easyvvuq

Python 3 framework to facilitate verification, validation and uncertainty quantification (VVUQ) for a wide variety of simulations.

https://github.com/ucl-ccs/easyvvuq

Science Score: 85.0%

This score indicates how likely this project is to be science-related based on various indicators:

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
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DOI references
Found 8 DOI reference(s) in README
✓
Academic publication links
Links to: researchgate.net
✓
Committers with academic emails
9 of 28 committers (32.1%) from academic institutions
✓
Institutional organization owner
Organization ucl-ccs has institutional domain (ccs.chem.ucl.ac.uk)
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (15.8%) to scientific vocabulary

Keywords

hpc-applications python simulation uncertainty-quantification verification vvuq

Last synced: 4 months ago · JSON representation ·

Repository

Python 3 framework to facilitate verification, validation and uncertainty quantification (VVUQ) for a wide variety of simulations.

Basic Info

Host: GitHub
Owner: UCL-CCS
License: lgpl-3.0
Language: Jupyter Notebook
Default Branch: dev
Homepage: https://easyvvuq.readthedocs.io/
Size: 32.7 MB

Statistics

Stars: 97
Watchers: 16
Forks: 28
Open Issues: 15
Releases: 39

Topics

hpc-applications python simulation uncertainty-quantification verification vvuq

Created over 7 years ago · Last pushed 4 months ago

Metadata Files

Readme Contributing License Code of conduct Citation Codemeta

EasyVVUQ

The aim of EasyVVUQ is to facilitate verification, validation and uncertainty quantification (VVUQ) for a wide variety of simulations. While very convenient for simple cases, EasyVVUQ is particularly well suited in situations where the simulations are computationally expensive, heterogeneous computing resources are necessary, the sampling space is very large or book-keeping is prohibitively complex. It coordinates execution using an efficient database, it is fault tolerant and all progress can be saved.

Here are some examples of questions EasyVVUQ can answer about your code:

Given the uncertainties in input parameters, what is the distribution of the output?
What percentage of the output variance each input parameter contributes?

It also lets you construct surrogate models that are cheaper to evaluate than the complete simulation.

The high-level overview of the library is available at our readthedocs.

Getting Started

For the quick start with EasyVVUQ we recommend to check our basic interactive tutorial available here.

Functionality

Available analysis and sampling methods:

Polynomial Chaos Expansion
Stochastic Collocation
Dimension-adaptive Stochastic Collocation for high-dimensional inputs (incl notebook in ./tutorials and theoretical tutorial)
Simplex Stochastic Collocation for irregular outputs (incl notebook in ./tutorials and article)
Monte Carlo Sensitivity Analysis
Markov-Chain Monte Carlo

EasyVVUQ also supports building surrogate models using:

Polynomial Chaos Expansion
Stochastic Collocation
Gaussian Processes

Supported computing resources:

Traditional clusters
Kubernetes clusters

The easiest way to get familiar with the provided functionality is to follow the tutorials (*.ipynb files) in our Binder.

Installation instructions

Requirements

To use the library you will need Python 3.7+.

Installation using pip

If you are unsure of the version of python your default pip works for type:

pip --version

If the output ends with (python 2.7) you should replace pip with pip3 in the following commands.

The following should fully install the library:

pip install easyvvuq

To upgrade the library use:

pip install easyvvuq --upgrade

Installation from the Repository via Bash Script (Recommended for Developers)

Alternatively, you can manually install EasyVVUQ. Note: As above, you need to be sure you are installing for Python3 - if necessary replace pip with pip3 and python with python3 in the commands below.

Clone the Repository:

git clone https://github.com/UCL-CCS/EasyVVUQ.git

Install with Bash Script:

The installation of dependencies and testing have been automated using bash script install_EasyVVUQ.sh included in the repository. To execute it:

cd EasyVVUQ/

Make bash script executable:

chmod +x install_EasyVVUQ.sh

Execute bash script:

bash install_EasyVVUQ.sh

Upon successful installation, the process will end with the following message:

EasyVVUQ installation and testing completed successfully!

Set the PYTHONPATH Environment Variable After installation:

You may need to manually set the PYTHONPATH to ensure EasyVVUQ can be found by Python. This step is required if the library is installed locally within the repository using the provided venv.

