src.amarium package

Submodules

src.amarium.checks module

Module to provide sanity checks for user inputs and other routine quality checks during execution.

author:

Julian M. Kleber

src.amarium.checks.check_delete_dir(dir_name: str) → None

The check_delete_dir function checks if a directory exists and deletes it.

Parameters:

dir_name – str: Used to Specify the directory name.

Returns:

None. :doc-author: Julian M. Kleber

src.amarium.checks.check_header_and_data(data: List[Any], header: List[Any]) → None

The check_header_and_data function checks that the length of the data and header lists are equal. If they are not, it raises a RuntimeError with an appropriate message.

Parameters:

• data – List[Any]: Used to Pass in the data to be written.

• header – List[Any]: Used to Ensure that the header and data have the same number of fields.

Returns:

A boolean value. :doc-author: Julian M. Kleber

src.amarium.checks.check_make_dir(dir_name: str) → None

The check_make_dir function checks if a directory exists. If it does not exist, the function creates it.

Parameters:

dir_name – str: Used to Specify the folder name.

Returns:

None. :doc-author: Trelent

src.amarium.checks.check_make_file_name_suffix(file_name: str, suffix: str = '') → str

The check_name_plot function checks that the file_name ends with .png. If it does not, then check_name_plot appends .png to the end of the file_name.

Parameters:

file_name – Used to Specify the name of the file to be plotted.

Returns:

The file_name with the correct file extension. :doc- author: Trelent

src.amarium.checks.check_make_subdirs(dir_names: Iterable[str]) → str

src.amarium.csv_utils module

src.amarium.encryption module

Module for encryption of files. Useful for all kinds of situtations.

author:

Julian M. Kleber

src.amarium.encryption.decrypt_file(encrypted_file: str, private_key_path: str)

The decrypt_file function takes in an encrypted file and a private key, then decrypts the file using the private key.

Parameters:

• encrypted_file – str: Used to Pass the file name of the encrypted file to be decrypted.

• private_key – str: Used to Read the private key file and decrypt the encrypted message.

Returns:

The original message. :doc-author: Julian M. Kleber

src.amarium.encryption.encrypt_file(file_name: str, public_key_file: str, in_place: bool = False, save_file: str | None = None) → None

The encrypt_file function takes a file name, public key, and optional in-place flag. It then encrypts the contents of the file using the provided public key. If in_place is True, it will overwrite the original file with its encrypted version. Otherwise it will create a new encrypted version of that file.

Parameters:

file_name:str – Used to Specify the name of the file to be

encrypted. :param public_key:str: Used to Specify the name of the public key file. :param in_place:bool=False: Used to Determine whether the file should be overwritten or not. :param save_ file:Optional[str]=None:

param file_name:

str: Used to Specify the name of the file to be

encrypted. :param public_key: str: Used to Specify the name of the public key file. :param in_place: bool=False: Used to Determine whether the file should be overwritten or not. :param save_ file:Optional[str]=None: :param file_name: str: Used to Specify the name of the file to be

encrypted.

Parameters:

• public_key – str: Used to Specify the name of the public key file.

• in_place – bool=False: Used to Determine whether the file should be overwritten or not. :param save_ file:Optional[str]=None:

• file_name – str: Used to Specify the name of the file to be encrypted.

• public_key – str: Used to Specify the name of the public key file.

• in_place – bool=False: Used to Determine whether the file should be overwritten or not. :param save_ file:Optional[str]=None:

• file_name – str: Used to Specify the name of the file to be encrypted.

• public_key – str: Used to Specify the name of the public key file.

• in_place – bool=False: Used to Determine whether the file should be overwritten or not.

• save_file – Optional[str]=None: Used to Allow the user to specify a file name for saving the encrypted file.

Returns:

None. :doc-author: Julian M. Kleber

src.amarium.encryption.generate_asymmetric_keys(key_size: int, private_key_name: str, public_key_name: str, write_secret: bool) → Tuple[bytes, bytes]

The generate_asymmetric_keys function generates a private key and public key pair. The keys are generated using the RSA algorithm with a specified bit size. The keys are then written to files in PEM format.

