updated C-code, removed old stuff

 * Include binary_C's API

 */

#include "binary_c.h"

//#include "binary_c_API.h"

//#include "binary_c_API_prototypes.h"

/* Binary_c's python API prototypes */

int run_system(char * argstring,

                size_t * const nbytes);

/* =================================================================== */

/* Functions to call other functionality                               */

/* Functions to handle memory                                          */

/* =================================================================== */

long int return_store_memaddr(char ** const buffer,

#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>

/*

 * 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 apitest.py for an example of how to use these functions.

 * See tests/python_API_test.py for an example of how to use these functions.

 *

 * See also

 * 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

 * 

 * Open tasks for the Extension:

 * TODO: Put in clear debug statements

 * TODO: properly return stderr

 * TODO: describe all functions with docstrings

 */

// TODO: Put in clear debug statements

/* list of variables used in the Py<>C interface */

/************************************************************/

/*

/************************************************************

 ************************************************************

 ** 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";

#ifdef __DEPRECATED

static char create_binary_docstring[] =

    "Allocate memory for a binary";

#endif

static char function_prototype_docstring[] =

    "The prototype for a binary_c python function";

static char new_binary_system_docstring[] =

    "Return an object containing a binary, ready for evolution";

// 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.";

static struct libbinary_c_store_t *store = NULL;

/* Initialize pyobjects */

// Old functions. Can be removed I think

#ifdef __DEPRECATED

static PyObject* binary_c_create_binary(PyObject *self, PyObject *args);

#endif

static PyObject* binary_c_function_prototype(PyObject *self, PyObject *args);

static PyObject* binary_c_new_binary_system(PyObject *self, PyObject *args);

// Evolution function headers

static PyObject* binary_c_run_system(PyObject *self, PyObject *args, PyObject *kwargs);

/* Set the module functions */

static PyMethodDef module_methods[] = {

#ifdef __DEPRECATED

    {"create_binary", 

        binary_c_create_binary, 

        METH_VARARGS, 

        create_binary_docstring

    },

#endif

    {"function_prototype", binary_c_function_prototype, METH_VARARGS, function_prototype_docstring},

    {"new_system", binary_c_new_binary_system, METH_VARARGS, new_binary_system_docstring},

    {"run_system", (PyCFunction)binary_c_run_system, METH_VARARGS|METH_KEYWORDS, run_system_docstring}, 

    // 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)binary_c_run_system, METH_VARARGS|METH_KEYWORDS, run_system_docstring}, 

    //

    {"return_arglines", binary_c_return_arglines, METH_VARARGS, return_arglines_docstring},

    {"return_help", binary_c_return_help_info, METH_VARARGS, return_help_info_docstring},

    {"return_help_all", binary_c_return_help_all_info, METH_VARARGS, return_help_all_info_docstring},

    {"return_version_info", binary_c_return_version_info, METH_VARARGS, return_version_info_docstring},

    //

    {"return_store_memaddr", binary_c_return_store_memaddr, METH_VARARGS, return_store_memaddr_docstring},

    {"return_persistent_data_memaddr", binary_c_return_persistent_data_memaddr, METH_NOARGS, return_persistent_data_memaddr_docstring},

    //

    {"free_persistent_data_memaddr_and_return_json_output", binary_c_free_persistent_data_memaddr_and_return_json_output, METH_VARARGS, free_persistent_data_memaddr_and_return_json_output_docstring},

    {"free_store_memaddr", binary_c_free_store_memaddr, METH_VARARGS, free_store_memaddr_docstring},

    //

    {NULL, NULL, 0, NULL}

};

{

    PyModuleDef_HEAD_INIT,

    "_binary_c_bindings", /* name of module */

    "TODO",          /* module documentation, may be NULL */

    "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

};

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

/* ============================================================================== */

#ifdef __DEPRECATED

static PyObject* binary_c_create_binary(PyObject *self, PyObject *args)

{

    double var1, var2;

    char * empty_str = "";

    int i;

    const int N = 1;

    /* Parse the input tuple */

    if(!PyArg_ParseTuple(args, "dd", &var1, &var2))

        return NULL;

    /* Binary structures */

    struct libbinary_c_stardata_t *stardata[N];

    struct libbinary_c_store_t *store = NULL;

    /* Allocate memory for binaries */

    for(i=0;i<N;i++){

        stardata[i] = NULL;

        binary_c_new_system(&stardata[i], NULL, NULL, &store, NULL, &empty_str, -1);

    }

    /* Return the evolved binary */

    PyObject *ret = Py_BuildValue("");

    return ret;

}

#endif //__DEPRECATED

static PyObject* binary_c_new_binary_system(PyObject *self, PyObject *args)

