functions module¶
Module containing most of the utility functions for the binarycpython package
Functions here are mostly functions used in other classes/functions, or useful functions for the user
- Tasks:
- TODO: change all prints to verbose_prints 
 
- class binarycpython.utils.functions.Capturing[source]¶
- Bases: - list- Context manager to capture output and store it 
- binarycpython.utils.functions.bin_data(value, binwidth)[source]¶
- Function that bins the data - Uses the absolute value of binwidth 
- binarycpython.utils.functions.call_binary_c_config(argument)[source]¶
- Function to interface with the binary_c config file - input:
- argument: argument for the binary_c config 
 
 - Returns
- raw output of binary_c-config 
 
 
- class binarycpython.utils.functions.catchtime[source]¶
- Bases: - object- Context manager to calculate time spent 
- binarycpython.utils.functions.check_if_in_shell()[source]¶
- Function to check whether the script is running from a shell 
- binarycpython.utils.functions.conv_time_units(t)[source]¶
- Converts time (t, in seconds, passing in as the only argument) to seconds, minutes or hours depending on its magnitude. Returns a tuple (t,units). 
- binarycpython.utils.functions.convert_bytes(size)[source]¶
- Function to return the size + a magnitude string 
- binarycpython.utils.functions.convfloat(x)[source]¶
- Convert scalar x to a float if we can, in which case return the float, otherwise just return x without changing it. Usually, x is a string, but could be anything that float() can handle without failure. 
- binarycpython.utils.functions.create_arg_string(arg_dict, sort=False, filter_values=False)[source]¶
- Function that creates the arg string for binary_c. Takes a dictionary containing the arguments and writes them to a string This string is missing the ‘binary_c ‘ at the start. - Parameters
- arg_dict ( - dict) – dictionary
- sort ( - bool) – (optional, default = False) Boolean whether to sort the order of the keys.
- filter_values ( - bool) – (optional, default = False) filters the input dict on keys that have NULL or function as value.
 
- Return type
- str
- Returns
- The string built up by combining all the key + value’s. 
 
- binarycpython.utils.functions.create_hdf5(data_dir, name)[source]¶
- Function to create an hdf5 file from the contents of a directory:
- settings file is selected by checking on files ending on settings 
- data files are selected by checking on files ending with .dat 
 
 - TODO: fix missing settings files - Parameters
- data_dir ( - str) – directory containing the data files and settings file
- name ( - str) – name of hdf5file.
 
- Return type
- None
 
- binarycpython.utils.functions.datalinedict(line, parameters)[source]¶
- Convert a line of data to a more convenient dictionary. :param line = a line of data as a string: :param parameters = a list of the parameter names: - Note: if the parameter is a floating point number, it will be converted to Python’s float type. 
- binarycpython.utils.functions.example_parse_output(output, selected_header)[source]¶
- Function that parses output of binary_c. This version serves as an example and is quite detailed. Custom functions can be easier: - This function works in two cases: if the caught line contains output like ‘example_header time=12.32 mass=0.94 ..’ or if the line contains output like ‘example_header 12.32 0.94’ Please don’t the two cases. - You can give a ‘selected_header’ to catch any line that starts with that. Then the values will be put into a dictionary. - Tasks:
- TODO: Think about exporting to numpy array or pandas instead of a defaultdict 
- TODO: rethink whether this function is necessary at all 
- TODO: check this function again 
 
 - Parameters
- output ( - str) – binary_c output string
- selected_header ( - str) – string header of the output (the start of the line that you want to process)
 
- Return type
- dict
- Returns
- dictionary containing parameters as keys and lists for the values 
 
- binarycpython.utils.functions.filter_arg_dict(arg_dict)[source]¶
- Function to filter out keys that contain values included in [‘NULL’, ‘Function’, ‘’] - This function is called by get_defaults() - Parameters
- arg_dict ( - dict) – dictionary containing the argument + default key pairs of binary_c
- Return type
- dict
- Returns
- filtered dictionary (pairs with NULL and Function values are removed) 
 
- binarycpython.utils.functions.get_arg_keys()[source]¶
- Function that return the list of possible keys to give in the arg string. This function calls get_defaults() - Return type
- list
- Returns
- list of all the parameters that binary_c accepts (and has default values for, since we call get_defaults()) 
 
- binarycpython.utils.functions.get_defaults(filter_values=False)[source]¶
- Function that calls the binaryc get args function and cast it into a dictionary. - All the values are strings - Parameters
- filter_values ( - bool) – whether to filter out NULL and Function defaults.
- Return type
- dict
- Returns
- dictionary containing the parameter name as key and the parameter default as value 
 
- binarycpython.utils.functions.get_help(param_name='', print_help=True, fail_silently=False)[source]¶
- Function that returns the help info for a given parameter, by interfacing with binary_c - Will check whether it is a valid parameter. - Binary_c will output things in the following order; - Did you mean? - binary_c help for variable - default - available macros - This function reads out that structure and catches the different components of this output - Tasks:
- TODO: consider not returning None, but return empty dict 
 
 - Parameters
- param_name ( - str) – name of the parameter that you want info from. Will get checked whether its a valid parameter name
- print_help ( - bool) – (optional, default = True) whether to print out the help information
- fail_silently ( - bool) – (optional, default = False) Whether to print the errors raised if the
- valid (parameter isn't) – 
 
- Return type
- Optional[- dict]
- Returns
- Dictionary containing the help info. This dictionary contains ‘parameter_name’, ‘parameter_value_input_type’, ‘description’, optionally ‘macros’ 
 
- binarycpython.utils.functions.get_help_all(print_help=True)[source]¶
- Function that reads out the output of the return_help_all API call to binary_c. This return_help_all binary_c returns all the information for the parameters, their descriptions and other properties. The output is categorised in sections. - Parameters
- print_help ( - bool) – (optional, default = True) prints all the parameters and their descriptions.
- Return type
- dict
- Returns
- returns a dictionary containing dictionaries per section. These dictionaries contain the parameters and descriptions etc for all the parameters in that section 
 
- binarycpython.utils.functions.get_help_super(print_help=False, fail_silently=True)[source]¶
- Function that first runs get_help_all, and then per argument also run the help function to get as much information as possible. - Parameters
- print_help ( - bool) – (optional, default = False) Whether to print the information
- fail_silently ( - bool) – (optional, default = True) Whether to fail silently or to print the errors
 
- Return type
- dict
- Returns
- dictionary containing all dictionaries per section, which then contain as much info as possible per parameter. 
 
