From e15e1ac1d88a2a4645b41ecd221e0b9c771e3405 Mon Sep 17 00:00:00 2001
From: David Hendriks <davidhendriks93@gmail.com>
Date: Sun, 15 Mar 2020 20:11:06 +0000
Subject: [PATCH] Changed the api code: removed all the functions that did a
slightly different thing. put them into 1 function that has several options.
Moreover, cleaned up code, test functions, and other functions throughout
code
---
.../utils/custom_logging_functions.py | 22 +-
binarycpython/utils/functions.py | 117 ++-----
binarycpython/utils/grid.py | 5 +-
binarycpython/utils/run_system_wrapper.py | 87 +++++
include/binary_c_python.h | 25 +-
src/binary_c_python.c | 252 +++-----------
src/binary_c_python_api.c | 315 +++---------------
tests/python_API_test.py | 99 +++---
8 files changed, 248 insertions(+), 674 deletions(-)
create mode 100644 binarycpython/utils/run_system_wrapper.py
diff --git a/binarycpython/utils/custom_logging_functions.py b/binarycpython/utils/custom_logging_functions.py
index 12af7c84b..4d8ee5f75 100644
--- a/binarycpython/utils/custom_logging_functions.py
+++ b/binarycpython/utils/custom_logging_functions.py
@@ -2,11 +2,11 @@ import os
import textwrap
import subprocess
import socket
-import tempfile
import ctypes
import random
import uuid
+from binarycpython.utils.functions import temp_dir
def autogen_C_logging_code(logging_dict, verbose=0):
"""
@@ -66,7 +66,7 @@ def autogen_C_logging_code(logging_dict, verbose=0):
####################################################################################
-def binary_c_log_code(code, verbose):
+def binary_c_log_code(code, verbose=0):
"""
Function to construct the code to construct the custom logging function
"""
@@ -292,23 +292,7 @@ def compile_shared_lib(code, sourcefile_name, outfile_name, verbose=0):
print("Output of compilation command:\n{}".format(res))
-def temp_dir():
- """
- Function to return the path the custom logging library shared object and script will be written to.
-
- Makes use of os.makedirs exist_ok which requires python 3.2+
- """
-
- tmp_dir = tempfile.gettempdir()
- path = os.path.join(tmp_dir, "binary_c_python")
-
- #
- os.makedirs(path, exist_ok=True)
-
- return path
-
-
-def create_and_load_logging_function(custom_logging_code, verbose):
+def create_and_load_logging_function(custom_logging_code, verbose=0):
"""
Function to automatically compile the shared library with the given custom logging code and load it with ctypes
diff --git a/binarycpython/utils/functions.py b/binarycpython/utils/functions.py
index 688ee8c44..dcdc4ffe7 100644
--- a/binarycpython/utils/functions.py
+++ b/binarycpython/utils/functions.py
@@ -2,13 +2,31 @@ import copy
import json
import os
import h5py
+import tempfile
+
from collections import defaultdict
import numpy as np
import binary_c_python_api
-from binarycpython.utils.custom_logging_functions import (
- create_and_load_logging_function,
-)
+
+# from binarycpython.utils.custom_logging_functions import (
+# create_and_load_logging_function,
+# )
+
+def temp_dir():
+ """
+ Function to return the path the custom logging library shared object and script will be written to.
+
+ Makes use of os.makedirs exist_ok which requires python 3.2+
+ """
+
+ tmp_dir = tempfile.gettempdir()
+ path = os.path.join(tmp_dir, "binary_c_python")
+
+ #
+ os.makedirs(path, exist_ok=True)
+
+ return path
def output_lines(output):
@@ -478,99 +496,6 @@ def get_help(param_name="", print_help=True, return_dict=False, fail_silently=Fa
)
return None
-
-def run_system(**kwargs):
- """
- Wrapper to run a system with settings
-
- This function determines which underlying python-c api function will be called based upon the arguments that are passed via kwargs.
