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Functions for creating and running Simulation Tools

Project description

SimTool Documentation Status

Functions for creating and running Simulation Tools on the HUBzero platform lead by nanoHUB


  • Easily declare and validate inputs and outputs of a simulation using Python and Jupyter notebooks. The entire simulation code can run inside a notebook or the notebook can be a wrapper that invokes complex external codes.

  • Uses papermill to run parameterized notebooks, saving a new copy for each run.

  • Results saved in a datastore (filesystem or web service based). The datastore can be used for machine learning and statistical analysis. Additionally, it functions as a cache.

  • Can be containerized for remote execution.


This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.


0.1.0 (2019-08-09)

  • First release on PyPI.

0.2.0 (2020-03-04)

  • Second release on PyPI.

0.2.1 (2020-03-08)

  • Third release on PyPI.

0.2.2 (2020-03-08)

  • PyPI release with updated documentation.

0.2.3 (2020-09-21)

  • Improved search function to locate simTool notebook

0.3.1 (2021-06-14)

  • Improved input data validation

  • Added web service based cacheing support

0.3.2 (2021-09-22)

  • Fixed for use outside of HUBzero environment

0.3.3 (2021-10-04)

  • Improved automatic documentation generation

  • Fixed Image value setting

0.3.4 (2022-05-10)

  • Verify location of installed or published sim2L notebook

  • Differentiate between missing path and wrong path type (file/directory)

  • Stricter enforcement of param attributes

  • Retain directory structure when saving results.

  • Close open files to avoid file descriptor leakage

  • Added magic functions needed to run notebooks in parallel (MPI)

0.3.5 (2022-05-16)

  • Trap missing simToolSaveErrorOccurred and simToolAllOutputsSaved in result notebook

  • Return list of input files whether inputs is specified as dictionary or YAML

  • Add run preparation method used for web service application. Previously used external shell script

0.3.6 (2022-08-11)

  • Extend utility functions for getting information about input files to use either parameter or simple dictionary description.

  • Prepare for newer papermill versions

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