Parameters:

• key_size – int: Used to specify the size of the key that will be generated.

• private_key_name – str: Used to Name the private key file.

• public_key_name – str: Used to specify the name of the public key file.

Returns:

The private and public keys. :doc-author: Julian M. Kleber

src.amarium.utils module

Collection of utitly functions for file I/O operations. The purpose is especially for scientific computing, thus numpy is involved in some functions. Copyright (C) 2022 Julian M. Kleber This program comes with ABSOLUTELY NO WARRANTY.”.

author: Julian M. Kleber

src.amarium.utils.attach_slash(raw_string: str) → str

The attach_slash function takes a string as input and returns the same string with a slash appended to it. If the input already ends in a slash, then no change is made.

Parameters:

raw_string – str: Used to Specify the type of data that is being passed into the function.

Returns:

A string with a trailing slash. :doc-author: Julian M. Kleber

src.amarium.utils.b64encode_string(input: str) → str

enocdes string to b64. Useful for APIs

Parameters:

input (str) – string to be encoded

Returns:

encoded input string

Return type:

str

src.amarium.utils.combine_dirs(dir_1: str, dir_2: str) → str

The combine dirs function chains two dir names

Parameters:

• dir_1 – str: Param for first dir

• dir_2 – str: Param for second dir

Returns:

A string with a trailing slash. :doc-author: Julian M. Kleber

src.amarium.utils.convert_str_to_bool(bool_str: str) → None

The convert_str_to_bool function takes a string and converts it to a boolean. The function is used in the main() function to convert the override value from a string to a boolean.

Parameters:

bool_str – str: Used to Specify the type of data that will be passed into the function.

Returns:

None. :doc-author: Julian M. Kleber

src.amarium.utils.copy_dir(old_dir: str, new_dir: str, overwrite=True) → None

The copy_dir function takes two arguments, old_dir and new_dir. It copies all files from the old directory to the new directory. If either of these directories do not end with a “/”, it will be added.

Parameters:

• old_dir – str: Used to Specify the directory that you want to copy from.

• new_dir – str: Used to Specify the new directory that you want to copy your files into.

Returns:

None. :doc-author: Julian M. Kleber

src.amarium.utils.copy_file(file_name: str, destination: str, overwrite: bool = False) → None

Function to copy a file with implemented checks and overwriting functionality.

Param:

file_name: str: specify the file to be copied

Param:

destination: str: specify the destination file name (not directory)

Param:

overwrite: bool: Defaults to false. :author: Julian M. Kleber

src.amarium.utils.delete_all_files_in_dir(dir_name: str) → None

The function deletes all files within the specified directory.

Parameters:

• dir_name – str: Used to specify the directory

• file_name – str=””: Used to specify the name of the file.

• suffix – str=”.out”: Used to specify the file extension.

Returns:

None :suffix: :doc-author: Julian M. Kleber

src.amarium.utils.delete_empty_dir(dir_name: str) → None

The delete_dir function deletes an empty directory.

Parameters:

file_name – str: Used to Specify the name of the file that will be deleted.

Returns:

None. :doc-author: Julian M. Kleber

src.amarium.utils.delete_file(file_name: str) → None

The delete_file function deletes a file from the local directory.

Parameters:

file_name – str: Used to Specify the name of the file that will be deleted.

Returns:

None. :doc-author: Julian M. Kleber

src.amarium.utils.insert_string_in_file_name(file_name: str, insertion: str, suffix: str) → str

The insert_string_in_file_name function takes a file_name and inserts a string into the name. The insertion is placed before the extension of the file_name, or if there is no extension, it will be placed at the end of the file_name with an suffix specified by you.

Parameters:

• file_name – str: Used to Specify the file name that you want to insert a string into.

• insertion – str: Used to Specify the string that will be inserted into the file name.

