diff --git a/TODO.org b/TODO.org
index d97a105f00188320fed74afd391368ea58c68ce8..7104038c6ef1370addcea51cfa3279a98b896b0c 100644
--- a/TODO.org
+++ b/TODO.org
@@ -17,7 +17,8 @@
** Features:
*** Help functionality
-**** TODO Add help functionality to the module by calling the binary_c help api
+**** DONE Add help functionality to the module by calling the binary_c help api
+ CLOSED: [2019-12-16 Mon 00:20]
**** TODO Add help_all functionality: to have binary_c return the whole set of parameter descriptions
*** Floors Stroopwafel
diff --git a/binarycpython/__init__.py b/binarycpython/__init__.py
index 4e61002d8790367b28495e2049dc1e1951af7651..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 100644
--- a/binarycpython/__init__.py
+++ b/binarycpython/__init__.py
@@ -1,2 +0,0 @@
-def ding():
- print("ding")
diff --git a/binarycpython/utils/custom_logging_functions.py b/binarycpython/utils/custom_logging_functions.py
index cd37988bc1f86ab8cfb1516389c2aa5f02bf0fb0..9f58b705a291e39df188765ba9b286a3b27bddff 100644
--- a/binarycpython/utils/custom_logging_functions.py
+++ b/binarycpython/utils/custom_logging_functions.py
@@ -5,6 +5,7 @@ import socket
import tempfile
import ctypes
+
def autogen_C_logging_code(logging_dict):
"""
Function that autogenerates PRINTF statements for binaryc. intput is a dictionary where the key is the header of that logging line and items which are lists of parameters\
@@ -206,7 +207,6 @@ def return_compilation_dict(verbose=False):
]
libs = "{} {}".format(" ".join(library_paths), " ".join(non_library_paths))
-
if verbose:
print(
"Building shared library for custom logging with (binary_c.h) at {} on {}\n".format(
diff --git a/binarycpython/utils/functions.py b/binarycpython/utils/functions.py
index 6d89b63ff1bd59ae3b8484bead10de5260847254..c65ca92db015fcacef934a4e1a67a28a69caa6a2 100644
--- a/binarycpython/utils/functions.py
+++ b/binarycpython/utils/functions.py
@@ -16,6 +16,7 @@ def create_arg_string(arg_dict):
arg_string = arg_string.strip()
return arg_string
+
def get_defaults():
"""
Function that calls the binaryc get args function and cast it into a dictionary
@@ -42,7 +43,8 @@ def get_arg_keys():
return get_defaults().keys()
-def get_help(param_name, return_dict):
+
+def get_help(param_name, return_dict=False):
"""
Function that returns the help info for a given parameter.
@@ -64,44 +66,57 @@ def get_help(param_name, return_dict):
if param_name in available_arg_keys:
help_info = binary_c_python_api.return_help(param_name)
- cleaned = [el for el in help_info.split('\n') if not el=='']
+ cleaned = [el for el in help_info.split("\n") if not el == ""]
# Get line numbers
- did_you_mean_nr = [i for i, el in enumerate(cleaned) if el.startswith('Did you mean')]
- parameter_line_nr = [i for i, el in enumerate(cleaned) if el.startswith('binary_c help')]
- default_line_nr = [i for i, el in enumerate(cleaned) if el.startswith('Default')]
- macros_line_nr = [i for i, el in enumerate(cleaned) if el.startswith('Available')]
+ did_you_mean_nr = [
+ i for i, el in enumerate(cleaned) if el.startswith("Did you mean")
+ ]
+ parameter_line_nr = [
+ i for i, el in enumerate(cleaned) if el.startswith("binary_c help")
+ ]
+ default_line_nr = [
+ i for i, el in enumerate(cleaned) if el.startswith("Default")
+ ]
+ macros_line_nr = [
+ i for i, el in enumerate(cleaned) if el.startswith("Available")
+ ]
help_info_dict = {}
# Get alternatives
if did_you_mean_nr:
- alternatives = cleaned[did_you_mean_nr[0]+1: parameter_line_nr[0]]
+ alternatives = cleaned[did_you_mean_nr[0] + 1 : parameter_line_nr[0]]
alternatives = [el.strip() for el in alternatives]
- help_info_dict['alternatives'] = alternatives
+ help_info_dict["alternatives"] = alternatives
# Information about the parameter
parameter_line = cleaned[parameter_line_nr[0]]
- parameter_name = parameter_line.split(":")[1].strip().split(' ')[0]