-
- - if custom_logging_code or custom_logging_dict is included in the kwargs then it will
- - if
-
- """
-
- # Load default args
- args = get_defaults()
- if "custom_logging_code" in kwargs:
- # Use kwarg value to override defaults and add new args
- for key in kwargs.keys():
- if not key == "custom_logging_code":
- args[key] = kwargs[key]
-
- # Generate library and get memaddr
- func_memaddr = create_and_load_logging_function(kwargs["custom_logging_code"])
-
- # Construct arguments string and final execution string
- arg_string = create_arg_string(args)
- arg_string = "binary_c {}".format(arg_string)
-
- # Run it and get output
- output = binary_c_python_api.run_binary_custom_logging(arg_string, func_memaddr)
- return output
-
- elif "log_filename" in kwargs:
- # Use kwarg value to override defaults and add new args
- for key in kwargs.keys():
- args[key] = kwargs[key]
-
- # Construct arguments string and final execution string
- arg_string = create_arg_string(args)
- arg_string = "binary_c {}".format(arg_string)
-
- # Run it and get output
- output = binary_c_python_api.run_binary_with_logfile(arg_string)
- return output
-
- else: # run the plain basic type
-
- # Use kwarg value to override defaults and add new args
- for key in kwargs.keys():
- args[key] = kwargs[key]
-
- # Construct arguments string and final execution string
- arg_string = create_arg_string(args)
- arg_string = "binary_c {}".format(arg_string)
-
- # Run it and get output
- output = binary_c_python_api.run_binary(arg_string)
-
- return output
-
-
-def run_system_with_log(**kwargs):
- """
- Wrapper to run a system with settings AND logs the files to a designated place defined by the log_filename parameter.
- """
-
- # Load default args
- args = get_defaults()
- # args = {}
-
- # For example
- # physics_args['M_1'] = 20
- # physics_args['separation'] = 0 # 0 = ignored, use period
- # physics_args['orbital_period'] = 100000000000 # To make it single
-
- # Use kwarg value to override defaults and add new args
- for key in kwargs.keys():
- args[key] = kwargs[key]
-
- # Construct arguments string and final execution string
- arg_string = create_arg_string(args)
- arg_string = "binary_c {}".format(arg_string)
-
- # print(arg_string)
-
- # Run it and get output
- output = binary_c_python_api.run_binary_with_logfile(arg_string)
-
- return output
-
-
-# run_system_with_log()
-
-
def parse_output(output, selected_header):
"""
Function that parses output of binary_c:
diff --git a/binarycpython/utils/grid.py b/binarycpython/utils/grid.py
index ddba33e74..6501ca2cd 100644
--- a/binarycpython/utils/grid.py
+++ b/binarycpython/utils/grid.py
@@ -513,10 +513,11 @@ class Population(object):
Function that the multiprocessing evolution method calls to evolve a system
"""
- out = binary_c_python_api.run_population(
- binary_cmdline_string,
+ out = binary_c_python_api.run_system(
+ arg_string=binary_cmdline_string,
self.grid_options["custom_logging_func_memaddr"],
self.grid_options["store_memaddr"],
+
)
if self.grid_options["parse_function"]:
self.grid_options["parse_function"](self, out)
diff --git a/binarycpython/utils/run_system_wrapper.py b/binarycpython/utils/run_system_wrapper.py
new file mode 100644
index 000000000..5de0de40c
--- /dev/null
+++ b/binarycpython/utils/run_system_wrapper.py
@@ -0,0 +1,87 @@
+def run_system(**kwargs):
+ """
+ Wrapper to run a system with settings
+
+ This function determines which underlying python-c api function will be called based upon the arguments that are passed via kwargs.
+
+ - if custom_logging_code or custom_logging_dict is included in the kwargs then it will
+ - if
+
+ """
+
+ # Load default args
+ args = get_defaults()
+ if "custom_logging_code" in kwargs:
+ # Use kwarg value to override defaults and add new args
+ for key in kwargs.keys():
+ if not key == "custom_logging_code":
+ args[key] = kwargs[key]
+
+ # Generate library and get memaddr
+ func_memaddr = create_and_load_logging_function(kwargs["custom_logging_code"])
+
+ # Construct arguments string and final execution string
+ arg_string = create_arg_string(args)
+ arg_string = "binary_c {}".format(arg_string)
+
+ # Run it and get output
+ output = binary_c_python_api.run_binary_custom_logging(arg_string, func_memaddr)
+ return output
+
+ elif "log_filename" in kwargs:
+ # Use kwarg value to override defaults and add new args
+ for key in kwargs.keys():
+ args[key] = kwargs[key]
+
+ # Construct arguments string and final execution string
+ arg_string = create_arg_string(args)
+ arg_string = "binary_c {}".format(arg_string)
+
+ # Run it and get output
+ output = binary_c_python_api.run_binary_with_logfile(arg_string)
+ return output
+
+ else: # run the plain basic type
+
+ # Use kwarg value to override defaults and add new args
+ for key in kwargs.keys():
+ args[key] = kwargs[key]
+
+ # Construct arguments string and final execution string
+ arg_string = create_arg_string(args)
+ arg_string = "binary_c {}".format(arg_string)
+
+ # Run it and get output
+ output = binary_c_python_api.run_binary(arg_string)
+
+ return output
+
+
+def run_system_with_log(**kwargs):
+ """
+ Wrapper to run a system with settings AND logs the files to a designated place defined by the log_filename parameter.
