Sindbad Module

Sindbad

Top-level orchestration package for Strategies to INtegrate Data and BiogeochemicAl moDels. Sindbad reexports the complete SindbadTEM modeling stack and combines the user-facing modules under src/ to offer a single public entry point for data ingest, configuration, simulation, optimization, machine learning, and visualization workflows.

Purpose:

• Provide a cohesive API that ties together process-level models from SindbadTEM with higher-level experiment tooling.

• Ensure every stage of a SINDBAD pipeline—data handling, setup, model execution, calibration, post-processing, and plotting—is available through one package.

Dependencies:

Related (SINDBAD ecosystem)

• ErrorMetrics: Model–observation metrics used across cost/diagnostics.

• TimeSamplers: Temporal sampling/aggregation helpers.

• OmniTools: Shared utilities used across modules.

External (third-party)

• CSV: Input/output of tabular forcing and calibration datasets.

• ConstructionBase: Shared constructors needed by downstream modules.

• JSON: Experiment metadata serialization (parsefile, json, print).

• JLD2: Persisting SINDBAD state, diagnostics, and trained artifacts.

• YAXArrays + YAXArrays.Datasets: Labeled n-dimensional arrays and dataset writers for model output.

Internal (within Sindbad)

• Sindbad.DataLoaders

• Sindbad.Experiment

• Sindbad.MachineLearning

• Sindbad.ParameterOptimization

• Sindbad.Setup

• Sindbad.Simulation

• Sindbad.Types

• Sindbad.Visualization

• SindbadTEM

Included Modules:

• DataLoaders (src/DataLoaders/):

  • Handles file IO, preprocessing, and conversion into SINDBAD-native data structures; exposes reusable loaders and utility helpers.

• Setup (src/Setup/):

  • Builds experiment info objects, validates model selections, and wires pools, spinup settings, and derived configuration metadata.

• Simulation (src/Simulation/):

  • Orchestrates terrestrial ecosystem simulations, including spinup, forward runs, diagnostics, and interaction with SindbadTEM.

• ParameterOptimization (src/ParameterOptimization/):

  • Provides parameter-calibration utilities and objective hooks.

  • Some optimizer backends are enabled via optional extensions (see Notes).

• MachineLearning (src/MachineLearning/):

  • Adds ML-assisted surrogates, emulators, and training pipelines that integrate with Sindbad outputs and optimization targets.

• Visualization (src/Visualization/):

  • Supplies plotting and reporting helpers for experiment evaluation (time series, spatial maps, diagnostic overlays, etc.).

• Experiment (src/Experiment/):

  • High-level experiment runner and output persistence helpers that tie together setup, loaders, simulation, optimization, ML, and visualization.

Notes:

• Each submodule is included and reexported so end users can call using Sindbad and immediately access Sindbad.DataLoaders, Sindbad.Simulation, and the rest without extra imports.

• Shared dependencies are loaded here to guarantee consistent versions across all components.

• Some functionality is enabled via Julia extensions (Project.toml [weakdeps] + [extensions] and ext/):

  • NLsolve → SindbadNLsolveExt

  • Optimization → SindbadOptimizationExt

  • CMAEvolutionStrategy → SindbadCMAEvolutionStrategyExt

Examples:

julia> using Sindbad

julia> # Prepare an experiment from a configuration file
julia> # info, forcing = prepExperiment("path/to/experiment_config.json")

julia> # Run a forward simulation
julia> # out = runExperimentForward("path/to/experiment_config.json")

Functions

addExtensionToSindbad

Sindbad.addExtensionToSindbad Function

addExtensionToSindbad(function_to_extend::Function, external_package::String) -> String

Convenience wrapper for this repo: asserts the function belongs to Sindbad and always uses folder layout.

Code

  function addExtensionToSindbad(function_to_extend::Function, external_package::String)
    root_pkg = Base.moduleroot(parentmodule(function_to_extend))
    nameof(root_pkg) == :Sindbad || error("Expected a Sindbad function; got root package $(root_pkg).")
    return add_extension_to_function(function_to_extend, external_package; extension_location=:Folder)
  end

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