- parameter_value_input_type = ' '.join(parameter_line.split(":")[1].strip().split(' ')[1:]).replace('<', '').replace('>', '')
+ parameter_name = parameter_line.split(":")[1].strip().split(" ")[0]
+ parameter_value_input_type = (
+ " ".join(parameter_line.split(":")[1].strip().split(" ")[1:])
+ .replace("<", "")
+ .replace(">", "")
+ )
- help_info_dict['parameter_name'] = parameter_name
- help_info_dict['parameter_value_input_type'] = parameter_value_input_type
+ help_info_dict["parameter_name"] = parameter_name
+ help_info_dict["parameter_value_input_type"] = parameter_value_input_type
- description_line = ' '.join(cleaned[parameter_line_nr[0]+1 : default_line_nr[0]])
- help_info_dict['description'] = description_line
+ description_line = " ".join(
+ cleaned[parameter_line_nr[0] + 1 : default_line_nr[0]]
+ )
+ help_info_dict["description"] = description_line
- # Default:
+ # Default:
default_line = cleaned[default_line_nr[0]]
- default_value = default_line.split(':')[-1].strip()
+ default_value = default_line.split(":")[-1].strip()
- help_info_dict['default'] = default_value
+ help_info_dict["default"] = default_value
# Get Macros:
if macros_line_nr:
- macros = cleaned[macros_line_nr[0]+1:]
- help_info_dict['macros'] = macros
-
+ 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]))
@@ -110,9 +125,17 @@ def get_help(param_name, return_dict):
return help_info_dict
else:
- print("{} is not a valid parameter name. Please choose from the following parameters:\n\t{}".format(param_name, list(available_arg_keys)))
+ print(
+ "{} is not a valid parameter name. Please choose from the following parameters:\n\t{}".format(
+ param_name, list(available_arg_keys)
+ )
+ )
return None
+
+get_help("RLOF_method")
+
+
def run_system(**kwargs):
"""
Wrapper to run a system with settings
@@ -197,11 +220,11 @@ def run_system_with_log(**kwargs):
# print(arg_string)
# Run it and get output
- buffer = ""
output = binary_c_python_api.run_binary_with_logfile(arg_string)
return output
+
def parse_output(output, selected_header):
"""
Function that parses output of binary_c:
@@ -216,8 +239,8 @@ def parse_output(output, selected_header):
TODO: Think about exporting to numpy array or pandas instead of a defaultdict
"""
- value_dicts = []
- val_lists = []
+ value_dicts = []
+ val_lists = []
# split output on newlines
for i, line in enumerate(output.split("\n")):
@@ -234,14 +257,16 @@ def parse_output(output, selected_header):
if header == selected_header:
# Check if the line contains '=' symbols:
value_dict = {}
- if all('=' in el for el in values_list):
+ if all("=" in el for el in values_list):
for el in values_list:
key, val = el.split("=")
value_dict[key.strip()] = val.strip()
value_dicts.append(value_dict)
else:
- if any('=' in el for el in values_list):
- raise ValueError('Caught line contains some = symbols but not all of them do. aborting run')
+ if any("=" in el for el in values_list):
+ raise ValueError(
+ "Caught line contains some = symbols but not all of them do. aborting run"
+ )
else:
for i, val in enumerate(values_list):
value_dict[i] = val
@@ -264,9 +289,8 @@ def parse_output(output, selected_header):
return final_values_dict
-
def load_logfile(logfile):
- with open(logfile, 'r') as f:
+ with open(logfile, "r") as f:
logfile_data = f.readlines()
time_list = []
@@ -296,6 +320,6 @@ def load_logfile(logfile):
ecc_list.append(split_line[6])
rel_r1_list.append(split_line[7])
rel_r2_list.append(split_line[8])
- event_list.append(' '.join(split_line[9:]))
+ event_list.append(" ".join(split_line[9:]))
- print(event_list)
\ No newline at end of file
+ print(event_list)
diff --git a/docs/source/conf.py b/docs/source/conf.py
index a7ec7ab840e67b77ca37f58c1b891d79b34e491c..e9df5d4be59ee15b89a4eae8f408b62d022fe1ad 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -14,20 +14,20 @@ import os
import sys
# Include paths for python code
-sys.path.insert(0, os.path.abspath('.'))
