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feat(bindings): ported most bindings over from serif

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Emily Boudreaux
2025-07-22 13:51:43 -04:00
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# Python
__pycache__/
*.py[cod]
*.pyo
*.pyd
*.env
*.venv
env/
venv/
ENV/
ENV.bak/
*.egg-info/
dist/
build/
*.egg
# C and C++ (using Meson)
build/
*.o
*.a
*.so
*.d
*.dSYM/
*.exe
*.out
*.obj
*.dll
*.lib
*.pdb
*.exp
*.log
*.stackdump
# Fortran
*.mod
*.o
*.a
*.so
*.exe
*.out
# Doxygen
latex/
xml/
man/
rtf/
tags
## Misc
*.swp
*._DS_Store
*.DS_Store
*.bak
*.tmp
*.log
*.cache
*.private
*.private/
subprojects/mfem/
subprojects/tetgen/
subprojects/yaml-cpp/
subprojects/quill/
subprojects/googletest-*/
subprojects/opat-core/
subprojects/pybind11*/
subprojects/packagecache/
subprojects/hypre/
subprojects/qhull/
subprojects/cppad/
subprojects/libcomposition/
subprojects/libconfig/
subprojects/libconstants/
subprojects/liblogging/
subprojects/eigen-*/
*.csv
*.dot
qhull.wrap
quill.wrap
yaml-cpp.wrap
pybind11.wrap
.vscode/
*.log
mpi-install-log.txt
output/
.boost_installed
4DSSE_logs/
.last_build_flags
.idea/
scratch/

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<one line to give the program's name and a brief idea of what it does.>
Copyright (C) <year> <name of author>
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
Also add information on how to contact you by electronic and paper mail.
If the program does terminal interaction, make it output a short
notice like this when it starts in an interactive mode:
<program> Copyright (C) <year> <name of author>
This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
This is free software, and you are welcome to redistribute it
under certain conditions; type `show c' for details.
The hypothetical commands `show w' and `show c' should show the appropriate
parts of the General Public License. Of course, your program's commands
might be different; for a GUI interface, you would use an "about box".
You should also get your employer (if you work as a programmer) or school,
if any, to sign a "copyright disclaimer" for the program, if necessary.
For more information on this, and how to apply and follow the GNU GPL, see
<http://www.gnu.org/licenses/>.
The GNU General Public License does not permit incorporating your program
into proprietary programs. If your program is a subroutine library, you
may consider it more useful to permit linking proprietary applications with
the library. If this is what you want to do, use the GNU Lesser General
Public License instead of this License. But first, please read
<http://www.gnu.org/philosophy/why-not-lgpl.html>.

8
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composition_p = subproject('libcomposition', default_options: ['pkg-config=false'])
comp_dep = composition_p.get_variable('composition_dep')
libcomposition = composition_p.get_variable('libcomposition')
spw_dep = composition_p.get_variable('species_weight_dep')
composition_dep = [
comp_dep,
spw_dep,
]

3
build-config/libconfig/meson.build Normal file
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config_p = subproject('libconfig', default_options:['pkg-config=false'])
config_dep = config_p.get_variable('config_dep')
libconfig = config_p.get_variable('libconfig')

3
build-config/libconstants/meson.build Normal file
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const_p = subproject('libconstants', default_options: ['pkg-config=false'])
const_dep = const_p.get_variable('const_dep')
libconst = const_p.get_variable('libconst')

7
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logging_p = subproject('liblogging', default_options: ['pkg-config=false'])
liblogging = logging_p.get_variable('liblogging')
logging_dep = logging_p.get_variable('logging_dep')
quill_dep = logging_p.get_variable('quill_dep')
log_dep = [logging_dep, quill_dep]

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subdir('libcomposition')
subdir('libconfig')
subdir('libconstants')
subdir('liblogging')
subdir('pybind')

