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links cecileane / crsl4 -> juliaphylo #13

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Jun 21, 2024
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links cecileane / crsl4 -> juliaphylo #13

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8 changes: 4 additions & 4 deletions README.md
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@@ -1,9 +1,9 @@
# PhyloCoalSimulations

[![stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://cecileane.github.io/PhyloCoalSimulations.jl/stable)
[![dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://cecileane.github.io/PhyloCoalSimulations.jl/dev)
[![Build Status](https://github.com/cecileane/PhyloCoalSimulations.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/cecileane/PhyloCoalSimulations.jl/actions/workflows/CI.yml?query=branch%3Amain)
[![Coverage](https://codecov.io/gh/cecileane/PhyloCoalSimulations.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/cecileane/PhyloCoalSimulations.jl)
[![stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://juliaphylo.github.io/PhyloCoalSimulations.jl/stable)
[![dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://juliaphylo.github.io/PhyloCoalSimulations.jl/dev)
[![Build Status](https://github.com/juliaphylo/PhyloCoalSimulations.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/juliaphylo/PhyloCoalSimulations.jl/actions/workflows/CI.yml?query=branch%3Amain)
[![Coverage](https://codecov.io/gh/juliaphylo/PhyloCoalSimulations.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/juliaphylo/PhyloCoalSimulations.jl)
[![Code Style: Blue](https://img.shields.io/badge/code%20style-blue-4495d1.svg)](https://github.com/invenia/BlueStyle)
[![ColPrac: Contributor's Guide on Collaborative Practices for Community Packages](https://img.shields.io/badge/ColPrac-Contributor's%20Guide-blueviolet)](https://github.com/SciML/ColPrac)
[![PkgEval](https://JuliaCI.github.io/NanosoldierReports/pkgeval_badges/P/PhyloCoalSimulations.svg)](https://JuliaCI.github.io/NanosoldierReports/pkgeval_badges/report.html)
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4 changes: 2 additions & 2 deletions docs/make.jl
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Expand Up @@ -9,7 +9,7 @@ makedocs(;
sitename="PhyloCoalSimulations.jl",
format=Documenter.HTML(;
prettyurls=get(ENV, "CI", "false") == "true",
canonical="https://cecileane.github.io/PhyloCoalSimulations.jl/stable/",
canonical="https://juliaphylo.github.io/PhyloCoalSimulations.jl/stable/",
assets=String[],
),
pages=[
Expand All @@ -29,7 +29,7 @@ makedocs(;
)

deploydocs(;
repo="github.com/cecileane/PhyloCoalSimulations.jl",
repo="github.com/JuliaPhylo/PhyloCoalSimulations.jl",
devbranch="main",
push_preview = true,
)
2 changes: 1 addition & 1 deletion docs/readme.md
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# notes to maintain documentation

- built with [Documenter](https://juliadocs.github.io/Documenter.jl)
- deployed [here](https://cecileane.github.io/PhyloCoalSimulations.jl/)
- deployed [here](https://juliaphylo.github.io/PhyloCoalSimulations.jl/)
(go to `dev/` or `stable/`)
using github and files committed to the `gh-pages` branch.

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8 changes: 4 additions & 4 deletions docs/src/index.md
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Expand Up @@ -4,14 +4,14 @@ CurrentModule = PhyloCoalSimulations

# PhyloCoalSimulations

[PhyloCoalSimulations](https://github.com/cecileane/PhyloCoalSimulations.jl)
[PhyloCoalSimulations](https://github.com/juliaphylo/PhyloCoalSimulations.jl)
is a [Julia](http://julialang.org) package to
simulate phylogenies under the coalescent.
It depends on [PhyloNetworks](https://github.com/crsl4/PhyloNetworks.jl)
It depends on [PhyloNetworks](https://github.com/juliaphylo/PhyloNetworks.jl)
for the phylogenetic data structures, and manipulation of phylogenies.

References:
please see [bibtex entries here](https://github.com/cecileane/PhyloCoalSimulations.jl/blob/main/CITATION.bib).
please see [bibtex entries here](https://github.com/juliaphylo/PhyloCoalSimulations.jl/blob/main/CITATION.bib).

- for this package and the network coalescent model with inheritance correlation:\
Fogg, Allman & Ané (2023).
Expand All @@ -21,7 +21,7 @@ please see [bibtex entries here](https://github.com/cecileane/PhyloCoalSimulatio
72(5):1171–1179.
[doi:10.1093/sysbio/syad030](https://doi.org/10.1093/sysbio/syad030).

- for [PhyloNetworks](https://github.com/crsl4/PhyloNetworks.jl),
- for [PhyloNetworks](https://github.com/juliaphylo/PhyloNetworks.jl),
which this package depends on:\
Solís-Lemus, Bastide & Ané (2017).
PhyloNetworks: a package for phylogenetic networks.
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