hybrid lambda dependency: v0.6.3-beta

bumped Documenter; migrated to travis-ci.com

Project.toml

@@ -1,7 +1,7 @@
 name = "QuartetNetworkGoodnessFit"
 uuid = "1382f7fc-2744-4d9d-8ec6-1e3efdec0746"
 authors = ["Cecile Ane <[email protected]>"]
-version = "0.2.1"
+version = "0.3.0"
 
 [deps]
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"

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)
 

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:

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"

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.

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.

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