binary_c_python.c

#include <Python.h>
#include "binary_c_python.h"
#include <time.h>
#include <sys/timeb.h>
#include <stdarg.h>
#include <stdio.h>
#include <stdlib.h>
#include <unistd.h>
#include <stdint.h>
#include <string.h>

/*
 * binary_c/PYTHON API interface functions
 *
 * This module will be available as _binary_c_bindings, as a part of the binarycpython package.
 * 
 * The first section contains the functions that will be available 
 * to python as part of the submodule _binary_c_bindings
 * 
 * The second section is composed of the functions that interface with the binary_c API 
 *
 * Written by David Hendriks (davidhendriks93@gmail.com), Robert Izzard (r.izzard@surrey.ac.uk). 
 * Based on initial work of Jeff Andrews
 * Remember: variables must be passed by references
 * (i.e. as pointers).
 *
 * See tests/python_API_test.py for an example of how to use these functions.
 *
 * Backup reading material for making C-extensions:
 * http://www-h.eng.cam.ac.uk/help/tpl/languages/mixinglanguages.html
 * https://realpython.com/build-python-c-extension-module/
 * https://docs.python.org/3/extending/extending.html
 * https://docs.python.org/3/c-api/arg.html#c.PyArg_ParseTuple
 * https://realpython.com/python-bindings-overview/
 * http://scipy-lectures.org/advanced/interfacing_with_c/interfacing_with_c.html
 * https://docs.python.org/3.6/c-api/capsule.html#c.PyCapsule_New
 * https://gist.github.com/Sleepingwell/5259476
 * https://bfroehle.com/2011/07/18/python-capsules/
 * https://docs.python.domainunion.de/3.6/howto/cporting.html
 * https://lappweb.in2p3.fr/~paubert/ASTERICS_HPC/5-6-3-651.html
 * https://www.geeksforgeeks.org/c-api-from-extension-module-in-python-set-1/
 * http://pageperso.lif.univ-mrs.fr/~francois.denis/IAAM1/python-3.6.5rc1-docs-html/howto/cporting.html
 * http://python3porting.com/cextensions.html
 * 
 * 
 * Open tasks for the Extension:
 * TODO: Put in clear debug statements
 * TODO: properly return stderr
 * TODO: describe all functions with docstrings
 * TODO: properly pass through all the pointers using Capsules:  
 */


/************************************************************
 ************************************************************
 ** Section 1: Python module functions and creation of module
 ************************************************************
 ************************************************************/

/************************************************************
 *
 * function prototypes : these are the functions
 * called by PYTHON code, without the trailing underscore.
 *
 ************************************************************/

/* Preparing all the functions of the module */
// Docstrings
static char module_docstring[] MAYBE_UNUSED =
    "This module is a python3 wrapper around binary_c";

// Evolution function docstrings
static char run_system_docstring[] = 
    "Function to run a system. This is a general function that will be able to handle different kinds of situations: single system run with different settings, population run with different settings, etc. To avoid having too many functions doing slightly different things.\n\nArguments:\n\targstring: argument string for binary_c\n\t(opt) custom_logging_func_memaddr: memory address value for custom logging function. Default = -1 (None)\n\t(opt) store_memaddr: memory adress of the store. Default = -1 (None)\n\t(opt) write_logfile: Boolean (in int form) for whether to enable the writing of the log function. Default = 0\n\t(opt) population: Boolean (in int form) for whether this system is part of a population run. Default = 0.";

// Utility function docstrings
static char return_arglines_docstring[] =
    "Return the default args for a binary_c system\n\nArguments:\n\tNo arguments.";
static char return_help_info_docstring[] = 
    "Return the help info for a given parameter\n\nArguments:\n\tparameter: parameter name.";
static char return_help_all_info_docstring[] = 
    "Return an overview of all the parameters, their description, categorized in sections\n\nArguments:\n\tNo arguments.";
static char return_version_info_docstring[] = 
    "Return the version information of the used binary_c build\n\nArguments:\n\tNo arguments.";
static char return_minimum_orbit_for_RLOF_docstring[] = 
    "Returns a string containing the minimum orbit and separation for which a binary system does not RLOF at ZAMS. Please use the wrapper functions in utils for this except when you know what you're doing.\n\nArguments:\n\targstring: argument string for binary_c\n\t(opt) store_capsule: capsule containing memory adress for the store object.unction. Default = Null";
static char return_maximum_mass_ratio_for_RLOF_docstring[] = 
    "Returns a string containing the maximum mass ratio for which a binary system does not RLOF at ZAMS. Please use the wrapper functions in utils for this except when you know what you're doing.\n\nArguments:\n\targstring: argument string for binary_c\n\t(opt) store_capsule: capsule containing memory adress for the store object.unction. Default = Null";

