use hpp

phreeqc-stubs/__init__.pyi

@@ -0,0 +1,44 @@
+from typing import List
+
+
+class Phreeqc:
+    def __init__(self) -> None:
+        """
+        Create a Phreeqc instance.
+        """
+        ...
+
+    def get_selected_output_string(self) -> str: ...
+
+    def load_database(self, path: str) -> None:
+        """
+        Load the specified database file into phreeqc.
+
+        :param path: The path of the phreeqc database to load. The full path (or relative path \
+            with respect to the working directory) will be required if the file is not in the current working directory
+        """
+        ...
+
+    def run_file(self, path: str) -> None:
+        """
+        Runs the specified phreeqc input file.
+
+        :param path: The path of the phreeqc input file to run.
+        """
+        ...
+
+    def run_string(self, input: str) -> None:
+        """
+        Runs the specified string as input to phreeqc.
+
+        :param input: String containing phreeqc input.
+        """
+        ...
+
+    def get_selected_output(self) -> List[List]:
+        """
+        Get the selected output.
+
+        :return: A 2d-array consisting of each row from the selected output
+        """
+        ...

setup.py

@@ -34,7 +34,8 @@ def build_extension(self, ext: CMakeExtension) -> None:
         # Using this requires trailing slash for auto-detection & inclusion of
         # auxiliary "native" libs
 
-        debug = int(os.environ.get("DEBUG", 0)) if self.debug is None else self.debug
+        debug = int(os.environ.get("DEBUG", 0)
+                    ) if self.debug is None else self.debug
         cfg = "Debug" if debug else "Release"
 
         # CMake lets you override the generator - we need to check this.
@@ -55,10 +56,12 @@ def build_extension(self, ext: CMakeExtension) -> None:
         # Adding CMake arguments set as environment variable
         # (needed e.g. to build for ARM OSx on conda-forge)
         if "CMAKE_ARGS" in os.environ:
-            cmake_args += [item for item in os.environ["CMAKE_ARGS"].split(" ") if item]
+            cmake_args += [
+                item for item in os.environ["CMAKE_ARGS"].split(" ") if item]
 
         # In this example, we pass in the version to C++. You might not need to.
-        cmake_args += [f"-DEXAMPLE_VERSION_INFO={self.distribution.get_version()}"]
+        cmake_args += [f"-DEXAMPLE_VERSION_INFO={
+            self.distribution.get_version()}"]
 
         if self.compiler.compiler_type != "msvc":
             # Using Ninja-build since it a) is available as a wheel and b)
@@ -73,14 +76,16 @@ def build_extension(self, ext: CMakeExtension) -> None:
                     ninja_executable_path = Path(ninja.BIN_DIR) / "ninja"
                     cmake_args += [
                         "-GNinja",
-                        f"-DCMAKE_MAKE_PROGRAM:FILEPATH={ninja_executable_path}",
+                        f"-DCMAKE_MAKE_PROGRAM:FILEPATH={
+                            ninja_executable_path}",
                     ]
                 except ImportError:
                     pass
 
         else:
             # Single config generators are handled "normally"
-            single_config = any(x in cmake_generator for x in {"NMake", "Ninja"})
+            single_config = any(
+                x in cmake_generator for x in {"NMake", "Ninja"})
 
             # CMake allows an arch-in-generator style for backward compatibility
             contains_arch = any(x in cmake_generator for x in {"ARM", "Win64"})
@@ -102,7 +107,8 @@ def build_extension(self, ext: CMakeExtension) -> None:
             # Cross-compile support for macOS - respect ARCHFLAGS if set
             archs = re.findall(r"-arch (\S+)", os.environ.get("ARCHFLAGS", ""))
             if archs:
-                cmake_args += ["-DCMAKE_OSX_ARCHITECTURES={}".format(";".join(archs))]
+                cmake_args += [
+                    "-DCMAKE_OSX_ARCHITECTURES={}".format(";".join(archs))]
 