+ """
+
+ # Load default args
+ args = get_defaults()
+ # args = {}
+
+ # For example
+ # physics_args['M_1'] = 20
+ # physics_args['separation'] = 0 # 0 = ignored, use period
+ # physics_args['orbital_period'] = 100000000000 # To make it single
+
+ # Use kwarg value to override defaults and add new args
+ for key in kwargs.keys():
+ args[key] = kwargs[key]
+
+ # Construct arguments string and final execution string
+ arg_string = create_arg_string(args)
+ arg_string = "binary_c {}".format(arg_string)
+
+ # print(arg_string)
+
+ # Run it and get output
+ output = binary_c_python_api.run_binary_with_logfile(arg_string)
+
+ return output
diff --git a/include/binary_c_python.h b/include/binary_c_python.h
index ee7544c26..9c65d7676 100644
--- a/include/binary_c_python.h
+++ b/include/binary_c_python.h
@@ -9,32 +9,11 @@
#include "binary_c_API_prototypes.h"
/* Binary_c's python API prototypes */
-int run_binary(char * argstring,
- char ** const outstring,
- char ** const errorstring,
- size_t * const nbytes);
-
-int run_binary_with_logfile(char * argstring,
- char ** const outstring,
- char ** const errorstring,
- size_t * const nbytes);
-
-int run_binary_custom_logging(char * argstring,
- long int custom_logging_func_memaddr,
- char ** const buffer,
- char ** const error_buffer,
- size_t * const nbytes);
-
-int run_population(char * argstring,
- long int custom_logging_func_memaddr,
- long int store_memaddr,
- char ** const buffer,
- char ** const error_buffer,
- size_t * const nbytes);
-
int run_system(char * argstring,
long int custom_logging_func_memaddr,
long int store_memaddr,
+ int write_logfile,
+ int population,
char ** const buffer,
char ** const error_buffer,
size_t * const nbytes);
diff --git a/src/binary_c_python.c b/src/binary_c_python.c
index 49fb8dbf7..3b7e91328 100644
--- a/src/binary_c_python.c
+++ b/src/binary_c_python.c
@@ -11,6 +11,11 @@
*
* See also
* 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
*/
/* list of variables used in the Py<>C interface */
@@ -22,9 +27,12 @@
*/
/************************************************************/
+/* Preparing all the functions of the module */
// Docstrings
static char module_docstring[] MAYBE_UNUSED =
"This module is a python wrapper around binary_c";
+
+
#ifdef __DEPRECATED
static char create_binary_docstring[] =
"Allocate memory for a binary";
@@ -35,16 +43,8 @@ static char new_binary_system_docstring[] =
"Return an object containing a binary, ready for evolution";
// Evolution function docstrings
-static char run_binary_docstring[] =
- "Run one binary using binary_c";
-static char run_binary_with_log_docstring[] =
- "Run one binary using binary_c and allow the logfile to be written. Do not use for populations!";
-static char run_binary_custom_logging_docstring[] =
- "TODO";
-static char run_population_docstring[] =
- "Run population of systems";
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.";
+ "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[] =
@@ -60,10 +60,10 @@ static char return_version_info_docstring[] =
static char return_store_docstring[] =
"Return the store memory adress that will be passed to run_population";
+// static struct libbinary_c_store_t *store = NULL;
-static struct libbinary_c_store_t *store = NULL;
-
-// Initialize pyobjects
+/* Initialize pyobjects */
+//
#ifdef __DEPRECATED
static PyObject* binary_c_create_binary(PyObject *self, PyObject *args);
#endif
@@ -71,11 +71,7 @@ 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_binary(PyObject *self, PyObject *args);
-static PyObject* binary_c_run_binary_with_logfile(PyObject *self, PyObject *args);
-static PyObject* binary_c_run_binary_custom_logging(PyObject *self, PyObject *args);
-static PyObject* binary_c_run_population(PyObject *self, PyObject *args);
-static PyObject* binary_c_run_system(PyObject *self, PyObject *args);
+static PyObject* binary_c_run_system(PyObject *self, PyObject *args, PyObject *kwargs);
// Utility function headers
static PyObject* binary_c_return_arglines(PyObject *self, PyObject *args);
@@ -86,13 +82,8 @@ static PyObject* binary_c_return_version_info(PyObject *self, PyObject *args);
