wholecell.utils.dependency_graph

Tools for working with dependency graphs

class wholecell.utils.dependency_graph.DependencyGraph

Bases: object

Represents a dependency graph

dependencies

Mapping from node to that node’s dependents

Initialize dependencies to empty dictionary

_topo_sort_dfs(node, explored, reverse_ordering)

Parameters:

• node (str)

• explored (dict[str, int])

• reverse_ordering (list[str])

add_dep_relation(a, b)

Add an edge such that a depends on b

If a or b does not exist yet as a node, it will be created.

Parameters:

• a (str) – The name of the node that depends on b

• b (str) – The name of the node that is depended-upon by a

add_nodes(nodes)

Add nodes with no dependencies

Parameters:

nodes (Iterable[str]) – Nodes to add

get_topological_ordering()

Get a topological ordering of the nodes

Returns:

List of dependency names such that the dependencies can be loaded in the order in which they appear in the list without violating dependency relationships.

Raises:

InvalidDependencyGraphError – If the graph contains a cycle

Return type:

list[str]

class wholecell.utils.dependency_graph.ExplorationStatus

Bases: object

EXPLORED = 3

Node has been visited and added to list.

EXPLORING = 2

Node has been visited but not added to list. This means that we have not yet finished with the node.

UNEXPLORED = 1

Node has not yet been visited.

exception wholecell.utils.dependency_graph.InvalidDependencyGraphError

Bases: Exception

Exception for invalid dependency graphs