change urls to JuliaPhylo (JuliaPhylo#213)

from crsl4 & cecileane  to juliaphylo, keep case in docs/make.jl

Author: crsl4

CONTRIBUTING.md

@@ -4,7 +4,7 @@ The following guidelines are designed for contributors of `PhyloNetworks`.
 
 ## Reporting Issues and Questions
 
-For reporting a bug, a failed function or requesting a new feature, you can simply open an issue in [the issue tracker](https://github.com/crsl4/PhyloNetworks.jl/issues).
+For reporting a bug, a failed function or requesting a new feature, you can simply open an issue in [the issue tracker](https://github.com/juliaphylo/PhyloNetworks.jl/issues).
 First, seach through existing issues (open or closed) that might have the answer to your question.
 If you are reporting a bug, please also include a minimal code example or all relevant information for us to replicate the issue.
 
@@ -30,7 +30,7 @@ Please use the following steps:
    Make sure that your code passes all the
    [tests](https://pkgdocs.julialang.org/v1/managing-packages/#Testing-packages).
 5. Push your changes to your fork
-6. [Submit a pull request](https://github.com/crsl4/PhyloNetworks.jl/pulls) against the `master` branch in `PhyloNetworks`. Make sure that your code passes all the automatic tests and that it is not in conflict with the current status of `master`
+6. [Submit a pull request](https://github.com/juliaphylo/PhyloNetworks.jl/pulls) against the `master` branch in `PhyloNetworks`. Make sure that your code passes all the automatic tests and that it is not in conflict with the current status of `master`
 
 Please make sure to follow the Julia package guidelines and conventions on your code. `PhyloNetworks` was created before these conventions were catalyzed, but we are attempting to follow them going forward. 
 

README.md

@@ -1,9 +1,9 @@
 # PhyloNetworks: analysis for phylogenetic networks <img src="docs/src/logo_text.png" align=right>
 
-[![doc stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://crsl4.github.io/PhyloNetworks.jl/stable)
-[![doc dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://crsl4.github.io/PhyloNetworks.jl/dev)
-[![Build status](https://github.com/crsl4/PhyloNetworks.jl/workflows/CI/badge.svg?branch=master)](https://github.com/crsl4/PhyloNetworks.jl/actions/workflows/ci.yml)
-[![coverage](https://codecov.io/gh/crsl4/PhyloNetworks.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/crsl4/PhyloNetworks.jl)
+[![doc stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://juliaphylo.github.io/PhyloNetworks.jl/stable)
+[![doc dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://juliaphylo.github.io/PhyloNetworks.jl/dev)
+[![Build status](https://github.com/juliaphylo/PhyloNetworks.jl/workflows/CI/badge.svg?branch=master)](https://github.com/juliaphylo/PhyloNetworks.jl/actions/workflows/ci.yml)
+[![coverage](https://codecov.io/gh/juliaphylo/PhyloNetworks.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/juliaphylo/PhyloNetworks.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/PhyloNetworks.svg)](https://JuliaCI.github.io/NanosoldierReports/pkgeval_badges/report.html)
@@ -25,14 +25,14 @@ PhyloNetworks is a [Julia](http://julialang.org) package with utilities to:
 - phylogenetic comparative methods for continuous trait evolution
   on species networks / trees
 - plot networks (and trees), via the companion package
-  [PhyloPlots](https://github.com/cecileane/PhyloPlots.jl)
+  [PhyloPlots](https://github.com/juliaphylo/PhyloPlots.jl)
 
 To get help, check
 
-- the [latest documentation](https://crsl4.github.io/PhyloNetworks.jl/dev)
-- the [wiki](https://github.com/crsl4/PhyloNetworks.jl/wiki) for a step-by-step tutorial
+- the [latest documentation](https://juliaphylo.github.io/PhyloNetworks.jl/dev)
+- the [wiki](https://github.com/juliaphylo/PhyloNetworks.jl/wiki) for a step-by-step tutorial
   with background on networks (last revised 2022)
-- [tutorial](https://cecileane.github.io/networkPCM-workshop/) for
+- [tutorial](https://juliaphylo.github.io/networkPCM-workshop/) for
   comparative methods, including network calibration (2023 workshop)
 - the [google group](https://groups.google.com/forum/#!forum/phylonetworks-users)
   for common questions. Join the group to post/email your questions,

