API Docs

Networkx Backend

geff.read_nx

read_nx(
    path: Path | str, validate: bool = True
) -> nx.Graph

Read a geff file into a networkx graph. Metadata attributes will be stored in the graph attributes, accessed via G.graph[key] where G is a networkx graph.

Parameters:

Name	Type	Description	Default
path	Path | str	The path to the root of the geff zarr, where the .attrs contains the geff metadata	required
validate	bool	Flag indicating whether to perform validation on the geff file before loading into memory. If set to False and there are format issues, will likely fail with a cryptic error. Defaults to True.	True

Returns:

Type	Description
Graph	A networkx graph containing the graph that was stored in the geff file format

geff.write_nx

write_nx(
    graph: Graph,
    path: str | Path,
    position_attr: str | None = None,
    axis_names: list[str] | None = None,
    axis_units: list[str] | None = None,
    zarr_format: int = 2,
    validate: bool = True,
)

Write a networkx graph to the geff file format

Parameters:

Name	Type	Description	Default
graph	Graph	A networkx graph	required
path	str | Path	The path to the output zarr. Opens in append mode, so will only overwrite geff-controlled groups.	required
position_attr	Optional[str]	The name of the position attribute present on every node, if present. Defaults to None.	None
axis_names	Optional[list[str]]	The names of the spatial dims represented in position attribute. Defaults to None. Will override value in graph attributes if provided.	None
axis_units	Optional[list[str]]	The units of the spatial dims represented in position attribute. Defaults to None. Will override value in graph attributes if provided.	None
zarr_format	int	The version of zarr to write. Defaults to 2.	2
validate	bool	Flag indicating whether to perform validation on the networkx graph before writing anything to disk. If set to False and there are missing attributes, will likely fail with a KeyError, leading to an incomplete graph written to disk. Defaults to True.	True

Utilities

geff.validate

validate(path: str | Path)

Check that the structure of the zarr conforms to geff specification

Parameters:

Name	Type	Description	Default
path	str | Path	Path to geff zarr	required

Raises:

Type	Description
AssertionError	If geff specs are violated

geff.GeffMetadata

Bases: BaseModel

Geff metadata schema to validate the attributes json file in a geff zarr

read classmethod

read(group: Group | Path) -> GeffMetadata

Helper function to read GeffMetadata from a zarr geff group.

Parameters:

Name	Type	Description	Default
group	Group | Path	The zarr group containing the geff metadata	required

Returns:

Name	Type	Description
GeffMetadata	GeffMetadata	The GeffMetadata object

write

write(group: Group | Path)

Helper function to write GeffMetadata into the zarr geff group.

Parameters:

Name	Type	Description	Default
group	Group | Path	The geff group to write the metadata to	required