libutil: utility functions

General utilities.

haddock.libs.libutil.copy_files_to_dir(paths: Iterable[str | Path], directory: str | Path) → None

Copy files to directory.

Parameters:

• paths (iterable of paths) – Source files.

• directory (path) – Where to copy files to.

haddock.libs.libutil.extract_keys_recursive(config: MutableMapping[str, Any]) → Generator[str, None, None]

Extract keys recursively for the needed modules.

haddock.libs.libutil.get_number_from_path_stem(path: str | Path) → int

Extract tail number from path.

Examples

>>> get_number_from_path_stem('src/file_1.pdb')
>>> 1

>>> get_number_from_path_stem('src/file_3.pdb')
>>> 3

>>> get_number_from_path_stem('file_1231.pdb')
>>> 1231

>>> get_number_from_path_stem('src/file11')
>>> 11

>>> get_number_from_path_stem('src/file_1234_1.pdb')
>>> 1

Parameters:

path (str or Path obj) – The path to evaluate.

Returns:

int – The tail integer of the path.

haddock.libs.libutil.get_result_or_same_in_list(function: Callable[[PT], AnyT], value: PT) → AnyT | list[PT]

Return the result if True or the value within a list.

Applies function to value and returns its result if it evaluates to True. Otherwise, return the value within a list.

function should receive a single argument, the value.

haddock.libs.libutil.log_error_and_exit() → Generator[None, None, None]

Exit with exception.

haddock.libs.libutil.make_list_if_string(item: str | list[str]) → list[str]

Put item into a list.

haddock.libs.libutil.non_negative_int(n: ~typing.Any, exception: type[Exception] = <class 'ValueError'>, emsg: str = '`n` do not satisfies') → int

Transform n in int and returns if compare evaluates to True.

Parameters:

• n (int-convertable) – Something that can be converted to int.

• exception (Exception) – The Exception to raise in case n is not a positive integer.

• emsg (str) – The error message to give to exception. May accept formatting to pass n.

Raises:

ValueError, TypeError – If n cannot be converted to int

haddock.libs.libutil.parse_ncores(n: int | str | None = None, njobs: int | None = None, max_cpus: bool | None = None) → int

Check the number of cores according to HADDOCK3 architecture.

Parameters:

• n (int or str) – The desired number of cores. If None is given, returns the maximum number of cores allowed, see max_cpus.

• njobs (int) – The number of jobs to execute. Optional. The number of cores will be compared to njobs.

• max_cpus (int) – The maximum number of CPUs allowed. If not specified, defaults to the available CPUs minus one.

Raises:

SetupError – If n is not positive or not convertable to int.

Returns:

int – A correct number of cores according to specifications.

haddock.libs.libutil.recursive_convert_paths_to_strings(params: ParamMapT) → ParamMapT

Convert paths to strings recursively over a dictionary.

Parameters:

params (dictionary)

Returns:

dictionary – A copy of the original dictionary with paths converted to strings.

haddock.libs.libutil.recursive_dict_update(d: ParamMapT, u: MutableMapping[str, Any]) → ParamMapT

Update dictionary d according to u recursively.

https://stackoverflow.com/questions/3232943

Returns:

dict – A new dict object with updated key: values. The original dictionaries are not modified.

haddock.libs.libutil.remove_dict_keys(d: MutableMapping[str, Any], keys: Container[str]) → dict[str, Any]

Remove keys from dictionary (d).

Returns:

dict – A copy of d dictionary without the keys.

haddock.libs.libutil.remove_folder(folder: str | Path) → None

Remove a folder if it exists.

Parameters:

folder (str or Path) – Path to folder to remove.

haddock.libs.libutil.sort_numbered_paths(*paths: FilePathT) → list[FilePathT]

Sort input paths to tail number.

If possible, sort criteria is provided by get_number_from_path_stem(). If paths do not have a numbered tag, sort paths alphabetically.

Parameters:

*inputs (str or pathlib.Path) – Paths to files.

Returns:

list – The sorted pathlist. The original types are not modified. If strings are given, strings are returns, if Paths are given paths are returned.

haddock.libs.libutil.transform_to_list(item: Iterable[AnyT] | AnyT) → list[AnyT] | tuple[AnyT, ...]

Put item into a list if not a list already.

If it is set, transforms the set into a list.

If it is a dict, returns a list of the keys.

If it is tuple, returns the tuple.

If a list, returns the same.

Everything else returns item inside a one element list.