// Other function headers
static PyObject* binary_c_return_store(PyObject *self, PyObject *args);
-/*
- * Python 3 interface is described at
- *
- * http://scipy-lectures.org/advanced/interfacing_with_c/interfacing_with_c.html
- */
-
+/* Set the module functions */
static PyMethodDef module_methods[] = {
#ifdef __DEPRECATED
{"create_binary",
@@ -104,13 +95,8 @@ static PyMethodDef module_methods[] = {
{"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_binary", binary_c_run_binary, METH_VARARGS, run_binary_docstring},
- {"run_binary_with_logfile", binary_c_run_binary_with_logfile, METH_VARARGS, run_binary_with_log_docstring},
- {"run_binary_custom_logging", binary_c_run_binary_custom_logging, METH_VARARGS, run_binary_custom_logging_docstring},
- {"run_population", binary_c_run_population, METH_VARARGS, run_population_docstring},
- {"run_system", binary_c_run_system, METH_VARARGS, run_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
{"return_arglines", binary_c_return_arglines, METH_VARARGS, return_arglines_docstring},
{"return_help", binary_c_return_help_info, METH_VARARGS, return_help_info_docstring},
@@ -122,6 +108,13 @@ static PyMethodDef module_methods[] = {
{NULL, NULL, 0, NULL}
};
+/* ============================================================================== */
+/* Making the module */
+/* ============================================================================== */
+
+
+/* */
+// TODO: enforce python3
#if PY_MAJOR_VERSION >= 3
/* Python 3+ */
@@ -155,6 +148,11 @@ PyMODINIT_FUNC initbinary_c(void)
}
#endif // Python version check
+/* ============================================================================== */
+/* Some wierd function */
+/* ============================================================================== */
+
+
#ifdef __DEPRECATED
static PyObject* binary_c_create_binary(PyObject *self, PyObject *args)
@@ -224,11 +222,9 @@ static PyObject* binary_c_function_prototype(PyObject *self, PyObject *args)
}
/*
- Below are the real funtions:
- binary_c_run_binary
- binary_c_run_binary_custom_logging
- binary_c_run_binary_with_logfile
+ Below are the real functions:
binary_c_run_population
+ binary_c_run_system
binary_c_return_arglines
binary_c_return_help_info
@@ -240,99 +236,33 @@ static PyObject* binary_c_function_prototype(PyObject *self, PyObject *args)
/* Wrappers to functions that evolve binary systems. */
/* ============================================================================== */
-
-static PyObject* binary_c_run_binary(PyObject *self, PyObject *args)
+static PyObject* binary_c_run_system(PyObject *self, PyObject *args, PyObject *kwargs)
{
- /* Parse the input tuple */
- char *argstring;
-
- /* Parse the input tuple */
- if(!PyArg_ParseTuple(args, "s", &argstring))
-
- return NULL;
-
- char * buffer;
- char * error_buffer;
- size_t nbytes;
- int out MAYBE_UNUSED = run_binary(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 binary_c run : %s\n",
- error_buffer);
- }
-
- Safe_free(buffer);
- Safe_free(error_buffer);
- /*
- * TODO
- * return the return_error_string as well!
- */
- return return_string;
-}
+ static char* keywords[] = {"argstring", "custom_logging_func_memaddr", "store_memaddr", "write_logfile", "population", NULL};
-static PyObject* binary_c_run_binary_custom_logging(PyObject *self, PyObject *args)
-{
- /* Parse the input tuple */
+ /* set vars and default values for some*/
char *argstring;
- long int func_memaddr;
-
- if(!PyArg_ParseTuple(args, "sl", &argstring, &func_memaddr))
- {
- return NULL;
- }
-
- char * buffer;
- char * error_buffer;
- size_t nbytes;
- int out MAYBE_UNUSED = run_binary_custom_logging(argstring,
- func_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);
+ long int custom_logging_func_memaddr = -1;
+ long int store_memaddr = -1;
+ int write_logfile = 0;
+ int population = 0;
- if(error_buffer != NULL && strlen(error_buffer)>0)
- {
- fprintf(stderr,
- "Error in binary_c run : %s\n",
- error_buffer);
- }
-
- Safe_free(buffer);
- Safe_free(error_buffer);
-
- /*
- * TODO
- * return the return_error_string as well!