3
build-config/pybind/meson.build Normal file
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pybind11_proj = subproject('pybind11')
pybind11_dep = pybind11_proj.get_variable('pybind11_dep')
python3_dep = dependency('python3')

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# --- Python Extension Setup ---
py_installation = import('python').find_installation('python3')
py_mod = py_installation.extension_module(
'fourdst', # Name of the generated .so/.pyd file (without extension)
sources: [
meson.project_source_root() + '/src-pybind/bindings.cpp',
meson.project_source_root() + '/src-pybind/composition/bindings.cpp',
meson.project_source_root() + '/src-pybind/constants/bindings.cpp',
meson.project_source_root() + '/src-pybind/config/bindings.cpp',
],
dependencies : [
pybind11_dep,
const_dep,
config_dep,
composition_dep,
],
cpp_args : ['-UNDEBUG'],
install : true,
)

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meson.build Normal file
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project('fourdst', 'cpp', version: 'v0.5.0', default_options: ['cpp_std=c++23'], meson_version: '>=1.5.0')
add_project_arguments('-fvisibility=default', language: 'cpp')
# Configure vendor libraries
subdir('build-config')
# Configure python bindings
subdir('build-python')
# Build python bindings
subdir('src-pybind')

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[build-system]
requires = [
"meson-python>=0.15.0", # Use a recent version
"meson>=1.6.0", # Specify your Meson version requirement
"pybind11>=2.10" # pybind11 headers needed at build time
]
build-backend = "mesonpy"
[project]
name = "fourdst" # Choose your Python package name
version = "0.5.0" # Your project's version
description = "Python interface to the utility fourdst modules from the 4D-STAR project"
readme = "readme.md"
license = { file = "LICENSE.txt" } # Reference your license file [cite: 2]
authors = [
{name = "Emily M. Boudreaux", email = "emily@boudreauxmail.com"},
]
maintainers = [
{name = "Emily M. Boudreaux", email = "emily@boudreauxmail.com"}
]

23
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#include <pybind11/pybind11.h>
#include <string>
#include "constants/bindings.h"
#include "composition/bindings.h"
#include "config/bindings.h"
PYBIND11_MODULE(fourdst, m) {
m.doc() = "Python bindings for the fourdst utility modules which are a part of the 4D-STAR project.";
auto compMod = m.def_submodule("composition", "Composition-module bindings");
register_comp_bindings(compMod);
auto atomicMod = m.def_submodule("atomic", "Species bindings");
register_species_bindings(atomicMod);
auto constMod = m.def_submodule("constants", "Constants-module bindings");
register_const_bindings(constMod);
auto configMod = m.def_submodule("config", "Configuration-module bindings");
register_config_bindings(configMod);
}