docs/make.jl

@@ -15,7 +15,7 @@ makedocs(
         prettyurls = get(ENV, "CI", nothing) == "true", # easier local build
         size_threshold = 600 * 2^10,
         size_threshold_warn = 500 * 2^10, # 600 KiB
-        canonical="https://crsl4.github.io/PhyloNetworks.jl/stable/",
+        canonical="https://juliaphylo.github.io/PhyloNetworks.jl/stable/",
         edit_link="master",
     ),
     # exception, so warning-only for :missing_docs. List all others:
@@ -48,7 +48,7 @@ makedocs(
 )
 
 deploydocs(
-    repo = "github.com/crsl4/PhyloNetworks.jl.git",
+    repo = "github.com/JuliaPhylo/PhyloNetworks.jl.git",
     push_preview = true,
     devbranch = "master",
 )

docs/readme.md

@@ -1,7 +1,7 @@
 # notes to maintain documentation
 
 - built with [Documenter](https://documenter.juliadocs.org/stable/).
-- deployed [here](https://crsl4.github.io/PhyloNetworks.jl/)
+- deployed [here](https://juliaphylo.github.io/PhyloNetworks.jl/)
   (go to `dev/` or `stable/`)
   using GitHub and files committed to the `gh-pages` branch.
 

docs/src/index.md

@@ -1,6 +1,6 @@
 # PhyloNetworks.jl
 
-[PhyloNetworks](https://github.com/crsl4/PhyloNetworks.jl)
+[PhyloNetworks](https://github.com/juliaphylo/PhyloNetworks.jl)
 is a [Julia](http://julialang.org) package for the
 manipulation, visualization, inference of phylogenetic networks,
 and their use for trait evolution.
@@ -9,10 +9,10 @@ and their use for trait evolution.
 
 **How to get help**
 
-- the package [wiki](https://github.com/crsl4/PhyloNetworks.jl/wiki) has a step-by-step
+- the package [wiki](https://github.com/juliaphylo/PhyloNetworks.jl/wiki) has a step-by-step
   tutorial, done for the MBL workshop (last revised 2022), with background on networks and
   explanations.
-- [tutorial](https://cecileane.github.io/networkPCM-workshop/) for
+- [tutorial](https://juliaphylo.github.io/networkPCM-workshop/) for
   comparative methods, including network calibration (2023 workshop)
 - the [google group](https://groups.google.com/forum/#!forum/phylonetworks-users)
   has answers to common questions.
@@ -22,7 +22,7 @@ and their use for trait evolution.
 
 ## References
 
-See their [bibtex format](https://github.com/crsl4/PhyloNetworks.jl/blob/master/CITATION.bib).
+See their [bibtex format](https://github.com/juliaphylo/PhyloNetworks.jl/blob/master/CITATION.bib).
 
 for the package:
 - Claudia Solís-Lemus, Paul Bastide and Cécile Ané (2017).

docs/src/man/bootstrap.md

@@ -19,7 +19,7 @@ bootnet = bootsnaq(startnetwork, df, hmax=1, filename="bootstrap")
 
 The names of all our bootstrap files are listed in "BSlistfiles".
 (ASTRAL can use the same file to do its own bootstrap, see the
-[wiki](https://github.com/crsl4/PhyloNetworks.jl/wiki/Gene-Trees:-RAxML)
+[wiki](https://github.com/juliaphylo/PhyloNetworks.jl/wiki/Gene-Trees:-RAxML)
 for more details).
 The function `readBootstrapTrees` can read this list of file names, then
 read each bootstrap file to get the bootstrap sample for each gene.

docs/src/man/inputdata.md

@@ -8,7 +8,7 @@ from multiple molecular sequence alignments. There are two alternatives for the
 
