Cache

Cache helpers from annnet.core._Matrix.

Use G.cache for graph-owned cache helpers. Direct imports from underscore modules follow the internal API policy.

annnet.core._Matrix.CacheManager

Derived sparse-matrix cache (CSR/CSC/adjacency), keyed on the structural clock.

Keys on _structure_version (see _derive.bump_structure), never on _version: that is a history counter which does not advance on removes.

Attributes

csr property

csr

Return the CSR (Compressed Sparse Row) matrix.

Returns:

Type	Description
csr_matrix

Notes

Built and cached on first access.

csc property

csc

Return the CSC (Compressed Sparse Column) matrix.

Returns:

Type	Description
csc_matrix

Notes

Built and cached on first access.

adjacency property

adjacency

Return the adjacency matrix computed from incidence.

Returns:

Type	Description
sparray

Notes

For incidence matrix B, adjacency is computed as A = B @ B.T. Boundary (half) edges — exchange/demand reactions flagged with the is_boundary edge attribute, which carry a single real endpoint and no partner — are dropped from B first, so they contribute neither spurious inter-metabolite links nor self-loop-like diagonal terms.

Functions

has_csr

has_csr()

Check whether a valid CSR cache exists.

Returns:

Type	Description
bool

has_csc

has_csc()

Check whether a valid CSC cache exists.

Returns:

Type	Description
bool

has_adjacency

has_adjacency()

Check whether a valid adjacency cache exists.

Returns:

Type	Description
bool

get_csr

get_csr()

Return the cached CSR matrix.

Returns:

Type	Description
csr_matrix

get_csc

get_csc()

Return the cached CSC matrix.

Returns:

Type	Description
csc_matrix

get_adjacency

get_adjacency()

Return the cached adjacency matrix.

Returns:

Type	Description
sparray

invalidate

invalidate(formats=None)

Invalidate cached formats.

Parameters:

Name	Type	Description	Default
formats	list[str]	Formats to invalidate ('csr', 'csc', 'adjacency'). If None, invalidate all.	None

Returns:

Type	Description
None

build

build(formats=None)

Pre-build specified formats (eager caching).

Parameters:

Name	Type	Description	Default
formats	list[str]	Formats to build ('csr', 'csc', 'adjacency'). If None, build all.	None

Returns:

Type	Description
None

clear

clear()

Clear all caches.

Returns:

Type	Description
None

info

info()

Get cache status and memory usage.

Returns:

Type	Description
dict	Status and size information for each cached format.