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Observation and Modeling","monthly_downloads":268,"total_dependent_repos":0,"total_dependent_packages":0,"readme":"# SINDBAD\n\n[![][docs-stable-img]][docs-stable-url][![][docs-dev-img]][docs-dev-url][![][ci-img]][ci-url] [![][codecov-img]][codecov-url][![Julia][julia-img]][julia-url][![License: EUPLv1.2](https://img.shields.io/badge/License-EUPLv1.2-seagreen)](https://github.com/LandEcosystems/Sindbad/blob/main/LICENSE)\n\n\u003cimg src=\"docs/src/assets/sindbad_logo.png\" align=\"right\" style=\"padding-left:10px;\" width=\"150\"/\u003e\n\n[docs-dev-img]: https://img.shields.io/badge/docs-dev-blue.svg\n[docs-dev-url]: https://landecosystems.github.io/Sindbad.jl/dev/\n\n[docs-stable-img]: https://img.shields.io/badge/docs-stable-blue.svg\n[docs-stable-url]: https://landecosystems.github.io/Sindbad.jl/stable/\n\n[codecov-img]: https://codecov.io/gh/LandEcosystems/Sindbad.jl/branch/main/graph/badge.svg\n[codecov-url]: https://codecov.io/gh/LandEcosystems/Sindbad.jl\n\n[ci-img]: https://github.com/LandEcosystems/Sindbad.jl/workflows/Sindbad.jl/badge.svg\n[ci-url]: https://github.com/LandEcosystems/Sindbad.jl/actions?query=workflow%3A%22Sindbad.jl%22\n\n[julia-img]: https://img.shields.io/badge/julia-v1.10+-blue.svg\n[julia-url]: https://julialang.org/\n\nWelcome to the repository for **S**trategies to **IN**tegrate **D**ata and **B**iogeochemic**A**l mo**D**els (SINDBAD).\n\n## Overview\n\nSINDBAD is a model data integration framework that encompasses the biogeochemical cycles of water and carbon, allowing for extensive and flexible integration of parsimonious models with a diverse set of observational data streams.\n\nThe framework provides a unified system for:\n- **Model Structure**: Adaptable ecosystem process representations\n- **Input Data**: Flexible data ingestion and processing\n- **Observation Data**: Versatile observational constraint integration\n- **Integration Methods**: Customizable optimization and assimilation approaches\n\n## Repository Structure\n\nThis repository contains the `Sindbad` package sources. The `Sindbad` package depends on several other registered packages (some maintained in separate repositories), which are installed automatically by Julia’s package manager.\n\n```\nSindbad.jl/\n├── src/                        `Sindbad` user-facing modules\n│   ├── DataLoaders/            Data loading and preprocessing\n│   ├── Setup/                  Experiment configuration and setup\n│   ├── Simulation/             Terrestrial ecosystem model execution\n│   ├── ParameterOptimization/  Parameter calibration and optimization\n│   ├── MachineLearning/        ML-assisted surrogates and emulators\n│   ├── Visualization/          Plotting and visualization tools\n│   ├── Experiment/             High-level experiment orchestration\n│   └── Types/                  Type definitions for SINDBAD structures\n├── SindbadTEM/                 Core terrestrial ecosystem models, types, and utilities\n│                                (own Project.toml; registered and versioned separately)\n├── ext/                        Package extensions for optional dependencies (see below)\n├── examples/                   Example experiments, scripts, and setups\n├── docs/                       Documentation source files\n├── test/                       Test suite for the `Sindbad` package\n├── tools/                      Standing developer tools (benchmarking, data I/O, feature testing)\n├── sandbox/                    Scratch directory for local, untracked dev environments\n└── .github/                    CI workflows and PR/issue templates\n```\n\nRelated packages (SINDBAD ecosystem, maintained in separate repositories):\n- **[ErrorMetrics.jl](https://github.com/LandEcosystems/ErrorMetrics.jl)**: Model–observation metrics ([docs](https://landecosystems.github.io/ErrorMetrics.jl))\n- **[TimeSamplers.jl](https://github.com/LandEcosystems/TimeSamplers.jl)**: Time aggregation / sampling utilities ([docs](https://landecosystems.github.io/TimeSamplers.jl))\n- **[OmniTools.jl](https://github.com/LandEcosystems/OmniTools.jl)**: Shared utility toolkit ([docs](https://landecosystems.github.io/OmniTools.jl))\n\n## Installation\n\n### From a Julia package registry (recommended)\n\n```julia\nusing Pkg\nPkg.add(\"Sindbad\")\n```\n\n\n### From source (development / monorepo checkout)\n\nIf you are working from a checkout of this repository:\n\n```julia\nusing Pkg\nPkg.activate(\"path/to/SINDBAD\")\nPkg.instantiate()\nusing Sindbad\n```\n\nIf you are using SSH-based package sources for SINDBAD ecosystem packages, you may need to tell Julia to use the system `git` client:\n\n```bash\nexport JULIA_PKG_USE_CLI_GIT=true\n```\n\nIf you want to develop `Sindbad` from a separate environment, you can also use:\n\n```julia\nusing Pkg\nPkg.develop(path=\"path/to/SINDBAD\")\n```\n\n### Optional