simtool 0.4.1

Functions for creating and running sim2Ls

SimTool

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

• Free software: MIT license

• Documentation: https://simtool.readthedocs.io.

Features

• 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.

Credits

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

History

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

0.4.1 (2022-12-13)

• Added new parameter classes Tag and File.

• Use checksum and file size to compute sim2L run squidId.

• Improve eapermill efficiency by reducing implicit I/O done during execution.

• Added support for sim2L metrics collection - record hit and miss by squidid.

• Added getParamsFromDictionary() and content() methods to standardize processing on INPUTS in sim2L notebooks.