Rename Python package from pysvzerod to svzerod

.github/scripts/record_release.sh

@@ -42,7 +42,7 @@ else
 
   GIT_AUTHOR_NAME="github-actions[bot]" GIT_AUTHOR_EMAIL="41898282+github-actions[bot]@users.noreply.github.com" \
     GIT_COMMITTER_NAME="github-actions[bot]" GIT_COMMITTER_EMAIL="41898282+github-actions[bot]@users.noreply.github.com" \
-    git -c commit.gpgSign=false commit -m "Release pysvzerod $RELEASE_VERSION"
+    git -c commit.gpgSign=false commit -m "Release svzerod $RELEASE_VERSION"
   commit_sha=$(git rev-parse HEAD)
   git tag "$tag" "$commit_sha"
   if ! git push --atomic origin "HEAD:refs/heads/$DEFAULT_BRANCH" "refs/tags/$tag"; then

.github/scripts/release_version.py

@@ -18,8 +18,8 @@
 
 VERSION = re.compile(r"(0|[1-9][0-9]*)\.(0|[1-9][0-9]*)")
 INDEX_URLS = {
-    "pypi": "https://pypi.org/pypi/pysvzerod/{version}/json",
-    "testpypi": "https://test.pypi.org/pypi/pysvzerod/{version}/json",
+    "pypi": "https://pypi.org/pypi/svzerod/{version}/json",
+    "testpypi": "https://test.pypi.org/pypi/svzerod/{version}/json",
 }
 
 
@@ -84,7 +84,7 @@ def set_version(path, version, expected_current):
 
 def check_metadata(content, version, filename):
     metadata = BytesParser().parsebytes(content)
-    for field, expected in (("Name", "pysvzerod"), ("Version", version)):
+    for field, expected in (("Name", "svzerod"), ("Version", version)):
         if metadata.get_all(field, []) != [expected]:
             raise ValueError(f"{filename}: expected exactly one {field}: {expected}")
 
@@ -93,7 +93,7 @@ def inspect_distributions(dist, version):
     parse_version(version)
     paths = sorted(Path(dist).iterdir())
     kinds = set()
-    prefix = f"pysvzerod-{version}"
+    prefix = f"svzerod-{version}"
     wheel_pattern = re.compile(
         re.escape(prefix) + r"-(?:[0-9][A-Za-z0-9_.]*-)?[A-Za-z0-9_.]+-[A-Za-z0-9_.]+-[A-Za-z0-9_.]+\.whl"
     )
@@ -223,13 +223,13 @@ def main():
             print(args.version)
         elif args.command == "verify-dist":
             paths = inspect_distributions(args.dist, args.version)
-            print(f"Verified {len(paths)} distributions for pysvzerod {args.version}")
+            print(f"Verified {len(paths)} distributions for svzerod {args.version}")
         elif args.command == "check-index":
             check_index(args.index, args.dist, args.version)
             print(f"Existing {args.index} files match the candidate distributions")
         else:
             verify_index(args.index, args.dist, args.version, args.attempts, args.delay)
-            print(f"Verified all distributions on {args.index} for pysvzerod {args.version}")
+            print(f"Verified all distributions on {args.index} for svzerod {args.version}")
     except (OSError, ValueError, tarfile.TarError, zipfile.BadZipFile) as error:
         parser.exit(1, f"Error: {error}\n")
 

.github/workflows/gui.yml

@@ -31,7 +31,7 @@ jobs:
           enable-cache: true
 
       - name: Install Flask dependencies
-        # The GUI only needs Flask, not the compiled pysvzerod extension.
+        # The GUI only needs Flask, not the compiled svzerod extension.
         run: uv sync --no-install-project --no-default-groups --group gui
 
       - name: Start Flask Application

.github/workflows/pypi.yml

@@ -27,7 +27,7 @@ on:
       - pyproject.toml
       - MANIFEST.in
       - CMakeLists.txt
-      - applications/pysvzerod.cpp
+      - applications/svzerod.cpp
 
 permissions:
   contents: read
@@ -115,7 +115,7 @@ jobs:
       - name: Build and verify source distribution
         run: |
           uv build --sdist
-          uv build --wheel dist/pysvzerod-*.tar.gz --out-dir /tmp/sdist-wheel
+          uv build --wheel dist/svzerod-*.tar.gz --out-dir /tmp/sdist-wheel
           uvx twine check --strict dist/*.tar.gz
       - uses: actions/upload-artifact@v4
         with:
@@ -374,7 +374,7 @@ jobs:
         uses: softprops/action-gh-release@v2
         with:
           tag_name: v${{ needs.prepare_release.outputs.release_version }}
-          name: pysvzerod ${{ needs.prepare_release.outputs.release_version }}
+          name: svzerod ${{ needs.prepare_release.outputs.release_version }}
           target_commitish: ${{ steps.record.outputs.commit_sha }}
           generate_release_notes: ${{ steps.release.outputs.exists != 'true' }}
           overwrite_files: false