- */
- return return_string;
-}
-
-static PyObject* binary_c_run_binary_with_logfile(PyObject *self, PyObject *args)
-{
/* Parse the input tuple */
- char *argstring;
-
- if(!PyArg_ParseTuple(args, "s", &argstring))
+ if(!PyArg_ParseTupleAndKeywords(args, kwargs, "s|llii", keywords, &argstring, &custom_logging_func_memaddr, &store_memaddr, &write_logfile, &population))
{
return NULL;
}
+ /* Call c-function */
char * buffer;
char * error_buffer;
size_t nbytes;
- int out MAYBE_UNUSED = run_binary_with_logfile(argstring,
+ int out MAYBE_UNUSED = run_system(argstring, // the argstring
+ custom_logging_func_memaddr, // memory adress for the function for custom logging
+ store_memaddr, // memory adress for the store object
+ write_logfile, // boolean for whether to write the logfile
+ population, // boolean for whether this is part of a population.
&buffer,
&error_buffer,
&nbytes);
@@ -341,10 +271,11 @@ static PyObject* binary_c_run_binary_with_logfile(PyObject *self, PyObject *args
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 binary_c run : %s\n",
+ "Error in binary_c run (via binary_c_run_system): %s\n",
error_buffer);
}
@@ -358,95 +289,6 @@ static PyObject* binary_c_run_binary_with_logfile(PyObject *self, PyObject *args
return return_string;
}
-static PyObject* binary_c_run_population(PyObject *self, PyObject *args)
-{
- /* Parse the input tuple */
- char *argstring;
- long int custom_logging_func_memaddr;
- long int store_memaddr;
-
-
- if(!PyArg_ParseTuple(args, "sll", &argstring, &custom_logging_func_memaddr, &store_memaddr))
- {
- return NULL;
- }
-
- char * buffer;
- char * error_buffer;
- size_t nbytes;
- int out MAYBE_UNUSED = run_population(argstring,
- custom_logging_func_memaddr,
- 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 binary_c run : %s\n",
- error_buffer);
- }
-
- Safe_free(buffer);
- Safe_free(error_buffer);
-
- /*
- * TODO
- * return the return_error_string as well!
- */
- return return_string;
-}
-
-static PyObject* binary_c_run_system(PyObject *self, PyObject *args)
-{
- /* Parse the input tuple */
- char *argstring;
- long int custom_logging_func_memaddr;
- long int store_memaddr;
-
- if(!PyArg_ParseTuple(args, "sll", &argstring, &custom_logging_func_memaddr, &store_memaddr))
- {
- return NULL;
- }
-
- char * buffer;
- char * error_buffer;
- size_t nbytes;
- int out MAYBE_UNUSED = run_system(argstring,
- custom_logging_func_memaddr,
- 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 binary_c run : %s\n",
- error_buffer);
- }
-
- Safe_free(buffer);
- Safe_free(error_buffer);
-
- /*
- * TODO
- * return the return_error_string as well!
- */
- return return_string;
-}
-
-
-
/* ============================================================================== */
/* Wrappers to functions that call other API functionality like help and arglines */
/* ============================================================================== */
@@ -593,7 +435,7 @@ static PyObject* binary_c_return_store(PyObject *self, PyObject *args)
&nbytes);
/* copy the buffer to a python string */
- PyObject * return_string = Py_BuildValue("s", buffer);
+ PyObject * return_string MAYBE_UNUSED = Py_BuildValue("s", buffer);
PyObject * return_error_string MAYBE_UNUSED = Py_BuildValue("s", error_buffer);
PyObject * return_store_memaddr = Py_BuildValue("l", out);
diff --git a/src/binary_c_python_api.c b/src/binary_c_python_api.c
index 68be4e74c..01fc7438e 100644
--- a/src/binary_c_python_api.c
+++ b/src/binary_c_python_api.c
@@ -7,34 +7,24 @@
#include <unistd.h>
#include <stdint.h>
-
-
-/*
- * apitest
- *
- * Short test programme to throw random binary systems at binary_c's
- * library via its API.
- *
- * Note that it looks more complicated than it is because I have included
- * code to capture binary_c's stdout stream and output it here.