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src-pybind/composition/bindings.cpp Normal file
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#include <pybind11/pybind11.h>
#include <pybind11/stl.h> // Needed for vectors, maps, sets, strings
#include <pybind11/stl_bind.h> // Needed for binding std::vector, std::map etc if needed directly
#include <string>
#include "fourdst/composition/composition.h"
#include "fourdst/composition/atomicSpecies.h"
#include "bindings.h"
#include "fourdst/composition/species.h"
namespace py = pybind11;
std::string sv_to_string(std::string_view sv) {
return std::string(sv);
}
std::string get_ostream_str(const fourdst::composition::Composition& comp) {
std::ostringstream oss;
oss << comp;
return oss.str();
}
void register_comp_bindings(pybind11::module &comp_submodule) {
// --- Bindings for composition and species module ---
py::class_<fourdst::composition::GlobalComposition>(comp_submodule, "GlobalComposition")
.def_readonly("specificNumberDensity", &fourdst::composition::GlobalComposition::specificNumberDensity)
.def_readonly("meanParticleMass", &fourdst::composition::GlobalComposition::meanParticleMass)
.def("__repr__", // Add a string representation for easy printing in Python
[](const fourdst::composition::GlobalComposition &gc) {
return "<GlobalComposition(specNumDens=" + std::to_string(gc.specificNumberDensity) +
", meanMass=" + std::to_string(gc.meanParticleMass) + ")>";
});
py::class_<fourdst::composition::CompositionEntry>(comp_submodule, "CompositionEntry")
.def("symbol", &fourdst::composition::CompositionEntry::symbol)
.def("mass_fraction",
py::overload_cast<>(&fourdst::composition::CompositionEntry::mass_fraction, py::const_),
"Gets the mass fraction of the species.")
.def("mass_fraction",
py::overload_cast<double>(&fourdst::composition::CompositionEntry::mass_fraction, py::const_),
py::arg("meanMolarMass"), // Name the argument in Python
"Gets the mass fraction of the species given the mean molar mass.")
.def("number_fraction",
py::overload_cast<>(&fourdst::composition::CompositionEntry::number_fraction, py::const_),
"Gets the number fraction of the species.")
.def("number_fraction",
py::overload_cast<double>(&fourdst::composition::CompositionEntry::number_fraction, py::const_),
py::arg("totalMoles"),
"Gets the number fraction of the species given the total moles.")
.def("rel_abundance", &fourdst::composition::CompositionEntry::rel_abundance)
.def("isotope", &fourdst::composition::CompositionEntry::isotope) // Assuming Species is bound or convertible
.def("getMassFracMode", &fourdst::composition::CompositionEntry::getMassFracMode)
.def("__repr__", // Optional: nice string representation
[](const fourdst::composition::CompositionEntry &ce) {
// You might want to include more info here now
return "<CompositionEntry(symbol='" + ce.symbol() + "', " +
"mass_frac=" + std::to_string(ce.mass_fraction()) + ", " +
"num_frac=" + std::to_string(ce.number_fraction()) + ")>";
});
// --- Binding for the main Composition class ---
py::class_<fourdst::composition::Composition>(comp_submodule, "Composition")
// Constructors
.def(py::init<>(), "Default constructor")
.def(py::init<const std::vector<std::string>&>(),
py::arg("symbols"),
"Constructor taking a list of symbols to register (defaults to mass fraction mode)")
// .def(py::init<const std::set<std::string>&>(), py::arg("symbols")) // Binding std::set constructor is possible but often less convenient from Python
.def(py::init<const std::vector<std::string>&, const std::vector<double>&, bool>(),
py::arg("symbols"), py::arg("fractions"), py::arg("massFracMode") = true,
"Constructor taking symbols, fractions, and mode (True=Mass, False=Number)")
// Methods
.def("finalize", &fourdst::composition::Composition::finalize, py::arg("norm") = false,
"Finalize the composition, optionally normalizing fractions to sum to 1.")
.def("registerSymbol", py::overload_cast<const std::string&, bool>(&fourdst::composition::Composition::registerSymbol),
py::arg("symbol"), py::arg("massFracMode") = true, "Register a single symbol.")
.def("registerSymbol", py::overload_cast<const std::vector<std::string>&, bool>(&fourdst::composition::Composition::registerSymbol),
py::arg("symbols"), py::arg("massFracMode") = true, "Register multiple symbols.")
.def("getRegisteredSymbols", &fourdst::composition::Composition::getRegisteredSymbols,
"Get the set of registered symbols.")
.def("setMassFraction", py::overload_cast<const std::string&, const double&>(&fourdst::composition::Composition::setMassFraction),
py::arg("symbol"), py::arg("mass_fraction"), "Set mass fraction for a single symbol (requires massFracMode). Returns old value.")
