I/O & model manipulation

I/O — {mod}`raven_toolbox.io`

raven-toolbox keeps everything as a {class}cobra.Model, so cobra's SBML I/O works unchanged. On top of that it adds the RAVEN-specific formats:

{func}raven_toolbox.io.read_yaml_model / {func}raven_toolbox.io.write_yaml_model — cobra-standard YAML (the !!omap layout), transparently handling .yml.gz. RAVEN-only and GECKO ec-* side-fields are preserved on each entry's notes so a read→write round-trip is lossless. The full schema (top-level layout, field order, quoting rules, the GECKO ec-* and metaData extensions) is documented in the YAML model format reference.
{func}raven_toolbox.io.export_model_to_sif — Cytoscape SIF (rc / rr / cc graphs).
{func}raven_toolbox.io.export_to_excel — the RAVEN 5-sheet workbook (RXNS / METS / COMPS / GENES / MODEL). Requires the excel extra. Excel import is intentionally not provided.
{func}raven_toolbox.io.export_for_git — the Standard-GEM repository layout (model/<fmt>/…), for version-controlled model repos.

Structural transforms that cobra does not cover cleanly:

Build / copy reactions: {func}raven_toolbox.manipulation.add_reactions_from_equations (equation-string → reactions, matching metabolites by id / name / name[comp]), {func}raven_toolbox.manipulation.add_transport_reactions, {func}raven_toolbox.manipulation.add_reactions_from_model.
Merge: {func}raven_toolbox.manipulation.merge_models (N-model merge, unify metabolites by name[comp]).
GPR / bounds: {func}raven_toolbox.manipulation.change_gene_reaction_rules, {func}raven_toolbox.manipulation.change_reaction_equations, {func}raven_toolbox.manipulation.set_variance_bounds.
Simplify: {func}raven_toolbox.manipulation.remove_dead_end_reactions, remove_duplicate_reactions, constrain_reversible_reactions, group_linear_reactions.
Topology: {func}raven_toolbox.manipulation.convert_to_irreversible, {func}raven_toolbox.manipulation.expand_model (split isozyme OR-GPRs), and the compartment helpers merge_compartments / copy_to_compartment.

See the migration map for which RAVEN functions these correspond to (and which became cobra one-liners), and the full io / manipulation API.