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Sciris

Sciris: Simplifying scientific software in Python - Published in JOSS (2023)

https://github.com/sciris/sciris

Science Score: 95.0%

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
    Found 1 DOI reference(s) in JOSS metadata
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 14 committers (7.1%) from academic institutions
  • ○
    Institutional organization owner
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software

Keywords

computational-science containers data-science matplotlib numpy parallelization plotting python scientific-computing utilities
Last synced: 6 months ago · JSON representation

Repository

Fast, flexible tools to simplify scientific Python

Basic Info
  • Host: GitHub
  • Owner: sciris
  • License: mit
  • Language: Python
  • Default Branch: main
  • Homepage: http://docs.sciris.org
  • Size: 13.7 MB
Statistics
  • Stars: 39
  • Watchers: 9
  • Forks: 13
  • Open Issues: 26
  • Releases: 9
Topics
computational-science containers data-science matplotlib numpy parallelization plotting python scientific-computing utilities
Created over 8 years ago · Last pushed 7 months ago
Metadata Files
Readme Changelog Contributing License Code of conduct

README.rst 

Welcome to Sciris
=================

.. image:: https://badgen.net/pypi/v/sciris/?color=blue
 :target: https://pypi.org/project/sciris

.. image:: https://static.pepy.tech/personalized-badge/sciris?period=total&units=international_system&left_color=grey&right_color=yellow&left_text=Downloads
 :target: https://pepy.tech/project/sciris

.. image:: https://img.shields.io/pypi/l/sciris.svg
 :target: https://github.com/sciris/sciris/blob/main/LICENSE

.. image:: https://github.com/sciris/sciris/actions/workflows/test_sciris.yaml/badge.svg
 :target: https://github.com/sciris/sciris/actions/workflows/test_sciris.yaml?query=workflow


What is Sciris?
---------------

Sciris is a library of tools that can help make writing scientific Python code easier and more pleasant. Built on top of `NumPy `_ and `Matplotlib `_, Sciris provides functions covering a wide range of common math, file I/O, and plotting operations. This means you can get more done with less code, so you can spend less time looking up answers on Stack Overflow or copy-pasting dubious solutions from ChatGPT. It was originally written to help epidemiologists and neuroscientists focus on doing science, rather than on writing code, but Sciris is applicable across scientific domains (and some nonscientific ones too).

For more information, see the full `documentation `_, the `paper `_, or `GitHub `_.

If you have questions, feature suggestions, or would like some help getting started, please reach out to us at info@sciris.org or `open an issue `_.


Installation
------------

Using pip: ``pip install sciris``

Using conda: ``conda install -c conda-forge sciris``

Using uv: ``uv add sciris``

*Requires Python >= 3.7*.


Tests
-----

Sciris comes with an automated test suite covering all functions. You almost certainly don't need to run these, but if you want to, go to the ``tests`` folder and run ``pytest``. See the readme in that folder for more information.

Owner

  • Name: Sciris
  • Login: sciris
  • Kind: organization
  • Email: info@sciris.org

Python and JavaScript tools for scientific simulations and webapps

JOSS Publication

Sciris: Simplifying scientific software in Python
Published
August 14, 2023
DOI
Volume 8, Issue 88, Page 5076
Authors
Cliff C. Kerr ORCID
Institute for Disease Modeling, Global Health Division, Bill \& Melinda Gates Foundation, Seattle, USA, School of Physics, University of Sydney, Sydney, Australia
Paula Sanz-Leon ORCID
Institute for Disease Modeling, Global Health Division, Bill \& Melinda Gates Foundation, Seattle, USA
Romesh G. Abeysuriya ORCID
Institute for Disease Modeling, Global Health Division, Bill \& Melinda Gates Foundation, Seattle, USA, Burnet Institute, Melbourne, Australia
George L. Chadderdon ORCID
Burnet Institute, Melbourne, Australia, CAE USA, Tampa, USA
Vlad-Ştefan Harbuz
Saffron Software, Bucharest, Romania
Parham Saidi
Saffron Software, Bucharest, Romania
Maria del Mar Quiroga ORCID
Burnet Institute, Melbourne, Australia, Melbourne Data Analytics Platform, The University of Melbourne, Melbourne, Australia
Rowan Martin-Hughes ORCID
Burnet Institute, Melbourne, Australia
Sherrie L. Kelly ORCID
Burnet Institute, Melbourne, Australia
Jamie A. Cohen ORCID
Institute for Disease Modeling, Global Health Division, Bill \& Melinda Gates Foundation, Seattle, USA
Robyn M. Stuart ORCID
Institute for Disease Modeling, Global Health Division, Bill \& Melinda Gates Foundation, Seattle, USA, Department of Mathematical Sciences, University of Copenhagen, Copenhagen, Denmark
Anna Nachesa
Google, Zürich, Switzerland
Editor
Daniel S. Katz ORCID
Tags
python scientific software development computational science numerical utilities containers plotting
View PDF Review Thread Software Archive

