Migrating to CORNETO 1.0#

The documented guides, tutorials, and API index define the supported CORNETO 1.0 surface. Undocumented beta-era experiments and duplicate implementations were removed instead of being carried as permanent compatibility aliases.

Canonical imports#

Earlier import

CORNETO 1.0 import

corneto.methods.future.CarnivalILP

corneto.methods.CarnivalILP

corneto.methods.future.CarnivalFlow

corneto.methods.CarnivalFlow

corneto.methods.future.MultiSampleFBA

corneto.methods.MultiSampleFBA

corneto.methods.future.MultiSampleIMAT

corneto.methods.MultiSampleIMAT

corneto.methods.future.PrizeCollectingSteinerTree

corneto.methods.PrizeCollectingSteinerTree

corneto.methods.future.SteinerTreeFlow

corneto.methods.SteinerTreeFlow

corneto.K or corneto.ops

corneto.opt

corneto._ml.build_dagnn

corneto.ml.build_dagnn

corneto.methods.shortest_path.create_multisample_shortest_path

corneto.methods.create_multisample_shortest_path

module-level graph serialization

Graph.save and Graph.load

The old future, K, and ops paths in this table remain warning compatibility paths throughout 1.x. The private _ml path and duplicate graph serialization functions do not have shims.

Removed without compatibility shims#

  • The legacy FBAProblem/fba_problem formulation and the old multicondition_imat implementation.

  • Undocumented beta-era method aliases such as runVanillaCarnival, runInverseCarnival, and fast_carnival.

  • Duplicate private graph, data, I/O, NetworkX, and legacy implementation modules (corneto._graph, corneto._data, corneto._io, corneto._nx, corneto._core, and corneto._legacy).

  • The British-spelling corneto.methods.signalling implementation and the old module-shaped corneto.methods.signaling, as well as the singular corneto.methods.signal compatibility namespace; signaling methods now live in the corneto.methods.signaling package.

  • Duplicate module-level graph serialization helpers from corneto.io.

Multi-condition convention#

Modern formulations use explicit method-specific arguments through build for one condition and named condition mappings through build_many. The advanced build_from_data(graph, data) interface accepts a corneto.Data object when custom feature metadata is needed. Passing Data directly to build is a deprecated compatibility path.

Choosing a CARNIVAL entry point#

  • milp_carnival(graph, perturbations, measurements, ...) is the supported simple single-condition ILP and accepts two mappings directly.

  • CarnivalILP(...).build(pkn, perturbations=..., transcription_factors=...) is the default single-condition ILP interface; use build_many for named conditions.

  • CarnivalFlow provides the same explicit inputs with a flow-based formulation.

Alternative-solution sampling#

The sampler used by the indexed tutorials remains supported:

from corneto.methods.sampler import sample_alternative_solutions