diff --git a/binarycpython/utils/custom_logging_functions.py b/binarycpython/utils/custom_logging_functions.py
index efad8c2bc17294a23619f6fabcebaa788f4d899b..763b4f143732ab161643c0d6b5a012d596d3513b 100644
--- a/binarycpython/utils/custom_logging_functions.py
+++ b/binarycpython/utils/custom_logging_functions.py
@@ -240,7 +240,7 @@ def return_compilation_dict(verbose=0):
def compile_shared_lib(code, sourcefile_name, outfile_name, verbose=0):
"""
Function to write the custom logging code to a file and then compile it.
-
+
TODO: nicely put in the -fPIC
"""
@@ -289,7 +289,8 @@ def compile_shared_lib(code, sourcefile_name, outfile_name, verbose=0):
def create_and_load_logging_function(custom_logging_code, verbose=0):
"""
- Function to automatically compile the shared library with the given custom logging code and load it with ctypes
+ Function to automatically compile the shared library with the given
+ custom logging code and load it with ctypes
returns:
memory adress of the custom logging function in a int type.
@@ -312,9 +313,10 @@ def create_and_load_logging_function(custom_logging_code, verbose=0):
print("loading shared library for custom logging")
# Loading library
- dll1 = ctypes.CDLL("libgslcblas.so", mode=ctypes.RTLD_GLOBAL)
- dll2 = ctypes.CDLL("libgsl.so", mode=ctypes.RTLD_GLOBAL)
- dll3 = ctypes.CDLL("libbinary_c.so", mode=ctypes.RTLD_GLOBAL)
+ _ = ctypes.CDLL("libgslcblas.so", mode=ctypes.RTLD_GLOBAL)
+ _ = ctypes.CDLL("libgsl.so", mode=ctypes.RTLD_GLOBAL)
+ _ = ctypes.CDLL("libbinary_c.so", mode=ctypes.RTLD_GLOBAL)
+
libcustom_logging = ctypes.CDLL(
library_name, mode=ctypes.RTLD_GLOBAL,
) # loads the shared library
diff --git a/binarycpython/utils/functions.py b/binarycpython/utils/functions.py
index 5e401986f9c7f810d1e944dbbbc208e7efd47425..516235312a79cffe5d4a9255af09056a2214c230 100644
--- a/binarycpython/utils/functions.py
+++ b/binarycpython/utils/functions.py
@@ -9,6 +9,7 @@ from collections import defaultdict
import numpy as np
import binary_c_python_api
+
def remove_file(file, verbose=0):
"""
Function to remove files but with verbosity
@@ -363,6 +364,7 @@ def get_help_all(print_help=True, return_dict=False):
else:
return None
+
def filter_arg_dict(arg_dict):
"""
Function to filter out keys that contain values included in ['NULL', 'Function', '']
@@ -370,7 +372,7 @@ def filter_arg_dict(arg_dict):
old_dict = arg_dict.copy()
new_dict = {}
-
+
for key in old_dict.keys():
if not old_dict[key] in ["NULL", "Function"]:
if not old_dict[key] == "":
@@ -379,7 +381,6 @@ def filter_arg_dict(arg_dict):
return new_dict
-
def create_arg_string(arg_dict, sort=False, filter_values=False):
"""
Function that creates the arg string
diff --git a/binarycpython/utils/grid.py b/binarycpython/utils/grid.py
index 311e740354350ab5c9303d887bc34987116c87de..a7c75e57a655bacff09d0e59631911e3fa2a37af 100644
--- a/binarycpython/utils/grid.py
+++ b/binarycpython/utils/grid.py
@@ -371,8 +371,10 @@ class Population(object):
)
if use_datadir:
- if not self.custom_options.get('base_filename', None):
- base_name = 'simulation_{}'.format(datetime.datetime.strftime(datetime.datetime.now(), '%Y%m%d_%H%M%S'))
+ if not self.custom_options.get("base_filename", None):
+ base_name = "simulation_{}".format(
+ datetime.datetime.strftime(datetime.datetime.now(), "%Y%m%d_%H%M%S")
+ )
else:
base_name = os.path.splitext(self.custom_options["base_filename"])[0]
@@ -466,7 +468,7 @@ class Population(object):
# Dry run and getting starcount
self.grid_options["probtot"] = 0
- # Put in check
+ # Put in check
if len(self.grid_options["grid_variables"]) == 0:
print("Error: you havent defined any grid variables! Aborting")
raise ValueError
@@ -1216,11 +1218,6 @@ class Population(object):