- binarycpython.utils.functions.get_moe_di_stefano_dataset(options, verbosity=0)[source]¶
- Function to get the default Moe and di Stefano dataset or accept a user input. - Returns a dict containing the (JSON) data. 
- binarycpython.utils.functions.load_logfile(logfile)[source]¶
- Experimental function that parses the generated log file of binary_c. - This function is not finished and shouldn’t be used yet. - Tasks:
- TODO: 
 
 - Parameters
- logfile (-) – filename of the log file you want to parse 
 - Returns: - Return type
- None
 
- binarycpython.utils.functions.make_build_text()[source]¶
- Function to make build text - Return type
- str
- Returns
- string containing information about the build and the git branch 
 
- binarycpython.utils.functions.mem_use()[source]¶
- Return current process memory use in MB. (Takes no arguments) Note: this is per-thread only. 
- binarycpython.utils.functions.output_lines(output)[source]¶
- Function that outputs the lines that were received from the binary_c run, but now as an iterator. - Parameters
- output ( - str) – raw binary_c output
- Return type
- list
- Returns
- Iterator over the lines of the binary_c output 
 
- binarycpython.utils.functions.pad_output_distribution(dist, binwidth)[source]¶
- Given a distribution, dist (a dictionary), which should be binned every binwidth (float), fill the distribution with zeros when there is no data. Note: this changes the data in place. 
- binarycpython.utils.functions.parse_binary_c_version_info(version_info_string)[source]¶
- Function that parses the binary_c version info. Long function with a lot of branches - TODO: fix this function. stuff is missing: isotopes, macros, nucleosynthesis_sources - Parameters
- version_info_string ( - str) – raw output of version_info call to binary_c
- Returns
- ‘isotopes’ for isotope info, ‘argpairs’ for argument pair info (TODO: explain), ‘ensembles’ for ensemble settings/info, ‘macros’ for macros, ‘elements’ for atomic element info, ‘DTlimit’ for (TODO: explain), ‘nucleosynthesis_sources’ for nucleosynthesis sources, and ‘miscellaneous’ for all those that were not caught by the previous groups. ‘git_branch’, ‘git_build’, ‘revision’ and ‘email’ are also keys, but its clear what those contain. 
- Return type
- Parsed version of the version info, which is a dictionary containing the keys 
 
- binarycpython.utils.functions.remove_file(file, verbosity=0)[source]¶
- Function to remove files but with verbosity - Parameters
- file ( - str) – full file path to the file that will be removed.
- verbosity ( - int) – current verbosity level (Optional)
 
- Return type
- None
- Returns
- the path of a sub directory called binary_c_python in the TMP of the file system 
 
- binarycpython.utils.functions.return_binary_c_version_info(parsed=True)[source]¶
- Function that returns the version information of binary_c. This function calls the function _binary_c_bindings.return_version_info() - Parameters
- parsed ( - bool) – Boolean flag whether to parse the version_info output of binary_c. default = False
- Return type
- Union[- str,- dict]
- Returns
- Either the raw string of binary_c or a parsed version of this in the form of a nested dictionary 
 
- binarycpython.utils.functions.temp_dir(*args)[source]¶
- Function to create directory within the TMP directory of the file system - Makes use of os.makedirs exist_ok which requires python 3.2+ - Parameters
- arguments (function) – str input where each next input will be a child of the previous full_path. e.g. temp_dir(‘tests’, ‘grid’) will become ‘/tmp/binary_c_python/tests/grid’ 
- Return type
- str
- Returns
- the path of a sub directory called binary_c_python in the TMP of the file system 
 
- binarycpython.utils.functions.timedelta(delta)[source]¶
- Function to convert a length of time (float, seconds) to a string for human-readable output. 
- binarycpython.utils.functions.trem(dt, count, dn, n)[source]¶
- Estimate time remaining (seconds) given a differential time and count (i.e. progress = $count/$n). $dt is the time since the last call, $count is the current progress count, $dn is the number run since the last call, and $n is the total number required. 
- binarycpython.utils.functions.verbose_print(message, verbosity, minimal_verbosity)[source]¶
- Function that decides whether to print a message based on the current verbosity and its minimum verbosity - if verbosity is equal or higher than the minimum, then we print - Parameters
- message ( - str) – message to print
- verbosity ( - int) – current verbosity level
- minimal_verbosity ( - int) – threshold verbosity above which to print
 
- Return type
- None
 
- binarycpython.utils.functions.write_binary_c_parameter_descriptions_to_rst_file(output_file)[source]¶
- Function that calls the get_help_super() to get the help text/descriptions for all the parameters available in that build. Writes the results to a .rst file that can be included in the docs. - Tasks:
- TODO: add the specific version git branch, git build, git commit, and binary_c version to
- this document 
 
 
 - Parameters
- output_file ( - str) – name of the output .rst file containing the ReStructuredText formatted output of all the binary_c parameters.
- Return type
- None