{

    /* Binary structures */

    struct libbinary_c_stardata_t *stardata;

    /* Allocate memory for binaries */

    char * empty_str = "";

    stardata = NULL;

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

    /* Return an object containing the stardata */

    PyObject *ret = Py_BuildValue("");

    return ret;

}

static PyObject* binary_c_function_prototype(PyObject *self, PyObject *args)

{

    // This function is an very bare example of how a function would look like.

    double var1, var2;

    /* Parse the input tuple */

    if(!PyArg_ParseTuple(args, "dd", &var1, &var2))

    {

        return NULL;

    }

    else

    {

        /* Return the evolved binary */

        PyObject *ret = Py_BuildValue("");

        return ret;

    }

}

/*

    Below are the real functions:

    binary_c_run_population

    Safe_free(buffer);

    Safe_free(error_buffer);

    // TODO: fix that the return_error_string is returned.

    return return_string;

}

    PyObject * return_error_string MAYBE_UNUSED = Py_BuildValue("s", error_buffer);

    PyObject * store_memaddr = Py_BuildValue("l", out);

    // printf("store_memaddr: %ld\n", out);

    if(error_buffer != NULL && strlen(error_buffer)>0)

    {

    /* Parse the input tuple */

    if(!PyArg_ParseTuple(args, "l", &store_memaddr))

    {

        // printf("Error: got a bad input\n");

        fprintf(stderr,

                "Error (in function: binary_c_free_store_memaddr): Got a bad input\n");

        return NULL;

    if(error_buffer != NULL && strlen(error_buffer)>0)

    {

        // printf("Error (in function: binary_c_free_store_memaddr): %s", error_buffer);

        fprintf(stderr,

                "Error (in function: binary_c_free_store_memaddr): %s\n",

                error_buffer);

    Safe_free(buffer);

    Safe_free(error_buffer);

    return Py_BuildValue("");

    Py_RETURN_NONE;

}

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

#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>

/************************************************************

 ************************************************************

 ** 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, first through binary_c_python.c, 

 * and there further instructions are given on how to interface

 * These functions are called by python, through the functions defined above. 

 * 

 * Contains several functions:

 * // evolution

 * // evolution functions:

 * run_system

 * // utility

 * // utility functions:

 * return_arglines

 * return_help_info

 * return_help_all_info

 * return_version_info

 * // other

 * create_store

 * // 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

}

/* =================================================================== */

/* Functions set up memoery adresses                                   */

/* Functions to set up memory                                          */

/* =================================================================== */

long int return_store_memaddr(char ** const buffer,

    );

    /* output to strings */

    // stardata->preferences->internal_buffering = INTERNAL_BUFFERING_STORE;

    // stardata->preferences->batchmode = BATCHMODE_LIBRARY;

    stardata->preferences->internal_buffering = INTERNAL_BUFFERING_STORE;

    stardata->preferences->batchmode = BATCHMODE_LIBRARY;

    /* 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) */

    /* free stardata (except the buffer and the store) */

    binary_c_free_memory(&stardata, // Stardata

        TRUE,                       // free_preferences

        TRUE,                       // free_stardata

    uintptr_t persistent_data_memaddr_int = (uintptr_t)stardata->persistent_data; // C Version converting ptr to int

    debug_printf("persistent_data is at address: %p persistent_data_memaddr_int: %ld\n", (void*)&stardata->persistent_data, persistent_data_memaddr_int);

    /* free stardata (except the buffer) */

    /* free stardata (except the buffer and the persistent data) */

    binary_c_free_memory(&stardata, // Stardata

        TRUE,                       // free_preferences

        TRUE,                       // free_stardata

}

/* =================================================================== */

/* Functions free memory                                               */

/* Functions to free memory                                            */

/* =================================================================== */

int free_persistent_data_memaddr_and_return_json_output(long int persistent_data_memaddr,

                        -1                  // argc

    );

    /* Set the model hash (usually done internally but we're not evolving a system here */

    stardata->model.ensemble_hash = stardata->persistent_data->ensemble_hash;

    /* output to strings */

    stardata->preferences->internal_buffering = INTERNAL_BUFFERING_STORE;

    stardata->preferences->batchmode = BATCHMODE_LIBRARY;

        TRUE,                       // free_stardata

        TRUE,                       // free_store

        FALSE,                      // free_raw_buffer

        FALSE                       // free_persistent

        FALSE                       // free_persistent. It already 

    );

    return 0;

                        -1                  // argc

    );

    printf("freed store memaddr\n");

    debug_printf("freed store memaddr\n");

    /* output to strings */

    stardata->preferences->internal_buffering = INTERNAL_BUFFERING_STORE;

    stardata->preferences->batchmode = BATCHMODE_LIBRARY;