// other functionality
static char return_store_memaddr_docstring[] = 
    "Return the store memory adress that will be passed to run_population\n\nArguments:\n\tNo arguments.";
static char return_persistent_data_memaddr_docstring[] = 
    "Return the store memory adress that will be passed to run_population\n\nArguments:\n\tNo arguments.";

static char free_persistent_data_memaddr_and_return_json_output_docstring[] = 
    "Frees the persistent_data memory and returns the json output.\n\nArguments:\n\tstore capsule: capsule containing the memory adress of the persistent data object (contains the ensemble)";
static char free_store_memaddr_docstring[] = 
    "Frees the store memaddr.\n\nArguments:\n\tstore capsule: capsule containing the memory adress of the store object";
static char test_func_docstring[] = 
    "Function that contains random snippets. Do not expect this to remain available, or reliable. i.e. dont use it. ";

/* Initialize pyobjects */

// Evolution function headers
static PyObject* python_run_system(PyObject *self, PyObject *args, PyObject *kwargs);

// Utility function headers
static PyObject* python_return_arglines(PyObject *self, PyObject *args);
static PyObject* python_return_help_info(PyObject *self, PyObject *args);
static PyObject* python_return_help_all_info(PyObject *self, PyObject *args);
static PyObject* python_return_version_info(PyObject *self, PyObject *args);
static PyObject* python_return_minimum_orbit_for_RLOF(PyObject *self, PyObject *args, PyObject *kwargs);
static PyObject* python_return_maximum_mass_ratio_for_RLOF(PyObject *self, PyObject *args, PyObject *kwargs);

// Other function headers
static PyObject* python_return_store_memaddr(PyObject *self, PyObject *args);
static PyObject* python_return_persistent_data_memaddr(PyObject *self, PyObject *args);

// Free functions
static PyObject* python_free_persistent_data_memaddr_and_return_json_output(PyObject *self, PyObject *args);
static PyObject* python_free_store_memaddr(PyObject *self, PyObject *args);
static PyObject* python_test_func(PyObject *self, PyObject *args);

/* Set the module functions */
static PyMethodDef module_methods[] = {
    // Wierdly, this casting to a PyCFunction, which usually takes only 2 args, now works when giving keywords. See https://stackoverflow.com/q/10264080
    {"run_system", (PyCFunction)python_run_system, METH_VARARGS|METH_KEYWORDS, run_system_docstring}, 

    //
    {"return_arglines", python_return_arglines, METH_VARARGS, return_arglines_docstring},
    {"return_help", python_return_help_info, METH_VARARGS, return_help_info_docstring},
    {"return_help_all", python_return_help_all_info, METH_VARARGS, return_help_all_info_docstring},
    {"return_version_info", python_return_version_info, METH_VARARGS, return_version_info_docstring},
    {"return_minimum_orbit_for_RLOF", (PyCFunction)python_return_minimum_orbit_for_RLOF, METH_VARARGS|METH_KEYWORDS, return_minimum_orbit_for_RLOF_docstring},
    {"return_maximum_mass_ratio_for_RLOF", (PyCFunction)python_return_maximum_mass_ratio_for_RLOF, METH_VARARGS|METH_KEYWORDS, return_maximum_mass_ratio_for_RLOF_docstring},

    // memory
    {"return_store_memaddr", python_return_store_memaddr, METH_VARARGS, return_store_memaddr_docstring},
    {"return_persistent_data_memaddr", python_return_persistent_data_memaddr, METH_NOARGS, return_persistent_data_memaddr_docstring},

    // freeing
    {"free_persistent_data_memaddr_and_return_json_output", python_free_persistent_data_memaddr_and_return_json_output, METH_VARARGS, free_persistent_data_memaddr_and_return_json_output_docstring},
    {"free_store_memaddr", python_free_store_memaddr, METH_VARARGS, free_store_memaddr_docstring},

    // dummy function
    {"test_func", python_test_func, METH_NOARGS, test_func_docstring},

    //
    {NULL, NULL, 0, NULL}
};

/* ============================================================================== */
/* Making the module                                                              */
/* ============================================================================== */