 This [pipeline](https://github.com/nstenz/TICR) can be used to obtain the table of
 quartet CF needed as input for SNaQ
-(see also the [wiki](https://github.com/crsl4/PhyloNetworks.jl/wiki/TICR:-from-alignments-to-quartet-concordance-factors).)
+(see also the [wiki](https://github.com/juliaphylo/PhyloNetworks.jl/wiki/TICR:-from-alignments-to-quartet-concordance-factors).)
 It starts from the sequence alignments,
 runs MrBayes and then BUCKy (both parallelized), producing the
 table of estimated CFs and their credibility intervals.
@@ -25,9 +25,9 @@ and run Julia from there.
 Suppose you have a file with a list of gene trees in parenthetical
 format called `raxmltrees.tre`.
 You can access the example file of input trees
-[here](https://github.com/crsl4/PhyloNetworks/blob/master/examples/raxmltrees.tre)
+[here](https://github.com/juliaphylo/PhyloNetworks/blob/master/examples/raxmltrees.tre)
 or
-[here](https://raw.githubusercontent.com/crsl4/PhyloNetworks/master/examples/raxmltrees.tre)
+[here](https://raw.githubusercontent.com/juliaphylo/PhyloNetworks/master/examples/raxmltrees.tre)
 for easier download.
 
 Do not copy-paste into a "smart" text-editor. Instead, save the file
@@ -59,7 +59,7 @@ genetrees = readMultiTopology(raxmltrees);
 genetrees[3]
 ```
 To visualize any of these input trees, use the
-[PhyloPlots](https://github.com/cecileane/PhyloPlots.jl) package:
+[PhyloPlots](https://github.com/juliaphylo/PhyloPlots.jl) package:
 ```@example qcf
 using PhyloPlots
 using RCall # hide
@@ -123,9 +123,9 @@ in a file `buckyCF.csv` in this format
 
 we would read it in one step like this: `readTableCF("buckyCF.csv")`.
 An example file comes with the package, available
-[here](https://github.com/crsl4/PhyloNetworks/blob/master/examples/buckyCF.csv)
+[here](https://github.com/juliaphylo/PhyloNetworks/blob/master/examples/buckyCF.csv)
 or
-[here](https://raw.githubusercontent.com/crsl4/PhyloNetworks/master/examples/buckyCF.csv).
+[here](https://raw.githubusercontent.com/juliaphylo/PhyloNetworks/master/examples/buckyCF.csv).
 
 ```@repl qcf
 buckyCFfile = joinpath(dirname(pathof(PhyloNetworks)), "..","examples","buckyCF.csv");
@@ -155,7 +155,7 @@ it can be used as a starting point for the optimization.
 From our gene trees, we estimated a species tree with
 [ASTRAL](https://github.com/smirarab/ASTRAL/blob/master/astral-tutorial.md).
 This tree comes with the package in file `astral.tre`
-[here](https://github.com/crsl4/PhyloNetworks/blob/master/examples/astral.tre).
+[here](https://github.com/juliaphylo/PhyloNetworks/blob/master/examples/astral.tre).
 This file has 102 trees: 100 bootstrap species trees,
 followed by their greedy consensus,
 followed by the best tree on the original data.

docs/src/man/installation.md

@@ -59,7 +59,7 @@ The PhyloNetworks package has dependencies like
 [DataFrames](http://juliadata.github.io/DataFrames.jl/stable/)
 (see the `Project.toml` file for the full list), but everything is installed automatically.
 
-The companion package [PhyloPlots](https://github.com/cecileane/PhyloPlots.jl)
+The companion package [PhyloPlots](https://github.com/juliaphylo/PhyloPlots.jl)
 has utilities to visualize networks, and for interoperability,
 such as to export networks to R (which can then be plotted via R).
 To install:

docs/src/man/multiplealleles.md

@@ -18,12 +18,12 @@ tm = CSV.read(mappingfile, DataFrame) # taxon map as a data frame
 taxonmap = Dict(row[:individual] => row[:species] for row in eachrow(tm)) # taxon map as a dictionary
 ```
 
-The [mapping file](https://github.com/crsl4/PhyloNetworks/blob/master/examples/mappingIndividuals.csv)
+The [mapping file](https://github.com/juliaphylo/PhyloNetworks/blob/master/examples/mappingIndividuals.csv)
 can be a text (or `csv`) file with two columns (at least):
 one for the individuals, named `allele` or `individual`,
 and one column containing the species names, named `species`.
 Each row should map an allele name to a species name.
-Next, read in the [gene trees](https://github.com/crsl4/PhyloNetworks/blob/master/examples/genetrees_alleletips.tre)
+Next, read in the [gene trees](https://github.com/juliaphylo/PhyloNetworks/blob/master/examples/genetrees_alleletips.tre)
 and calculate the quartet CFs at the species level:
 
 

docs/src/man/parsimony.md

@@ -16,9 +16,9 @@ The data table may have missing data, and may contain extra taxa
 that we might want to exclude.
 