While in EasyVVUQ directory, activate the virtual environment (Linux/macOS):

source venv/bin/activate

For Windows users, activate virtual environment using:

venv\Scripts\activate

Export PYTHONPATH:

export PYTHONPATH=$(pwd):$PYTHONPATH

Export PYTHONPATH site-packages according to your Python version (e.g., python3.10):

export PYTHONPATH=$(pwd)/venv/lib/python3.10/site-packages:$PYTHONPATH

Check PYTHONPATH:

python python -c "import sys; print('\n'.join(sys.path))"

Manual Developer Installation From the Repository

Clone the Repository: git clone https://github.com/UCL-CCS/EasyVVUQ.git
Navigate to the EasyVVUQ directory:

cd EasyVVUQ
Create and Activate Virtual Environment:

Using a virtual environment isolates EasyVVUQ's dependencies and prevents conflicts with other Python projects.

You can create a Python Virtual Environment inside EasyVVUQ directory or outside it. Git is set to ignore venv

python3 -m venv venv

Activate the virtual environment (Linux/macOS):

source venv/bin/activate
Install Required Packages using requirements.txt pip install -r requirements.txt
Install EasyVVUQ in Editable Mode in Virtual Environment:

pip install -e .

The -e flag (editable mode) means any changes you make to the EasyVVUQ source code will be immediately reflected without needing to reinstall.

To see easyvvuq in the list of the installed packages in the virtual environment:

pip list
Installation Verification:

After installation, verify the installation:

python python -c "import easyvvuq; print('EasyVVUQ version:', easyvvuq.__version__)"

Output:

EasyVVUQ version: 1.2.3

API

You can find the EasyVVUQ API documentation on our GitHub Pages.

Contributing

We welcome contributions! Please see our Contributing Guidelines for details on:

Setting up a development environment
Code style and testing requirements
Git commit guidelines
Submitting pull requests
Community guidelines

For bug reports and feature requests, please use GitHub Issues.

Citing EasyVVUQ

Richardson, R A, Wright, D W, Edeling, W, Jancauskas, V, Lakhlili, J and Coveney, P V. 2020 EasyVVUQ: A Library for Verification, Validation and Uncertainty Quantification in High Performance Computing. Journal of Open Research Software, 8: 11. DOI: 10.5334/jors.303.

Wright, D.W., Richardson, R.A., Edeling, W., Lakhlili, J., Sinclair, R.C., Jancauskas, V., Suleimenova, D., Bosak, B., Kulczewski, M., Piontek, T., Kopta, P., Chirca, I., Arabnejad, H., Luk, O.O., Hoenen, O., Weglarz, J., Crommelin, D., Groen, D. and Coveney, P.V. (2020), Building Confidence in Simulation: Applications of EasyVVUQ. Adv. Theory Simul., 3: 1900246. DOI: 10.1002/adts.201900246.

Acknowledgments

Development was funded by the EU Horizon 2020 project VECMA.

Owner

Name: Centre for Computational Science (UCL)
Login: UCL-CCS
Kind: organization
Location: London

Website: http://ccs.chem.ucl.ac.uk/
Repositories: 32
Profile: https://github.com/UCL-CCS

Citation (CITATION.cff)

# YAML 1.2
---

abstract: "EasyVVUQ is an open source Python library designed to facilitate verification, validation and uncertainty quantification (VVUQ) for a wide variety of simulations. The goal of EasyVVUQ is to make it as easy as possible to implement advanced VVUQ techniques for existing application codes or workflows. Our aim is to expose these features in an accessible way for users of scientific software, in particular for simulation codes running on high performance computers."

