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Open Source Science

https://github.com/21cmfast/21cmmc

Constrain 21cmFAST parameters using MCMC

https://github.com/21cmfast/21cmmc

Science Score: 36.0%

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
  • ✓
    DOI references
    Found 8 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    5 of 12 committers (41.7%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.3%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Constrain 21cmFAST parameters using MCMC

Basic Info
  • Host: GitHub
  • Owner: 21cmfast
  • License: mit
  • Language: Python
  • Default Branch: master
  • Size: 19.5 MB
Statistics
  • Stars: 8
  • Watchers: 3
  • Forks: 12
  • Open Issues: 19
  • Releases: 0
Created about 7 years ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog Contributing License Authors

README.rst 

======
21CMMC
======

.. start-badges
.. image:: https://github.com/21cmfast/21CMMC/actions/workflows/test_suite.yaml/badge.svg
    :target: https://github.com/21cmfast/21CMMC/actions/workflows/test_suite.yaml
.. image:: https://codecov.io/gh/21cmfast/21CMMC/branch/master/graph/badge.svg
    :target: https://codecov.io/gh/21cmfast/21CMMC
.. image:: https://img.shields.io/badge/code%20style-black-000000.svg
    :target: https://github.com/ambv/black
.. image:: https://readthedocs.org/projects/21cmmc/badge/?version=latest
    :target: https://21cmmc.readthedocs.io/en/latest/?badge=latest
    :alt: Documentation Status
.. end-badges

An extensible MCMC framework for 21cmFAST.


This code uses `semantic versioning `_, though this will strictly
begin when `v1.0.0` is officially shipped.

* Free software: MIT license

Features
========

* Seamless integration with ``emcee``-based MCMC.
* Supports the ``MultiNest`` sampler.
* Supports the ``zeus`` sampler.
* MCMC is easily extensible via the addition of different likelihoods using the same underlying data.

Scalability
===========

.. image:: docs/multinest_scalability.jpg
    :width: 866
This plot shows the number of test models (see details `here `_) performed using the MultiNest sampler as a function of thread number, illustrating an almost ideal scalability where #model per human hour scales linearly with #thread. There are three runs for each thread number, which are indicated by the filled circles with errorbar. The double sided arrows show the relative (w.r.t. the 24-thread case) loss when scaling up the calculation. Note that a typical inference study, working with more complex models and therefore performing much fewer models per human hour, is expected to remain the same level of scalability.

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

See https://21CMMC.readthedocs.org.

Acknowledging
=============
If you find `21CMMC` useful in your research please cite at least one of the following
(whichever is most suitable to you):

    Bradley Greig and Andrei Mesinger, "21CMMC: an MCMC analysis tool enabling
    astrophysical parameter studies of the cosmic 21 cm signal", Monthly Notices of the
    Royal Astronomical Society, Volume 449, Issue 4, p.4246-4263 (2015),
    https://doi.org/10.1093/mnras/stv571

    Bradley Greig and Andrei Mesinger, "Simultaneously constraining the astrophysics of
    reionization and the epoch of heating with 21CMMC", Monthly Notices of the Royal
    Astronomical Society, Volume 472, Issue 3, p.2651-2669 (2017),
    https://doi.org/10.1093/mnras/stx2118

    Bradley Greig and Andrei Mesinger, "21CMMC with a 3D light-cone: the impact of the
    co-evolution approximation on the astrophysics of reionization and cosmic dawn",
    Monthly Notices of the Royal Astronomical Society, Volume 477, Issue 3, p.3217-3229
    (2018), https://doi.org/10.1093/mnras/sty796

    Jaehong Park et al.,  "Inferring the astrophysics of reionization and cosmic dawn
    from galaxy luminosity functions and the 21-cm signal", Monthly Notices of the
    Royal Astronomical Society, Volume 484, Issue 1, p.933-949 (2018),
    https://doi.org/10.1093/mnras/stz032

Owner

  • Name: 21cmFAST Collaboration
  • Login: 21cmfast
  • Kind: organization
  • Email: 21cmfast.coredev@gmail.com

Core team that develops 21cmFAST and associated packages

GitHub Events

Total
  • Watch event: 1
  • Push event: 12
  • Fork event: 2
Last Year
  • Watch event: 1
  • Push event: 12
  • Fork event: 2