dependencies (extensions)\n\nSome functionality is enabled via Julia package extensions (see `Project.toml` `[weakdeps]` + `[extensions]` and `ext/`):\n\n- **`NLsolve`**: enables parts of the spinup workflow (`SindbadNLsolveExt`)\n- **`DifferentialEquations`**: enables ODE-based spinup solvers (`SindbadDifferentialEquationsExt`)\n- **`Optimization`**: enables SciML Optimization-based optimizers (`SindbadOptimizationExt`)\n- **`CMAEvolutionStrategy`**: enables CMA-ES optimizer bridge (`SindbadCMAEvolutionStrategyExt`)\n- **`Enzyme`**: enables Enzyme-based gradients for hybrid ML (`SindbadEnzymeExt`)\n- **`ForwardDiff`**: enables ForwardDiff-based gradients for hybrid ML (`SindbadForwardDiffExt`)\n- **`PolyesterForwardDiff`**: enables threaded ForwardDiff-based gradients for hybrid ML (`SindbadPolyesterForwardDiffExt`)\n- **`FiniteDiff`**: enables FiniteDiff-based gradients for hybrid ML (`SindbadFiniteDiffExt`)\n- **`FiniteDifferences`**: enables FiniteDifferences-based gradients for hybrid ML (`SindbadFiniteDifferencesExt`)\n- **`Zygote`**: enables Zygote-based gradients for hybrid ML (`SindbadZygoteExt`)\n- **`Flux`**: enables Flux-based ML models for hybrid ML (`SindbadFluxExt`)\n- **`Lux`**: enables Lux-based ML models for hybrid ML (`SindbadLuxExt`)\n- **`Optimisers`**: enables Optimisers.jl-based ML model updates (`SindbadOptimisersExt`)\n- **`PreallocationTools`**: enables cache-based ML output handling (`SindbadPreallocationToolsExt`)\n- **`Plots`**: enables Plots.jl-based visualization (`SindbadPlotsExt`)\n\nTo enable an extension, add the corresponding package **in the same environment** where you use `Sindbad`:\n\n```julia\nusing Pkg\nPkg.add(\"NLsolve\")  # or any of the other extension trigger packages listed above\n```\n\nFor development setup and usage instructions, see [CONTRIBUTING.md](./CONTRIBUTING.md).\n\n## Quick Start\n\n```julia\nusing Sindbad\n\n# Run a forward simulation for an experiment configuration\nout = Sindbad.Experiment.runExperimentForward(\"experiment_config.json\")\n\n# `out` contains `out.info`, `out.forcing`, and `out.output`\n```\n\n## Documentation\n\nComprehensive documentation is available at:\n- **Stable**: [landecosystems.github.io/Sindbad.jl/stable](https://landecosystems.github.io/Sindbad.jl/stable/)\n- **Development**: [landecosystems.github.io/Sindbad.jl/dev](https://landecosystems.github.io/Sindbad.jl/dev/)\n\n## SINDBAD Contributors\n\nSINDBAD is developed at the Department of Biogeochemical Integration of the Max Planck Institute for Biogeochemistry in Jena, Germany with active contributions from [Sujan Koirala](https://www.bgc-jena.mpg.de/person/skoirala/2206), [Xu Shan](https://www.bgc-jena.mpg.de/person/138641/2206), [Jialiang Zhou](https://www.bgc-jena.mpg.de/person/137086/2206), [Lazaro Alonso](https://www.bgc-jena.mpg.de/person/lalonso/2206), [Fabian Gans](https://www.bgc-jena.mpg.de/person/fgans/4777761), [Felix Cremer](https://www.bgc-jena.mpg.de/person/fcremer/2206), [Nuno Carvalhais](https://www.bgc-jena.mpg.de/person/ncarval/2206).\n\nFor a full list of current and previous contributors, see [sindbad-mdi.org team page](http://sindbad-mdi.org/pages/about/team.html)\n\n## Contributing\n\nWe welcome contributions! Please see [CONTRIBUTING.md](./CONTRIBUTING.md) for guidelines on:\n- Development setup\n- Code style and conventions\n- Submitting pull requests\n- Reporting issues\n\n## Copyright and License\n\n**SINDBAD: Strategies to Integrate Data and Biogeochemical Models**\n\n**Copyright © 2025**  \nMax-Planck-Gesellschaft zur Förderung der Wissenschaften\n\nFor copyright details, see the [NOTICE](./NOTICE) file.\n\n---\n\n### License\n\nSINDBAD is free and open-source software, licensed under the [European Union Public License v1.2 (EUPL)](https://eupl.eu/1.2/en).\n\n---\n\n### Your Rights\n\nYou are free to:\n\n- Copy, modify, and redistribute the code  \n- Use the software as a package in your own projects, regardless of their license or copyright status  \n- Apply the software in both commercial and non-commercial contexts  \n\n---\n\n### Your Responsibilities\n\nIf you modify the code — excluding changes made solely for interoperability — you **must redistribute the modified version under the EUPL v1.2 or a compatible license**. This ensures the long-term sustainability of the project and supports an open, inclusive, and collaborative community.\n\n---\n\n### Disclaimer\n\nThis software is provided in the hope that it will be useful, but **without any warranty** — including, without limitation, the implied warranties of merchantability or fitness for a particular purpose.\n","funding_links":[],"readme_doi_urls":[],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":["arrays","gdal","geo","geospatial-data"],"project_url":"https://ost.ecosyste.ms/api/v1/projects/356481","html_url":"https://ost.ecosyste.ms/projects/356481"}