-sys.path.insert(0, os.path.abspath('../../binarycpython'))
+sys.path.insert(0, os.path.abspath("."))
+sys.path.insert(0, os.path.abspath("../../binarycpython"))
# sys.path.insert(0, os.path.abspath('../../examples'))
-sys.path.insert(0, os.path.abspath('../../binarycpython/utils'))
+sys.path.insert(0, os.path.abspath("../../binarycpython/utils"))
sys.path.insert(0, os.path.join(os.getenv("BINARY_C"), "src/API/"))
# include paths for c code
-cautodoc_root = os.path.abspath('../../')
+cautodoc_root = os.path.abspath("../../")
# -- Project information -----------------------------------------------------
-project = 'binary_c-python'
-copyright = '2019, Jeff Andrews, Robert Izzard, David Hendriks'
-author = 'Jeff Andrews, Robert Izzard, David Hendriks'
+project = "binary_c-python"
+copyright = "2019, Jeff Andrews, Robert Izzard, David Hendriks"
+author = "Jeff Andrews, Robert Izzard, David Hendriks"
# -- General configuration ---------------------------------------------------
@@ -36,16 +36,16 @@ author = 'Jeff Andrews, Robert Izzard, David Hendriks'
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
extensions = [
- 'sphinx.ext.autodoc',
- 'sphinx.ext.doctest',
- 'hawkmoth',
- 'm2r',
+ "sphinx.ext.autodoc",
+ "sphinx.ext.doctest",
+ "hawkmoth",
+ "m2r",
]
-source_suffix = ['.rst', '.md']
+source_suffix = [".rst", ".md"]
# Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
@@ -58,9 +58,9 @@ exclude_patterns = []
# The theme to use for HTML and HTML Help pages. See the documentation for
# a list of builtin themes.
#
-html_theme = 'alabaster'
+html_theme = "alabaster"
# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]
diff --git a/examples/examples.py b/examples/examples.py
index ab728b6e4679484d265be8068ed00d8ca4fe2dbf..e81878fd70a8f62d9bd345453d93ed25f7e85fc4 100644
--- a/examples/examples.py
+++ b/examples/examples.py
@@ -45,6 +45,7 @@ def run_example_binary():
output = binary_c_python_api.run_binary(argstring)
print(output)
+
run_example_binary()
@@ -83,7 +84,6 @@ def run_example_binary_with_run_system():
# Or put them into a pandas array
-
# Cast the data into a dataframe.
# This example automatically catches the column names because the binary_c output line is constructed as 'example_header_1 time=<number>..'
df = pd.DataFrame.from_dict(result_example_header_1, dtype=np.float64)
@@ -91,7 +91,7 @@ def run_example_binary_with_run_system():
# This example has column headers which are numbered, but we can override that with custom headers.
df2 = pd.DataFrame.from_dict(result_example_header_2, dtype=np.float64)
- df2.columns=['time', 'mass_1', 'mass_2', 'st1', 'st2', 'sep', 'ecc']
+ df2.columns = ["time", "mass_1", "mass_2", "st1", "st2", "sep", "ecc"]
print(df2)
# print(df)
@@ -100,8 +100,10 @@ def run_example_binary_with_run_system():
