VmaxOrchestrator

class VmaxBuilder.api.orchestrator.VmaxOrchestrator(config: APIConfig | None = None, *, model_stage: StageProtocol | None = None, gpr_stage: StageProtocol | None = None, protein_stage: StageProtocol | None = None, allocation_stage: StageProtocol | None = None, vmax_stage: StageProtocol | None = None, diagnostics_runner: DiagnosticsRunnerProtocol | None = None, diagnostics_hooks: Sequence[DiagnosticsHookProtocol] | None = None)[source]

Generated: validation needed.

Description:

Orchestrate configured pipeline stages over shared scaffold.

Parameters:

  • config (APIConfig) – Root API config object.

  • model_stage (StageProtocol | None) – Optional model stage implementation override.

  • protein_stage (StageProtocol | None) – Optional protein stage implementation override.

  • allocation_stage (StageProtocol | None) – Optional allocation stage implementation override.

  • vmax_stage (StageProtocol | None) – Optional vmax stage implementation override.

  • diagnostics_runner (DiagnosticsRunnerProtocol | None) – Optional diagnostics runner override.

  • diagnostics_hooks (Sequence[DiagnosticsHookProtocol] | None) – Optional diagnostics hooks.

Public Methods

run(…)

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run_all(…)

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run_allocation(…)

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run_gpr(…)

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run_model(…)

Generated: validation needed.

run_protein(…)

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run_vmax(…)

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_resolve_implementation(category: type, method_key: str) → type[source]

Generated: validation needed.

Description:

Resolve implementation class for given category and method key.

Parameters:

  • category (type) – Implementation category type.

  • method_key (str) – Method key for implementation lookup.

Returns:

type – Resolved implementation class.

Raises:

ConfigurationError – When no implementation is registered for the method key.

run_model(scaffold: Scaffold | None = None) → Scaffold[source]

Generated: validation needed.

Description:

Execute model stage and return updated scaffold.

Parameters:

scaffold (Scaffold | None) – Optional existing scaffold.

Returns:

Scaffold – Updated scaffold after model stage execution.

Modifies:

scaffold payload.

run_gpr(scaffold: Scaffold | None = None) → Scaffold[source]

Generated: validation needed.

Description:

Execute GPR stage and return updated scaffold.

Parameters:

scaffold (Scaffold | None) – Optional existing scaffold.

Returns:

Scaffold – Updated scaffold after GPR stage execution.

Modifies:

scaffold payload.

run_protein(scaffold: Scaffold | None = None) → Scaffold[source]

Generated: validation needed.

Description:

Execute protein stage and return updated scaffold.

Parameters:

scaffold (Scaffold | None) – Optional existing scaffold.

Returns:

Scaffold – Updated scaffold after protein stage execution.

Modifies:

scaffold payload.

run_allocation(scaffold: Scaffold | None = None) → Scaffold[source]

Generated: validation needed.

Description:

Execute allocation stage and return updated scaffold.

Parameters:

scaffold (Scaffold | None) – Optional existing scaffold.

Returns:

Scaffold – Updated scaffold after allocation stage execution.

Modifies:

scaffold payload.

run_vmax(scaffold: Scaffold | None = None) → Scaffold[source]

Generated: validation needed.

Description:

Execute vmax stage and return updated scaffold.

Parameters:

scaffold (Scaffold | None) – Optional existing scaffold.

Returns:

Scaffold – Updated scaffold after vmax stage execution.

Raises:

None. –

Requires:

None.

Modifies:

scaffold payload.

run(stages: Sequence[StageName]) → Scaffold[source]

Generated: validation needed.

Description:

Execute selected stages in provided order.

Parameters:

stages (Sequence[StageName]) – Ordered list of stage names to execute.

Returns:

Scaffold – Updated scaffold after requested stage execution.

Raises:

ValueError – When unsupported stage name is provided.

Modifies:

scaffold payload across stage runs.

run_all() → Scaffold[source]

Generated: validation needed.

Description:

Execute all top-level stages in default pipeline order.

Returns:

Scaffold – Updated scaffold after full pipeline traversal.

Modifies:

scaffold payload.

static _initialise_scaffold(scaffold: Scaffold | None = None) → Scaffold[source]

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Description:

Ensure scaffold contains required top-level payload sections.

Parameters:

scaffold (Scaffold | None) – Optional existing scaffold payload.

Returns:

Scaffold – Normalized scaffold object.

Modifies:

scaffold dictionary keys when missing.

