From 47376ac67c9f262e3972ae883315a0e92e6f11c1 Mon Sep 17 00:00:00 2001
From: David Hendriks <davidhendriks93@gmail.com>
Date: Fri, 8 Nov 2019 17:22:10 +0000
Subject: [PATCH] Alot of API visibility and binary_c_exit errors
---
Makefile | 2 +-
TODO.org | 4 +-
binary_c_python.c | 118 ++++++++++-----
binary_c_python.h | 12 +-
binary_c_python_api.c | 135 ++++++++++++------
.../custom_logging_functions.py | 9 +-
custom_logging.c | 5 +-
testing.py | 8 +-
8 files changed, 205 insertions(+), 88 deletions(-)
diff --git a/Makefile b/Makefile
index f04d68ef2..a327be900 100644
--- a/Makefile
+++ b/Makefile
@@ -16,7 +16,7 @@ LIBS := -lbinary_c $(shell $(BINARY_C)/binary_c-config --libs)
C_SRC := binary_c_python_api.c
OBJECTS := $(C_SRC:.c=.o)
OBJ_FLAGS := -c
-CFLAGS := -fPIC $(shell $(BINARY_C)/binary_c-config --flags) -I$(BINARY_C)/src/ -I$(BINARY_C)/src/API
+CFLAGS := -fPIC $(shell $(BINARY_C)/binary_c-config --flags | sed s/-fvisibility=hidden// ) -I$(BINARY_C)/src/ -I$(BINARY_C)/src/API
SO_FLAGS := -shared -o
SO_NAME := libbinary_c_api.so
diff --git a/TODO.org b/TODO.org
index 9fec89639..6f73f99db 100644
--- a/TODO.org
+++ b/TODO.org
@@ -141,11 +141,13 @@ That went very deep haha. alot of memory allocation stuff
CLOSED: [2019-11-08 Fri 15:00]
*** DONE make tag of old master branch for future reference
CLOSED: [2019-11-08 Fri 15:00]
-*** TODO Implement the autogeneration of the library
+*** DONE Implement the autogeneration of the library
+ CLOSED: [2019-11-08 Fri 15:48]
*** TODO Load all the things with the c-types
*** TODO Implement new function for run_binary_with_custom_logging
*** TODO Make new c function run_binary_with_custom_logging
*** TODO Put in some new tests in the python test api
+
** General:
*** DONE Get a more reliable way of loading the default values (running a ./tbse echo or something?)
CLOSED: [2019-10-29 Tue 17:44]
diff --git a/binary_c_python.c b/binary_c_python.c
index a44f974b1..ff67ec101 100644
--- a/binary_c_python.c
+++ b/binary_c_python.c
@@ -22,7 +22,7 @@
*/
/************************************************************/
-
+// Docstrings
static char module_docstring[] MAYBE_UNUSED =
"This module is a python wrapper around binary_c";
#ifdef __DEPRECATED
@@ -33,6 +33,8 @@ static char run_binary_docstring[] =
"Run one binary using binary_c";
static char run_binary_with_logdocstring[] =
"Run one binary using binary_c and allow the logfile to be written. Do not use for populations!";
+static char run_binary_custom_loggingdocstring[] =
+ "TODO";
static char new_binary_system_docstring[] =
"Return an object containing a binary, ready for evolution";
static char function_prototype_docstring[] =
@@ -41,32 +43,38 @@ static char return_arglines_docstring[] =
"Return the default args for a binary_c system";
static struct libbinary_c_store_t *store = NULL;
+// Initialize pyobjects
#ifdef __DEPRECATED
static PyObject* binary_c_create_binary(PyObject *self, PyObject *args);
#endif
static PyObject* binary_c_run_binary(PyObject *self, PyObject *args);
static PyObject* binary_c_run_binary_with_log(PyObject *self, PyObject *args);
+static PyObject* binary_c_run_binary_custom_logging(PyObject *self, PyObject *args);
static PyObject* binary_c_function_prototype(PyObject *self, PyObject *args);
static PyObject* binary_c_new_binary_system(PyObject *self, PyObject *args);
static PyObject* binary_c_return_arglines(PyObject *self, PyObject *args);
-
-
/*
* Python 3 interface is described at
*
* http://scipy-lectures.org/advanced/interfacing_with_c/interfacing_with_c.html
*/
+
static PyMethodDef module_methods[] = {
#ifdef __DEPRECATED
- {"create_binary", binary_c_create_binary, METH_VARARGS, create_binary_docstring},
+ {"create_binary",
+ binary_c_create_binary,
+ METH_VARARGS,
+ create_binary_docstring
