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demes

Tools for describing and manipulating demographic models.

https://github.com/popsim-consortium/demes-python

Science Score: 54.0%

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
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    3 of 7 committers (42.9%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (6.0%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

Tools for describing and manipulating demographic models.

Basic Info
Statistics
  • Stars: 19
  • Watchers: 5
  • Forks: 6
  • Open Issues: 23
  • Releases: 10
Created over 5 years ago · Last pushed 10 months ago
Metadata Files
Readme Changelog License Citation

README.md

Tools for describing and manipulating demographic models.

A demographic model describes one or more demes (or populations), how they change over time, and their relationships to one another. demes provides a self-contained and unambiguous in-memory description of a demographic model.

Please see the documentation for more details.

Goals

  • A simple declarative high-level format for specifying demographic models. This format is intended to be human-readable and to make it easy to correctly specify models.
  • A corresponding low-level format that is an entirely unambiguous and portable description of a model, which can be used by many different simulation frameworks as input. Thus, we can see part of the role of this package as compiling the high-level description of a model into the corresponding low-level description.
  • Robust validation of models and reporting of errors for invalid models.

Owner

  • Name: PopSim Consortium
  • Login: popsim-consortium
  • Kind: organization

A community-driven effort to standardize population genetics

Citation (CITATION.md) 

(sec_citation)=
# Citing Demes

If you use Demes in your work, please cite the
[2022 Genetics paper](https://doi.org/10.1093/genetics/iyac131).

```bibtex
@article{gower_demes_2022,
  title        = {Demes: a standard format for demographic models},
  url          = {https://doi.org/10.1093/genetics/iyac131},
  doi          = {10.1093/genetics/iyac131},
  journal      = {Genetics},
  author       = {Gower, Graham and Ragsdale, Aaron P and Bisschop,
    Gertjan and Gutenkunst, Ryan N and Hartfield, Matthew and Noskova,
    Ekaterina and Schiffels, Stephan and Struck, Travis J and
    Kelleher, Jerome and Thornton, Kevin R},
  month        = sep,
  year         = 2022,
  pages        = {iyac131},
}
```

GitHub Events

Total
  • Issues event: 5
  • Watch event: 1
  • Delete event: 11
  • Issue comment event: 42
  • Push event: 30
  • Pull request review event: 4
  • Pull request event: 24
  • Create event: 8
Last Year
  • Issues event: 5
  • Watch event: 1
  • Delete event: 11
  • Issue comment event: 42
  • Push event: 30
  • Pull request review event: 4
  • Pull request event: 24
  • Create event: 8

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 307
  • Total Committers: 7
  • Avg Commits per committer: 43.857
  • Development Distribution Score (DDS): 0.459
Past Year
  • Commits: 43
  • Committers: 3
  • Avg Commits per committer: 14.333
  • Development Distribution Score (DDS): 0.488
Top Committers
Name Email Commits
Graham Gower g****r@g****m 166
dependabot[bot] 4****]@u****m 92
Aaron Ragsdale a****e@m****a 33
Arjun Biddanda a****a@g****m 6
Aaron Ragsdale a****e@w****u 4
Ekaterina k****3@g****m 3
Jerome Kelleher jk@w****k 3
Committer Domains (Top 20 + Academic)
well.ox.ac.uk: 1 wisc.edu: 1 mail.mcgill.ca: 1

Packages

  • Total packages: 2
  • Total downloads:
    • pypi 14,956 last-month
  • Total dependent packages: 10
    (may contain duplicates)
  • Total dependent repositories: 37
    (may contain duplicates)
  • Total versions: 16
  • Total maintainers: 2
pypi.org: demes

tools for describing demographic models

  • Versions: 11
  • Dependent Packages: 8
  • Dependent Repositories: 32
  • Downloads: 14,956 Last month
Rankings
Dependent packages count: 1.6%
Dependent repos count: 2.6%
Downloads: 4.4%
Average: 7.3%
Forks count: 13.3%
Stargazers count: 14.5%
Maintainers (2)
jerome.kelleher grahamgower
Last synced: 7 months ago
conda-forge.org: demes
  • Versions: 5
  • Dependent Packages: 2
  • Dependent Repositories: 5
Rankings
Dependent repos count: 14.8%
Dependent packages count: 19.6%
Average: 34.2%
Forks count: 50.6%
Stargazers count: 51.9%
Last synced: 6 months ago

Dependencies

requirements/docs.txt pypi
  • demesdraw ==0.3.0
  • jupyter-book ==0.12.3
  • sphinx ==4.5.0
  • sphinx_issues ==3.0.1
  • sphinxcontrib-programoutput ==0.17
requirements/lint.txt pypi
  • black ==22.3.0
  • flake8 ==4.0.1
  • mypy ==0.960
requirements/minimal.txt pypi
  • attrs ==21.4.0
  • ruamel.yaml ==0.17.21
requirements/tests.txt pypi
  • numpy *
  • numpy ==1.22.4
  • pytest ==7.1.2
  • pytest-cov ==3.0.0
  • pytest-xdist ==2.5.0
.github/workflows/dev.yaml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
.github/workflows/docs.yaml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
.github/workflows/lint.yaml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
.github/workflows/tests.yaml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
  • codecov/codecov-action v3.1.0 composite
  • styfle/cancel-workflow-action 0.10.0 composite
.github/workflows/wheel.yaml actions
  • actions/checkout v3 composite
  • actions/download-artifact v3 composite
  • actions/setup-python v4 composite
  • actions/upload-artifact v3 composite
  • pypa/gh-action-pypi-publish release/v1 composite