 An example file comes with the package, available
-[here](https://github.com/crsl4/PhyloNetworks/blob/master/examples/Swadesh.csv)
+[here](https://github.com/juliaphylo/PhyloNetworks/blob/master/examples/Swadesh.csv)
 or
-[here](https://raw.githubusercontent.com/crsl4/PhyloNetworks/master/examples/Swadesh.csv).
+[here](https://raw.githubusercontent.com/juliaphylo/PhyloNetworks/master/examples/Swadesh.csv).
 
 ```@setup parsimony
 using PhyloNetworks

docs/src/man/snaq_plot.md

@@ -297,7 +297,7 @@ plot(x=collect(0:3), y=scores, Geom.point, Geom.line)
 ## Network Visualization
 
 To visualize the estimated network, we can use the companion package
-[PhyloPlots](https://github.com/cecileane/PhyloPlots.jl).
+[PhyloPlots](https://github.com/juliaphylo/PhyloPlots.jl).
 In the example below, julia creates and sends the plot to R
 via [RCall](https://github.com/JuliaInterop/RCall.jl),
 so we can tweak the plot in various ways via commands sent to R.
@@ -379,7 +379,7 @@ lower the better. See the section to get the score of [Candidate Networks](@ref)
 ## SNaQ error reporting
 
 Please report any bugs and errors by opening an
-[issue](https://github.com/crsl4/PhyloNetworks.jl/issues/new).
+[issue](https://github.com/juliaphylo/PhyloNetworks.jl/issues/new).
 The easiest way to provide information on the error is by checking the
 `.err` file, which will show the number of runs that
 failed and the corresponding seed to replicate the run.

docs/src/man/ticr_howtogetQuartetCFs.md

@@ -1,14 +1,14 @@
 # TICR pipeline
 
-PhyloNetworks' [wiki](https://github.com/crsl4/PhyloNetworks.jl/wiki/TICR:-from-alignments-to-quartet-concordance-factors)
+PhyloNetworks' [wiki](https://github.com/juliaphylo/PhyloNetworks.jl/wiki/TICR:-from-alignments-to-quartet-concordance-factors)
 has a step-by-step tutorial,
 to go from multiple sequence alignments
 to a table of quartet gene frequencies (concordance factors: CFs),
 through BUCKy (to integrate out gene tree uncertainty) or through RAxML.
 To get the `raxml.pl` perl script to run RAxML on each gene,
 download the content of that wiki with
 
-`git clone https://github.com/crsl4/PhyloNetworks.jl.wiki.git`
+`git clone https://github.com/juliaphylo/PhyloNetworks.jl.wiki.git`
 
 then go to the `script/` folder.  
 Full information and code is [here](https://github.com/nstenz/TICR).

docs/src/man/trait_tree.md

@@ -196,7 +196,7 @@ the `level` of the prediction interval. If not given, the default value is
 It is also possible to plot both the reconstructed state and the predicted value
 on the same plot, using the optional keyword argument `withExp`.
 As shown below, we could also use the `RCall` method from the
-[`plot`](https://cecileane.github.io/PhyloPlots.jl/stable/lib/public/) function.
+[`plot`](https://juliaphylo.github.io/PhyloPlots.jl/stable/lib/public/) function.
 ```@example tree_trait
 plot(truenet, nodelabel = predintPlot(ancTrait1, withExp=true));
 nothing # hide

src/manipulateNet.jl

@@ -239,7 +239,7 @@ number 'nodeNumber' (by default) or with index 'nodeNumber' if index=true.
 Attributes isChild1 and containRoot are updated along the way.
 Use `plot(net, shownodenumber=true, showedgelength=false)` to
 visualize and identify a node of interest.
-(see package [PhyloPlots](https://github.com/cecileane/PhyloPlots.jl))
+(see package [PhyloPlots](https://github.com/juliaphylo/PhyloPlots.jl))
 
 Return the network.
 