/* Initialise the module. Removed the part which supports python 2 here on 17-03-2020 */
/* Python 3+ */
static struct PyModuleDef Py__binary_c_bindings =
{
    PyModuleDef_HEAD_INIT,
    "_binary_c_bindings", /* name of module */
    "Module to interface the Binary_c API with python.",          /* module documentation, may be NULL */
    -1,          /* size of per-interpreter state of the module, or -1 if the module keeps state in global variables. */
    module_methods
};

PyMODINIT_FUNC PyInit__binary_c_bindings(void)
{
    return PyModule_Create(&Py__binary_c_bindings);
}

/* ============================================================================== */
/* Some function that we started out with. Unused now.                            */
/* ============================================================================== */

/*
    TODO: update this list
    Below are the real functions:
    binary_c_run_population
    binary_c_run_system

    binary_c_return_arglines
    binary_c_return_help_info
    binary_c_return_help_all_info
    binary_c_return_version_info
*/

/* ============================================================================== */
/* Wrappers to functions that evolve binary systems.                              */
/* ============================================================================== */

static PyObject* python_run_system(PyObject *self, PyObject *args, PyObject *kwargs)
{

    static char* keywords[] = {"argstring", "custom_logging_func_memaddr", "store_memaddr", "persistent_data_memaddr", "write_logfile", "population", NULL};

    /* set vars and default values for some*/
    char *argstring;
    long int custom_logging_func_memaddr = -1;
    PyObject *  store_capsule = NULL;
    PyObject * persistent_data_capsule = NULL;
    int write_logfile = 0;
    int population = 0;

    /* Parse the input tuple */
    // By using the keywords argument it scans over the given set of kwargs, but if they are not given then the default value is used
    if(!PyArg_ParseTupleAndKeywords(args, kwargs, "s|lOOii", keywords, &argstring, &custom_logging_func_memaddr, &store_capsule, &persistent_data_capsule, &write_logfile, &population))
    {
        return NULL;
    }

    // TODO: Build in checks for all the capsules

    /* Unpack the capsules */
    // Persistent data
    struct libbinary_c_persistent_data_t * persistent_data = NULL;
    if (persistent_data_capsule != NULL)
    {
        if (PyCapsule_IsValid(persistent_data_capsule, "PERSISTENT_DATA"))
        {
            if (!(persistent_data = (struct libbinary_c_persistent_data_t *) PyCapsule_GetPointer(persistent_data_capsule, "PERSISTENT_DATA")))
                return NULL;   
            debug_printf("Unpacked persistent_data pointer %p from capsule\n", persistent_data);                
        }
    }

    // Store
    struct libbinary_c_store_t * store = NULL;
    if (store_capsule != NULL)
    {
        if (PyCapsule_IsValid(store_capsule, "STORE"))
        {
            if (!(store = (struct libbinary_c_store_t *) PyCapsule_GetPointer(store_capsule, "STORE")))
                return NULL;   
            debug_printf("Unpacked store pointer %p from capsule\n", store_capsule);            
        }
    }

    /* Call c-function */
    char * buffer;
    char * error_buffer;
    size_t nbytes;
    int out MAYBE_UNUSED = run_system(argstring,                    // the argstring
                                      custom_logging_func_memaddr,  // memory adress for the function for custom logging
                                      store,                // TODO: change. memory adress for the store object
                                      persistent_data,      // TODO: change. memory adress for the persistent data
                                      write_logfile,                // boolean for whether to write the logfile
                                      population,                   // boolean for whether this is part of a population.
                                      &buffer,
                                      &error_buffer,
                                      &nbytes);

    /* copy the buffer to a python string */
    PyObject * return_string = Py_BuildValue("s", buffer);
    PyObject * return_error_string MAYBE_UNUSED = Py_BuildValue("s", error_buffer);

    /* Display error */
    if(error_buffer != NULL && strlen(error_buffer)>0)
    {
        fprintf(stderr,
                "Error (in function: binary_c_run_system): %s\n",
                error_buffer);
    }

    Safe_free(buffer);
    Safe_free(error_buffer);

    return return_string;
}

/* ============================================================================== */
/* Wrappers to functions that call other API functionality like help and arglines */
/* ============================================================================== */

static PyObject* python_return_arglines(PyObject *self, PyObject *args)
{
    char * buffer;
    char * error_buffer;
    size_t nbytes;
    int out MAYBE_UNUSED = return_arglines(&buffer,
                                          &error_buffer,
                                          &nbytes);

    /* copy the buffer to a python string */
    PyObject * return_string = Py_BuildValue("s", buffer);
    PyObject * return_error_string MAYBE_UNUSED = Py_BuildValue("s", error_buffer);

    if(error_buffer != NULL && strlen(error_buffer)>0)
    {
        fprintf(stderr,
                "Error (in function: binary_c_return_arglines): %s\n",
                error_buffer);
    }

