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PhyloX

PhyloX: A Python package for complete phylogenetic network workflows - Published in JOSS (2024)

https://github.com/remiejanssen/phylox

Science Score: 93.0%

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 2 DOI reference(s) in README and JOSS metadata
  • ✓
    Academic publication links
    Links to: joss.theoj.org, zenodo.org
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software

Scientific Fields

Sociology Social Sciences - 64% confidence
Last synced: 4 months ago · JSON representation

Repository

A python package with tools for constructing, manipulating, and analyzing phylogenetic networks.

Basic Info
  • Host: GitHub
  • Owner: RemieJanssen
  • License: bsd-3-clause
  • Language: Python
  • Default Branch: main
  • Size: 280 KB
Statistics
  • Stars: 1
  • Watchers: 1
  • Forks: 2
  • Open Issues: 13
  • Releases: 9
Created over 2 years ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog Contributing License Zenodo

README.md

DOI JOSS Documentation Status

PhyloX

PhyloX is a python package with tools for constructing, manipulating, and analyzing phylogenetic networks.

Installation as pypi package phylox is simple via pip or conda: pip install phylox You can load the package methods with import phylox in python.

For more information, see the documentation.

Citing PhyloX

For now, simply refer to the github page to cite PhyloX. Registering the software for a DOI is still on the to do list.

Use of NetworkX

The implementation of PhyloX is based on NetworkX (NetworkX is distributed with the 3-clause BSD license):

Aric A. Hagberg, Daniel A. Schult and Pieter J. Swart, “Exploring network structure, dynamics, and function using NetworkX”, in Proceedings of the 7th Python in Science Conference (SciPy2008), Gäel Varoquaux, Travis Vaught, and Jarrod Millman (Eds), (Pasadena, CA USA), pp. 11–15, Aug 2008

Citing specific functions

When citing PhyloX, you are most likely also using specific methods, which can be traced back to their original papers. Please take care to cite the original papers as well. A reference to the original paper should be found in the documentation of the method, or of the module containing the method.

Development

For a development version, simply pull the project and in the home of the project do: pip install -e . This installs the phylox package from the source. When you change things in the source, the package gets updated as well.

Release

set new version number in master branch - CHANGELOG.md - pyproject.toml

release current version git checkout release git merge main git tag [version number] git push --atomic origin release [version number]

Linting

precommit is yet to be configured, for now, simply run black and isort.

Documentation

Documentation is in the docs folder, and is created uses sphinx.

Requirements

You may need to install the requirements from docs/requirements.txt first. Make sure to use python<=3.11., for example: ``` conda create -n phylox-sphinx conda activate phylox-sphinx python install python==3.11. pip install -r docs/requirements.txt ```

Creating documentation

to build the documentation, go to the docs folder and run: make html the docs will be in docs/build/html.

If you re-run the build, you can first remove the old autosummary files. If you do not, it will not update them.

Owner

  • Login: RemieJanssen
  • Kind: user

JOSS Publication

PhyloX: A Python package for complete phylogenetic network workflows
Published
November 24, 2024
DOI
Volume 9, Issue 103, Page 6427
Authors
Remie Janssen ORCID
National Institute for Public Health and the Environment, Bioinformatics and Computing group, Bilthoven, The Netherlands
Editor
Frederick Boehm ORCID
Tags
Bioinformatics Phylogenetics Graph theory
View PDF Review Thread Software Archive

GitHub Events

Total
  • Watch event: 1
  • Delete event: 3
  • Push event: 3
  • Pull request event: 6
  • Create event: 3
Last Year
  • Watch event: 1
  • Delete event: 3
  • Push event: 3
  • Pull request event: 6
  • Create event: 3

Committers

Last synced: 5 months ago

All Time
  • Total Commits: 69
  • Total Committers: 3
  • Avg Commits per committer: 23.0
  • Development Distribution Score (DDS): 0.058
Past Year
  • Commits: 6
  • Committers: 1
  • Avg Commits per committer: 6.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
RemieJanssen 2****n 65
Benjamin M. Gyori b****i@g****m 2
Remie Janssen j****r@r****l 2
Committer Domains (Top 20 + Academic)
rivm-biohn-l08p.int.ssc-campus.nl: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time
  • Total issues: 31
  • Total pull requests: 45
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 3 days
  • Total issue authors: 2
  • Total pull request authors: 2
  • Average comments per issue: 0.39
  • Average comments per pull request: 0.09
  • Merged pull requests: 44
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 8
  • Average time to close issues: N/A
  • Average time to close pull requests: about 12 hours
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 8
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • RemieJanssen (28)
  • abhishektiwari (3)
Pull Request Authors
  • RemieJanssen (60)
  • bgyori (4)
Top Labels
Issue Labels
joss (5) enhancement (3) bug (2) epic (1)
Pull Request Labels
joss (4)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 20 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 8
  • Total maintainers: 1
pypi.org: phylox

A package with tools for constructing, manipulating, and analyzing phylogenetic networks.

  • Versions: 8
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 20 Last month
Rankings
Dependent packages count: 10.0%
Dependent repos count: 21.7%
Forks count: 22.6%
Average: 27.0%
Stargazers count: 38.8%
Downloads: 42.0%
Maintainers (1)
RemieJanssen
Last synced: 4 months ago

Dependencies

.github/workflows/python-package.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
pyproject.toml pypi
  • networkx >=2.6
  • numpy >=1.21.6
.github/workflows/pypi-release.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
  • pypa/gh-action-pypi-publish release/v1 composite
docs/requirements.in pypi
  • phylox *
  • sphinx ==7.0.1
docs/requirements.txt pypi
  • alabaster ==0.7.13
  • babel ==2.12.1
  • certifi ==2023.5.7
  • charset-normalizer ==3.2.0
  • docutils ==0.20.1
  • idna ==3.4
  • imagesize ==1.4.1
  • jinja2 ==3.1.2
  • markupsafe ==2.1.3
  • networkx ==3.1
  • numpy ==1.25.1
  • packaging ==23.1
  • phylox ==0.0.2
  • pygments ==2.15.1
  • requests ==2.31.0
  • snowballstemmer ==2.2.0
  • sphinx ==7.0.1
  • sphinxcontrib-applehelp ==1.0.4
  • sphinxcontrib-devhelp ==1.0.2
  • sphinxcontrib-htmlhelp ==2.0.1
  • sphinxcontrib-jsmath ==1.0.1
  • sphinxcontrib-qthelp ==1.0.3
  • sphinxcontrib-serializinghtml ==1.1.5
  • urllib3 ==2.0.4