- *
- * This code sends output to stderr : you should use apitest.sh to run it
- * and hence force output to your terminal's stdout.
- *
- * Output lines:
- *
- * APITEST .... is information about what this code is doing.
- * STATUS .... is information about the binary system.
- * BINARY_C .... is output from binary_c (see iterate_logging.c etc.)
- * which would have gone to stdout
- *
- * If you define the NO_OUTPUT macro, there will be no output except
- * the memory allocation and test system information. This is useful for speed tests,
- * but note that you may end up in a race condition where the pipe which replaces
- * stdout's buffer fills and hence the code stops.
+/* 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
+ *
+ * Contains several functions:
+ * // evolution
+ * run_system
+
+ * // utility
+ * return_arglines
+ * return_help_info
+ * return_help_all_info
+ * return_version_info
+
+ * // other
+ * create_store
*
- * Note:
- * I have tested this with gcc 4.7.2 (Ubuntu 12.10) only.
*/
// #define _CAPTURE
@@ -47,250 +37,23 @@ static void capture_stdout(void);
int out_pipe[2];
int stdoutwas;
-/*
-Below are the real calls to the API of binary_c. Currently these are the functions:
-
-// evolution
-run_binary
-run_binary_custom_logging
-run_binary_with_logfile
-run_population
-
-
-// utility
-return_arglines
-return_help_info
-return_help_all_info
-return_version_info
-
-// other
-create_store
-
-*/
-
-
/* =================================================================== */
/* Functions to evolve systems */
/* =================================================================== */
-
-int run_binary(char * argstring,
- char ** const buffer,
- char ** const error_buffer,
- size_t * const nbytes)
-{
- /* memory for N binary systems */
- struct libbinary_c_stardata_t *stardata;
- struct libbinary_c_store_t * store = NULL;
-
- /* make new stardata */
- stardata = NULL;
- binary_c_new_system(&stardata,
- NULL,
- NULL,
- &store,
- &argstring,
- -1);
-
- /* 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;
-
- /* 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);
-
- /* set raw_buffer_size = -1 to prevent it being freed */
- stardata->tmpstore->raw_buffer_size = -1;
-
- /* free stardata (except the buffer) */
- binary_c_free_memory(&stardata,TRUE,TRUE,FALSE,FALSE);
- binary_c_free_store_contents(store);
-
- return 0;
-}
-
-int run_binary_custom_logging(char * argstring,
- long int custom_logging_func_memaddr,
- char ** const buffer,
- char ** const error_buffer,
- size_t * const nbytes)
-{
- /* memory for N binary systems */
- struct libbinary_c_stardata_t *stardata;
- struct libbinary_c_store_t * store = NULL;
-
- /* make new stardata */
- stardata = NULL;
- binary_c_new_system(&stardata,
- NULL,
- NULL,
- &store,
- &argstring,
- -1);
-
- /* 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;
- stardata->preferences->custom_output_function = (void*)(struct stardata_t *)custom_logging_func_memaddr;
-
- /* 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);
-
- /* set raw_buffer_size = -1 to prevent it being freed */
- stardata->tmpstore->raw_buffer_size = -1;
-
- /* free stardata (except the buffer) */
- binary_c_free_memory(&stardata,TRUE,TRUE,FALSE,FALSE);
- binary_c_free_store_contents(store);
-
- return 0;
-}
-
-int run_binary_with_logfile(char * argstring,
- char ** const buffer,
- char ** const error_buffer,
- size_t * const nbytes)
-{
- /* memory for N binary systems */
- struct libbinary_c_stardata_t *stardata;
- struct libbinary_c_store_t * store = NULL;
-
- /* make new stardata */
- stardata = NULL;
- binary_c_new_system(&stardata,
- NULL,
- NULL,
- &store,
- &argstring,
- -1);
-
- /* output to strings */
- stardata->preferences->internal_buffering = INTERNAL_BUFFERING_STORE;
- stardata->preferences->batchmode = BATCHMODE_LIBRARY;
-
- /* 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);
-
- /* set raw_buffer_size = -1 to prevent it being freed */
- stardata->tmpstore->raw_buffer_size = -1;
-
- /* free stardata (except the buffer) */
- binary_c_free_memory(&stardata,TRUE,TRUE,FALSE,FALSE);
- binary_c_free_store_contents(store);
- return 0;
-}
-
-int run_population(char * argstring,
- long int custom_logging_func_memaddr,
- long int store_memaddr,
- char ** const buffer,
- char ** const error_buffer,
- size_t * const nbytes)
-{
- /* memory for N binary systems */
- struct libbinary_c_stardata_t *stardata;
-
- // load the store from the integer that has been passed
- struct libbinary_c_store_t * store = (void*)store_memaddr;
-
- /* make new stardata */
- stardata = NULL;
- binary_c_new_system(&stardata,
- NULL,
- NULL,
- &store,
- &argstring,
- -1);
-
- /* 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;
-
- /* 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;
- }
-
- /* 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);
-
- /* set raw_buffer_size = -1 to prevent it being freed */
- stardata->tmpstore->raw_buffer_size = -1;
-
- /* free stardata (except the buffer) */
- binary_c_free_memory(&stardata,TRUE,TRUE,FALSE,FALSE);
-
- // TODO: Ask rob whether to free the memory here or not? or to free it manually.