authors:
  -
    affiliation: "Netherlands eScience Center"
    family-names: Richardson
    given-names: Robin A.
    orcid: https://orcid.org/0000-0002-9984-2720
  -
    affiliation: "University College London"
    family-names: Wright
    given-names: David W.
    orcid: https://orcid.org/0000-0002-5124-8044
  -
    affiliation: "Leibniz Supercomputing Centre"
    family-names: Jancauskas
    given-names: Vytautas
    orcid: https://orcid.org/0000-0002-6051-210X
  -
    affiliation: "Centrum voor Wiskunde en Informatica"
    family-names: Edeling
    given-names: Wouter
    orcid: https://orcid.org/0000-0003-4734-7960
  -
    affiliation: "Max-Planck-Institut für Plasmaphysik"
    family-names: Lakhlili
    given-names: Jalal
    orcid: https://orcid.org/0000-0003-2900-1026
  -
    affiliation: "Max Planck Institute for Plasma Physics"
    family-names: Coster
    given-names: David P.
    orcid: https://orcid.org/0000-0002-2470-9706
  -
    affiliation: "Universita della Svizzera italiana, Lugano"
    family-names: Kardoš
    given-names: Juraj
    orcid: https://orcid.org/0000-0002-0197-5470
  -
    affiliation: "Brunel University London"
    family-names: Groen
    given-names: Derek
    orcid: https://orcid.org/0000-0001-7463-3765
  -
    affiliation: "Poznań Supercomputing and Networking Centre"
    family-names: Bosak
    given-names: Bartosz
    orcid: https://orcid.org/0000-0002-9331-3166
  -
    affiliation: "Centre for Computational Science, University College London"
    family-names: McCullough
    given-names: Jon
    orcid: https://orcid.org/0000-0002-9606-0408
  -
    affiliation: "Brunel University London"
    family-names: Suleimenova
    given-names: Diana
    orcid: https://orcid.org/0000-0003-4474-0943
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    affiliation: "Brunel University London"
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    given-names: Hamid
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    given-names: Peter
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    family-names: Ghorbani
    given-names: Maziar
    orcid: https://orcid.org/0000-0001-7284-9853
  -
    affiliation: "University College London"
    family-names: Sinclair
    given-names: Robert
    orcid: https://orcid.org/0000-0003-0418-6415
  -
    affiliation: "Centrum Wiskunde en Informatica Amsterdam"
    family-names: Jansson
    given-names: Fredrik
    orcid: https://orcid.org/0000-0003-4712-5938
  -
    affiliation: "University of Amsterdam"
    family-names: van der Kolk
    given-names: Max
    orcid: https://orcid.org/0000-0001-5761-5776
  -
    affiliation: "Poznań Supercomputing and Networking Centre"
    family-names: Chodkowski
    given-names: Miłosz
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    affiliation: "University of York"
    family-names: Dickinson
    given-names: David
    orcid: https://orcid.org/0000-0002-0868-211X
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    family-names: Harbach
    given-names: Laura
    orcid: https://orcid.org/0000-0001-7944-0292
  -
    family-names: Lebedev
    given-names: Anton

keywords:
  - "Validation"
  - "Verification"
  - "Uncertainty Quantification"
  - "VVUQ"
  - "HPC"
license: "GNU Lesser General Public License v3.0"
repository-code: "https://github.com/UCL-CCS/EasyVVUQ"
message: "If you use this software, please cite it using these metadata."
title: "EasyVVUQ: A Library for Verification, Validation and Uncertainty Quantification in High Performance Computing"
version: "0.7.1"
cff-version: "1.0.3"
references:
  - type: article
    title: "EasyVVUQ: A Library for Verification, Validation and Uncertainty Quantification in High Performance Computing"
    doi: 10.5334/jors.303
  - type: article
    title: "Building Confidence in Simulation: Applications of EasyVVUQ"
    doi: 10.1002/adts.201900246

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GitHub Events

Total

Create event: 22
Release event: 5
Issues event: 28
Watch event: 8
Delete event: 20
Member event: 3
Issue comment event: 46
Push event: 198
Pull request review comment event: 7
Pull request event: 48
Pull request review event: 42
Fork event: 2

Last Year

Create event: 22
Release event: 5
Issues event: 28
Watch event: 8
Delete event: 20
Member event: 3
Issue comment event: 46
Push event: 198
Pull request review comment event: 7
Pull request event: 48
Pull request review event: 42
Fork event: 2

Committers

Last synced: about 2 years ago

All Time

Total Commits: 3,201
Total Committers: 28
Avg Commits per committer: 114.321
Development Distribution Score (DDS): 0.579

Past Year

Commits: 97
Committers: 6
Avg Commits per committer: 16.167
Development Distribution Score (DDS): 0.526

Top Committers

Name	Email	Commits
Vytautas Jancauskas	u**o@g**m	1,347
David W Wright	d**t@g**m	452
Robin Richardson	r**n@u**k	437
Robin Richardson	r**n@g**m	188
di73kuj2	v**s@l**e	184
wouteredeling@gmail.com	w**g@g**m	162
Jalal Lakhlili	j**i@g**m	121
David Coster	D**r@i**e	81
Robin Richardson	r****1	48
Juraj Kardos	g****o	46
Bartosz Bosak	b**k@m**l	38
Derek Groen	d**l@g**m	26
Robert Sinclair	r**5@u**k	13
Jalal Lakhlili	l**a@d**e	12
Jalal Lakhlili	j**i@i**e	9
Fredrik Jansson	j**n@c**l	8
Vytautas Janc_auskas	d**2@m**e	6
Diana Suleimenova	d**a@b**k	5
Hamid	h**d@g**m	4
Wouter Edeling	e**g@k**l	3
Peter Hill	z**e@g**m	3
Max van der Kolk	m**k@u**l	2
Jalal Lakhlili	l**a@d**e	1
Jalal	j**l@x**p	1
David Dickinson	d****9	1
Anton-Le	l**t@g**t	1
LGTM Migrator	l****r	1
DianaS	1**0@m**k	1