         # Set CMAKE_BUILD_PARALLEL_LEVEL to control the parallel build level
         # across all generators.
@@ -132,10 +138,12 @@ def build_extension(self, ext: CMakeExtension) -> None:
     version="0.0.1",
     author="Haohan Yang",
     description="Python bindings for PHREEQC Version 3",
-    long_description="",
+    long_description="Python bindings for PHREEQC Version 3",
+    packages=["phreeqc-stubs"],
+    package_data={"phreeqc-stubs": ["*.pyi"]},
     ext_modules=[CMakeExtension("phreeqc")],
     cmdclass={"build_ext": CMakeBuild},
     zip_safe=False,
     extras_require={"test": ["pytest>=6.0"]},
     python_requires=">=3.7",
-)
+)

src/main.cpp

@@ -1,25 +1,27 @@
 #include <exception>
 #include <pybind11/pybind11.h>
-#include "IPhreeqc.h"
+#include "IPhreeqc.hpp"
 
 namespace py = pybind11;
 
 struct Phreeqc
 {
     Phreeqc()
     {
-        int res = CreateIPhreeqc();
-        if (res < 0)
+        instance = new IPhreeqc();
+    }
+
+    ~Phreeqc()
+    {
+        if (instance != nullptr)
         {
-            throw std::runtime_error("Failed to create an IPhreeqc instance");
+            delete instance;
         }
-
-        id = res;
     }
 
     void loadDatabase(const char *path)
     {
-        int errors = LoadDatabase(id, path);
+        int errors = instance->LoadDatabase(path);
         if (errors > 0)
         {
             throw std::runtime_error("Failed to load database");
@@ -28,7 +30,7 @@ struct Phreeqc
 
     void runString(const char *input)
     {
-        int errors = RunString(id, input);
+        int errors = instance->RunString(input);
         if (errors > 0)
         {
             throw std::runtime_error("Failed to run string");
@@ -37,19 +39,60 @@ struct Phreeqc
 
     void runFile(const char *path)
     {
-        int errors = RunFile(id, path);
+        int errors = instance->RunFile(path);
         if (errors > 0)
         {
             throw std::runtime_error("Failed to run path");
         }
     }
 
-    const char *getSelectedOutputString()
+    const py::list getSelectedOutput()
     {
-        return GetSelectedOutputString(id);
+        py::list output;
+
+        VAR var;
+        VarInit(&var);
+
+        const int colCount = instance->GetSelectedOutputColumnCount();
+        const int rowCount = instance->GetSelectedOutputRowCount();
+
+        for (int row = 0; row < rowCount; row++)
+        {
+            py::list rowData;
+            for (int col = 0; col < colCount; col++)
+            {
+                if (instance->GetSelectedOutputValue(row, col, &var) != VR_OK)
+                {
+                    rowData.append(py::str("error"));
+                }
+                else
+                {
+                    if (var.type == TT_LONG)
+                    {
+                        rowData.append(py::int_(var.lVal));
+                    }
+                    else if (var.type == TT_DOUBLE)
+                    {
+                        rowData.append(py::float_(var.dVal));
+                    }
+                    else if (var.type == TT_STRING)
+                    {
+                        rowData.append(py::str(var.sVal));
+                    }
+                    else
+                    {
+                        rowData.append(py::none());
+                    }
+                }
+            }
+
+            output.append(rowData);
+        }
+
+        return output;
     }
 
-    int id;
+    IPhreeqc *instance;
 };
 
 PYBIND11_MODULE(phreeqc, m)
@@ -60,5 +103,5 @@ PYBIND11_MODULE(phreeqc, m)
         .def("load_database", &Phreeqc::loadDatabase)
         .def("run_string", &Phreeqc::runString)
         .def("run_file", &Phreeqc::runFile)
-        .def("get_selected_output_string", &Phreeqc::getSelectedOutputString);
+        .def("get_selected_output", &Phreeqc::getSelectedOutput);
 }