.github/workflows/test_visualization.yml

@@ -21,7 +21,7 @@ jobs:
 
       - name: Install dependencies
         # The dirgraph test only needs the Python dev tooling, not the compiled
-        # pysvzerod extension, so skip building the project.
+        # svzerod extension, so skip building the project.
         run: uv sync --no-install-project --no-default-groups --group dev
 
       - name: Install Graphviz

CMakeLists.txt

@@ -176,16 +176,16 @@ add_executable(svzerodcalibrator applications/svzerodcalibrator.cpp
 )
 
 # -----------------------------------------------------------------------------
-# Setup building of the pysvzerod Python extension module.
+# Setup building of the svzerod Python extension module.
 # -----------------------------------------------------------------------------
 # Replace EXCLUDE_FROM_ALL with SHARED to test building the Python 
 # shared library.
 
-pybind11_add_module(pysvzerod applications/pysvzerod.cpp)
-set(PYSVZEROD_VERSION "dev" CACHE STRING "Python package version")
-target_compile_definitions(pysvzerod PRIVATE PYSVZEROD_VERSION="${PYSVZEROD_VERSION}")
+pybind11_add_module(svzerod applications/svzerod.cpp)
+set(SVZEROD_VERSION "dev" CACHE STRING "Python package version")
+target_compile_definitions(svzerod PRIVATE SVZEROD_VERSION="${SVZEROD_VERSION}")
 if(WIN32 AND "${CMAKE_GENERATOR}" STREQUAL "MinGW Makefiles")
-    message(STATUS ">> Applying static‑link flags to pysvzerod")
+    message(STATUS ">> Applying static‑link flags to svzerod")
 
     include(CheckCXXCompilerFlag)
     set(_static_flags
@@ -199,20 +199,20 @@ if(WIN32 AND "${CMAKE_GENERATOR}" STREQUAL "MinGW Makefiles")
         list(APPEND _static_flags -static-libwinpthread)
     else()
         find_package(Threads REQUIRED)
-        target_link_libraries(pysvzerod PRIVATE Threads::Threads)
+        target_link_libraries(svzerod PRIVATE Threads::Threads)
     endif()
     # apply to compile *and* link
     foreach(_f IN LISTS _static_flags)
-        target_compile_options(pysvzerod PRIVATE ${_f})
+        target_compile_options(svzerod PRIVATE ${_f})
         # CMake ≥3.13:
-        target_link_options   (pysvzerod PRIVATE ${_f})
+        target_link_options   (svzerod 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}")
+    get_target_property(_ccopts svzerod COMPILE_OPTIONS)
+    message(STATUS ">>> svzerod COMPILE_OPTIONS = ${_ccopts}")
+    get_target_property(_lnkopts svzerod LINK_OPTIONS)
+    message(STATUS ">>> svzerod LINK_OPTIONS   = ${_lnkopts}")
 endif()
 
 # -----------------------------------------------------------------------------
@@ -241,7 +241,7 @@ target_include_directories(svzerodcalibrator PUBLIC
   ${CMAKE_SOURCE_DIR}/src/solve 
 )
 
-target_include_directories(pysvzerod PUBLIC 
+target_include_directories(svzerod PUBLIC 
   ${CMAKE_SOURCE_DIR}/src/algebra
   ${CMAKE_SOURCE_DIR}/src/model 
   ${CMAKE_SOURCE_DIR}/src/optimize
@@ -259,13 +259,13 @@ 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(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)
+target_link_libraries(svzerod PRIVATE Eigen3::Eigen)
+target_link_libraries(svzerod PRIVATE nlohmann_json::nlohmann_json)
+target_link_libraries(svzerod PRIVATE pybind11_json)
+target_link_libraries(svzerod PRIVATE svzero_algebra_library)
+target_link_libraries(svzerod PRIVATE svzero_model_library)
+target_link_libraries(svzerod PRIVATE svzero_optimize_library)
+target_link_libraries(svzerod PRIVATE svzero_solve_library)
 