Committer Domains (Top 20 + Academic)

ipp.mpg.de: 2 ucl.ac.uk: 2 my.brunel.ac.uk: 1 gmx.net: 1 xps15-notebook.speedport.ip: 1 draco01.mpcdf.mpg.de: 1 uva.nl: 1 komi.sc.cwi.nl: 1 brunel.ac.uk: 1 mpp2-login7.cos.lrz.de: 1 cwi.nl: 1 draco02.mpcdf.mpg.de: 1 man.poznan.pl: 1 lrz.de: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 89
Total pull requests: 61
Average time to close issues: 4 months
Average time to close pull requests: about 1 month
Total issue authors: 11
Total pull request authors: 10
Average comments per issue: 3.51
Average comments per pull request: 0.41
Merged pull requests: 51
Bot issues: 0
Bot pull requests: 5

Past Year

Issues: 8
Pull requests: 19
Average time to close issues: about 1 month
Average time to close pull requests: 18 days
Issue authors: 4
Pull request authors: 6
Average comments per issue: 0.63
Average comments per pull request: 0.47
Merged pull requests: 14
Bot issues: 0
Bot pull requests: 5

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raar1 (32)
dww100 (29)
DavidPCoster (12)
djgroen (7)
wedeling (5)
lauraharbach (3)
bartoszbosak (2)
mzrghorbani (1)
jlakhlili (1)
NicolasMonnier (1)
mbergmann1324 (1)
cspgdds (1)
mvassaux (1)

Pull Request Authors

raar1 (14)
dww100 (13)
bartoszbosak (11)
DavidPCoster (10)
djgroen (7)
wedeling (5)
dependabot[bot] (5)
orbitfold (4)
mzrghorbani (4)
ZedThree (2)

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Discussion (19) enhancement (15) M12 review (15) bug (9) documentation (2) question (1) future-proofing (1)

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Packages

Total packages: 1
Total downloads:
- pypi 364 last-month

Total dependent packages: 0
Total dependent repositories: 4
Total versions: 56
Total maintainers: 3

pypi.org: easyvvuq

Library to facilitate simple Verification, Validation and Uncertainty Quantification of simulation codes

Documentation: https://easyvvuq.readthedocs.io/en/dev/
License: LGPL-3.0 AND GPL-3.0
Latest release: 1.2.3
published 7 months ago

Versions: 56
Dependent Packages: 0
Dependent Repositories: 4
Downloads: 364 Last month

Rankings

Dependent repos count: 7.5%

Dependent packages count: 10.1%

Average: 12.5%

Downloads: 19.9%

Maintainers (3)

dww100 orbitfold rrichardson

Last synced: 4 months ago

Dependencies

docs/requirements.txt pypi

easyvvuq *

requirements.txt pypi

SALib *
SQLAlchemy *
autopep8 *
cerberus *
chaospy ==4.3.2
cloudpickle *
dask *
dask_jobqueue *
dill *
jinja2 *
kubernetes *
numpoly ==1.1.3
numpy *
pandas *
pytest *
pytest-benchmark *
pytest-dependency *
pytest-pep8 *
qcg-pilotjob *
qcg-pilotjob-executor-api *
scikit-learn *
scipy *
squarify *
tqdm *
wheel *

.github/workflows/benchmark.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite
rhysd/github-action-benchmark v1 composite

.github/workflows/codeql.yml actions

actions/checkout v3 composite
github/codeql-action/analyze v2 composite
github/codeql-action/autobuild v2 composite
github/codeql-action/init v2 composite

.github/workflows/coveralls.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite

.github/workflows/docker.yml actions

actions/checkout v2 composite
mr-smithers-excellent/docker-build-push v3.3 composite

.github/workflows/pdocs.yml actions

JamesIves/github-pages-deploy-action 4.1.2 composite
actions/checkout v2.3.1 composite
actions/checkout v2 composite
actions/setup-python v2 composite

.github/workflows/python-package.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite

.github/workflows/pythonpublish.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite

tutorials/kubernetes/Dockerfile docker

ubuntu latest build

setup.py pypi

easyvvuq

Science Score: 85.0%

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EasyVVUQ

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pypi.org: easyvvuq

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