- return 0;
-}
-
-
-// This one will replace the different ones above. needs to handle multiple input choices and decide what to do.
+/* Function that runs a system. Has multiple input parameters:
+Big function. Takes several arguments. See binary_c_python.c docstring.
+*/
int run_system(char * argstring,
long int custom_logging_func_memaddr,
long int store_memaddr,
+ int write_logfile,
+ int population,
char ** const buffer,
char ** const error_buffer,
size_t * const nbytes)
{
- /* memory for N binary systems */
+ /* memory for system */
struct libbinary_c_stardata_t *stardata;
// Store:
@@ -317,15 +80,19 @@ int run_system(char * argstring,
&argstring,
-1);
+ // Add flag to enable
/* 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");
+ 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;
@@ -352,12 +119,17 @@ int run_system(char * argstring,
/* free stardata (except the buffer) */
binary_c_free_memory(&stardata,TRUE,TRUE,FALSE,FALSE); // CHeck if this is good for single runs.. TODO:
-
+
+ // add flag or logic to free store contents.
+ if (store_memaddr == -1)
+ {
+ binary_c_free_store_contents(store);
+ }
+
// TODO: Ask rob whether to free the memory here or not? or to free it manually.
return 0;
}
-
/* =================================================================== */
/* Functions to call other API functionality like help and arglines */
/* =================================================================== */
@@ -454,6 +226,7 @@ int return_help_info(char * argstring,
return 0;
}
+
int return_help_all_info(char ** const buffer,
char ** const error_buffer,
size_t * const nbytes)
@@ -494,6 +267,7 @@ int return_help_all_info(char ** const buffer,
return 0;
}
+
int return_version_info(char ** const buffer,
char ** const error_buffer,
size_t * const nbytes)
@@ -538,7 +312,6 @@ int return_version_info(char ** const buffer,
/* Functions to call other functionality */
/* =================================================================== */
-
long int return_store(char * argstring,
char ** const buffer,
char ** const error_buffer,
diff --git a/tests/python_API_test.py b/tests/python_API_test.py
index 8e05cd65e..e70f0ed8f 100755
--- a/tests/python_API_test.py
+++ b/tests/python_API_test.py
@@ -7,15 +7,22 @@ from binarycpython.utils.custom_logging_functions import (
binary_c_log_code,
create_and_load_logging_function,
)
+from binarycpython.utils.functions import (
+ temp_dir,
+)
import tempfile
############################################################
# Test script for the api functions
+# TODO: Add asserts to these functions and use em as
+# unittests
############################################################
-def test_run_binary():
+# Evolution functionality
+
+def test_run_system():
m1 = 15.0 # Msun
m2 = 14.0 # Msun
separation = 0 # 0 = ignored, use period
@@ -33,23 +40,12 @@ def test_run_binary():
max_evolution_time,
)
- output = binary_c_python_api.run_binary(argstring)
+ output = binary_c_python_api.run_system(argstring=argstring)
print("\n\nBinary_c output:")
print(output)
-
-def test_return_help():
- out = binary_c_python_api.return_help("M_1")
- print(out)
-
-
-def test_return_arglines():
- out = binary_c_python_api.return_arglines()
- print(out)
-
-
-def test_run_binary_with_log():
+def test_run_system_with_log():
m1 = 15.0 # Msun
m2 = 14.0 # Msun
separation = 0 # 0 = ignored, use period
@@ -58,8 +54,8 @@ def test_run_binary_with_log():
metallicity = 0.02
max_evolution_time = 15000
- log_filename = tempfile.gettempdir() + "/test_log.txt"
- api_log_filename_prefix = tempfile.gettempdir() + "/test_log"