GitHub Events

Total
  • Issues event: 84
  • Watch event: 7
  • Delete event: 6
  • Issue comment event: 60
  • Push event: 81
  • Pull request review comment event: 1
  • Pull request review event: 4
  • Pull request event: 15
  • Create event: 10
Last Year
  • Issues event: 84
  • Watch event: 7
  • Delete event: 6
  • Issue comment event: 60
  • Push event: 81
  • Pull request review comment event: 1
  • Pull request review event: 4
  • Pull request event: 15
  • Create event: 10

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 2,396
  • Total Committers: 14
  • Avg Commits per committer: 171.143
  • Development Distribution Score (DDS): 0.179
Past Year
  • Commits: 140
  • Committers: 3
  • Avg Commits per committer: 46.667
  • Development Distribution Score (DDS): 0.064
Top Committers
Name Email Commits
cliffckerr q****y@g****m 1,968
George Chadderdon g****3@g****m 249
Paula Sanz-Leon p****n@q****u 75
Romesh Abeysuriya r****y@g****m 66
James Jansson j****n@g****m 10
Vlad-Ștefan Harbuz v****d@v****t 9
Kelvin Burke k****e@g****m 6
Eloisa Perez-Bennetts 4****s 3
Thomas A Caswell t****l@g****m 3
Rowanmh r****h@g****m 2
mariadelmarq m****q 2
David Kedziora d****z 1
Robyn Stuart r****s@g****m 1
appsplash99 6****9 1
Committer Domains (Top 20 + Academic)
vladh.net: 1 qimrberghofer.edu.au: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 220
  • Total pull requests: 65
  • Average time to close issues: 2 months
  • Average time to close pull requests: 20 days
  • Total issue authors: 11
  • Total pull request authors: 8
  • Average comments per issue: 1.31
  • Average comments per pull request: 0.25
  • Merged pull requests: 58
  • Bot issues: 0
  • Bot pull requests: 2
Past Year
  • Issues: 58
  • Pull requests: 22
  • Average time to close issues: 2 months
  • Average time to close pull requests: about 1 month
  • Issue authors: 5
  • Pull request authors: 3
  • Average comments per issue: 0.93
  • Average comments per pull request: 0.18
  • Merged pull requests: 18
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • cliffckerr (194)
  • kelvinburke (10)
  • aflaxman (5)
  • tacaswell (4)
  • pausz (2)
  • clorton (1)
  • RomeshA (1)
  • fabmazz (1)
  • daniel-klein (1)
  • dstansby (1)
  • krosenfeld (1)
  • vsbuffalo (1)
Pull Request Authors
  • cliffckerr (48)
  • RomeshA (13)
  • kelvinburke (5)
  • tacaswell (3)
  • vladh (3)
  • dependabot[bot] (2)
  • Rowanmh (1)
  • epbennetts (1)
  • danielskatz (1)
Top Labels
Issue Labels
enhancement (68) bug (45) refactor (23) documentation (16) lowpriority (12) admin (9) test (5) big (4) quick (1)
Pull Request Labels
enhancement (4) dependencies (2) python (2) bug (1)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 14,730 last-month
  • Total dependent packages: 8
  • Total dependent repositories: 18
  • Total versions: 70
  • Total maintainers: 3
pypi.org: sciris

Fast, flexible tools to simplify scientific Python

  • Versions: 70
  • Dependent Packages: 8
  • Dependent Repositories: 18
  • Downloads: 14,730 Last month
Rankings
Dependent packages count: 1.6%
Dependent repos count: 3.5%
Downloads: 6.2%
Average: 6.9%
Forks count: 10.6%
Stargazers count: 12.7%
Maintainers (3)
romesh sciris cliffckerr
Last synced: 6 months ago

Dependencies

.github/workflows/tests.yaml actions
  • actions/checkout v2 composite
  • actions/setup-python master composite
  • actions/upload-artifact v1 composite
docs/requirements.txt pypi
  • pandoc *
  • pypandoc *
  • pytest *
  • pytest-xdist *
  • recommonmark *
  • sphinx >=1.8
  • sphinx-autodoc-typehints *
  • sphinx-rtd-theme *
requirements.txt pypi
  • colorama *
  • dill *
  • gitpython *
  • jellyfish *
  • jsonpickle *
  • line_profiler *
  • matplotlib *
  • memory_profiler *
  • multiprocess *
  • numpy *
  • openpyxl *
  • packaging *
  • pandas *
  • psutil *
  • python-dateutil *
  • pyyaml *
  • setuptools *
  • tqdm *
  • xlsxwriter *
  • zstandard *
setup.py pypi
tests/requirements.txt pypi
  • pytest >=7.3 test
  • pytest-cov * test
  • pytest-env * test
  • pytest-xdist * test