.def("setMassFraction", py::overload_cast<const std::vector<std::string>&, const std::vector<double>&>(&fourdst::composition::Composition::setMassFraction),
py::arg("symbols"), py::arg("mass_fractions"), "Set mass fractions for multiple symbols (requires massFracMode). Returns list of old values.")
.def("setNumberFraction", py::overload_cast<const std::string&, const double&>(&fourdst::composition::Composition::setNumberFraction),
py::arg("symbol"), py::arg("number_fraction"), "Set number fraction for a single symbol (requires !massFracMode). Returns old value.")
.def("setNumberFraction", py::overload_cast<const std::vector<std::string>&, const std::vector<double>&>(&fourdst::composition::Composition::setNumberFraction),
py::arg("symbols"), py::arg("number_fractions"), "Set number fractions for multiple symbols (requires !massFracMode). Returns list of old values.")
.def("mix", &fourdst::composition::Composition::mix, py::arg("other"), py::arg("fraction"),
"Mix with another composition. Returns new Composition.")
.def("getMassFraction", py::overload_cast<const std::string&>(&fourdst::composition::Composition::getMassFraction, py::const_),
py::arg("symbol"), "Get mass fraction for a symbol (calculates if needed). Requires finalization.")
.def("getMassFraction", py::overload_cast<>(&fourdst::composition::Composition::getMassFraction, py::const_),
"Get dictionary of all mass fractions. Requires finalization.")
.def("getNumberFraction", py::overload_cast<const std::string&>(&fourdst::composition::Composition::getNumberFraction, py::const_),
py::arg("symbol"), "Get number fraction for a symbol (calculates if needed). Requires finalization.")
.def("getNumberFraction", py::overload_cast<>(&fourdst::composition::Composition::getNumberFraction, py::const_),
"Get dictionary of all number fractions. Requires finalization.")
// Note: pybind11 automatically converts std::pair to a Python tuple
.def("getComposition", py::overload_cast<const std::string&>(&fourdst::composition::Composition::getComposition, py::const_),
py::arg("symbol"), "Returns a tuple (CompositionEntry, GlobalComposition) for the symbol. Requires finalization.")
// Binding the version returning map<string, Entry> requires a bit more care or helper function
// to convert the map to a Python dict if needed directly. Let's bind the pair version for now.
.def("getComposition", py::overload_cast<>(&fourdst::composition::Composition::getComposition, py::const_),
"Returns a tuple (dict[str, CompositionEntry], GlobalComposition) for all symbols. Requires finalization.")
.def("subset", &fourdst::composition::Composition::subset, py::arg("symbols"), py::arg("method") = "norm",
"Create a new Composition containing only the specified symbols.")
.def("hasSymbol", &fourdst::composition::Composition::hasSymbol, py::arg("symbol"),
"Check if a symbol is registered.")
.def("setCompositionMode", &fourdst::composition::Composition::setCompositionMode, py::arg("massFracMode"),
"Set the mode (True=Mass, False=Number). Requires finalization before switching.")
// Operator overload
.def(py::self + py::self, "Mix equally with another composition.") // Binds operator+
// Add __repr__ or __str__
.def("__repr__", [](const fourdst::composition::Composition &comp) {
return get_ostream_str(comp); // Use helper for C++ operator<<
});
}
void register_species_bindings(pybind11::module &chem_submodule) {
// --- Bindings for species module ---
py::class_<fourdst::atomic::Species>(chem_submodule, "Species")
.def("mass", &fourdst::atomic::Species::mass, "Get atomic mass (amu)")
.def("massUnc", &fourdst::atomic::Species::massUnc, "Get atomic mass uncertainty (amu)")
.def("bindingEnergy", &fourdst::atomic::Species::bindingEnergy, "Get binding energy (keV/nucleon?)") // Check units
.def("betaDecayEnergy", &fourdst::atomic::Species::betaDecayEnergy, "Get beta decay energy (keV?)") // Check units
.def("betaCode", [](const fourdst::atomic::Species& s){ return sv_to_string(s.betaCode()); }, "Get beta decay code") // Convert string_view
.def("name", [](const fourdst::atomic::Species& s){ return sv_to_string(s.name()); }, "Get species name (e.g., 'H-1')") // Convert string_view
.def("el", [](const fourdst::atomic::Species& s){ return sv_to_string(s.el()); }, "Get element symbol (e.g., 'H')") // Convert string_view
.def("nz", &fourdst::atomic::Species::nz, "Get NZ value")
.def("n", &fourdst::atomic::Species::n, "Get neutron number N")
.def("z", &fourdst::atomic::Species::z, "Get proton number Z")
.def("a", &fourdst::atomic::Species::a, "Get mass number A")
.def("__repr__",
[](const fourdst::atomic::Species &s) {
std::ostringstream oss;
oss << s;
return oss.str();
});
chem_submodule.attr("species") = py::cast(fourdst::atomic::species); // Expose the species map
}