 
 # Create distribution
@@ -289,20 +289,20 @@ add_custom_target(codecheck
   COMMAND npm run check
   COMMAND find ${SDIR}/*.h ${SDIR}/*.cpp | xargs clang-format -style=file:${PROJECT_SOURCE_DIR}/.clang-format --dry-run --Werror)
 
-set_target_properties(pysvzerod PROPERTIES
+set_target_properties(svzerod PROPERTIES
         LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/python
 )
 
 # standard install target locations
-install(TARGETS pysvzerod
+install(TARGETS svzerod
         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
+    set_target_properties(svzerod PROPERTIES
             PREFIX ""
             SUFFIX ".pyd"
     )

README.md

@@ -25,8 +25,8 @@ You can find more information under the following links:
 Install the Python bindings from PyPI with:
 
 ```sh
-python -m pip install pysvzerod
+python -m pip install svzerod
 ```
 
-Use `pysvzerod.simulate("model.json")` to run a model from Python. The package
+Use `svzerod.simulate("model.json")` to run a model from Python. The package
 also installs the `svzerodsolver` and `svzerodcalibrator` commands.

applications/svZeroDTuner/examples/closed_loop_Regazzoni/main.py

@@ -16,7 +16,7 @@
 import sys
 import numpy as np
 import pandas as pd
-import pysvzerod
+import svzerod
 
 # Add src to path
 sys.path.insert(0, os.path.join(os.path.dirname(__file__), '../..'))
@@ -51,7 +51,7 @@ def run_baseline(config_file):
 
     # Run baseline simulation
     try:
-        solver = pysvzerod.Solver(config_file)
+        solver = svzerod.Solver(config_file)
         solver.run()
         print("✓ Simulation completed successfully\n")
     except Exception as e:

applications/svZeroDTuner/examples/closed_loop_Regazzoni/tuning_job.sh

@@ -51,7 +51,7 @@ module load cmake
 # Relative paths (submit from this directory)
 VENV_DIR="../../venv"
 REQUIREMENTS="../../requirements.txt"
-SVZEROD_ROOT="../../../.."   # svZeroDSolver repo root (for pip install -e pysvzerod)
+SVZEROD_ROOT="../../../.."   # svZeroDSolver repo root (for pip install -e svzerod)
 
 # Check if virtual environment exists and has Python; if not, create and install
 if [[ ! -f "$VENV_DIR/bin/python" ]]; then

applications/svZeroDTuner/examples/closed_loop_Zingaro/main.py

@@ -16,7 +16,7 @@
 import sys
 import numpy as np
 import pandas as pd
-import pysvzerod
+import svzerod
 
 # Add src to path
 sys.path.insert(0, os.path.join(os.path.dirname(__file__), '../..'))
@@ -51,7 +51,7 @@ def run_baseline(config_file):
 
     # Run baseline simulation
     try:
-        solver = pysvzerod.Solver(config_file)
+        solver = svzerod.Solver(config_file)
         solver.run()
         print("✓ Simulation completed successfully\n")
     except Exception as e:

applications/svZeroDTuner/examples/closed_loop_Zingaro/tuning_job.sh

@@ -51,7 +51,7 @@ module load cmake
 # Relative paths (submit from this directory)
 VENV_DIR="../../venv"
 REQUIREMENTS="../../requirements.txt"
-SVZEROD_ROOT="../../../.."   # svZeroDSolver repo root (for pip install -e pysvzerod)
+SVZEROD_ROOT="../../../.."   # svZeroDSolver repo root (for pip install -e svzerod)
 
 # Check if virtual environment exists and has Python; if not, create and install
 if [[ ! -f "$VENV_DIR/bin/python" ]]; then

applications/svZeroDTuner/examples/right_heart_pa/main.py

@@ -15,7 +15,7 @@
 import sys
 import numpy as np
 import pandas as pd
-import pysvzerod
+import svzerod
 
