From 3c444a1b8f49cbebc9dd723652018960d527abdb Mon Sep 17 00:00:00 2001
From: David Hendriks <davidhendriks93@gmail.com>
Date: Wed, 18 Dec 2019 16:31:22 +0000
Subject: [PATCH] added help_all functionality and began writing the grid
script
---
binarycpython/utils/functions.py | 132 ++++++++++++++++--
binarycpython/utils/grid.py | 41 ++++++
.../example_run_binary_with_custom_logging.py | 6 +-
include/binary_c_python.h | 4 +-
src/binary_c_python.c | 84 +++++++++--
src/binary_c_python_api.c | 76 ++++++++--
tests/python_API_test.py | 18 ++-
7 files changed, 326 insertions(+), 35 deletions(-)
create mode 100644 binarycpython/utils/grid.py
diff --git a/binarycpython/utils/functions.py b/binarycpython/utils/functions.py
index c65ca92db..df087d4e2 100644
--- a/binarycpython/utils/functions.py
+++ b/binarycpython/utils/functions.py
@@ -1,3 +1,5 @@
+import copy
+import json
from collections import defaultdict
import binary_c_python_api
@@ -5,6 +7,110 @@ from binarycpython.utils.custom_logging_functions import (
create_and_load_logging_function,
)
+def get_help_all(print_help=True, return_dict=False):
+ """
+ Function that reads out the output of the help_all api call to binary_c
+
+ prints all the parameters and their descriptions.
+
+ return_dict: returns a dictionary
+ """
+
+ # Call function
+ help_all = binary_c_python_api.return_help_all()
+
+ # String manipulation
+ split = help_all.split(
+ "############################################################\n"
+ )
+ cleaned = [el for el in split if not el == "\n"]
+
+ section_nums = [i for i in range(len(cleaned)) if cleaned[i].startswith("#####")]
+
+ # Create dicts
+ help_all_dict = {}
+
+ # Select the section name and the contents of that section. Note, not all sections have content!
+ for i in range(len(section_nums)):
+ if not i == len(section_nums) - 1:
+ params = cleaned[section_nums[i] + 1 : section_nums[i + 1]]
+ else:
+ params = cleaned[section_nums[i] + 1 : len(cleaned)]
+ section_name = (
+ cleaned[section_nums[i]]
+ .lstrip("#####")
+ .strip()
+ .replace("Section ", "")
+ .lower()
+ )
+
+ #
+ params_dict = {}
+
+ if params:
+
+ # Clean it, replace in-text newlines with a space and then split on newlines.
+ split_params = params[0].strip().replace("\n ", " ").split("\n")
+
+ # Process params and descriptions per section
+ for el in split_params:
+ split_param_info = el.split(" : ")
+ if not len(split_param_info) == 3:
+ # there are ocassions where the semicolon is used in the description text itself.
+ if len(split_param_info) == 4:
+ split_param_info = [
+ split_param_info[0],
+ ": ".join([split_param_info[1], split_param_info[2]]),
+ split_param_info[3],
+ ]
+
+ # other occassions?
+
+ # Put the information in a dict
+ param_name = split_param_info[0]
+ param_description = split_param_info[1]
+ rest = split_param_info[2]
+
+ params_dict[param_name] = {
+ "param_name": param_name,
+ "description": param_description,
+ "rest": rest,
+ }
+
+ # make section_dict
+ section_dict = {"section_name": section_name, "parameters": params_dict.copy()}
+
+ # Put in the total dict
+ help_all_dict[section_name] = section_dict.copy()
+
+ # Print things
+ if print_help:
+ for section in sorted(help_all_dict.keys()):
+ print(
+ "##################\n###### Section {}\n##################".format(
+ section
+ )
+ )
+ section_dict = help_all_dict[section]
+ for param_name in sorted(section_dict["parameters"].keys()):
+ param = section_dict["parameters"][param_name]
+ print(
+ "\n{}:\n\t{}: {}".format(
+ param["param_name"], param["description"], param["rest"]
+ )
+ )
+
+ # Loop over all the parameters an call the help() function on it. Takes a long time but this is for testing
+ # for section in help_all_dict.keys():
+ # section_dict = help_all_dict[section]
+ # for param in section_dict['parameters'].keys():
+ # get_help(param)
+
+ if return_dict:
+ return help_all_dict
+ else:
+ return None
+
def create_arg_string(arg_dict):
"""
@@ -17,11 +123,14 @@ def create_arg_string(arg_dict):
return arg_string
-def get_defaults():
+def get_defaults(filter_values=False):
"""
Function that calls the binaryc get args function and cast it into a dictionary
All the values are strings
+
+ filter_values: whether to filter out NULL and Function defaults.