    Safe_free(buffer);
    Safe_free(error_buffer);

    return return_string;
}

static PyObject* python_return_help_info(PyObject *self, PyObject *args)
{
    /* Parse the input tuple */
    char *argstring;
    
    if(!PyArg_ParseTuple(args, "s", &argstring))
    {
        return NULL;
    }

    char * buffer;
    char * error_buffer;
    size_t nbytes;
    int out MAYBE_UNUSED = return_help_info(argstring,
                                          &buffer,
                                          &error_buffer,
                                          &nbytes);

    /* copy the buffer to a python string */
    PyObject * return_string = Py_BuildValue("s", buffer);
    PyObject * return_error_string MAYBE_UNUSED = Py_BuildValue("s", error_buffer);

    if(error_buffer != NULL && strlen(error_buffer)>0)
    {
        fprintf(stderr,
                "Error (in function: binary_c_return_help_info): %s\n",
                error_buffer);
    }
    
    Safe_free(buffer);
    Safe_free(error_buffer);

    return return_string;
}

static PyObject* python_return_help_all_info(PyObject *self, PyObject *args)
{
    char * buffer;
    char * error_buffer;
    size_t nbytes;
    int out MAYBE_UNUSED = return_help_all_info(&buffer,
                                          &error_buffer,
                                          &nbytes);

    /* copy the buffer to a python string */
    PyObject * return_string = Py_BuildValue("s", buffer);
    PyObject * return_error_string MAYBE_UNUSED = Py_BuildValue("s", error_buffer);

    if(error_buffer != NULL && strlen(error_buffer)>0)
    {
        fprintf(stderr,
                "Error (in function: binary_c_return_help_all_info): %s\n",
                error_buffer);
    }
    
    Safe_free(buffer);
    Safe_free(error_buffer);

    return return_string;
}

static PyObject* python_return_version_info(PyObject *self, PyObject *args)
{
    char * buffer;
    char * error_buffer;
    size_t nbytes;
    int out MAYBE_UNUSED = return_version_info(&buffer,
                                          &error_buffer,
                                          &nbytes);

    /* copy the buffer to a python string */
    PyObject * return_string = Py_BuildValue("s", buffer);
    PyObject * return_error_string MAYBE_UNUSED = Py_BuildValue("s", error_buffer);

    if(error_buffer != NULL && strlen(error_buffer)>0)
    {
        fprintf(stderr,
                "Error (in function: binary_c_return_version_info): %s\n",
                error_buffer);
    }
    
    Safe_free(buffer);
    Safe_free(error_buffer);

    return return_string;
}

static PyObject* python_return_minimum_orbit_for_RLOF(PyObject *self, PyObject *args, PyObject *kwargs)
{
    /* set vars and default values for some */
    char *argstring;
    PyObject *  store_capsule = NULL;

    static char* keywords[] = {"argstring", "store_capsule", NULL};

    /* Parse the input tuple */
    // By using the keywords argument it scans over the given set of kwargs, but if they are not given then the default value is used
    if(!PyArg_ParseTupleAndKeywords(args, kwargs, "s|O", keywords, &argstring, &store_capsule))
    {
        return NULL;
    }

    // Store
    struct libbinary_c_store_t * store = NULL;
    if (store_capsule != NULL)
    {
        if (PyCapsule_IsValid(store_capsule, "STORE"))
        {
            if (!(store = (struct libbinary_c_store_t *) PyCapsule_GetPointer(store_capsule, "STORE")))
                return NULL;   
            debug_printf("Unpacked store pointer %p from capsule\n", store_capsule);            
        }
    }

    // Setup buffers
    char * buffer;
    char * error_buffer;
    size_t nbytes;

    /* Call c-function */
    int out MAYBE_UNUSED = return_minimum_orbit_for_RLOF(
                                        argstring, // String containing the arguments for the system
                                        store, // value for store memaddr
                                        &buffer,
                                        &error_buffer,
                                        &nbytes);

    /* copy the buffer to a python string */
    PyObject * return_string = Py_BuildValue("s", buffer);
    PyObject * return_error_string MAYBE_UNUSED = Py_BuildValue("s", error_buffer);

    if(error_buffer != NULL && strlen(error_buffer)>0)
    {
        fprintf(stderr,
                "Error (in function: binary_c_return_minimum_orbit_for_RLOF): %s\n",
                error_buffer);
    }

