Commit 67eef507 authored by David Hendriks's avatar David Hendriks
Browse files

resolved todo conflict

parents f7f5730d 42abf4ec

TODO.org

+2 −1
Original line number Diff line number Diff line
@@ -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

binarycpython/__init__.py

+0 −2
Original line number Diff line number Diff line 
def ding():

	print("ding")

binarycpython/utils/custom_logging_functions.py

+1 −1
Original line number Diff line number Diff line
@@ -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(

binarycpython/utils/functions.py

+55 −31
Original line number Diff line number Diff line
@@ -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.
@@ -64,13 +66,21 @@ 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 = {}
@@ -78,30 +88,35 @@ def get_help(param_name, return_dict): 
        if did_you_mean_nr:

            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_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



            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:
@@ -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)

docs/source/conf.py

+15 −15
Original line number Diff line number Diff line
@@ -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"]