SpECTRE  v2024.05.11
Writing Python Bindings

CMake and Directory Layout

To allow users to analyze output from simulations and take advantage of SpECTRE's data structures and functions in python, bindings must sometimes be written. SpECTRE uses pybind11 to aid with generating the bindings. The C++ code for the bindings should generally go in a Python subdirectory. For example, the bindings for the DataStructures library would go in src/DataStructures/Python/. SpECTRE provides the spectre_python_add_module CMake function to make adding a new python module, be it with or without bindings, easy. The python bindings are built only if -D BUILD_PYTHON_BINDINGS=ON is passed when invoking cmake (enabled by default). You can specify the Python version, interpreter and libraries used for compiling and testing the bindings by setting the -D Python_EXECUTABLE to an absolute path such as /usr/bin/python3.

The function spectre_python_add_module takes as its first argument the module, in our case DataStructures. Optionally, a list of SOURCES can be passed to the CMake function. If you specify SOURCES, you must also specify a LIBRARY_NAME. A good LIBRARY_NAME is the name of the C++ library for which bindings are being built prefixed with Py, e.g. PyDataStructures. If the Python module will only consist of Python files, then the SOURCES option should not be specified. Python files that should be part of the module can be passed with the keyword PYTHON_FILES. Finally, the MODULE_PATH named argument can be passed with a string that is the path to where the module should be. For example, MODULE_PATH "submodule0/submodule1/" would mean the module is accessed from python using import spectre.submodule0.submodule1.MODULE_NAME.

Here is a complete example of how to call the spectre_python_add_module function:

LIBRARY_NAME "PyExtraDataStructures"
MODULE_PATH "DataStructures/"
SOURCES Bindings.cpp MyCoolDataStructure.cpp
PYTHON_FILES CoolPythonDataStructure.py

The library that is added has the name PyExtraDataStructures. Make sure to call spectre_python_link_libraries for every Python module that compiles SOURCES. For example,


You may also call spectre_python_add_dependencies for Python modules that have SOURCES, e.g.


Note that these functions will skip adding or configure any C++ libraries if the BUILD_PYTHON_BINDINGS flag is OFF.

Writing Bindings

Once a python module has been added you can write the actual bindings. You should structure your bindings directory to reflect the structure of the library you're writing bindings for. For example, say we want bindings for DataVector and Matrix then we should have one source file for each class's bindings inside src/DataStructures/Python. The functions that generate the bindings should be in the py_bindings namespace and have a reasonable name such as bind_datavector. There should be a file named Bindings.cpp which calls all the bind_* functions. The Bindings.cpp file is quite simple and should include <pybind11/pybind11.h>, forward declare the bind_* functions, and then have a PYBIND11_MODULE function. For example,

#include <pybind11/pybind11.h>
namespace py = pybind11;
namespace py_bindings {
void bind_datavector(py::module& m);
} // namespace py_bindings
PYBIND11_MODULE(_Pybindings, m) {

Note that the library name is passed to PYBIND11_MODULE and is prefixed with an underscore. The underscore is important and the library name must be the same that is passed as LIBRARY_NAME to spectre_python_add_module (see above).

The DataVector bindings serve as an example with code comments on how to write bindings for a class. There is also extensive documentation available directly from pybind11.

If you are binding a library full of similarly structured free functions, such as libraries in src/PointwiseFunctions/, you can bind all functions directly in the Bindings.cpp file to avoid unnecessary boilerplate code. See src/PointwiseFunctions/GeneralRelativity/Python/Bindings.cpp for an example.

Exceptions should be allowed to propagate through the bindings so that error handling via exceptions is possible from python rather than having the python interpreter being killed with a call to abort.

Testing Python Bindings and Code

All the python bindings must be tested. SpECTRE uses the unittest framework provided as part of python. To register a test file with CMake use the SpECTRE-provided function spectre_add_python_test passing as the first argument the test name (e.g. "Unit.DataStructures.Python.DataVector"), the file as the second argument (e.g. Test_DataVector.py), and a semicolon separated list of labels as the last (e.g. "unit;datastructures;python"). All the test cases should be in a single class so that the python unit testing framework will run all test functions on a single invocation to avoid startup cost.

Below is an example of registering a python test file for bindings:


Python code that does not use bindings must also be tested. You can register the test file using the spectre_add_python_test CMake function with the same signature as shown above.

Using The Bindings

See Using SpECTRE's Python


  • All python libraries are dynamic/shared libraries.
  • Exceptions should be allowed to propagate through the bindings so that error handling via exceptions is possible from python rather than having the python interpreter being killed with a call to abort.
  • All function arguments in Python bindings should be named using py::arg. See the Python bindings in IO/H5/ for examples. Using the named arguments in Python code is optional, but preferred when it makes code more readable. In particular, use the argument names in the tests for the Python bindings so they are being tested as well.

Guidelines for writing command-line interfaces (CLIs)

  • List all CLI endpoints in support/Python/__main__.py.
  • Follow the recommendations in the click documentation.
  • Split your code into free functions that know nothing about the CLI and can just as well be called independently from Python, and the CLI commands that call the functions. Test both.
  • Take only input files that the script operates on as positional arguments (like H5 data files or YAML input files) and everything else as options.
  • Choose option names and shorthands consistent with other CLI endpoints in the repository. For example, H5 subfile names are specified with '–subfile-name' / '-d' and output files are specified with '–output' / '-o'. Look at other CLI endpoints before making choices for option names.
  • Never read or write files to or from "default" locations. Instead, take all input files as arguments and write all output files to locations specified explicitly by the user. This is important so users are not afraid of moving and renaming files, and are not left wondering where the script wrote its output. Examples:
    • Don't try to read a file like "spectre.out" from the current directory just because it might be there by convention. Instead, add an argument or option like --out-filename so the user can specify it.
    • Don't write a file like "plot.pdf" to the current directory without telling the user. Instead, add an option like --output / -o for the user to specify explicitly so they know exactly where output is written to.
  • Operate on files instead of directories when possible. For example, prefer taking many H5 volume data files as arguments instead of the directory that contains them. This helps with operating on H5 files in segments or other subdirectory structures. Passing many files to a script is easy for the user by using a glob (note: don't take the glob as a string argument, take the expanded list of files directly using click.argument(..., nargs=-1, type=click.Path(...))).
  • Never overwrite or delete files without prompting the user or asking them to run with --force.
  • When the input to a script is empty, gracefully degrade to a noop.
  • When the user did not specify an option, print possible values for it and return instead of raising an exception. For example, print the subfile names in an H5 file if no subfile name was specified. This allows the user to make selections incrementally.
  • When the user did not specify an output file, write the output to sys.stdout if possible instead of raising an exception. This allows the user to use pipes and chain commands if they want, or add a quick -o option to write to a file.
  • Always use Python's logging module over plain print statements. This allows the user to control the verbosity.