Committers

Last synced: over 3 years ago

All Time
  • Total Commits: 670
  • Total Committers: 12
  • Avg Commits per committer: 55.833
  • Development Distribution Score (DDS): 0.552
Top Committers
Name Email Commits
Steven Murray s****y@c****u 300
Yuxiang Qin Y****n@g****m 106
BradGreig b****g@s****u 100
Yuxiang Qin y****n@s****t 80
Steven Murray s****y@a****u 48
David Prelogovic d****c@g****m 10
pre-commit-ci[bot] 6****]@u****m 9
Samuel Gagnon-Hartman s****n@g****m 6
yuxiang qin y****n@g****m 5
Vivian Poulin p****n@l****r 3
Thomas J Binnie t****6@p****k 2
BradGreig b****g@g****m 1
Committer Domains (Top 20 + Academic)
ph-jpritcha-1.ph.ic.ac.uk: 1 lapth.cnrs.fr: 1 asu.edu: 1 sns.it: 1 student.unimelb.edu.au: 1 curtin.edu.au: 1

Issues and Pull Requests

Last synced: 12 months ago

All Time
  • Total issues: 36
  • Total pull requests: 46
  • Average time to close issues: 4 months
  • Average time to close pull requests: about 1 month
  • Total issue authors: 14
  • Total pull request authors: 8
  • Average comments per issue: 3.28
  • Average comments per pull request: 3.61
  • Merged pull requests: 39
  • Bot issues: 0
  • Bot pull requests: 7
Past Year
  • Issues: 4
  • Pull requests: 6
  • Average time to close issues: 14 days
  • Average time to close pull requests: 6 days
  • Issue authors: 4
  • Pull request authors: 4
  • Average comments per issue: 1.5
  • Average comments per pull request: 1.5
  • Merged pull requests: 4
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • steven-murray (14)
  • qyx268 (5)
  • NGillet (4)
  • binnietom (2)
  • dprelogo (2)
  • jpober (1)
  • BradGreig (1)
  • dkn16 (1)
  • wps2n (1)
  • SuvedhaNaik (1)
  • HoisW (1)
  • keelder (1)
  • parphyam (1)
  • ashishbijlani (1)
Pull Request Authors
  • steven-murray (17)
  • qyx268 (8)
  • pre-commit-ci[bot] (7)
  • DanielaBreitman (7)
  • dprelogo (4)
  • Kojobu (2)
  • samgagnon (1)
  • binnietom (1)
Top Labels
Issue Labels
type: feature: code (7) context: mcmc (7) API Breaking (6) bug (6) type: documentation (4) type: bug (4) context: io (2) documentation (2) type: refactor (2) context: framework (2) question (2) docs (2) type: performance: memory (1) type: performance: speed (1) type: question (1) status: requires research (1) context: error-handling (1) type: maintenance (1) enhancement (1)
Pull Request Labels
context: mcmc (3) documentation (1) enhancement (1) type: feature: physical (1)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 87 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 4
  • Total maintainers: 1
pypi.org: 21cmmc

An extensible MCMC framework for 21cmFAST

  • Versions: 4
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 87 Last month
Rankings
Dependent packages count: 10.0%
Forks count: 11.4%
Downloads: 14.3%
Stargazers count: 19.3%
Average: 24.5%
Dependent repos count: 67.6%
Maintainers (1)
stevenjeanette
Last synced: 12 months ago

Dependencies

docs/requirements.txt pypi
  • cached_property *
  • emcee <3
  • ipython *
  • nbsphinx *
  • numpydoc *
  • powerbox *
  • sphinx >=1.3
  • sphinx-rtd-theme *
setup.py pypi
  • 21cmFAST *
  • cached_property *
  • click *
  • cosmoHammer *
  • emcee <3
  • matplotlib >=2.1
  • numpy *
  • powerbox >=0.5.7
  • pymultinest *
  • scipy *
.github/workflows/test_suite.yaml actions
  • actions/cache v2 composite
  • actions/checkout master composite
  • codecov/codecov-action v2 composite
  • conda-incubator/setup-miniconda v2.1.1 composite