# warning; dont use yet. not fully tested.
"""
-
-
-
-
-
if self.grid_options["system_generator"]:
# Check if there is an output dir configured
if self.custom_options.get("data_dir", None):
diff --git a/binarycpython/utils/plot_functions.py b/binarycpython/utils/plot_functions.py
index 0529702932f4fc1c82f853d24bcafc3fe42a9b56..4d7a88b03db7d0f74eb7b218c1acd909cc7c286f 100644
--- a/binarycpython/utils/plot_functions.py
+++ b/binarycpython/utils/plot_functions.py
@@ -11,13 +11,17 @@ import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
-from david_phd_functions.plotting.plot_functions import plot_orbit, plot_masses, plot_HR_diagram
+from david_phd_functions.plotting.plot_functions import (
+ plot_orbit,
+ plot_masses,
+ plot_HR_diagram,
+)
from binarycpython.utils.functions import get_arg_keys, output_lines
from binarycpython.utils.run_system_wrapper import run_system
from binarycpython.utils.custom_logging_functions import binary_c_log_code
-# Define the custom_logging_strings. These are kept to the minimum necessary for each plotting routine.
+# Define the custom_logging_strings. These are kept to the minimum necessary for each plotting routine.
custom_logging_string_masses = ""
custom_logging_string_orbit = ""
@@ -44,18 +48,11 @@ Printf("HR_PLOTTING %30.12e %d %d %g %g %g %g %g %g\\n",
"""
-
-
-
-
-
-
# Define the parse functions for the plotting routines
def dummy():
pass
-
def parse_function_hr_diagram(output):
"""
Parsing function for the HR plotting routine
@@ -65,30 +62,37 @@ def parse_function_hr_diagram(output):
values_list = []
- parameters = ['time',
- 'stellar_type_1', 'stellar_type_2',
- 'luminosity_1', 'luminosity_2',
- 'radius_1', 'radius_2', 'pms_mass_1', 'pms_mass_2']
+ parameters = [
+ "time",
+ "stellar_type_1",
+ "stellar_type_2",
+ "luminosity_1",
+ "luminosity_2",
+ "radius_1",
+ "radius_2",
+ "pms_mass_1",
+ "pms_mass_2",
+ ]
# Go over the output.
for el in output_lines(output):
headerline = el.split()[0]
# Check the header and act accordingly
- if (headerline=='HR_PLOTTING'):
+ if headerline == "HR_PLOTTING":
values = el.split()[1:]
values_list.append(values)
df = pd.DataFrame(values_list)
df.columns = parameters
-
df = df.astype(np.float64)
- df['stellar_type_1'] = df['stellar_type_1'].astype(np.int64)
- df['stellar_type_2'] = df['stellar_type_2'].astype(np.int64)
+ df["stellar_type_1"] = df["stellar_type_1"].astype(np.int64)
+ df["stellar_type_2"] = df["stellar_type_2"].astype(np.int64)
return df
+
def plot_system(plot_type, **kwargs):
"""
TODO: Complex Function!
@@ -119,24 +123,40 @@ def plot_system(plot_type, **kwargs):
show_stellar_types = False
plot_types_dict = {
- 'mass_evolution': {'plot_function': plot_masses, 'custom_logging_string': custom_logging_string_masses, 'parse_function': dummy},
- 'orbit_evolution': {'plot_function': plot_orbit, 'custom_logging_string': custom_logging_string_orbit, 'parse_function': dummy},
- 'hr_diagram': {'plot_function': plot_HR_diagram, 'custom_logging_string': custom_logging_string_HR_diagram, 'parse_function': parse_function_hr_diagram},
- }
- plot_system_specific_keywords = ['plot_type', 'show_plot', 'show_stellar_types']
+ "mass_evolution": {
+ "plot_function": plot_masses,
+ "custom_logging_string": custom_logging_string_masses,
+ "parse_function": dummy,
+ },
+ "orbit_evolution": {
+ "plot_function": plot_orbit,
+ "custom_logging_string": custom_logging_string_orbit,
+ "parse_function": dummy,
+ },
+ "hr_diagram": {
+ "plot_function": plot_HR_diagram,
+ "custom_logging_string": custom_logging_string_HR_diagram,
+ "parse_function": parse_function_hr_diagram,
+ },
+ }
+ plot_system_specific_keywords = ["plot_type", "show_plot", "show_stellar_types"]
# First check on the plot_type input
if not plot_type in plot_types_dict.keys():
- print("Warning, the provided plot type is not known. Please choose one from the following:\n\t{}".format(plot_types_dict.keys()))
+ print(
+ "Warning, the provided plot type is not known. Please choose one from the following:\n\t{}".format(
+ plot_types_dict.keys()
+ )
+ )
raise ValueError
