From 7734e9aeebc9bd9b79867f3c6b4af7f655e89c94 Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Sat, 19 Feb 2022 16:20:17 -0600
Subject: [PATCH] ready for v0.3.3

- bump compat: CSV 0.10 (#17), julia v1.7 (updated tests to new RNG)
  thanks CompatHelper and gh-actions!
- complete ref in doc
---
 Project.toml         |  6 +++---
 docs/src/index.md    |  3 ++-
 src/quarnetGoF.jl    |  4 ++--
 test/test_qnetGoF.jl | 13 ++++++++++---
 4 files changed, 17 insertions(+), 9 deletions(-)

diff --git a/Project.toml b/Project.toml
index 7602118..d74aa97 100644
--- a/Project.toml
+++ b/Project.toml
@@ -1,7 +1,7 @@
 name = "QuartetNetworkGoodnessFit"
 uuid = "1382f7fc-2744-4d9d-8ec6-1e3efdec0746"
 authors = ["Cecile Ane <cecileane@users.noreply.github.com>"]
-version = "0.3.2"
+version = "0.3.3"
 
 [deps]
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
@@ -17,10 +17,10 @@ Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 StatsFuns = "4c63d2b9-4356-54db-8cca-17b64c39e42c"
 
 [compat]
-CSV = "0.4, 0.5, 0.6, 0.7, 0.8, 0.9"
+CSV = "0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 0.10"
 DataFrames = "0.13, 0.14, 0.15, 0.16, 0.17, 0.18, 0.19, 0.20, 0.21, 0.22, 1.0"
 NLopt = "0.5.1, 0.6"
 PhyloNetworks = "0.11, 0.12, 0.13, 0.14"
 SpecialFunctions = "0.8, 0.9, 0.10, 1.0, 2"
 StatsFuns = "0.7, 0.8, 0.9"
-julia = "1.2, 1.3, 1.4, 1.5, 1.6"
+julia = "1.2, 1.3, 1.4, 1.5, 1.6, 1.7"
diff --git a/docs/src/index.md b/docs/src/index.md
index f7f3e9c..0d47bf7 100644
--- a/docs/src/index.md
+++ b/docs/src/index.md
@@ -21,7 +21,8 @@ References:
 
 - 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)
+  [Bioinformatics](https://doi.org/10.1093/bioinformatics/btaa863),
+  37(5):634-641.
 - 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 7880760..68c569e 100644
--- a/src/quarnetGoF.jl
+++ b/src/quarnetGoF.jl
@@ -105,8 +105,8 @@ Note that `net` is **not** modified.
 
 - 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
+  Bioinformatics, 37(5):634-641.
+  doi: [10.1093/bioinformatics/btaa863](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 68c2921..9845ab0 100644
--- a/test/test_qnetGoF.jl
+++ b/test/test_qnetGoF.jl
@@ -63,11 +63,18 @@ Distributed.addprocs(2)
 # start with: julia -p 2 --project
 # or: using Distributed; @everywhere begin; using Pkg; Pkg.activate("."); using PhyloNetworks; end
 @everywhere using QuartetNetworkGoodnessFit
-netresult1 = quarnetGoFtest!(net3,d,false; seed=2298, nsim=5);
+netresult1 = quarnetGoFtest!(net3,d,false; seed=245, nsim=5);
 @test netresult1[4] ≈ [0.0024449826689709165,0.01496306673600063,0.01496306673600063,0.0024449826689709165,0.04086460431063039,0.9998541057240138,0.1901450501005025,0.8909735618259936,0.9058717147295428,0.8909735618259936,0.1901450501005025,0.9058717147295428,0.9913859984840471,0.3656465603640152,0.04086460431063039]
 @test netresult1[2] ≈ 6.21966321647047 # z stat, uncorrected
-@test netresult1[3] ≈ 3.405362128771355 # sigma
-@test netresult1[6] ≈ vcat(7.4043609719886545, repeat([-0.8885233166386386],4))
+#= with some fiddling with the seed, we could get:
+netresult1[3] ≈ 3.405362128771355 # sigma
+netresult1[6] ≈ vcat(7.4043609719886545, repeat([-0.8885233166386386],4))
+Without this fiddling, all 5 simulated z's are -0.8885233166386386 and
+we get the warning about the simulated z's being far from 0
+=#
+@test netresult1[3] > 0.888 # sigma
+@test length(netresult1[6]) == 5
+@test sort(netresult1[6])[1:4] ≈ repeat([-0.8885233166386386],4)
 netresult1 = (@test_logs (:warn, r"far from 0") quarnetGoFtest!(net3,d,true; seed=182, nsim=2, quartetstat=:Qlog));
 # just because 2 simulated z's only, and same values bc tiny network. may break with different RNG
 # note: with verbose=true, we see hybrid-lambda's warnings: