update urls to JuliaPhylo (#13)

JuliaPhylo · Jun 19, 2024 · c08758c · c08758c
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diff --git a/CITATION.bib b/CITATION.bib
@@ -4,7 +4,7 @@ @users.noreply.github.com>
       Paul Bastide <pbastide@users.noreply.github.com> and
       contributors},
     title   = {PhyloGaussianBeliefProp.jl},
-    url     = {https://github.com/cecileane/PhyloGaussianBeliefProp.jl},
+    url     = {https://github.com/JuliaPhylo/PhyloGaussianBeliefProp.jl},
     version = {v0.0.1},
     year    = {2023},
 }

diff --git a/README.md b/README.md
@@ -1,17 +1,17 @@
 # PhyloGaussianBeliefProp
 
-[![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://cecileane.github.io/PhyloGaussianBeliefProp.jl/stable/)
-[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://cecileane.github.io/PhyloGaussianBeliefProp.jl/dev/)
-[![Build Status](https://github.com/cecileane/PhyloGaussianBeliefProp.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/cecileane/PhyloGaussianBeliefProp.jl/actions/workflows/CI.yml?query=branch%3Amain)
-[![Coverage](https://codecov.io/gh/cecileane/PhyloGaussianBeliefProp.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/cecileane/PhyloGaussianBeliefProp.jl)
+[![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://JuliaPhylo.github.io/PhyloGaussianBeliefProp.jl/stable/)
+[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://JuliaPhylo.github.io/PhyloGaussianBeliefProp.jl/dev/)
+[![Build Status](https://github.com/JuliaPhylo/PhyloGaussianBeliefProp.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/JuliaPhylo/PhyloGaussianBeliefProp.jl/actions/workflows/CI.yml?query=branch%3Amain)
+[![Coverage](https://codecov.io/gh/JuliaPhylo/PhyloGaussianBeliefProp.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/JuliaPhylo/PhyloGaussianBeliefProp.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/PhyloGaussianBeliefProp.svg)](https://JuliaCI.github.io/NanosoldierReports/pkgeval_badges/report.html)
 
 [Julia](http://julialang.org) package for the analysis of Gaussian models on
 phylogenetic networks and admixture graphs
 using belief propagation (aka message passing).
-It depends on utilities from [PhyloNetworks](https://github.com/crsl4/PhyloNetworks.jl).
+It depends on utilities from [PhyloNetworks](https://github.com/JuliaPhylo/PhyloNetworks.jl).
 
 ## Citing
 

diff --git a/docs/make.jl b/docs/make.jl
@@ -14,7 +14,7 @@ makedocs(;
         mathengine=Documenter.KaTeX(),
         prettyurls=get(ENV, "CI", "false") == "true",
         size_threshold = 600 * 2^10, size_threshold_warn = 500 * 2^10, # 600 KiB
-        canonical="https://cecileane.github.io/PhyloGaussianBeliefProp.jl/stable/",
+        canonical="https://JuliaPhylo.github.io/PhyloGaussianBeliefProp.jl/stable/",
         edit_link="main",
         assets=String["assets/citations.css"],
     ),
@@ -38,7 +38,7 @@ makedocs(;
 )
 
 deploydocs(;
-    repo="github.com/cecileane/PhyloGaussianBeliefProp.jl.git",
+    repo="github.com/JuliaPhylo/PhyloGaussianBeliefProp.jl.git",
     push_preview=true,
     devbranch="main",
 )
diff --git a/docs/src/index.md b/docs/src/index.md
@@ -4,7 +4,7 @@ CurrentModule = PhyloGaussianBeliefProp
 
 # PhyloGaussianBeliefProp
 
-[PhyloGaussianBeliefProp](https://github.com/cecileane/PhyloGaussianBeliefProp.jl)
+[PhyloGaussianBeliefProp](https://github.com/JuliaPhylo/PhyloGaussianBeliefProp.jl)
 is a [Julia](http://julialang.org) package for the analysis of Gaussian models on
 phylogenetic networks using belief propagation (aka message passing).
 

diff --git a/docs/src/man/installation.md b/docs/src/man/installation.md
@@ -1,10 +1,10 @@
 # Installation
 
 For information on how to install Julia and PhyloNetworks, see
-[here](https://crsl4.github.io/PhyloNetworks.jl/dev/man/installation/#Installation).
+[here](https://JuliaPhylo.github.io/PhyloNetworks.jl/dev/man/installation/#Installation).
 PhyloGaussianBeliefProp depends on PhyloNetworks.
 
-To install [PhyloGaussianBeliefProp](https://github.com/cecileane/PhyloGaussianBeliefProp.jl)
+To install [PhyloGaussianBeliefProp](https://github.com/JuliaPhylo/PhyloGaussianBeliefProp.jl)
 in the Julia REPL, do:
 ```julia
 julia> using Pkg
@@ -18,7 +18,7 @@ pkg> add PhyloGaussianBeliefProp
 ```
 
 In this manual, we will also use
-[PhyloNetworks](https://github.com/crsl4/PhyloNetworks.jl) and other packages,
+[PhyloNetworks](https://github.com/JuliaPhylo/PhyloNetworks.jl) and other packages,
 to be installed similarly, here in package mode:
 ```
 pkg> add PhyloNetworks

diff --git a/src/clustergraph.jl b/src/clustergraph.jl
@@ -131,7 +131,7 @@ all of the parents' indices are listed after the node (their child) index.
 A given node and its parents is called a "node family".
 
 **Warning**: `net` is assumed preordered, see [`preprocessnet!`](@ref) and
-[`PhyloNetworks.preorder!`](https://crsl4.github.io/PhyloNetworks.jl/latest/lib/public/#PhyloNetworks.preorder!)).
+[`PhyloNetworks.preorder!`](https://JuliaPhylo.github.io/PhyloNetworks.jl/latest/lib/public/#PhyloNetworks.preorder!)).
 """
 function nodefamilies(net::HybridNetwork)
     T = vgraph_eltype(net)
@@ -162,7 +162,7 @@ Tuple `(ispreserving, isfamily_incluster)`:
     contains at least 1 true value.
 
 **Warning**: assumes that `net` is preordered, see
-[`PhyloNetworks.preorder!`](https://crsl4.github.io/PhyloNetworks.jl/latest/lib/public/#PhyloNetworks.preorder!)).
+[`PhyloNetworks.preorder!`](https://JuliaPhylo.github.io/PhyloNetworks.jl/latest/lib/public/#PhyloNetworks.preorder!)).
 
 See also [`nodefamilies`](@ref) to get node families.
 """