 # Add src to path
 sys.path.insert(0, os.path.join(os.path.dirname(__file__), '../..'))
@@ -42,7 +42,7 @@ def run_baseline(config_file):
     print()
 
     try:
-        solver = pysvzerod.Solver(config_file)
+        solver = svzerod.Solver(config_file)
         solver.run()
         print("\u2713 Simulation completed successfully\n")
     except Exception as e:

applications/svZeroDTuner/requirements.txt

@@ -4,5 +4,5 @@ pandas>=1.3.0
 pyyaml>=6.0
 matplotlib>=3.5.0
 
-# pysvzerod is a requirement, but it is not available on PyPI, so we need to 
-#install it from source using "pip install -e ." from the svZeroDSolver repo root
+# svzerod is also required. Install it from PyPI with "pip install svzerod",
+# or from source using "pip install -e ." from the svZeroDSolver repo root.

applications/svZeroDTuner/svzerodtuner/output_extractor.py

@@ -8,7 +8,7 @@
 import numpy as np
 import pandas as pd
 from typing import Union, Literal, Optional
-import pysvzerod
+import svzerod
 
 
 class OutputExtractor:
@@ -19,12 +19,12 @@ class OutputExtractor:
     Supports extraction of time series or scalar metrics (min, max, mean).
     """
 
-    def __init__(self, solver: pysvzerod.Solver):
+    def __init__(self, solver: svzerod.Solver):
         """
         Initialize output extractor with a solver instance.
 
         Args:
-            solver: pysvzerod.Solver instance (must have run() called)
+            solver: svzerod.Solver instance (must have run() called)
         """
         self.solver = solver
         self._result_df = None

applications/svZeroDTuner/svzerodtuner/simulation.py

@@ -6,7 +6,7 @@
 """
 
 import numpy as np
-import pysvzerod
+import svzerod
 from typing import List, Dict, Any, Tuple
 
 from .parameter_handler import ParameterHandler
@@ -17,7 +17,7 @@ def run_simulation(
     param_handler: ParameterHandler,
     parameters: List[Dict[str, Any]],
     param_values: np.ndarray,
-) -> Tuple[pysvzerod.Solver, OutputExtractor]:
+) -> Tuple[svzerod.Solver, OutputExtractor]:
     """
     Run sv0D simulation with given parameter values.
 
@@ -42,7 +42,7 @@ def run_simulation(
         param_handler.set_parameter(name, value)
 
     config_dict = param_handler.get_config()
-    solver = pysvzerod.Solver(config_dict)
+    solver = svzerod.Solver(config_dict)
     solver.run()
     extractor = OutputExtractor(solver)
     return solver, extractor

applications/svZeroDTuner/svzerodtuner/sv0d_tuner.py

@@ -97,7 +97,7 @@ def __init__(self, config_file: str):
     def __getstate__(self):
         """
         Make tuner pickle-safe for multiprocessing objective dispatch.
-        `pysvzerod.Solver`/extractor instances are runtime-only and not pickleable.
+        `svzerod.Solver`/extractor instances are runtime-only and not pickleable.
         """
         state = self.__dict__.copy()
         state["solver"] = None

applications/svZeroDVisualization/visualize_simulation.py

@@ -3,7 +3,7 @@
 
 import sys
 import argparse
-import pysvzerod
+import svzerod
 import pandas as pd
 import matplotlib.pyplot as plt
 import networkx as nx
@@ -27,7 +27,7 @@
 '''
 
 def dirgraph(filepath, output_dir, export_csv):
-    solver = pysvzerod.Solver(filepath)
+    solver = svzerod.Solver(filepath)
     solver.run()
     results = pd.DataFrame(solver.get_full_result())
 

applications/pysvzerod.cpp → applications/svzerod.cpp

@@ -1,7 +1,7 @@
 // SPDX-FileCopyrightText: Copyright (c) Stanford University, The Regents of the
 // University of California, and others. SPDX-License-Identifier: BSD-3-Clause
 /**
- * @file pysvzerod.cpp
+ * @file svzerod.cpp
  * @brief Python interface for svZeroDSolver
  */
 #include <pybind11/eigen.h>
@@ -15,8 +15,8 @@
 
 namespace py = pybind11;
 
-PYBIND11_MODULE(pysvzerod, m) {
-  m.attr("__version__") = PYSVZEROD_VERSION;
+PYBIND11_MODULE(svzerod, m) {
+  m.attr("__version__") = SVZEROD_VERSION;
   using Solver = Solver;
   py::class_<Solver>(m, "Solver")
       .def(py::init([](py::dict& config) {