"""
+
default_output = binary_c_python_api.return_arglines()
default_dict = {}
@@ -30,9 +139,15 @@ def get_defaults():
key, value = default.split(" = ")
# Filter out NULLS (not compiled anyway)
- if not value in ["NULL", "Function"]:
- if not value == "":
- default_dict[key] = value
+ if filter_values:
+ if not value in ["NULL", "Function"]:
+ if not value == "":
+ default_dict[key] = value
+
+ # On default, just show everything
+ else:
+ default_dict[key] = value
+
return default_dict
@@ -118,8 +233,8 @@ def get_help(param_name, return_dict=False):
macros = cleaned[macros_line_nr[0] + 1 :]
help_info_dict["macros"] = macros
- for key in help_info_dict.keys():
- print("{}:\n\t{}".format(key, help_info_dict[key]))
+ # for key in help_info_dict.keys():
+ # print("{}:\n\t{}".format(key, help_info_dict[key]))
if return_dict:
return help_info_dict
@@ -133,7 +248,7 @@ def get_help(param_name, return_dict=False):
return None
-get_help("RLOF_method")
+# get_help("RLOF_method")
def run_system(**kwargs):
@@ -223,7 +338,7 @@ def run_system_with_log(**kwargs):
output = binary_c_python_api.run_binary_with_logfile(arg_string)
return output
-
+# run_system_with_log()
def parse_output(output, selected_header):
"""
@@ -323,3 +438,4 @@ def load_logfile(logfile):
event_list.append(" ".join(split_line[9:]))
print(event_list)
+# load_logfile()
\ No newline at end of file
diff --git a/binarycpython/utils/grid.py b/binarycpython/utils/grid.py
new file mode 100644
index 000000000..57937bb40
--- /dev/null
+++ b/binarycpython/utils/grid.py
@@ -0,0 +1,41 @@
+import binary_c_python_api
+
+from binarycpython.utils.functions import (
+ get_defaults,
+)
+
+import binarycpython
+
+
+class Population(object):
+ def __init__(self):
+ """
+ Lots of initialisation
+ """
+
+ self.defaults = get_defaults()
+ pass
+
+ def evolve(self):
+ pass
+
+ def evolve_single(self):
+ arg_string = "binary_c "
+ for param in self.defaults.keys():
+ print(param, self.defaults[param])
+ if self.defaults[param]=='':
+ print(self.defaults[param])
+
+ # arg_string += "{} {} ".format(param, self.defaults[param])
+
+ # arg_string = arg_string.strip()
+ out = binary_c_python_api.run_binary(arg_string)
+ print(out)
+ # print( arg_string)
+
+
+test_pop = Population()
+
+# print(test_pop.defaults)
+
+test_pop.evolve_single()
\ No newline at end of file
diff --git a/examples/example_run_binary_with_custom_logging.py b/examples/example_run_binary_with_custom_logging.py
index 83ab013a0..ac6cfc7b9 100644
--- a/examples/example_run_binary_with_custom_logging.py
+++ b/examples/example_run_binary_with_custom_logging.py
@@ -2,14 +2,14 @@ import ctypes
import tempfile
import os
-from binaryc_python_utils.custom_logging_functions import (
+from binarycpython.utils.custom_logging_functions import (
autogen_C_logging_code,
binary_c_log_code,
compile_shared_lib,
temp_custom_logging_dir,
create_and_load_logging_function,
)
-import binary_c
+import binary_c_python_api
# generate logging lines
logging_line = autogen_C_logging_code(
@@ -36,5 +36,5 @@ max_evolution_time = 15000
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
)
-output = binary_c.run_binary_custom_logging(argstring, func_memaddr)
+output = binary_c_python_api.run_binary_custom_logging(argstring, func_memaddr)
print(output)
diff --git a/include/binary_c_python.h b/include/binary_c_python.h
index e2a48e16f..01aca72ea 100644
--- a/include/binary_c_python.h
+++ b/include/binary_c_python.h
@@ -34,7 +34,9 @@ int return_help_info(char * argstring,
char ** const errorstring,
size_t * const nbytes);
-
+int return_help_all_info(char ** const outstring,
+ char ** const errorstring,
+ size_t * const nbytes);
/* C macros */
#define BINARY_C_APITEST_VERSION 0.1
diff --git a/src/binary_c_python.c b/src/binary_c_python.c
index bd0ffd741..726752d97 100644
--- a/src/binary_c_python.c
+++ b/src/binary_c_python.c
@@ -29,20 +29,26 @@ static char module_docstring[] MAYBE_UNUSED =
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_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[] =
- "The prototype for a binary_c python function";
+
+// Utility function docstrings
static char return_arglines_docstring[] =
"Return the default args for a binary_c system";
static char return_help_info_docstring[] =
"Return the help info for a given parameter";
+static char return_help_all_info_docstring[] =
+ "Return an overview of all the parameters, their description, categorized in sections";
static struct libbinary_c_store_t *store = NULL;
@@ -50,14 +56,18 @@ static struct libbinary_c_store_t *store = NULL;
#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_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_function_prototype(PyObject *self, PyObject *args);
-static PyObject* binary_c_new_binary_system(PyObject *self, PyObject *args);
+
+// Utility function headers
static PyObject* binary_c_return_arglines(PyObject *self, PyObject *args);