    Safe_free(buffer);
    Safe_free(error_buffer);

    return return_string;
}

static PyObject* python_return_maximum_mass_ratio_for_RLOF(PyObject *self, PyObject *args, PyObject *kwargs)
{
    static char* keywords[] = {"argstring", "store_capsule", NULL};

    /* set vars and default values for some*/
    char *argstring;
    PyObject *  store_capsule = NULL;

    /* Parse the input tuple */
    // By using the keywords argument it scans over the given set of kwargs, but if they are not given then the default value is used
    if(!PyArg_ParseTupleAndKeywords(args, kwargs, "s|O", keywords, &argstring, &store_capsule))
    {
        return NULL;
    }

    // Store
    struct libbinary_c_store_t * store = NULL;
    if (store_capsule != NULL)
    {
        if (PyCapsule_IsValid(store_capsule, "STORE"))
        {
            if (!(store = (struct libbinary_c_store_t *) PyCapsule_GetPointer(store_capsule, "STORE")))
                return NULL;   
            debug_printf("Unpacked store pointer %p from capsule\n", store_capsule);            
        }
    }

    // Setup buffers
    char * buffer;
    char * error_buffer;
    size_t nbytes;

    /* Call c-function */
    int out MAYBE_UNUSED = return_maximum_mass_ratio_for_RLOF(
                                        argstring, // String containing the arguments for the system
                                        store, // value for store memaddr
                                        &buffer,
                                        &error_buffer,
                                        &nbytes);

    /* copy the buffer to a python string */
    PyObject * return_string = Py_BuildValue("s", buffer);
    PyObject * return_error_string MAYBE_UNUSED = Py_BuildValue("s", error_buffer);

    if(error_buffer != NULL && strlen(error_buffer)>0)
    {
        fprintf(stderr,
                "Error (in function: python_return_maximum_mass_ratio_for_RLOF): %s\n",
                error_buffer);
    }

    Safe_free(buffer);
    Safe_free(error_buffer);

    return return_string;
}


int return_maximum_mass_ratio_for_RLOF(char * argstring,
                                   struct libbinary_c_store_t * store,
                                   char ** buffer,
                                   char ** error_buffer,
                                   size_t * nbytes)
{
    /*
     * Return the maximum mass ratio for RLOF given M1 and period
     * If a valid store is passed in then we use it. otherwise a new store is made and released
     */
    struct libbinary_c_stardata_t *stardata = NULL;

    /* Determine whether to free the store memory adress*/
    Boolean free_store = FALSE;
    if (store==NULL)
    {
        debug_printf("Decided to free the store memaddr\n");
        free_store = TRUE;
    }

    binary_c_new_system(&stardata,
                        NULL,
                        NULL,
                        &store,
                        NULL,   
                        &argstring,
                        -1);

    // Set preferences. 
    stardata->preferences->show_maximum_mass_ratio_for_instant_RLOF = TRUE;
    snprintf(stardata->preferences->log_filename,
             STRING_LENGTH-1,"%s","/dev/null");
    snprintf(stardata->preferences->api_log_filename_prefix,
             STRING_LENGTH-1,"%s","/dev/null");
    stardata->preferences->internal_buffering = INTERNAL_BUFFERING_STORE;
    stardata->preferences->batchmode = BATCHMODE_LIBRARY;

    /* Actually show the instant_rlof */
    binary_c_show_instant_RLOF(stardata); // prints to the buffer. 

    /* put results in buffer */
    binary_c_buffer_info(stardata, buffer, nbytes);

    /* Put errors in error buffer */
    binary_c_error_buffer(stardata, error_buffer);
 
    Boolean free_persistent_data = TRUE;

    /* free stardata (except the buffer) */
    binary_c_free_memory(&stardata, // Stardata
        TRUE,                       // free_preferences
        TRUE,                       // free_stardata
        free_store,                 // free_store
        FALSE,                      // free_raw_buffer TODO: fix this
        free_persistent_data        // free_persistent
    );

    return 0;
}

/* ============================================================================== */
/* Wrappers to functions that call other functionality */
/* ============================================================================== */

/* Memory setting functions */
static PyObject* python_return_store_memaddr(PyObject *self, PyObject *args)
{
    char * buffer;
    char * error_buffer;
    size_t nbytes;
    struct libbinary_c_store_t * store MAYBE_UNUSED = return_store_memaddr(&buffer,
                                      &error_buffer,
                                      &nbytes);

