{"id":26766302,"url":"https://github.com/ucl/neso-calibration","last_synced_at":"2025-08-13T07:06:42.421Z","repository":{"id":183521284,"uuid":"670302340","full_name":"UCL/neso-calibration","owner":"UCL","description":"Examples of calibrating Neptune Exploratory Software (NESO) 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NESO calibration\n\n[![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit\u0026logoColor=white)](https://github.com/pre-commit/pre-commit)\n[![Tests](https://github.com/UCL/neso-calibration/actions/workflows/tests.yml/badge.svg)](https://github.com/UCL/neso-calibration/actions/workflows/tests.yml)\n[![Linting](https://github.com/UCL/neso-calibration/actions/workflows/linting.yml/badge.svg)](https://github.com/UCL/neso-calibration/actions/workflows/linting.yml)\n[![Documentation](https://github.com/UCL/neso-calibration/actions/workflows/docs.yml/badge.svg)](https://github-pages.ucl.ac.uk/neso-calibration/)\n[![Licence][licence-badge]](./LICENCE.md)\n\n\u003c!-- prettier-ignore-start --\u003e\n[actions-badge]:            https://github.com/UCL/neso-calibration/workflows/CI/badge.svg\n[actions-link]:             https://github.com/UCL/neso-calibration/actions\n[licence-badge]:            https://img.shields.io/badge/License-MIT-yellow.svg\n\u003c!-- prettier-ignore-end --\u003e\n\nThe aim is for this repository to illustrate examples of calibrating\n[Neptune Exploratory Software (NESO)](https://github.com/ExCALIBUR-NEPTUNE/NESO) models.\n\nTo facilitate this, this repository contains a Python package `nesopy` which provides a\nsimple interface for executing NESO solvers with specified parameter values and\nextracting the generated outputs.\n\nAn example of using this interface to run and extract outputs from a NESO solver built and\ninstalled in a Docker image is given in\n[a tutorial notebook](examples/two_stream/docker_example.ipynb) and an example of inferring\nthe posterior on parameters of a model using a NESO solver in a simulated data setting\nusing [the PyVBMC package](https://acerbilab.github.io/pyvbmc/index.html) is given in\n[a separate notebook](examples/two_stream/pyvbmc_calibration_example.ipynb).\n\nThis project is developed in collaboration with the\n[Centre for Advanced Research Computing](https://ucl.ac.uk/arc), University College London.\n\n## About\n\n### Project team\n\n- Matt Graham ([matt-graham](https://github.com/matt-graham))\n- Serge Guillas ([sguillas](https://github.com/sguillas))\n\n### Research software engineering contact\n\nCentre for Advanced Research Computing, University College London ([arc.collaborations@ucl.ac.uk](mailto:arc.collaborations.@ucl.ac.uk))\n\n## Getting started\n\n### Prerequisites\n\nThe `nesopy` package requires Python 3.10 or above. To use the NESO model wrapper\nclasses you will need to either locally build the required NESO solvers or build NESO\nwithin a Docker image. If you wish to run the solver in parallel using MPI you will need\nto build NESO against an appropriate MPI implementation.\n\n### Installation\n\nTo install the latest development version of `nesopy` using `pip` run\n\n```sh\npip install git+https://github.com/UCL/neso-calibration.git\n```\n\nAlternatively create a local clone of the repository with\n\n```sh\ngit clone https://github.com/UCL/neso-calibration.git\n```\n\nand then install in editable mode by running\n\n```sh\npip install -e .\n```\n\nfrom the root directory of your clone of the repository.\n\n### Running tests\n\nTests can be run across all compatible Python versions in isolated environments using\n[`tox`](https://tox.wiki/en/latest/) by running\n\n```sh\ntox\n```\n\nTo run tests manually in a Python environment with `pytest` installed run\n\n```sh\npytest tests\n```\n\nagain from the root of the repository.\n\n## Acknowledgements\n\nThis work was funded by a grant from the ExCALIBUR programme.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fucl%2Fneso-calibration","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fucl%2Fneso-calibration","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fucl%2Fneso-calibration/lists"}