From f9d92042ed51024e8308e344befd0b87448ba773 Mon Sep 17 00:00:00 2001
From: David Hendriks <davidhendriks93@gmail.com>
Date: Sun, 29 Nov 2020 19:53:22 +0000
Subject: [PATCH] updated binarycpython to handle the c_bindings as part of the
module
---
binarycpython/utils/functions.py | 38 ++++++++++++++++++-----
binarycpython/utils/grid.py | 29 ++++++-----------
binarycpython/utils/run_system_wrapper.py | 5 +--
3 files changed, 43 insertions(+), 29 deletions(-)
diff --git a/binarycpython/utils/functions.py b/binarycpython/utils/functions.py
index 85cfc27e9..27a325312 100644
--- a/binarycpython/utils/functions.py
+++ b/binarycpython/utils/functions.py
@@ -10,13 +10,14 @@ import os
import tempfile
import copy
import inspect
+import ast
from collections import defaultdict
import h5py
import numpy as np
-import binary_c_python_api
+from binarycpython import _binary_c_bindings
########################################################
# utility functions
@@ -140,7 +141,7 @@ def return_binary_c_version_info(parsed=False):
Function that returns the version information of binary_c
"""
- version_info = binary_c_python_api.return_version_info().strip()
+ version_info = _binary_c_bindings.return_version_info().strip()
if parsed:
version_info = parse_binary_c_version_info(version_info)
@@ -407,7 +408,7 @@ def get_defaults(filter_values=False):
filter_values: whether to filter out NULL and Function defaults.
"""
- default_output = binary_c_python_api.return_arglines()
+ default_output = _binary_c_bindings.return_arglines()
default_dict = {}
for default in default_output.split("\n"):
@@ -500,7 +501,7 @@ def get_help(param_name="", print_help=True, fail_silently=False):
return None
if param_name in available_arg_keys:
- help_info = binary_c_python_api.return_help(param_name)
+ help_info = _binary_c_bindings.return_help(param_name)
cleaned = [el for el in help_info.split("\n") if not el == ""]
# Get line numbers
@@ -580,7 +581,7 @@ def get_help_all(print_help=True):
"""
# Call function
- help_all = binary_c_python_api.return_help_all()
+ help_all = _binary_c_bindings.return_help_all()
# String manipulation
split = help_all.split(
@@ -633,12 +634,16 @@ def get_help_all(print_help=True):
# Put the information in a dict
param_name = split_param_info[0]
param_description = split_param_info[1]
- rest = split_param_info[2]
+
+ if len(split_param_info) > 2:
+ rest = split_param_info[2:]
+ else:
+ rest = None
params_dict[param_name] = {
"param_name": param_name,
"description": param_description,
- "rest": rest,
+ "rest": ''.join(rest) if rest else '',
}
# make section_dict
@@ -937,3 +942,22 @@ def binaryc_json_serializer(obj):
if inspect.isfunction(obj):
return str(obj)
return obj
+
+def handle_ensemble_string_to_json(raw_output):
+ """
+ Function that deals with the raw output of the ensemble and
+ creates a working JSON dictionary out of it.
+
+ It seems that JSON does not like strings that contain dictionaries which have a number as a key, but more specifically it is the fact that binary-c outputs as 5e2 instead of
+
+ e.g. with python 3.6.4: json.loads("{5e2: 10}") leads to a JSONDecodeError. To fix this, I do the following:
+
+ with ensemble_output being the literal string of output, and json_output the correct jsonified version of that.
+
+ eval_dict = ast.literal_eval(ensemble_output)
+ json_output = json.loads(json.dumps(eval_dict), cls=binarycDecoder)
+
+ Note: this does pose somewhat of a risk, since eval'ing something might lead to unexpected behaviour.