6
src-pybind/composition/bindings.h Normal file
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#pragma once
#include <pybind11/pybind11.h>
void register_comp_bindings(pybind11::module &m);
void register_species_bindings(pybind11::module &m);

17
src-pybind/composition/meson.build Normal file
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@@ -0,0 +1,17 @@
# Define the library
bindings_sources = files('bindings.cpp')
bindings_headers = files('bindings.h')
dependencies = [
composition_dep,
python3_dep,
pybind11_dep,
]
shared_module('py_composition',
bindings_sources,
cpp_args: ['-fvisibility=default'],
install : true,
dependencies: dependencies,
include_directories: include_directories('.')
)

55
src-pybind/config/bindings.cpp Normal file
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@@ -0,0 +1,55 @@
#include <pybind11/pybind11.h>
#include <pybind11/stl.h> // Needed for vectors, maps, sets, strings
#include <pybind11/stl_bind.h> // Needed for binding std::vector, std::map etc if needed directly
#include <string>
#include "bindings.h"
#include "fourdst/config/config.h"
namespace py = pybind11;
// Helper function template for binding Config::get
template <typename T>
void def_config_get(py::module &m) {
m.def("get",
[](const std::string &key, T defaultValue) {
return fourdst::config::Config::getInstance().get<T>(key, defaultValue);
},
py::arg("key"), py::arg("defaultValue"),
"Get configuration value (type inferred from default)");
}
void register_config_bindings(pybind11::module &config_submodule) {
def_config_get<int>(config_submodule);
def_config_get<double>(config_submodule);
def_config_get<std::string>(config_submodule);
def_config_get<bool>(config_submodule);
config_submodule.def("loadConfig",
[](const std::string& configFilePath) {
return fourdst::config::Config::getInstance().loadConfig(configFilePath);
},
py::arg("configFilePath"),
"Load configuration from a YAML file.");
config_submodule.def("has",
[](const std::string &key) {
return fourdst::config::Config::getInstance().has(key);
},
py::arg("key"),
"Check if a key exists in the configuration.");
config_submodule.def("keys",
[]() {
return py::cast(fourdst::config::Config::getInstance().keys());
},
"Get a list of all configuration keys.");
config_submodule.def("__repr__",
[]() {
std::ostringstream oss;
oss << fourdst::config::Config::getInstance(); // Use the existing operator<<
return std::string("<fourdsse_bindings.config module accessing C++ Singleton>\n") + oss.str();
});
}

5
src-pybind/config/bindings.h Normal file
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#pragma once
#include <pybind11/pybind11.h>
void register_config_bindings(pybind11::module &config_submodule);

17
src-pybind/config/meson.build Normal file
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@@ -0,0 +1,17 @@
# Define the library
bindings_sources = files('bindings.cpp')
bindings_headers = files('bindings.h')
dependencies = [
config_dep,
python3_dep,
pybind11_dep,
]
shared_module('py_config',
bindings_sources,
include_directories: include_directories('.'),
cpp_args: ['-fvisibility=default'],
install : true,
dependencies: dependencies,
)