_ensure_runtime_ready(*, stage_name: StageName, scaffold: Scaffold) → None[source]

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Description:

Prime output directories and validate stage runtime prerequisites.

Parameters:

  • stage_name (StageName) – Stage that is about to run.

  • scaffold (Scaffold) – Shared pipeline scaffold.

Raises:

ConfigurationError – When required stage inputs are missing.

_validate_model_inputs(*, scaffold: Scaffold) → None[source]

Generated: validation needed.

Description:

Validate model-stage input is available from in-memory object or path config.

Parameters:

scaffold (Scaffold) – Shared pipeline scaffold.

Raises:

ConfigurationError – When no model object/path/discovery roots are configured.

_validate_protein_inputs(*, scaffold: Scaffold) → None[source]

Generated: validation needed.

Description:

Validate protein-stage inputs are available from in-memory objects or path config. Required inputs depend on protein.source_mode (expression+ptr or proteomics).

Parameters:

scaffold (Scaffold) – Shared pipeline scaffold.

Raises:

ConfigurationError – When required protein inputs are missing.

_prime_output_directories(*, scaffold: Scaffold) → None[source]

Generated: validation needed.

Description:

Ensure configured output directories exist, and re-prime when paths change.

Parameters:

scaffold (Scaffold) – Shared pipeline scaffold.

Modifies:

Filesystem output directories and scaffold metadata.

_persist_runtime_state(*, scaffold: Scaffold, stage_name: StageName) → None[source]

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Description:

Persist scaffold artifacts, diagnostics, outputs, and metadata into resolved run output directories.

Parameters:

  • scaffold (Scaffold) – Shared pipeline scaffold.

  • stage_name (StageName) – Stage most recently executed.

Modifies:

Filesystem output directory contents and scaffold metadata manifest paths.

_persist_named_payloads(*, payload: dict[str, Any], save_directory: Path) → dict[str, dict[str, str]][source]

Generated: validation needed.

Description:

Persist serialisable scaffold payload entries and return save manifest.

Parameters:

  • payload (dict[str, Any]) – Named scaffold section payload.

  • save_directory (Path) – Directory receiving persisted files.

Returns:

dict[str, dict[str, str]] – Per-entry save status manifest.

_persist_named_value(*, payload_name: str, payload_value: Any, save_directory: Path) → dict[str, str][source]

Generated: validation needed.

Description:

Persist one named scaffold value when supported by runtime serializers.

Parameters:

  • payload_name (str) – Stable scaffold payload key.

  • payload_value (Any) – Payload value to persist.

  • save_directory (Path) – Target directory.

Returns:

dict[str, str] – Save status, type, and optional path or skip reason.

static _save_tabular_payload(*, payload: DataFrame | Series, filename: str, save_directory: Path, include_index: bool) → Path[source]

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Description:

Save tabular runtime payload as CSV for user inspection.

Parameters:

  • payload (pd.DataFrame | pd.Series) – Tabular payload.

  • filename (str) – Output filename stem.

  • save_directory (Path) – Target directory.

  • include_index (bool) – Whether to include index column.

Returns:

Path – Saved CSV path.

static _save_json_payload(*, payload: dict[str, Any] | list[Any], filename: str, save_directory: Path) → Path[source]

Generated: validation needed.

Description:

Save JSON-serialisable runtime payload.

Parameters:

  • payload (dict[str, Any] | list[Any]) – JSON-safe payload.

  • filename (str) – Output filename stem.

  • save_directory (Path) – Target directory.

Returns:

Path – Saved JSON path.

static _save_text_payload(*, payload: str, filename: str, save_directory: Path) → Path[source]

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Description:

Save scalar runtime payload as plain text.

Parameters:

  • payload (str) – Text payload.

  • filename (str) – Output filename stem.

  • save_directory (Path) – Target directory.

Returns:

Path – Saved text path.

classmethod _make_json_safe(value: Any) → Any[source]

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Description:

Convert nested runtime payloads into JSON-safe builtin values.

Parameters:

value (Any) – Runtime payload value.

Returns:

Any – JSON-safe builtin representation.

static _build_output_signature(output_directories: tuple[Path, ...]) → tuple[str, ...][source]

Generated: validation needed.

Description:

Build stable output-directory signature used for output re-prime checks.

Parameters:

output_directories (tuple[Path, …]) – Candidate output directories.

Returns:

tuple[str, …] – Sorted normalized output path strings.