+ },
#endif
{"run_binary", binary_c_run_binary, METH_VARARGS, run_binary_docstring},
{"run_binary_with_log", binary_c_run_binary_with_log, METH_VARARGS, run_binary_with_logdocstring},
+ // {"run_binary_custom_logging", binary_c_run_binary_custom_logging, METH_VARARGS, run_binary_custom_loggingdocstring},
{"function_prototype", binary_c_function_prototype, METH_VARARGS, function_prototype_docstring},
{"new_system", binary_c_new_binary_system, METH_VARARGS, new_binary_system_docstring},
- {"return_arglines", binary_c_return_arglines, METH_VARARGS, return_arglines_docstring},
+ // {"return_arglines", binary_c_return_arglines, METH_VARARGS, return_arglines_docstring},
{NULL, NULL, 0, NULL}
};
@@ -74,7 +82,6 @@ static PyMethodDef module_methods[] = {
#if PY_MAJOR_VERSION >= 3
/* Python 3+ */
-
static struct PyModuleDef Py_binary_c =
{
PyModuleDef_HEAD_INIT,
@@ -215,6 +222,48 @@ static PyObject* binary_c_run_binary(PyObject *self, PyObject *args)
}
}
+// static PyObject* binary_c_run_binary_custom_logging(PyObject *self, PyObject *args)
+// {
+// /* Parse the input tuple */
+// char *argstring;
+// long int str_1;
+
+// if(!PyArg_ParseTuple(args, "sl", &argstring, &str_1))
+// {
+// return NULL;
+// }
+// else
+// {
+// char * buffer;
+// char * error_buffer;
+// size_t nbytes;
+// int out MAYBE_UNUSED = run_binary_custom_logging(argstring,
+// str_1,
+// &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_binary_with_log(PyObject *self, PyObject *args)
{
/* Parse the input tuple */
@@ -256,33 +305,32 @@ static PyObject* binary_c_run_binary_with_log(PyObject *self, PyObject *args)
}
}
-static PyObject* binary_c_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 binary_c run : %s\n",
- error_buffer);
- }
+// static PyObject* binary_c_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 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;
-}
-
+// Safe_free(buffer);
+// Safe_free(error_buffer);
+
+// /*
+// * TODO
+// * return the return_error_string as well!
+// */
+// return return_string;
+// }
\ No newline at end of file
diff --git a/binary_c_python.h b/binary_c_python.h
index 04a1a1257..7643dcfcc 100644
--- a/binary_c_python.h
+++ b/binary_c_python.h
@@ -19,9 +19,15 @@ int run_binary_with_log (char * argstring,
char ** const errorstring,
size_t * const nbytes);
-int return_arglines(char ** const outstring,
- char ** const errorstring,
- size_t * const nbytes);
+// int run_binary_custom_logging(char * argstring,
+// long int str_1,
+// char ** const buffer,
+// char ** const error_buffer,
+// size_t * const nbytes);
+
+// int return_arglines(char ** const outstring,
+// char ** const errorstring,
+// size_t * const nbytes);
/* C macros */
#define BINARY_C_APITEST_VERSION 0.1
diff --git a/binary_c_python_api.c b/binary_c_python_api.c
index d160ef857..00ddc349d 100644
--- a/binary_c_python_api.c
+++ b/binary_c_python_api.c
@@ -128,56 +128,109 @@ int run_binary(char * argstring,
return 0;
}
-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;
- struct libbinary_c_store_t * store = NULL;
+// int run_binary_custom_logging(char * argstring,
+// long int str_1,
+// char ** const buffer,
+// char ** const error_buffer,
+// size_t * const nbytes)
+// {
+// /* memory for N binary systems */
+// struct libbinary_c_store_t * store = NULL;
- /* make new stardata */
- stardata = NULL;
- char * empty_str = "";
- binary_c_new_system(&stardata,
- NULL,
- NULL,
- &store,
- &empty_str,
- -1);
+// /* 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 = str_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");
+// /* 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;
+// }
- /* output to strings */
- stardata->preferences->internal_buffering = INTERNAL_BUFFERING_STORE;