@@ -320,7 +320,7 @@ Attributes `isChild1` and `containRoot` are updated along the way.
 This adds a new node and a new edge to the network.
 Use `plot(net, showedgenumber=true, showedgelength=false)` to
 visualize and identify an edge of interest.
-(see package [PhyloPlots](https://github.com/cecileane/PhyloPlots.jl))
+(see package [PhyloPlots](https://github.com/juliaphylo/PhyloPlots.jl))
 
 See also: [`rootatnode!`](@ref).
 """
@@ -799,7 +799,7 @@ and the optional argument `orderedEdgeNum` is ignored.
 
 Use `plot(net, shownodenumber=true, showedgenumber=false)` to map node and edge numbers
 on the network, as shown in the examples below.
-(see package [PhyloPlots](https://github.com/cecileane/PhyloPlots.jl))
+(see package [PhyloPlots](https://github.com/juliaphylo/PhyloPlots.jl))
 
 Warning: assumes that edges are correctly directed (isChild1 updated). This is done
 by `plot(net)`. Otherwise run `directEdges!(net)`.

src/traits.jl

@@ -3125,7 +3125,7 @@ end
 
 Compute and format the expected reconstructed states for the plotting function.
 The resulting dataframe can be readily used as a `nodelabel` argument to
-`plot` from package [`PhyloPlots`](https://github.com/cecileane/PhyloPlots.jl).
+`plot` from package [`PhyloPlots`](https://github.com/juliaphylo/PhyloPlots.jl).
 Keyword argument `markMissing` is a string that is appended to predicted
 tip values, so that they can be distinguished from the actual datapoints. Default to
 "*". Set to "" to remove any visual cue.
@@ -3181,7 +3181,7 @@ end
 
 Compute and format the prediction intervals for the plotting function.
 The resulting dataframe can be readily used as a `nodelabel` argument to
-`plot` from package [`PhyloPlots`](https://github.com/cecileane/PhyloPlots.jl).
+`plot` from package [`PhyloPlots`](https://github.com/juliaphylo/PhyloPlots.jl).
 Keyworks argument `level` control the confidence level of the
 prediction interval. If `withExp` is set to true, then the best
 predicted value is also shown along with the interval.
@@ -3401,7 +3401,7 @@ julia> ancStates = ancestralStateReconstruction(fitBM) # Should produce a warnin
 │ assuming that the estimated variance rate of evolution is correct.
 │ Additional uncertainty in the estimation of this variance rate is
 │ ignored, so prediction intervals should be larger.
-└ @ PhyloNetworks ~/build/crsl4/PhyloNetworks.jl/src/traits.jl:3359
+└ @ PhyloNetworks ~/build/juliaphylo/PhyloNetworks.jl/src/traits.jl:3359
 ReconstructedStates:
 ───────────────────────────────────────────────
   Node index      Pred.        Min.  Max. (95%)
@@ -3548,7 +3548,7 @@ julia> ancStates = ancestralStateReconstruction(fitBM);
 │ assuming that the estimated variance rate of evolution is correct.
 │ Additional uncertainty in the estimation of this variance rate is
 │ ignored, so prediction intervals should be larger.
-└ @ PhyloNetworks ~/build/crsl4/PhyloNetworks.jl/src/traits.jl:3166
+└ @ PhyloNetworks ~/build/juliaphylo/PhyloNetworks.jl/src/traits.jl:3166
 
 julia> first(expectations(ancStates), 3) # looking at first 3 nodes only
 3×2 DataFrame

test/test_lm.jl

@@ -11,7 +11,7 @@ preorder!(net)
 # one another (Especialy for hybrids) ?
 # see QuartetNetworkGoodnessFit.ultrametrize! which can detect if the network is
 # time-consistent: all paths from the root to a given node have the same length
-# https://github.com/cecileane/QuartetNetworkGoodnessFit.jl
+# https://github.com/juliaphylo/QuartetNetworkGoodnessFit.jl
 
 # Ancestral state reconstruction with ready-made matrices
 params = ParamsBM(10, 1)