almost there i think

Makefile

@@ -9,6 +9,9 @@ endif
 # Name of program
 PROGRAM := binary_c_python_api
 
+SRC_DIR := src
+OBJ_DIR := obj
+
 # some commands
 CC      	:= gcc
 LD      	:= gcc
@@ -20,28 +23,32 @@ LIBS 		:= -lbinary_c $(shell $(BINARY_C)/binary_c-config --libs)
 # Source files and cflags
 C_SRC   	:= binary_c_python_api.c
 CFLAGS 		:= -fPIC $(shell $(BINARY_C)/binary_c-config --flags | sed s/-fvisibility=hidden// )
+C_SRC_NEW	:= src/binary_c_python_api.c
+
+# SRC = $(wildcard $(SRC_DIR)/binary_c_python_api.c)
+# OBJECTS = $(C_SRC:$(SRC_DIR)/%.c=$(OBJ_DIR)/%.o)
 
 # Incdirs
-INCDIRS 	:= -I$(BINARY_C)/src/ -I$(BINARY_C)/src/API
+INCDIRS 	:= -I$(BINARY_C)/src/ -I$(BINARY_C)/src/API -Iinclude/
 
 # Object files and flags
 OBJECTS 	:= $(C_SRC:.c=.o)
 OBJ_FLAGS 	:= -c
+OBJ_NEW		:= $(C_SRC:$(SRC_DIR)/%.c=$(OBJ_DIR)/%.o)
 
 # Shared lib files and flags
 SO_NAME 	:= libbinary_c_api.so
-SO_FLAGS 	:= -shared -o
+SO_FLAGS 	:= -shared
 
 # To create python shared library
 PY_EXEC 	:= python3
 PY_SETUP 	:= setup.py
 PY_OPTIONS 	:= build_ext --inplace
 
-
 all:
-	$(CC) -DBINARY_C=$(BINARY_C) $(CFLAGS) $(INCDIRS) $(C_SRC) $(OBJ_FLAGS) $(LIBS) 
-	$(CC) -DBINARY_C=$(BINARY_C) $(SO_FLAGS) $(SO_NAME) $(OBJECTS)
-	$(PY_EXEC) $(PY_SETUP) $(PY_OPTIONS) 
+	$(CC) -DBINARY_C=$(BINARY_C) $(CFLAGS) $(INCDIRS) $(C_SRC) -o $(OBJECTS) $(OBJ_FLAGS) $(LIBS) 
+	$(CC) -DBINARY_C=$(BINARY_C) $(SO_FLAGS) -o $(SO_NAME) $(OBJECTS)
+# 	$(PY_EXEC) $(PY_SETUP) $(PY_OPTIONS) 
 
 test:	
 	@echo Objects: $(OBJECTS)
@@ -49,7 +56,9 @@ test:
 	@echo C_SRC: $(C_SRC)
 	@echo CFLAGS: $(CFLAGS)
 	@echo INCDIRS: $(INCDIRS)
+	@echo OBJS_NEW: $(OBJ_NEW)
+
 
 clean:
-	rm -f *.o *.so
-	rm -rf build/
+	$(RM) -f *.o *.so
+	$(RM) -r build/
\ No newline at end of file

setup.py

@@ -67,6 +67,7 @@ setup(
             include_dirs=[
                 os.environ["BINARY_C"] + "/src",
                 os.environ["BINARY_C"] + "/src/API",
+                'include',
             ]
             + binary_c_incdirs,
             library_dirs=[os.environ["BINARY_C"] + "/src", "./"] + binary_c_libdirs,

src/binary_c_python_api.c

+#include "binary_c_python.h"
+#include <time.h>
+#include <sys/timeb.h>
+#include <stdarg.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <unistd.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.
+ *
+ * Note:
+ * I have tested this with gcc 4.7.2 (Ubuntu 12.10) only.
+ */
+
+// #define _CAPTURE
+#ifdef _CAPTURE
+static void show_stdout(void);
+static void capture_stdout(void);
+#endif
+
+/* global variables */
+int out_pipe[2];
+int stdoutwas;
+
+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 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 *)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 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;
+
+    /* 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);
+    
+    /* 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;
+}
\ No newline at end of file