+ """
+
+ return json.loads(json.dumps(ast.literal_eval(raw_output)), cls=binarycDecoder)
diff --git a/binarycpython/utils/grid.py b/binarycpython/utils/grid.py
index 1d8bae3d4..14036a907 100644
--- a/binarycpython/utils/grid.py
+++ b/binarycpython/utils/grid.py
@@ -49,8 +49,7 @@ from binarycpython.utils.hpc_functions import (
get_python_details,
)
-
-import binary_c_python_api
+from binarycpython import _binary_c_bindings
# Tasks
# TODO: add functionality to 'on-init' set arguments
@@ -349,9 +348,7 @@ class Population:
def _return_binary_c_version_info(self, parsed=False):
"""
Function that returns the version information of binary_c
- """
-
- version_info = binary_c_python_api.return_version_info().strip()
+ """.return_version_info().strip()
if parsed:
version_info = parse_binary_c_version_info(version_info)
@@ -534,8 +531,7 @@ class Population:
"""
for thread_nr in self.grid_options["amt_cores"]:
- persistent_data_memaddr = (
- binary_c_python_api.binary_c_return_persistent_data_memaddr()
+ persistent_data_memad.binary_c_return_persistent_data_memaddr()
)
self.persistent_data_memory_dict[thread_nr] = persistent_data_memaddr
verbose_print(
@@ -567,8 +563,7 @@ class Population:
1,
)
- # Get the output and decode it correctly to get the numbers correct
- ensemble_json_output = binary_c_python_api.binary_c_free_persistent_data_memaddr_and_return_json_output(
+ # Get the output and decode it correctly.binary_c_free_persistent_data_memaddr_and_return_json_output(
persistent_data_memaddr
)
parsed_json = json.loads(
@@ -700,8 +695,7 @@ class Population:
full_system_dict = self.bse_options.copy()
full_system_dict.update(system)
- binary_cmdline_string = self._return_argline(full_system_dict)
- out = binary_c_python_api.run_system(
+ binary_cmdline_string =.run_system(
argstring=binary_cmdline_string,
custom_logging_func_memaddr=self.grid_options[
"custom_logging_func_memaddr"
@@ -719,9 +713,7 @@ class Population:
def evolve_system_mp(self, binary_cmdline_string):
"""
Function that the multiprocessing evolution method calls to evolve a system
- """
-
- out = binary_c_python_api.run_system(
+ """.run_system(
argstring=binary_cmdline_string,
custom_logging_func_memaddr=self.grid_options[
"custom_logging_func_memaddr"
@@ -766,8 +758,7 @@ class Population:
argline = self._return_argline(self.bse_options)
verbose_print("Running {}".format(argline), self.grid_options["verbosity"], 1)
- # Run system
- out = binary_c_python_api.run_system(
+ # Run syste.run_system(
argstring=argline,
custom_logging_func_memaddr=self.grid_options[
"custom_logging_func_memaddr"
@@ -811,8 +802,7 @@ class Population:
### Custom logging code:
self._set_custom_logging()
- ### Load store
- self.grid_options["store_memaddr"] = binary_c_python_api.return_store_memaddr()
+ ### Load stor.return_store_memaddr()
### ensemble:
## check the settings:
@@ -930,8 +920,7 @@ class Population:
# Unload functions
- # Unload store
- binary_c_python_api.free_store_memaddr(self.grid_options["store_memaddr"])
+ # Unload stor.free_store_memaddr(self.grid_options["store_memaddr"])
###################################################
# Gridcode functions
diff --git a/binarycpython/utils/run_system_wrapper.py b/binarycpython/utils/run_system_wrapper.py
index 7b726892e..e13535cd4 100644
--- a/binarycpython/utils/run_system_wrapper.py
+++ b/binarycpython/utils/run_system_wrapper.py
@@ -13,7 +13,8 @@ from binarycpython.utils.functions import (
from binarycpython.utils.custom_logging_functions import (
create_and_load_logging_function,
)
-import binary_c_python_api
+
+from binarycpython import _binary_c_bindings
def run_system(**kwargs):
@@ -87,7 +88,7 @@ def run_system(**kwargs):
binary_c_command = "binary_c {}".format(arg_string)
# Call binary_c
- output = binary_c_python_api.run_system(
+ output = _binary_c_bindings.run_system(
binary_c_command,
custom_logging_func_memaddr=func_memaddr,
write_logfile=write_logfile,
--
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