    /* copy the buffer to a python string */
    PyObject * return_string MAYBE_UNUSED = Py_BuildValue("s", buffer);
    PyObject * return_error_string MAYBE_UNUSED = Py_BuildValue("s", error_buffer);

    debug_printf("Packing up store pointer %p into capsule\n", store);
    PyObject * store_memaddr_capsule = PyCapsule_New(store, "STORE", NULL);

    if(error_buffer != NULL && strlen(error_buffer)>0)
    {
        fprintf(stderr,
                "Error (in function: binary_c_return_store_memaddr): %s\n",
                error_buffer);
        printf("Error (in function: binary_c_return_store_memaddr): %s\n",
                error_buffer);
    }
    
    Safe_free(buffer);
    Safe_free(error_buffer);

    return store_memaddr_capsule;
}

static PyObject* python_return_persistent_data_memaddr(PyObject *self, PyObject *args)
{
    /* Python binding that wraps the c function which calls the binary_c api endpoint. */
    char * buffer;
    char * error_buffer;
    size_t nbytes;
    struct libbinary_c_persistent_data_t * persistent_data MAYBE_UNUSED = return_persistent_data_memaddr(&buffer,
                                      &error_buffer,
                                      &nbytes);

    /* copy the buffer to a python string */
    PyObject * return_string MAYBE_UNUSED = Py_BuildValue("s", buffer);
    PyObject * return_error_string MAYBE_UNUSED = Py_BuildValue("s", error_buffer);

    debug_printf("Packing up persistent_data pointer %p into capsule\n", persistent_data);
    PyObject * persistent_data_memaddr_capsule = PyCapsule_New(persistent_data, "PERSISTENT_DATA", NULL);

    if(error_buffer != NULL && strlen(error_buffer)>0)
    {
        fprintf(stderr,
                "Error (in function: binary_c_return_persistent_data_memaddr): %s\n",
                error_buffer);
        printf("Error (in function: binary_c_return_persistent_data_memaddr): %s\n",
                error_buffer);
    }
    
    Safe_free(buffer);
    Safe_free(error_buffer);

    return persistent_data_memaddr_capsule;
}

/* Memory freeing functions */
static PyObject* python_free_persistent_data_memaddr_and_return_json_output(PyObject *self, PyObject *args)
{
    /* Python binding that calls the c function that free's the persistent data memory and prints out the json */

    // Unpack the input
    PyObject *persistent_data_memaddr_capsule = NULL;
    if (!PyArg_ParseTuple(args, "O", &persistent_data_memaddr_capsule))
    {
        fprintf(stderr,
                "Error (in function: binary_c_free_persistent_data_memaddr_and_return_json_output): Got a bad input\n");
        printf("Error (in function: binary_c_free_persistent_data_memaddr_and_return_json_output): Got a bad input\n");
        return NULL; // Add message for input        
    }

    // Unpack the capsule
    struct libbinary_c_persistent_data_t * persistent_data = NULL;
    if (!(persistent_data = (struct libbinary_c_persistent_data_t *) PyCapsule_GetPointer(persistent_data_memaddr_capsule, "PERSISTENT_DATA")))
        return NULL;   
    debug_printf("Unpacked persistent_data pointer %p from capsule\n", persistent_data);

    // Interface with binary_c API
    char * buffer;
    char * error_buffer;
    size_t nbytes;

    int out MAYBE_UNUSED = free_persistent_data_memaddr_and_return_json_output(persistent_data,
                                      &buffer,
                                      &error_buffer,
                                      &nbytes);

    /* copy the buffer to a python string */
    PyObject * return_string MAYBE_UNUSED = Py_BuildValue("s", buffer);
    PyObject * return_error_string MAYBE_UNUSED = Py_BuildValue("s", error_buffer);

    if(error_buffer != NULL && strlen(error_buffer)>0)
    {
        fprintf(stderr,
                "Error (in function: binary_c_free_persistent_data_memaddr_and_return_json_output): %s\n",
                error_buffer);
        printf("Error (in function: binary_c_free_persistent_data_memaddr_and_return_json_output): %s\n",
                error_buffer);
    }
    
    Safe_free(buffer);
    Safe_free(error_buffer);

    return return_string;
}

static PyObject* python_free_store_memaddr(PyObject *self, PyObject *args)
{
    /* Python binding that calls the c function that free's the store memory */
    char * buffer;
    char * error_buffer;
    size_t nbytes;

    PyObject *store_memaddr_capsule = NULL;
    if (!PyArg_ParseTuple(args, "O", &store_memaddr_capsule))
    {
        fprintf(stderr,
                "Error (in function: binary_c_free_store_memaddr): Got a bad input\n");
        printf("Error (in function: binary_c_free_store_memaddr): Got a bad input\n");
        return NULL; // Add message for input        
    }
    // TODO: Add checks for validity of capsule


