corneto package

Subpackages

• corneto.backend package
  • Module contents
    • Backend
      • Backend.is_available()
      • Backend.version()
      • Backend.get_symbols()
      • Backend.available_solvers()
      • Backend.Constant()
      • Backend.Variable()
      • Backend.Parameter()
      • Backend.Problem()
      • Backend.build()
      • Backend.solve()
      • Backend.Flow()
      • Backend.Acyclic()
      • Backend.AcyclicFlow()
      • Backend.Indicator()
      • Backend.NonZeroIndicator()
      • Backend.Indicators()
      • Backend.Xor()
      • Backend.linear_or()
      • Backend.linear_and()
      • Backend.linear_xor()
      • Backend.vstack()
      • Backend.hstack()
      • Backend.zero_function()
    • VarType
      • VarType.INTEGER
      • VarType.CONTINUOUS
      • VarType.BINARY
    • CvxpyBackend
      • CvxpyBackend.available_solvers()
      • CvxpyBackend.Constant()
      • CvxpyBackend.Variable()
      • CvxpyBackend.Parameter()
      • CvxpyBackend.build()
    • PicosBackend
      • PicosBackend.available_solvers()
      • PicosBackend.build()
      • PicosBackend.Constant()
      • PicosBackend.Variable()
      • PicosBackend.Parameter()
• corneto.methods package
  • Subpackages
    • corneto.methods.metabolism package
      • Submodules
      • corneto.methods.metabolism.fba module
      • Module contents
  • Submodules
  • corneto.methods.carnival module
    • read_dataset()
    • preprocess_graph()
    • runVanillaCarnival()
    • runInverseCarnival()
    • heuristic_carnival()
    • get_result()
    • get_selected_edges()
    • reachability_graph()
    • bfs_search()
    • create_flow_carnival_v4()
    • create_flow_carnival_v3()
    • create_flow_carnival_v2()
    • create_flow_carnival()
    • runCARNIVAL_AcyclicFlow()
    • runCARNIVAL_Flow_Acyclic()
    • runCARNIVAL_Flow_Acyclic_Signal()
    • milp_carnival()
  • corneto.methods.shortest_path module
    • create_multisample_shortest_path()
    • shortest_path()
    • solve_shortest_path()
  • corneto.methods.signaling module
    • create_flow_graph()
    • signflow_constraints()
    • default_sign_loss()
    • signflow()
    • expand_graph_for_flows()
  • corneto.methods.steiner module
    • exact_steiner_tree()
    • create_exact_multi_steiner_tree()
  • Module contents
• corneto.utils package
  • Module contents
    • OptionalModule
    • OptionalNumba
    • get_library_version()
    • import_optional_module()

Module contents

class corneto.Attr(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)

Bases: str, Enum

Enum class representing predefined attribute names used in the Attributes class.

VALUE

Represents the key for a value attribute.

EDGE_TYPE

Represents the key for an edge type attribute.

SOURCE_ATTR

Represents the key for a source attribute.

TARGET_ATTR

Represents the key for a target attribute.

CUSTOM_ATTR

Represents the key for a custom attribute.

VALUE = '__value'

EDGE_TYPE = '__edge_type'

SOURCE_ATTR = '__source_attr'

TARGET_ATTR = '__target_attr'

CUSTOM_ATTR = '__custom_attr'

class corneto.EdgeType(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)

Bases: str, Enum

DIRECTED = 'directed'

UNDIRECTED = 'undirected'

class corneto.Attributes

Bases: dict

A dictionary-based class to manage attributes.

Uses reserved attributes used by CORNETO Graphs.

set_attr(key, value)

Set an attribute in the dictionary using an Attr key.

Parameters:

• key (Attr) – The key for the attribute, represented as an Attr enum.

• value (Any) – The value to assign to the key. If the value is an enum, its value is used.

Return type:

None

has_attr(key, value=None)

Check if a given attribute exists in the dictionary, optionally with a specific value.

Parameters:

• key (Attr) – The key for the attribute, represented as an Attr enum.

• value (Optional[Any]) – The optional value to check for.

Returns:

True if the attribute exists and matches the value (if provided),

otherwise False.

Return type:

bool

get_attr(key, default=None)

Retrieve the value of an attribute, or return a default value if not found.

Parameters:

• key (Attr) – The key for the attribute, represented as an Attr enum.

• default (Any) – The default value to return if the attribute does not exist.

Returns:

The value of the attribute, or the default value if not found.

Return type:

Any

class corneto.Graph(default_edge_type=EdgeType.DIRECTED, **kwargs)

Bases: BaseGraph

Default Graph class with support for undirected, directed, parallel and hypergedes.

Parameters:

• default_edge_type (EdgeType (default: <EdgeType.DIRECTED: 'directed'>)) – Default edge type EdgeType.

• Examples

• --------

• corneto.Graph() (>>> graph =)

• graph.add_edge(1 (>>>)

• 2)

• graph.plot() (>>>)

get_edge(index)

Return type:

Tuple[FrozenSet[Any], FrozenSet[Any]]

Parameters:

index (int)

get_graph_attributes()

Return type:

Attributes

extract_subgraph(vertices=None, edges=None)

Parameters:

• vertices (Iterable | None)

• edges (Iterable[int] | None)

reverse()

Create a new graph and reverse the direction of all edges in the graph.

Return type:

Graph

filter_graph(filter_vertex=None, filter_edge=None)

Parameters:

• filter_vertex (Callable[[Any], bool] | None)

• filter_edge (Callable[[int], bool] | None)

copy()

Return type:

Graph

static from_sif(sif_file, delimiter='\\t', has_header=False, discard_self_loops=True, column_order=[0, 1, 2])

Parameters:

• sif_file (str)

• delimiter (str)

• has_header (bool)

• discard_self_loops (bool | None)

• column_order (List[int])

static from_sif_tuples(tuples)

Parameters:

tuples (Iterable[Tuple])

static from_cobra_model(model)

Parameters:

model (CobraModel)

static from_miom_model(model)

corneto.info()

corneto.available_backends()