54
src-pybind/constants/bindings.cpp Normal file
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#include <pybind11/pybind11.h>
#include <pybind11/stl.h> // Needed for vectors, maps, sets, strings
#include <pybind11/stl_bind.h> // Needed for binding std::vector, std::map etc if needed directly
#include <string>
#include "fourdst/constants/const.h"
#include "bindings.h"
namespace py = pybind11;
void register_const_bindings(pybind11::module &const_submodule) {
py::class_<fourdst::constant::Constant>(const_submodule, "Constant")
.def_readonly("name", &fourdst::constant::Constant::name)
.def_readonly("value", &fourdst::constant::Constant::value)
.def_readonly("uncertainty", &fourdst::constant::Constant::uncertainty)
.def_readonly("unit", &fourdst::constant::Constant::unit)
.def_readonly("reference", &fourdst::constant::Constant::reference)
.def("__repr__", [](const fourdst::constant::Constant &c) {
return "<Constant(name='" + c.name + "', value=" + std::to_string(c.value) +
", uncertainty=" + std::to_string(c.uncertainty) +
", unit='" + c.unit + "')>";
});
py::class_<fourdst::constant::Constants>(const_submodule, "Constants")
.def_property_readonly("loaded", &fourdst::constant::Constants::isLoaded)
.def_static("get",
[](const std::string &name) {
return py::cast(
fourdst::constant::Constants::getInstance().get(name)
);
},
"Get a constant by name. Returns None if not found."
)
.def_static("has",
[](const std::string &name) {
return fourdst::constant::Constants::getInstance().has(name);
},
"Check if a constant exists by name.")
.def_static("keys",
[]() {
return py::cast(
fourdst::constant::Constants::getInstance().keys()
);
},
"Get a list of all constant names.")
.def_static("__class_getitem__",
[](const std::string &name) {
return py::cast(
fourdst::constant::Constants::getInstance().get(name)
);
});
}

5
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#pragma once
#include <pybind11/pybind11.h>
void register_const_bindings(pybind11::module &const_submodule);

17
src-pybind/constants/meson.build Normal file
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@@ -0,0 +1,17 @@
# Define the library
bindings_sources = files('bindings.cpp')
bindings_headers = files('bindings.h')
dependencies = [
const_dep,
python3_dep,
pybind11_dep,
]
shared_module('py_const',
bindings_sources,
include_directories: include_directories('.'),
cpp_args: ['-fvisibility=default'],
install : true,
dependencies: dependencies,
)

0
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4
src-pybind/meson.build Normal file
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subdir('composition')
subdir('constants')
subdir('config')

16
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[wrap-file]
directory = googletest-1.15.2
source_url = https://github.com/google/googletest/archive/refs/tags/v1.15.2.tar.gz
source_filename = gtest-1.15.2.tar.gz
source_hash = 7b42b4d6ed48810c5362c265a17faebe90dc2373c885e5216439d37927f02926
patch_filename = gtest_1.15.2-2_patch.zip
patch_url = https://wrapdb.mesonbuild.com/v2/gtest_1.15.2-2/get_patch
patch_hash = 641a16b33c96cd32a593537bc30eb7d853c5cc361fa1ee96884f0e2fca21e2d3
source_fallback_url = https://github.com/mesonbuild/wrapdb/releases/download/gtest_1.15.2-2/gtest-1.15.2.tar.gz
wrapdb_version = 1.15.2-2
[provide]
gtest = gtest_dep
gtest_main = gtest_main_dep
gmock = gmock_dep
gmock_main = gmock_main_dep

4
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[wrap-git]
url = https://github.com/4D-STAR/libcomposition.git
revision = v1.5.1
depth = 1

4
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@@ -0,0 +1,4 @@
[wrap-git]
url = https://github.com/4D-STAR/libconfig.git
revision = v1.1.0
depth = 1

4
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@@ -0,0 +1,4 @@
[wrap-git]
url = https://github.com/4D-STAR/libconstants.git
revision = v1.1.0
depth = 1

4
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@@ -0,0 +1,4 @@
[wrap-git]
url = https://github.com/4D-STAR/liblogging.git
revision = v1.1.0
depth = 1