• suffix – str: Used to Specify the file suffix.

Returns:

A string. :doc-author: Julian M. Kleber

src.amarium.utils.load_json_from_file(file_name: str) → Dict[Any, Any]

The load_json_from_file function takes a file name as input and returns the contents of that file in JSON format.

Parameters:

file_name – str: Used to Specify the file name of the json file to be loaded.

Returns:

A dictionary of the data in the file. :doc-author: Julian M. Kleber

src.amarium.utils.make_date_file_name(prefix: str = '', file_name: str = '', suffix: str = '') → str

The make_date_file_name function creates a file name with the date and time stamp in the format YYYY-MM-DD_HH:MM:SS.out. The prefix, file_name, and suffix are optional arguments that can be used to specify what string should precede the date stamp in the file_name (prefix), what string should be appended after the date stamp (suffix), or both (file_name). If no arguments are provided, then make_date_file_name will use default values for all three arguments.

Parameters:

• prefix – str=””: Used to ddd a prefix to the file name.

• file_name – str=””: Used to specify the name of the file.

• suffix – str=”.out”: Used to specify the file extension.

Returns:

A string that is the combination of prefix, file_name and suffix. :doc-author: Julian M. Kleber

src.amarium.utils.make_full_filename(prefix: str, file_name: str) → str

The make_full_filename function takes a prefix and a file_name as input. If the prefix is None, then the file_name is returned unchanged. Otherwise, if the file name starts with ‘http://’ or ‘ftp://’, then it’s assumed to be an URL and the full_filename will contain both the prefix and file_name; otherwise, only return full_filename = file_name.

Parameters:

• prefix – Used to Add a prefix to the file_name.

• file_name – Used to Create a full file_name for the file to be downloaded.

Returns:

The full file_name with the prefix added to the beginning of the file_name.

Doc-author:

Trelent

src.amarium.utils.prepare_file_name_saving(file_name: str, prefix: str | Type[None] | None = None, suffix: str | Type[None] | None = None) → str

The prepare_file_name_saving function takes a prefix and file name as input. It checks to see if the directory exists, and makes it if not. Then it returns the full path of the file.

Parameters:

• prefix – str: Used to specify the folder where the file will be saved.

• file_name – str: Used to specify the name of the file to be saved.

Returns:

The full path of the file name. :doc-author: Julian M. Kleber

src.amarium.utils.read_file(file_name: str, encoding='ISO-8859-1') → str

src.amarium.utils.remove_all_files_from_dir(dir: str) → None

Removes all files in the specified directory without deleting the directory

Parameters:

dir (str) – Path to the directory that shall be cleared

src.amarium.utils.save_json_to_file(dictionary: Dict[Any, Any], file_name: str) → None

The save_json function saves a dictionary to a json file.

Parameters:

• dictionary – Used to store the data that will be saved.

• file_name – str=None: Used to specify a file name.

Returns:

A string with the name of the file that was just created. :doc-author: Julian M. Kleber

src.amarium.utils.search_subdirs(dir_name: str) → Tuple[List[str], List[str]]

The search_subdirs function takes a directory name as input and returns a tuple of two lists. The first list contains all the files in the directory, including those in subdirectories. The second list contains all the subdirectories.

Parameters:

dir_name – str: Used to Specify the directory that we want to search.

Returns:

A tuple of two lists. :doc-author: Julian M. Kleber

src.amarium.utils.write_file(content: str, file_name: str, encoding: str = 'ISO-8859-1')

src.amarium.utils.write_list_to_file(list, file_name) → str

src.amarium.utils.write_tar(target_dir: str, file_name: str) → None

The write_tar function takes a target directory and an output name as arguments. It then creates a tar file with the given output name, and adds all files in the target directory to it.

Parameters:

• target_dir – str: Used to Specify the directory that you want to compress.

• out_name – str: Used to Specify the name of the tar file that will be created.

Returns:

None. :doc-author: Julian M. Kleber

Module contents