# Some routine to plot.
+
run_example_binary_with_run_system()
+
def run_example_binary_with_custom_logging():
"""
Function that will use a automatically generated piece of logging code. Compile it, load it
@@ -143,8 +145,10 @@ def run_example_binary_with_custom_logging():
# Do whatever you like with the dataframe.
print(df)
+
run_example_binary_with_custom_logging()
+
def run_example_binary_with_writing_logfile():
"""
Same as above but when giving the log_filename argument the log filename will be written
@@ -161,7 +165,7 @@ def run_example_binary_with_writing_logfile():
separation=0,
orbital_period=100000000000,
log_filename=tempfile.gettempdir() + "/test_log.txt",
-
)
-run_example_binary_with_writing_logfile()
\ No newline at end of file
+
+run_example_binary_with_writing_logfile()
diff --git a/setup.py b/setup.py
index 9e97e0f499f50bd70ca9917da1818511cc0b08f1..cd1c0651982b182a6337e32bdb0f2cda244020c9 100644
--- a/setup.py
+++ b/setup.py
@@ -1,4 +1,5 @@
from distutils.core import setup, Extension
+
# from setuptools import find_packages
# from setuptools import setup, find_packages, Extension
import os
@@ -88,10 +89,12 @@ binary_c_python_api_module = Extension(
language="C",
)
+
def readme():
- with open('README.md') as f:
+ with open("README.md") as f:
return f.read()
+
setup(
name="binarycpython",
version="0.1",
@@ -101,22 +104,18 @@ setup(
long_description=readme(),
url="https://gitlab.eps.surrey.ac.uk/ri0005/binary_c-python",
license="",
- package_dir = {
- 'binarycpython': 'binarycpython',
- 'binarycpython.utils': 'binarycpython/utils',
+ package_dir={
+ "binarycpython": "binarycpython",
+ "binarycpython.utils": "binarycpython/utils",
# 'binarycpython.core': 'lib',
},
packages=[
- 'binarycpython',
- 'binarycpython.utils',
+ "binarycpython",
+ "binarycpython.utils",
# 'binarycpython.core',
],
-
# package_data={
# 'binarycpython.core': ['libbinary_c_api.so'],
# },
-
- ext_modules=[
- binary_c_python_api_module
- ], # binary_c must be loaded
+ ext_modules=[binary_c_python_api_module], # binary_c must be loaded
)
diff --git a/tests/python_API_test.py b/tests/python_API_test.py
index 18c9ad8a002c7c82637578f4cdb980a8138d219e..e24a7906ee2bf516bd3d953d0969689b369ec8be 100755
--- a/tests/python_API_test.py
+++ b/tests/python_API_test.py
@@ -14,6 +14,7 @@ import tempfile
# Test script for the api functions
############################################################
+
def test_run_binary():
m1 = 15.0 # Msun
m2 = 14.0 # Msun
@@ -37,14 +38,17 @@ def test_run_binary():
print("\n\nBinary_c output:")
print(output)
+
def test_return_help():
- out = binary_c_python_api.return_help('M_1')
+ out = binary_c_python_api.return_help("M_1")
print(out)
+
def test_return_arglines():
out = binary_c_python_api.return_arglines()
print(out)
+
def test_run_binary_with_log():
m1 = 15.0 # Msun
m2 = 14.0 # Msun
@@ -55,7 +59,7 @@ def test_run_binary_with_log():
max_evolution_time = 15000
log_filename = tempfile.gettempdir() + "/test_log.txt"
- api_log_filename_prefix = tempfile.gettempdir()+'/test_log'
+ api_log_filename_prefix = tempfile.gettempdir() + "/test_log"
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} log_filename {7:s} api_log_filename_prefix {8:s}".format(
m1,
@@ -73,6 +77,7 @@ def test_run_binary_with_log():
print("\n\nBinary_c output:")
print(output)
+
def test_run_binary_with_custom_logging():
"""
"""
@@ -111,13 +116,14 @@ def test_run_binary_with_custom_logging():
out = binary_c_python_api.run_binary_custom_logging(argstring, func_memaddr)
print(out)
+
####
# test_run_binary()
-test_run_binary_with_log()
+# test_run_binary_with_log()
# test_return_help()
# test_return_arglines()
-# test_run_binary_with_custom_logging()
\ No newline at end of file
+# test_run_binary_with_custom_logging()