static PyObject* binary_c_return_help_info(PyObject *self, PyObject *args);
-
+static PyObject* binary_c_return_help_all_info(PyObject *self, PyObject *args);
/*
* Python 3 interface is described at
@@ -80,8 +90,10 @@ static PyMethodDef module_methods[] = {
{"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_logdocstring},
{"run_binary_custom_logging", binary_c_run_binary_custom_logging, METH_VARARGS, run_binary_custom_loggingdocstring},
+
{"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},
{NULL, NULL, 0, NULL}
};
@@ -92,8 +104,8 @@ static PyMethodDef module_methods[] = {
static struct PyModuleDef Py_binary_c_python_api =
{
PyModuleDef_HEAD_INIT,
- "binary_c", /* name of module */
- "binary_c docs", /* module documentation, may be NULL */
+ "binary_c_python_api", /* name of module */
+ "binary_c_python_api docs", /* 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
};
@@ -187,6 +199,22 @@ 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
+
+binary_c_return_arglines
+binary_c_return_help_info
+binary_c_return_help_all_info
+
+
+*/
+
+/* Wrappers to functions that evolve binary systems. */
+
static PyObject* binary_c_run_binary(PyObject *self, PyObject *args)
{
/* Parse the input tuple */
@@ -310,6 +338,8 @@ static PyObject* binary_c_run_binary_with_logfile(PyObject *self, PyObject *args
}
}
+/* Wrappers to functions that call other API functionality like help and arglines*/
+
static PyObject* binary_c_return_arglines(PyObject *self, PyObject *args)
{
char * buffer;
@@ -375,4 +405,40 @@ static PyObject* binary_c_return_help_info(PyObject *self, PyObject *args)
return return_string;
}
+}
+
+static PyObject* binary_c_return_help_all_info(PyObject *self, PyObject *args)
+{
+ /* Parse the input tuple */
+ // char *argstring;
+
+ // if(!PyArg_ParseTuple(args, "s", &argstring))
+ // {
+ // return NULL;
+ // }
+ // else
+ // {
+ char * buffer;
+ char * error_buffer;
+ size_t nbytes;
+ int out MAYBE_UNUSED = return_help_all_info(&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);
+
+ return return_string;
+ // }
}
\ No newline at end of file
diff --git a/src/binary_c_python_api.c b/src/binary_c_python_api.c
index f8e1d11bf..10ab6147a 100644
--- a/src/binary_c_python_api.c
+++ b/src/binary_c_python_api.c
@@ -45,6 +45,23 @@ 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:
+
+run_binary
+run_binary_custom_logging
+return_arglines
+run_binary_with_logfile
+return_help_info
+return_help_all_info
+
+
+*/
+
+
+
+/* Functions to evolve binary systems */
+
int run_binary(char * argstring,
char ** const buffer,
char ** const error_buffer,
@@ -149,6 +166,48 @@ int run_binary_custom_logging(char * argstring,
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;
+}
+
+/* Functions to call other API functionality like help and arglines */
int return_arglines(char ** const buffer,
char ** const error_buffer,
size_t * const nbytes)
@@ -200,7 +259,8 @@ int return_arglines(char ** const buffer,
return 0;
}
-int run_binary_with_logfile(char * argstring,
+
+int return_help_info(char * argstring,
char ** const buffer,
char ** const error_buffer,
size_t * const nbytes)
@@ -222,9 +282,8 @@ int run_binary_with_logfile(char * argstring,
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);
+ /* Ask the help api */
+ binary_c_help(stardata, argstring);
/* get buffer pointer */
binary_c_buffer_info(stardata,buffer,nbytes);
@@ -241,9 +300,7 @@ int run_binary_with_logfile(char * argstring,
return 0;
}
-
-int return_help_info(char * argstring,
- char ** const buffer,
+int return_help_all_info(char ** const buffer,
char ** const error_buffer,
size_t * const nbytes)
{
@@ -253,11 +310,12 @@ int return_help_info(char * argstring,
/* make new stardata */
stardata = NULL;
+ char * empty_str = "";
binary_c_new_system(&stardata,
NULL,
NULL,
&store,
- &argstring,
+ &empty_str,
-1);
/* output to strings */
@@ -265,7 +323,7 @@ int return_help_info(char * argstring,
stardata->preferences->batchmode = BATCHMODE_LIBRARY;
/* Ask the help api */
- binary_c_help(stardata, argstring);
+ binary_c_help_all(stardata);
/* get buffer pointer */
binary_c_buffer_info(stardata,buffer,nbytes);
diff --git a/tests/python_API_test.py b/tests/python_API_test.py
index e24a7906e..cc373d2a4 100755
--- a/tests/python_API_test.py
+++ b/tests/python_API_test.py
@@ -117,13 +117,21 @@ def test_run_binary_with_custom_logging():
print(out)
+def test_return_help_all():
+ out = binary_c_python_api.return_help_all("M_1")
+ print(out)
+
+
####
-# test_run_binary()
+if __name__ == "__main__":
+ test_run_binary()
+
+ test_run_binary_with_log()
-# test_run_binary_with_log()
+ test_run_binary_with_custom_logging()
-# test_return_help()
+ test_return_help()
-# test_return_arglines()
+ test_return_arglines()
-# test_run_binary_with_custom_logging()
+ test_return_help_all()
--
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