From 708bcaa1d3d59defe08e83ccc7c900d0e0544054 Mon Sep 17 00:00:00 2001 From: Paul Bastide Date: Wed, 19 Jun 2024 22:34:42 +0200 Subject: [PATCH 1/3] Update urls to JuliaPhylo --- CITATION.bib | 2 +- README.md | 8 ++++---- docs/make.jl | 4 ++-- docs/src/index.md | 2 +- docs/src/man/installation.md | 2 +- 5 files changed, 9 insertions(+), 9 deletions(-) diff --git a/CITATION.bib b/CITATION.bib index 0418b90..f5a4144 100644 --- a/CITATION.bib +++ b/CITATION.bib @@ -4,7 +4,7 @@ @users.noreply.github.com> Paul Bastide 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 index f0ea1a8..d977aa1 100644 --- a/README.md +++ b/README.md @@ -1,9 +1,9 @@ # 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) diff --git a/docs/make.jl b/docs/make.jl index 943fc62..7bf13ad 100644 --- 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 index b07df7a..735a413 100644 --- 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 index 36bb359..30fed5b 100644 --- a/docs/src/man/installation.md +++ b/docs/src/man/installation.md @@ -4,7 +4,7 @@ For information on how to install Julia and PhyloNetworks, see [here](https://crsl4.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 From 098289ded7e6df6a79edc44b34dcc49dedcf623c Mon Sep 17 00:00:00 2001 From: Paul Bastide Date: Wed, 19 Jun 2024 22:49:46 +0200 Subject: [PATCH 2/3] crsl4 to JuliaPhylo --- README.md | 2 +- docs/src/man/installation.md | 2 +- src/clustergraph.jl | 4 ++-- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index d977aa1..07cfd10 100644 --- a/README.md +++ b/README.md @@ -11,7 +11,7 @@ [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/src/man/installation.md b/docs/src/man/installation.md index 30fed5b..6419eb4 100644 --- a/docs/src/man/installation.md +++ b/docs/src/man/installation.md @@ -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 index d6d6661..ed339b4 100644 --- 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. """ From 91198ddfa5acfcff2f995a7b78ead25acdb51ffe Mon Sep 17 00:00:00 2001 From: Paul Bastide Date: Wed, 19 Jun 2024 22:53:59 +0200 Subject: [PATCH 3/3] forgotten crsl4 --- docs/src/man/installation.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/src/man/installation.md b/docs/src/man/installation.md index 6419eb4..4ed7a6f 100644 --- a/docs/src/man/installation.md +++ b/docs/src/man/installation.md @@ -1,7 +1,7 @@ # 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/JuliaPhylo/PhyloGaussianBeliefProp.jl)