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tensiometer

https://github.com/mraveri/tensiometer

Science Score: 46.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ✓
    Academic publication links
    Links to: arxiv.org
  • ✓
    Committers with academic emails
    2 of 5 committers (40.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.6%) to scientific vocabulary
Last synced: 7 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: mraveri
  • License: gpl-3.0
  • Language: Python
  • Default Branch: master
  • Size: 105 MB
Statistics
  • Stars: 26
  • Watchers: 6
  • Forks: 10
  • Open Issues: 1
  • Releases: 4
Created almost 6 years ago · Last pushed 7 months ago
Metadata Files
Readme License

README.rst 

============
Tensiometer
============
-------------------------------
 Test a model until it breaks!
-------------------------------
:Tensiometer: A tool to test the level of agreement/disagreement between high dimensional posterior distributions.
:Author: Marco Raveri and Cyrille Doux
:Homepage: https://tensiometer.readthedocs.io
:Source: https://github.com/mraveri/tensiometer
:References: `2105.03324 `_ (non-Gaussian tension metrics), 
             `1806.04649 `_ and 
             `1912.04880 `_ (Gaussian tension metrics),
             `2112.05737 `_ (measured parameters).

.. image:: https://github.com/mraveri/tensiometer/actions/workflows/test.yml/badge.svg
    :target: https://github.com/mraveri/tensiometer/actions/workflows/test.yml
.. image:: https://readthedocs.org/projects/tensiometer/badge/?version=latest
    :target: https://tensiometer.readthedocs.org/en/latest
.. image:: https://coveralls.io/repos/github/mraveri/tensiometer/badge.svg?branch=master
    :target: https://coveralls.io/github/mraveri/tensiometer?branch=master
.. image:: https://img.shields.io/pypi/v/tensiometer.svg?style=flat
    :target: https://pypi.python.org/pypi/tensiometer/

Description
============

The tensiometer package is a collection of tools to help understanding the structure of high 
dimensional posterior distributions. 
In particular it implements a number of metrics to quantify the level of agreement/disagreement
between different distributions.
Some of these methods are based on a `Gaussian approximation `_.
Others are capable of capturing `non-Gaussian features `_ of the distributions 
thanks to machine learning techniques.

The best way to get up to speed is to walk through some worked example, based on 
what is needed:

* `Normalizing flow models for posterior distributions `_;
* `Tension between two Gaussian posteriors `_;
* `Tension between two non-Gaussian posteriors `_;
* `Posterior profiles `_;
* `Measured parameters `_;
* `Quantify convergence of chains `_;


Installation
=============

The tensiometer package is available on PyPI and can be easily installed with::

  pip install tensiometer

Alternatively one can download the source code from github::

  git clone https://github.com/mraveri/tensiometer.git

and install it locally with the shortcut::

  make install

You can test that the code is working properly by using::

  make test

Dependencies
=============

Tensiometer uses mostly standard python packages.
Notable exceptions are GetDist, Tensorflow and Tensorflow Probability.
Installing the last two is likely painful and we advice to not delegate that to 
automatic dependency resolvers...

For the full list of requirements see the `requirements.txt` file.

Testing the code
================

Tensiometer has a suite of unit tests to make sure everything is properly installed. 
This is especially useful considering that tensiometer relies on a number of external libraries.

To run all tests give the command::

  make test

To run tests and get coverage statistics first make sure that the package `coverage `_ is installed. 
Then you can use the command::

  make test_with_coverage

As you can see coverage is not complete, pull requests improving test coverage are most welcome.

Documentation
=============

The documentation is automatically built for each release on `readthedocs `_.

If you want to build locally the documentation you shoud install `sphinx `_.
Then you can install the readthedocs documentation format with::

  pip install sphinx-rtd-theme

Then you can issue the command::

  make documentation

Acknowledgements
================

We thank Samuel Goldstein, Shivam Pandey for help developing the code.

****************

Owner

  • Name: Marco Raveri
  • Login: mraveri
  • Kind: user
  • Company: University of Pennsylvania

GitHub Events

Total
  • Watch event: 13
  • Push event: 11
  • Pull request event: 4
  • Fork event: 2
Last Year
  • Watch event: 13
  • Push event: 11
  • Pull request event: 4
  • Fork event: 2

Committers

Last synced: about 3 years ago

All Time
  • Total Commits: 27
  • Total Committers: 5
  • Avg Commits per committer: 5.4
  • Development Distribution Score (DDS): 0.407
Top Committers
Name Email Commits
mraveri m****i@s****u 16
mraveri m****1@y****t 5
Cyrille Doux c****x@s****u 3
Cyrille Doux x****d@u****m 2
Michael Rashkovetskyi m****h@g****m 1
Committer Domains (Top 20 + Academic)
sas.upenn.edu: 2 yahoo.it: 1

Issues and Pull Requests

Last synced: 8 months ago

All Time
  • Total issues: 1
  • Total pull requests: 8
  • Average time to close issues: over 4 years
  • Average time to close pull requests: about 4 hours
  • Total issue authors: 1
  • Total pull request authors: 6
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.25
  • Merged pull requests: 7
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 4
  • Average time to close issues: N/A
  • Average time to close pull requests: about 7 hours
  • Issue authors: 0
  • Pull request authors: 3
  • Average comments per issue: 0
  • Average comments per pull request: 0.25
  • Merged pull requests: 4
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • mraveri (1)
Pull Request Authors
  • mraveri (4)
  • MariaLuisaGallavotti (2)
  • xuod (2)
  • gcampailla (2)
  • misharash (1)
  • msyriac (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 150 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 11
  • Total maintainers: 1
pypi.org: tensiometer

Tension tools for posterior distributions

  • Versions: 11
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 150 Last month
Rankings
Dependent packages count: 10.0%
Stargazers count: 16.5%
Forks count: 16.8%
Average: 18.6%
Dependent repos count: 21.7%
Downloads: 27.8%
Maintainers (1)
mraveri
Last synced: 8 months ago

Dependencies

requirements.txt pypi
  • GetDist >=1.1.2
  • autograd *
  • coverage >=5.5
  • joblib >=1.0.1
  • matplotlib >=2.2.0
  • numba >=0.53.0
  • numpy >=1.19.1
  • pymanopt >=0.2.5
  • scipy >=1.6.2
  • tensorflow >=2.0.0
  • tensorflow_probability >=0.11.1
  • tqdm *