# First: check all the arguments. Chosen to not check all the keywords for run_system and binary_c specifically, but just to pick out the ones needed for this routine. run_system will handle the rest
run_system_arg_dict = {}
for key in kwargs.keys():
- if key == 'show_plot':
+ if key == "show_plot":
show_plot = kwargs[key]
- elif key == 'show_stellar_types':
+ elif key == "show_stellar_types":
show_stellar_types = kwargs[key]
# The rest will be passed to run_system
@@ -144,19 +164,29 @@ def plot_system(plot_type, **kwargs):
run_system_arg_dict[key] = kwargs[key]
# TODO: When a list of plot_types is passed, make it so that the strings are chained, and that the output of the binary_c call is handled by multiple parsers
- custom_logging_code = binary_c_log_code(plot_types_dict[plot_type]['custom_logging_string'])
- run_system_arg_dict['custom_logging_code'] = custom_logging_code
+ custom_logging_code = binary_c_log_code(
+ plot_types_dict[plot_type]["custom_logging_string"]
+ )
+ run_system_arg_dict["custom_logging_code"] = custom_logging_code
- run_system_arg_dict['parse_function'] = plot_types_dict[plot_type]['parse_function']
+ run_system_arg_dict["parse_function"] = plot_types_dict[plot_type]["parse_function"]
# Run and get the output of the parse function
binary_c_output_df = run_system(**run_system_arg_dict)
-
- fig = plot_types_dict[plot_type]['plot_function'](binary_c_output_df, show_plot=show_plot, show_stellar_types=show_stellar_types)
+ fig = plot_types_dict[plot_type]["plot_function"](
+ binary_c_output_df, show_plot=show_plot, show_stellar_types=show_stellar_types
+ )
if not show_plot:
return fig
-plot_system(plot_type='hr_diagram', M_1=10, M_2=5, orbital_period=100000, max_evolution_time=15000, show_plot=True)
\ No newline at end of file
+plot_system(
+ plot_type="hr_diagram",
+ M_1=10,
+ M_2=5,
+ orbital_period=100000,
+ max_evolution_time=15000,
+ show_plot=True,
+)
diff --git a/binarycpython/utils/run_system_wrapper.py b/binarycpython/utils/run_system_wrapper.py
index 0a247f1f0074c7568445dad536bacbefa3a63bdf..4237548dc3cb232d461a189074144508e5ca55c4 100644
--- a/binarycpython/utils/run_system_wrapper.py
+++ b/binarycpython/utils/run_system_wrapper.py
@@ -38,7 +38,7 @@ def run_system(**kwargs):
# Load available arg keywords
available_binary_c_arg_keywords = get_arg_keys()
- other_keywords = ['custom_logging_code', 'log_filename', 'parse_function']
+ other_keywords = ["custom_logging_code", "log_filename", "parse_function"]
# Set default values
func_memaddr = -1
@@ -55,8 +55,11 @@ def run_system(**kwargs):
# Notify user when this key wont be used
else:
if not key in other_keywords:
- print("The following keyword was not recognized and wont be used:\n\t{}".format(key))
-
+ print(
+ "The following keyword was not recognized and wont be used:\n\t{}".format(
+ key
+ )
+ )
# Check if custom logging is required
if "custom_logging_code" in kwargs:
diff --git a/docs/source/conf.py b/docs/source/conf.py
index e9df5d4be59ee15b89a4eae8f408b62d022fe1ad..85556cc802d9f72698a56799987c0ff568f8e3e9 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -26,8 +26,8 @@ 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"
+copyright = "2020, David Hendriks, Robert Izzard, Jeff Andrews"
+author = "David Hendriks, Robert Izzard, Jeff Andrews"
# -- General configuration ---------------------------------------------------
diff --git a/test_systems/README.md b/examples/example_systems/README.md
similarity index 100%
rename from test_systems/README.md
rename to examples/example_systems/README.md
diff --git a/pathos_worker_objects.py b/pathos_worker_objects.py
deleted file mode 100644
index 26e4e0017145d52ebf0b765e69c57289b7b8e217..0000000000000000000000000000000000000000
--- a/pathos_worker_objects.py
+++ /dev/null
@@ -1,17 +0,0 @@
-import multiprocessing as mp
-
-from pathos.multiprocessing import ProcessingPool as Pool
-
-
-# Create pool
-p = Pool(processes=1, ncpus=3)
-
-
-print(dir(p))
-print(p)
-
-
-quit()
-# Execute
-# TODO: calculate the chunksize value based on: total starcount and cores used.
-r = list(p.imap_unordered(self.evolve_system_mp, self.yield_system_mp(), chunksize=20))