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Model Metadata

Project description

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model_metadata

Tools for working with CSDMS Model Metadata

The CSDMS Model Metadata provides a detailed and formalized description of a model. This includes information about:

  • Identifying information about the model. For example, model author(s), citations for the model, URL to the source code, etc.
  • A description of the model API, if it has been wrapped with a Basic Model Interface. This includes, for instance, how to build the model, depending on the language, what include statements are needed, etc.
  • A description of input file parameters. This includes default values, acceptable parameter ranges, units, etc.
  • Template input files. These are a set of input files that contain special markup where parameters from the metadata parameter description can be placed.
  • A description of how to run the model from the command line.

The CSDMS Model Metadata is extensible and not yet complete. New metadata will most certainly be added in the future. We believe the current specification provides a minimum amount of information needed to describe a model to be either run as a standalone model or, possibly, to couple with another model.

Whereas the BMI answers run-time queries of a model (e.g. the current time of a model simulation, the value of a particular output variable), the CSDMS Model Metadata provides a static description of a model. The Model Metadata, along with a BMI implementation, allows a model to automatically be incorporated as a component in the CSDMS PyMT.

Info section

Identifying information about the model.

info:
    summary:
      Sedflux3D is a basin filling stratigraphic model. Sedflux3d simulates
      long-term marine sediment transport and accumulation into a
      three-dimensional basin over time scales of tens of thousands of years. It
      simulates the dynamics of strata formation of continental margins based on
      distribution of river plumes and tectonics.
    url: http://csdms.colorado.edu/wiki/Model_help:Sedflux
    author: Eric Hutton
    email: eric.hutton@colorado.edu
    version: "2.1"
    license: MIT
    doi: "10.1594/IEDA/100161"
    cite_as: |
      @article{hutton2008sedflux,
      title={Sedflux 2.0: An advanced process-response model that generates three-dimensional stratigraphy},
      author={Hutton, Eric WH and Syvitski, James PM},
      journal={Computers \& Geosciences},
      volume={34},
      number={10},
      pages={1319--1337},
      year={2008},
      publisher={Pergamon}
      }

API Section

A description of the model API.

api:
    name: Sedflux3D
    language: c
    register: register_bmi_sedflux3d
    includes:
      - "#include <sedflux3d/bmi_sedflux3d.h>"
    cflags:
      pkgconfig: sedflux3d
    libs:
      pkgconfig: sedflux3d

Parameters Section

A description of the parameters in the input files.

parameters:
    slope_gradient:
      description: Gradient of slope
      value:
        default: 0.01
        range:
          max: 0.1
          min: 0.0
        type: float
        units: m

    shelf_width:
      description: Width of shelf
      value:
        default: 100000.0
        range:
          max: 1000000.0
          min: 1000.0
        type: float
        units: m

Run Section

How the model is to be run.

run:
    config_file: sedflux_3d_init.kvf

Model Metadata Tools

The CSDMS model_metadata Python package provides tools for working with CSDMS Model Metadata. Contained within this package are tools for:

  • Reading and parsing model metadata that follow the CSDMS Model Metadata Standards.
  • Setting up model simulations either programmatically or through a commandline interface. Although model metadata may describe models with different interfaces, the model metadata tools provides a common interface for staging simulations.
  • Validing input parameter units, ranges, and type checking. If, for instance, a user provides an input value that is out of range, an error can be issued.
  • Running simulations, which have already been staged, through a common interface.

These tools are currently used by:

  • The Web Modeling Tool server to validate input parameters and stage model simulations.
  • The CSDMS Execution Server and PyMT for running BMI-enabled models.
  • Commandline utilities for quering model metadata, and staging model simulations.

Credits

Development Lead

  • Eric Hutton

Contributors

  • Mark Piper

Changelog for model_metadata

0.7.0 (2020-09-22)

  • Added constructor for ModelMetadata that accepts an object rather than a string, better searching for metadata.

0.6.2 (2020-09-17)

  • Fixed a bug that raised “object has no attribute ‘__module__’” exception when looking for metadata of an instance from an extension module (#22)

0.6.1 (2020-09-01)

  • Removed versioneer; use zest.releaser instead

0.6.0 (2019-11-12)

  • Changed command line interface to use click (#20)

0.5.0 (2019-05-15)

  • Query a model by class or name

0.4.4 (2019-04-09)

  • Deploy to PyPI from Travis
  • Fixed continuous integration on Travis
  • General package clean up

0.4.3 (2019-03-15)

  • Fixed a bug where the yaml loader failed to correctly parse numbers represented in scientific notation

0.4.2 (2018-10-08)

  • Fixed a typo in mmd-stage command that caused it to crash

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