlus manually from source, clone the repository
+If you want to build svZeroDSolver manually from source, clone the repository
 and run the following commands from the top directory of the project:
 
 ```bash
@@ -115,38 +115,38 @@ For some applications it is beneficial to run svZeroDSolver directly
 from within another program. For example, this can be
 useful when many simulations need to be performed (e.g. for 
 calibration, uncertainty quantification, ...). It is also allows using
-svZeroDPlus with other solvers, for example as boundary conditions or
+svZeroDSolver with other solvers, for example as boundary conditions or
 forcing terms.
 
 ### In C++
 
-SvZeroDPlus needs to be built using CMake to use the shared library interface.
+SvZeroDSolver needs to be built using CMake to use the shared library interface.
 
-Detailed examples of interfacing with svZeroDPlus from C++ codes are available 
-in the test cases at `svZeroDPlus/tests/test_interface`. 
+Detailed examples of interfacing with svZeroDSolver from C++ codes are available 
+in the test cases at `svZeroDSolver/tests/test_interface`. 
 
 ### In Python
 
 Please make sure that
-you installed svZerodPlus via pip to enable this feature. We start by
-importing svzerodplus:
+you installed svZerodSolver via pip to enable this feature. We start by
+importing pysvzerod:
 
 ```python
->>> import svzerodplus
+>>> import pysvzerod
 ```
 
 Next, we create a solver from our configuration. The configuration can
 be specified by either a path to a JSON file:
 
 ```python
->>> solver = svzerodplus.Solver("tests/cases/steadyFlow_RLC_R.json")
+>>> solver = pysvzerod.Solver("tests/cases/steadyFlow_RLC_R.json")
 ```
 
 or as a Python dictionary:
 
 ```python
 >>> my_config = {...}
->>> solver = svzerodplus.Solver(my_config)
+>>> solver = pysvzerod.Solver(my_config)
 ```
 
 To run the simulation we add:
@@ -202,7 +202,7 @@ There is also a function to retrieve the full result directly based on a given c
 ```python
 
 >>> my_config = {...}
->>> svzerodplus.simulate(my_config)
+>>> pysvzerod.simulate(my_config)
 
              name  time  flow_in  flow_out  pressure_in  pressure_out
 0    branch0_seg0  0.00      5.0       5.0       1100.0         600.0
@@ -342,14 +342,14 @@ The result will be written to a JSON file.
 ### In Python
 
 svZeroDCalibrator can also be called directly from Python.
-Please make sure that you installed svZerodPlus via pip to enable this feature. We start by
-importing svzerodplus:
+Please make sure that you installed svZerodSolver via pip to enable this feature. We start by
+importing pysvzerod:
 
 ```python
-import svzerodplus
+import pysvzerod
 
 my_unoptimized_config = {...}
-my_optimized_config = svzerodplus.calibrate(my_unoptimized_config)
+my_optimized_config = pysvzerod.calibrate(my_unoptimized_config)
 ```
 
 ## Configuration (file)

setup.cfg

@@ -1,5 +1,5 @@
 [metadata]
-name = svzerodplus
+name = pysvzerod
 version = 2.0
 description = A fast C++ application for working with 0D models.
 long_description = file: README.md
@@ -18,5 +18,5 @@ dev =
 
 [options.entry_points]
 console_scripts =
-    svzerodsolver = svzerodplus:run_simulation_cli
-    svzerodcalibrator = svzerodplus:run_calibration_cli
+    svzerodsolver = pysvzerod:run_simulation_cli
+    svzerodcalibrator = pysvzerod:run_calibration_cli

setup.py

@@ -2,6 +2,6 @@
 from cmake_setuptools import CMakeExtension, CMakeBuildExt
 
 setup(
-    ext_modules=[CMakeExtension("svzerodplus")],
+    ext_modules=[CMakeExtension("pysvzerod")],
     cmdclass={"build_ext": CMakeBuildExt},
 )

src/interface/interface.cpp

@@ -172,12 +172,13 @@ void initialize(std::string input_file_arg, int& problem_id, int& pts_per_cycle,
     num_output_steps = 1;
     throw std::runtime_error(
         "ERROR: Option output_mean_only has not been implemented when "
-        "using the svZeroDPlus interface library.");
+        "using the svZeroDSolver interface library.");
   } else if (!simparams.output_all_cycles) {
     num_output_steps = interface->pts_per_cycle_;
     throw std::runtime_error(
         "ERROR: Option output_last_cycle_only has been implemented but not "
-        "tested when using the svZeroDPlus interface library. Please test this "
+        "tested when using the svZeroDSolver interface library. Please test "
+        "this "
         "functionality before removing this message.");
   } else {
     num_output_steps = interface->num_time_steps_;
@@ -510,7 +511,8 @@ void run_simulation(int problem_id, const double external_time,
     start_time = interface->times_[start_idx];
     throw std::runtime_error(
         "ERROR: Option output_last_cycle_only has been implemented but not "
-        "tested when using the svZeroDPlus interface library. Please test this "
+        "tested when using the svZeroDSolver interface library. Please test "
+        "this "
         "functionality before removing this message.");
   }
   for (int t = start_idx; t < num_output_steps; t++) {

svzerodplus.pyi

@@ -1,7 +1,7 @@
-# This file contains the stubs for the public Python interface of svZeroDPlus.
+# This file contains the stubs for the public Python interface of svZeroDSolver.
 # This is necessary for supporting auto-completion in Visual Studio Code or
 # PyCharm.
-"""svZeroDPlus Python interface."""
+"""svZeroDSolver Python interface."""
 from __future__ import annotations
 import numpy
 import typing