From e27ce13f5a8c96cda1d76db138f78ffde31d207f Mon Sep 17 00:00:00 2001 From: Cecile Ane Date: Mon, 18 Jan 2021 21:41:05 -0600 Subject: [PATCH] hybrid lambda dependency: v0.6.3-beta bumped Documenter; migrated to travis-ci.com --- Project.toml | 2 +- README.md | 2 +- deps/build.jl | 18 +++++++++--------- docs/Project.toml | 2 +- docs/src/index.md | 3 ++- src/quarnetGoF.jl | 4 +++- test/test_qnetGoF.jl | 2 +- 7 files changed, 18 insertions(+), 15 deletions(-) diff --git a/Project.toml b/Project.toml index 4518d4a..3ab7ea0 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "QuartetNetworkGoodnessFit" uuid = "1382f7fc-2744-4d9d-8ec6-1e3efdec0746" authors = ["Cecile Ane "] -version = "0.2.1" +version = "0.3.0" [deps] CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b" diff --git a/README.md b/README.md index c644f83..44f6698 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -[![Build Status](https://travis-ci.org/cecileane/QuartetNetworkGoodnessFit.jl.svg?branch=master)](https://travis-ci.org/cecileane/QuartetNetworkGoodnessFit.jl) +[![Build Status](https://travis-ci.com/cecileane/QuartetNetworkGoodnessFit.jl.svg?branch=master)](https://travis-ci.com/cecileane/QuartetNetworkGoodnessFit.jl) [![Coverage Status](https://coveralls.io/repos/cecileane/QuartetNetworkGoodnessFit.jl/badge.svg?branch=master&service=github)](https://coveralls.io/github/cecileane/QuartetNetworkGoodnessFit.jl?branch=master) [![codecov.io](http://codecov.io/github/cecileane/QuartetNetworkGoodnessFit.jl/coverage.svg?branch=master)](http://codecov.io/github/cecileane/QuartetNetworkGoodnessFit.jl?branch=master) diff --git a/deps/build.jl b/deps/build.jl index b763b79..7dabc02 100644 --- a/deps/build.jl +++ b/deps/build.jl @@ -8,18 +8,18 @@ products = [ ] # Download binaries from hosted location -bin_prefix = "https://github.com/cecileane/HybridLambdaBuilder/releases/download/v0.6.2-beta" +bin_prefix = "https://github.com/cecileane/HybridLambdaBuilder/releases/download/v0.6.3-beta" # Listing of files generated by BinaryBuilder: download_info = Dict( - Linux(:aarch64, libc=:glibc) => ("$bin_prefix/HybridLambda.v0.6.2-beta.aarch64-linux-gnu.tar.gz", "cb9723304dfc7a4d67ba305d6a7c3041c665c8db53b170fde320d9533f7cb367"), - Linux(:aarch64, libc=:musl) => ("$bin_prefix/HybridLambda.v0.6.2-beta.aarch64-linux-musl.tar.gz", "6291d48b2e6b569dbc2bc011f5d768eb44e5611aa1943faae720cb1ce281b5d3"), - Linux(:armv7l, libc=:glibc, call_abi=:eabihf) => ("$bin_prefix/HybridLambda.v0.6.2-beta.arm-linux-gnueabihf.tar.gz", "807aafa70fb1d022b0b796abc9e2a89a030ef79357cc3880e1a8dcae3823a667"), - Linux(:armv7l, libc=:musl, call_abi=:eabihf) => ("$bin_prefix/HybridLambda.v0.6.2-beta.arm-linux-musleabihf.tar.gz", "381f40c0d6892bd7ceafdf2cce0d35b06617388ff9d090dcc6a7fa93bc2bc006"), - Linux(:i686, libc=:glibc) => ("$bin_prefix/HybridLambda.v0.6.2-beta.i686-linux-gnu.tar.gz", "c49e49736aa7cc5b82f9d40fdffd7effba2f2aaaf77a8090dee5c3c064c0895d"), - Linux(:powerpc64le, libc=:glibc) => ("$bin_prefix/HybridLambda.v0.6.2-beta.powerpc64le-linux-gnu.tar.gz", "8643c0708d1cce0080984e08168a68f1361a2ae1876cf95da8ab39a0cd1a2423"), - MacOS(:x86_64) => ("$bin_prefix/HybridLambda.v0.6.2-beta.x86_64-apple-darwin14.tar.gz", "4ed16d6775ddcef45e63c1a769d9bdf731fc9eeeb5d44572a486548f53c27f71"), - Linux(:x86_64, libc=:glibc) => ("$bin_prefix/HybridLambda.v0.6.2-beta.x86_64-linux-gnu.tar.gz", "cf27dbf2ced3b6d167112a8ca6c7c2aa818cc622494bfc5bca8ede03c5da6ea8"), + Linux(:aarch64, libc=:glibc) => ("$bin_prefix/HybridLambda.v0.6.3-beta.aarch64-linux-gnu.tar.gz", "25fd9884732898a05f61402ed94252f17ed0afb861cdc5ea5495fa80550b823f"), + Linux(:aarch64, libc=:musl) => ("$bin_prefix/HybridLambda.v0.6.3-beta.aarch64-linux-musl.tar.gz", "1d2f70519d060ca16df0219d3acd78eea93fb06601be2634689770d34866d86b"), + Linux(:armv7l, libc=:glibc, call_abi=:eabihf) => ("$bin_prefix/HybridLambda.v0.6.3-beta.arm-linux-gnueabihf.tar.gz", "c8cc211510d585f8fa785f59d246c7c79a4de4588c3a43b127e440f040959c49"), + Linux(:armv7l, libc=:musl, call_abi=:eabihf) => ("$bin_prefix/HybridLambda.v0.6.3-beta.arm-linux-musleabihf.tar.gz", "e11086ad9ff34a73442958426368b48f747638c0815b8b7e13719cc2a47f4eca"), + Linux(:i686, libc=:glibc) => ("$bin_prefix/HybridLambda.v0.6.3-beta.i686-linux-gnu.tar.gz", "bb46daceeb2194fe8d353d60dac82923136ff1e62414e475bdca3c816027c59c"), + Linux(:powerpc64le, libc=:glibc) => ("$bin_prefix/HybridLambda.v0.6.3-beta.powerpc64le-linux-gnu.tar.gz", "604778b3565f42040b915aab6a04da973cfc2010b913107eb258e32d8d99ec28"), + MacOS(:x86_64) => ("$bin_prefix/HybridLambda.v0.6.3-beta.x86_64-apple-darwin14.tar.gz", "e07e30037a168bc88b68fd03c5e0640582a3c6e8b5339a37418a58ab9e2134f7"), + Linux(:x86_64, libc=:glibc) => ("$bin_prefix/HybridLambda.v0.6.3-beta.x86_64-linux-gnu.tar.gz", "799aa1470211f58a641f71ec5e5059f9ae49dd73a957000a4d948b52cbbab063"), ) # Install unsatisfied or updated dependencies: diff --git a/docs/Project.toml b/docs/Project.toml index d417794..612219a 100644 --- a/docs/Project.toml +++ b/docs/Project.toml @@ -8,4 +8,4 @@ PhyloNetworks = "33ad39ac-ed31-50eb-9b15-43d0656eaa72" [compat] CSV = "0.7" DataFrames = "0.21" -Documenter = "~0.24" +Documenter = "~0.26" diff --git a/docs/src/index.md b/docs/src/index.md index 018f2cf..f7f3e9c 100644 --- a/docs/src/index.md +++ b/docs/src/index.md @@ -19,8 +19,9 @@ Depth = 1 References: -- Ruoyi Cai & Cécile Ané (in prep). +- Ruoyi Cai & Cécile Ané (2021). Assessing the fit of the multi-species network coalescent to multi-locus data. + [Bioinformatics](https://doi.org/10.1093/bioinformatics/btaa863) - Noah W. M. Stenz, Bret Larget, David A. Baum, and Cécile Ané (2015). Exploring tree-like and non-tree-like patterns using genome sequences: An example using the inbreeding plant species *Arabidopsis thaliana* (L.) Heynh. [Systematic Biology](https://doi.org/10.1093/sysbio/syv039), 64(5):809-823. diff --git a/src/quarnetGoF.jl b/src/quarnetGoF.jl index 5a9842a..7880760 100644 --- a/src/quarnetGoF.jl +++ b/src/quarnetGoF.jl @@ -103,8 +103,10 @@ Note that `net` is **not** modified. # references -- Ruoyi Cai & Cécile Ané (in prep). +- Ruoyi Cai & Cécile Ané (2021). Assessing the fit of the multi-species network coalescent to multi-locus data. + Bioinformatics, + https://doi.org/10.1093/bioinformatics/btaa863 - Lorenzen (1995). A new family of goodness-of-fit statistics for discrete multivariate data. diff --git a/test/test_qnetGoF.jl b/test/test_qnetGoF.jl index 58f1862..3247da7 100644 --- a/test/test_qnetGoF.jl +++ b/test/test_qnetGoF.jl @@ -80,7 +80,7 @@ Distributed.rmprocs(workers()) # network that caused a bug in hybrid-Lambda v0.6.2-beta, see # https://github.com/hybridLambda/hybrid-Lambda/issues/36 net = readTopology("(((A:7.13,(B:5.98)#H18:1.15::0.79):0.1,C:7.23):0.07,((D:0.0)#H19:6.2::0.89,(E:5.64,(O:0.0,#H19:0.0::0.11):5.64):0.56):1.1,#H18:1.32::0.21);") -@test_logs (:warn,r"^The simulated z values") quarnetGoFtest!(net,d,false; seed=419, nsim=5); +@test_logs quarnetGoFtest!(net,d,false; seed=419, nsim=5); end