- stardata->preferences->batchmode = BATCHMODE_LIBRARY;
- /* List available arguments */
- binary_c_list_args(stardata);
+// 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;
+// struct libbinary_c_store_t * store = NULL;
- /* get buffer pointer */
- binary_c_buffer_info(stardata,buffer,nbytes);
+// /* make new stardata */
+// stardata = NULL;
+// char * empty_str = "";
+// binary_c_new_system(&stardata,
+// NULL,
+// NULL,
+// &store,
+// &empty_str,
+// -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;
+
+// /* 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);
+// /* 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;
+// /* 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);
+// /* free stardata (except the buffer) */
+// binary_c_free_memory(&stardata,TRUE,TRUE,FALSE,FALSE);
+// binary_c_free_store_contents(store);
- return 0;
-}
+// return 0;
+// }
int run_binary_with_log(char * argstring,
char ** const buffer,
diff --git a/binaryc_python_utils/custom_logging_functions.py b/binaryc_python_utils/custom_logging_functions.py
index 49919e6b9..bfd3c2f98 100644
--- a/binaryc_python_utils/custom_logging_functions.py
+++ b/binaryc_python_utils/custom_logging_functions.py
@@ -65,8 +65,9 @@ def binary_c_log_code(code):
#undef MIN
#include \"binary_c.h\"
-void custom_output_function(struct stardata_t * stardata);
-void custom_output_function(struct stardata_t * stardata)
+// add visibility __attribute__ ((visibility ("default"))) to it
+void binary_c_API_function custom_output_function(struct stardata_t * stardata);
+void binary_c_API_function custom_output_function(struct stardata_t * stardata)
{{
// struct stardata_t * stardata = (struct stardata_t *)x;
{};
@@ -175,6 +176,10 @@ def return_compilation_dict():
# you must define _SEARCH_H to prevent it being loaded twice
ccflags += ' -shared -D_SEARCH_H'
+ # remove the visibility=hidden for this compilation
+ ccflags = ccflags.replace('-fvisibility=hidden', '')
+
+
# ensure library paths to the front of the libs:
libs_content = libs.split(' ')
library_paths = [el for el in libs_content if el.startswith('-L')]
diff --git a/custom_logging.c b/custom_logging.c
index ef5b587fb..57b6574fa 100644
--- a/custom_logging.c
+++ b/custom_logging.c
@@ -4,8 +4,9 @@
#undef MIN
#include "binary_c.h"
-void custom_output_function(struct stardata_t * stardata);
-void custom_output_function(struct stardata_t * stardata)
+// add visibility __attribute__ ((visibility ("default"))) to it
+void binary_c_API_function custom_output_function(struct stardata_t * stardata);
+void binary_c_API_function custom_output_function(struct stardata_t * stardata)
{
// struct stardata_t * stardata = (struct stardata_t *)x;
Printf("MY_STELLAR_DATA %g %g\n",((double)stardata->model.time),((double)stardata->star[0].mass));
diff --git a/testing.py b/testing.py
index 688e77020..f0f5a52e1 100644
--- a/testing.py
+++ b/testing.py
@@ -1,7 +1,7 @@
import ctypes
from binaryc_python_utils.custom_logging_functions import autogen_C_logging_code, binary_c_log_code, compile_shared_lib
-
+# import binary_c
# generate logging lines
logging_line = autogen_C_logging_code(
@@ -18,7 +18,9 @@ created_code = binary_c_log_code(logging_line)
compile_shared_lib(created_code, sourcefile_name='custom_logging.c', outfile_name='libcustom_logging.so')
# Loading library
-libmean = ctypes.CDLL("libcustom_logging.so") # loads the shared library
+libmean = ctypes.CDLL("libcustom_logging.so", mode=1) # loads the shared library
# Get memory adress of function. mimicking a pointer
-mem = ctypes.cast(libmean.custom_output_function, ctypes.c_void_p).value
\ No newline at end of file
+mem = ctypes.cast(libmean.custom_output_function, ctypes.c_void_p).value
+
+
--
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