From a3a46b4fbefaf2ca7a93f623a3ef25b12921e1d2 Mon Sep 17 00:00:00 2001
From: David Hendriks <davidhendriks93@gmail.com>
Date: Mon, 18 Nov 2019 15:42:41 +0000
Subject: [PATCH] almost there i think
---
Makefile | 25 +-
.../binary_c_python.h | 0
setup.py | 1 +
src/binary_c_python_api.c | 242 ++++++++++++++++++
4 files changed, 260 insertions(+), 8 deletions(-)
rename binary_c_python.h => include/binary_c_python.h (100%)
create mode 100644 src/binary_c_python_api.c
diff --git a/Makefile b/Makefile
index c0b18ca30..687115f05 100644
--- a/Makefile
+++ b/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
diff --git a/binary_c_python.h b/include/binary_c_python.h
similarity index 100%
rename from binary_c_python.h
rename to include/binary_c_python.h
diff --git a/setup.py b/setup.py
index 84868603a..c955c7583 100644
--- a/setup.py
+++ b/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,
diff --git a/src/binary_c_python_api.c b/src/binary_c_python_api.c
new file mode 100644
index 000000000..98aa26883
--- /dev/null
+++ b/src/binary_c_python_api.c
@@ -0,0 +1,242 @@
+#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
--
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