diff --git a/README.md b/README.md index e8bad28..a93b7d7 100644 --- a/README.md +++ b/README.md @@ -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) diff --git a/docs/make.jl b/docs/make.jl index 1dc73ae..e96ba21 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -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=[ @@ -29,7 +29,7 @@ makedocs(; ) deploydocs(; - repo="github.com/cecileane/PhyloCoalSimulations.jl", + repo="github.com/JuliaPhylo/PhyloCoalSimulations.jl", devbranch="main", push_preview = true, ) diff --git a/docs/readme.md b/docs/readme.md index cf808f4..967aeca 100644 --- a/docs/readme.md +++ b/docs/readme.md @@ -1,7 +1,7 @@ # 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. diff --git a/docs/src/index.md b/docs/src/index.md index f1ab590..cca21fe 100644 --- a/docs/src/index.md +++ b/docs/src/index.md @@ -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). @@ -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.