+ log_filename = temp_dir() + "/test_log.txt"
+ api_log_filename_prefix = temp_dir() + "/test_log"
argstring = "binary_c M_1 {0:g} M_2 {1:g} separation {2:g} orbital_period {3:g} eccentricity {4:g} metallicity {5:g} max_evolution_time {6:g} log_filename {7:s} api_log_filename_prefix {8:s}".format(
m1,
@@ -73,12 +69,12 @@ def test_run_binary_with_log():
api_log_filename_prefix,
)
- output = binary_c_python_api.run_binary_with_logfile(argstring)
+ output = binary_c_python_api.run_system(argstring=argstring, write_logfile=1)
+
print("\n\nBinary_c output:")
print(output)
-
-def test_run_binary_with_custom_logging():
+def test_run_system_with_custom_logging():
"""
"""
@@ -92,8 +88,9 @@ def test_run_binary_with_custom_logging():
custom_logging_code = binary_c_log_code(logging_line)
# Load memory adress
- func_memaddr = create_and_load_logging_function(custom_logging_code)
+ func_memaddr, shared_lib_filename = create_and_load_logging_function(custom_logging_code)
+ # Some values
m1 = 15.0 # Msun
m2 = 14.0 # Msun
separation = 0 # 0 = ignored, use period
@@ -101,8 +98,8 @@ def test_run_binary_with_custom_logging():
eccentricity = 0.0
metallicity = 0.02
max_evolution_time = 15000
- log_filename = tempfile.gettempdir() + "/test_log.txt"
- argstring = "binary_c M_1 {0:g} M_2 {1:g} separation {2:g} orbital_period {3:g} eccentricity {4:g} metallicity {5:g} max_evolution_time {6:g} log_filename {7:s}".format(
+
+ argstring = "binary_c M_1 {0:g} M_2 {1:g} separation {2:g} orbital_period {3:g} eccentricity {4:g} metallicity {5:g} max_evolution_time {6:g}".format(
m1,
m2,
separation,
@@ -110,12 +107,23 @@ def test_run_binary_with_custom_logging():
eccentricity,
metallicity,
max_evolution_time,
- log_filename,
)
- out = binary_c_python_api.run_binary_custom_logging(argstring, func_memaddr)
+ print(func_memaddr)
+
+ out = binary_c_python_api.run_system(argstring, custom_logging_func_memaddr=func_memaddr)
print(out)
+# Testing other utility functions
+
+def test_return_help():
+ out = binary_c_python_api.return_help("M_1")
+ print(out)
+
+
+def test_return_arglines():
+ out = binary_c_python_api.return_arglines()
+ print(out)
def test_return_help_all():
out = binary_c_python_api.return_help_all("M_1")
@@ -126,52 +134,27 @@ def test_return_version_info():
out = binary_c_python_api.return_version_info()
print(out)
+# Testing other functions
def test_return_store():
out = binary_c_python_api.return_store("")
print(out)
-
-def test_run_system():
-
- m1 = 15.0 # Msun
- m2 = 14.0 # Msun
- separation = 0 # 0 = ignored, use period
- orbital_period = 4530.0 # days
- eccentricity = 0.0
- metallicity = 0.02
- max_evolution_time = 15000
- log_filename = tempfile.gettempdir() + "/test_log.txt"
- argstring = "binary_c M_1 {0:g} M_2 {1:g} separation {2:g} orbital_period {3:g} eccentricity {4:g} metallicity {5:g} max_evolution_time {6:g}".format(
- m1,
- m2,
- separation,
- orbital_period,
- eccentricity,
- metallicity,
- max_evolution_time,
- log_filename,
- )
- out = binary_c_python_api.run_system(argstring, -1, -1)
- print(out)
-
-
####
if __name__ == "__main__":
- # test_run_binary()
+ test_run_system()
- # test_run_binary_with_log()
+ test_run_system_with_log()
- # test_run_binary_with_custom_logging()
+ test_run_system_with_custom_logging()
- # test_return_help()
+ test_return_help()
- # test_return_arglines()
+ test_return_arglines()
- # test_return_help_all()
+ test_return_help_all()
- # test_return_version_info()
+ test_return_version_info()
- # test_return_store()
+ test_return_store()
- test_run_system()
--
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