vivarium.cluster_tools Utilities

Making directories is hard.

vivarium.cluster_tools.utilities.get_cluster_name()

Returns the hostname

Return type:

str

vivarium.cluster_tools.utilities.hash_output_path(output_path, length=8)

Return a short, stable hash of an output path.

Used to disambiguate Jobmon workflow identifiers between concurrent pipelines that share the same name and timestamp but write to different output directories.

Return type:

str

Parameters:

• output_path (str | Path) – The output path to hash.

• length (int) – Number of leading hex characters of the digest to return.

Returns:

The first length characters of the MD5 hex digest of output_path.

vivarium.cluster_tools.utilities.mkdir(path, umask=2, exists_ok=False, parents=False)

Utility method to create a directory with specified permissions.

Return type:

None

Parameters:

• path (str | Path) – Path of the directory to create.

• umask (int) – Umask specifying the desired permissions - defaults to 0o002.

• exists_ok (bool) – If False, raises FileExistsError if the directory already exists.

• parents (bool) – If False, raises FileNotFoundError if the directory’s parent doesn’t exist.

vivarium.cluster_tools.utilities.backoff_and_retry(backoff_seconds=30, num_retries=3, log_function=<built-in function warn>)

Adds a retry handler to the decorated function.

Return type:

Callable[[Callable[[ParamSpec(P, bound= None)], TypeVar(T)]], Callable[[ParamSpec(P, bound= None)], TypeVar(T)]]

Parameters:

• backoff_seconds (int | float) – Number of seconds to wait until retrying the operation.

• num_retries (int) – Number of times to retry before failing.

• log_function (Callable[[str], None]) – A callable used to emit retry messages. Defaults to emitting a standard library warning.

Returns:

A function that retries the decorated function a specified number of times.