    // Unpack the capsule
    struct libbinary_c_store_t * store = NULL;
    if (!(store = (struct libbinary_c_store_t *) PyCapsule_GetPointer(store_memaddr_capsule, "STORE")))
        return NULL;   
    debug_printf("Unpacked store pointer %p from capsule\n", store);

    int out MAYBE_UNUSED = free_store_memaddr(store,
                                      &buffer,
                                      &error_buffer,
                                      &nbytes);

    /* copy the buffer to a python string */
    PyObject * return_string MAYBE_UNUSED = Py_BuildValue("s", buffer);
    PyObject * return_error_string MAYBE_UNUSED = Py_BuildValue("s", error_buffer);

    if(error_buffer != NULL && strlen(error_buffer)>0)
    {
        fprintf(stderr,
                "Error (in function: binary_c_free_store_memaddr): %s\n",
                error_buffer);
        printf("Error (in function: binary_c_free_store_memaddr): %s\n",
                error_buffer);
    }
    
    Safe_free(buffer);
    Safe_free(error_buffer);

    Py_RETURN_NONE;
}

static PyObject* python_test_func(PyObject *self, PyObject *args)
{
    // function to see if we can access the stability string
    printf("%s", RLOF_stability_string(1));

    Py_RETURN_NONE;
}

/////////////////////////////////////////////////////////////////////////////////////////////////////////

/************************************************************
 ************************************************************
 ** Section 2: binary_c interfacing functions
 **
 ** These functions call the binary_c API 
 ************************************************************
 ************************************************************/

/* Binary_c python API 
 * Set of c-functions that interface with the binary_c api.
 * These functions are called by python, through the functions defined above. 
 * 
 * Contains several functions:
 * // evolution functions:
 * run_system

 * // utility functions:
 * return_arglines
 * return_help_info
 * return_help_all_info
 * return_version_info
 * return_minimum_orbit_for_RLOF

 * // memory allocating functions:
 * return_store_memaddr
 * free_persistent_data_memaddr_and_return_json_output
 * 
 * // Memory freeing functions:
 * free_store_memaddr 
 * free_persistent_data_memaddr_and_return_json_output
 */

// #define _CAPTURE
#ifdef _CAPTURE
static void show_stdout(void);
static void capture_stdout(void);
#endif

/* global variables */
int out_pipe[2];
int stdoutwas;

/* =================================================================== */
/* Functions to evolve systems                                         */
/* =================================================================== */

/* 
Function that runs a system. Has multiple input parameters:
Big function. Takes several arguments. See binary_c_python.c docstring.
TODO: Describe each input
*/
int run_system(char * argstring,
               long int custom_logging_func_memaddr,
               struct libbinary_c_store_t * store,
               struct persistent_data_t * persistent_data,
               int write_logfile,
               int population,
               char ** const buffer,
               char ** const error_buffer,
               size_t * const nbytes)
{
    /* memory for system */
    struct libbinary_c_stardata_t *stardata = NULL;
    // store can be NULL, but could be a valid pointer to a store
    // persistent_data can be NULL, but could be a valid pointer to a persistent_data

    /* Determine whether to free the store memory adress*/
    Boolean free_store = FALSE;
    if (store==NULL)
    {
        debug_printf("Decided to free the store memaddr\n");
        free_store = TRUE;
    }

    /* Determine whether to free the persistent data memory adress*/
    Boolean free_persistent_data = FALSE;
    if (persistent_data == NULL)
    {
        debug_printf("Decided to free the persistent_data memaddr\n");
        free_persistent_data = TRUE;
    }

    /* Set up new system */
    binary_c_new_system(&stardata,          // stardata
                        NULL,               // previous_stardatas
                        NULL,               // preferences
                        &store,             // store
                        &persistent_data,   // persistent_data
                        &argstring,         // argv
                        -1                  // argc
    );

    // Add flag to enable
    /* disable logging */
    if(write_logfile != 1)
    {
        snprintf(stardata->preferences->log_filename,
                 STRING_LENGTH-1,
                 "%s",
                 "/dev/null");
        snprintf(stardata->preferences->api_log_filename_prefix,
                 STRING_LENGTH-1,
                 "%s",
                 "/dev/null");
    }

    /* output to strings */
    stardata->preferences->internal_buffering = INTERNAL_BUFFERING_STORE;
    stardata->preferences->batchmode = BATCHMODE_LIBRARY;

    /* Check the value of the custom_logging_memaddr */
    if(custom_logging_func_memaddr != -1)
    {
        stardata->preferences->custom_output_function = (void*)(struct stardata_t *)custom_logging_func_memaddr;
    }

    debug_printf("ensemble_defer: %d\n", stardata->preferences->ensemble_defer);

    /* do binary evolution */
    binary_c_evolve_for_dt(stardata,
                           stardata->model.max_evolution_time);
        
    /* get buffer pointer */
    binary_c_buffer_info(stardata, buffer, nbytes);
    
    /* get error buffer pointer */
    binary_c_error_buffer(stardata, error_buffer);

    /* free stardata (except the buffer) */
    binary_c_free_memory(&stardata, // Stardata
        TRUE,                       // free_preferences
        TRUE,                       // free_stardata
        free_store,                 // free_store
        FALSE,                      // free_raw_buffer
        free_persistent_data        // free_persistent
    );

    return 0;
}

/* =================================================================== */
/* Functions to call other API functionality like help and arglines    */
/* =================================================================== */

int return_arglines(char ** const buffer,
               char ** const error_buffer,
               size_t * const nbytes)
{
    /* memory for N binary systems */
    struct libbinary_c_stardata_t *stardata = NULL;
    struct libbinary_c_store_t *store = NULL;
    char *empty_str = "";

    /* Set up new system */
    binary_c_new_system(&stardata,          // stardata
                        NULL,               // previous_stardatas
                        NULL,               // preferences
                        &store,             // store
                        NULL,               // persistent_data
                        &empty_str,         // argv
                        -1                  // argc
    );

    /* disable logging */
    snprintf(stardata->preferences->log_filename,
             STRING_LENGTH-1,
             "%s",
             "/dev/null");
    snprintf(stardata->preferences->api_log_filename_prefix,
             STRING_LENGTH-1,
             "%s",
             "/dev/null");

    /* output to strings */
    stardata->preferences->internal_buffering = INTERNAL_BUFFERING_STORE;
    stardata->preferences->batchmode = BATCHMODE_LIBRARY;

    /* List available arguments */
    binary_c_list_args(stardata);

    /* get buffer pointer */
    binary_c_buffer_info(stardata,buffer,nbytes);
    
    /* get error buffer pointer */
    binary_c_error_buffer(stardata,error_buffer);
    
    /* free stardata (except the buffer) */
    binary_c_free_memory(&stardata, // Stardata
        TRUE,                       // free_preferences
        TRUE,                       // free_stardata
        TRUE,                       // free_store
        FALSE,                      // free_raw_buffer
        TRUE                        // free_persistent
    );
    
    return 0;
}


int return_help_info(char * argstring,
               char ** const buffer,
               char ** const error_buffer,
               size_t * const nbytes)
{
    struct libbinary_c_stardata_t *stardata = NULL;
    struct libbinary_c_store_t *store = NULL;

    /* Set up new system */
    binary_c_new_system(&stardata,          // stardata
                        NULL,               // previous_stardatas
                        NULL,               // preferences
                        &store,             // store
                        NULL,               // persistent_data
                        &argstring,         // argv
                        -1                  // argc
    );

    /* output to strings */
    stardata->preferences->internal_buffering = INTERNAL_BUFFERING_STORE;
    stardata->preferences->batchmode = BATCHMODE_LIBRARY;

    /* Ask the help api */
    binary_c_help(stardata, argstring);
        
    /* get buffer pointer */
    binary_c_buffer_info(stardata, buffer, nbytes);
    
    /* get error buffer pointer */
    binary_c_error_buffer(stardata, error_buffer);
        
    /* free stardata (except the buffer) */
    binary_c_free_memory(&stardata, // Stardata
        TRUE,                       // free_preferences
        TRUE,                       // free_stardata
        TRUE,                       // free_store
        FALSE,                      // free_raw_buffer
        TRUE                        // free_persistent
    );

    return 0;
}


int return_help_all_info(char ** const buffer,
               char ** const error_buffer,
               size_t * const nbytes)
{
    struct libbinary_c_stardata_t *stardata = NULL;
    struct libbinary_c_store_t *store = NULL;
    char * empty_str = "";

    /* Set up new system */
    binary_c_new_system(&stardata,          // stardata
                        NULL,               // previous_stardatas
                        NULL,               // preferences
                        &store,             // store
                        NULL,               // persistent_data
                        &empty_str,         // argv
                        -1                  // argc
    );