From f95ee8eecb5aef61b571835fc726ffddb0e6b2da Mon Sep 17 00:00:00 2001
From: paril <Jeff Paril>
Date: Sat, 1 Feb 2025 11:42:17 +1100
Subject: [PATCH] trying to fix CI with RCall, R::BGLR and GLMakie.jl

---
 .github/workflows/CI.yml | 8 ++++++++
 docs/make.jl             | 7 +++----
 test/runtests.jl         | 6 +++---
 3 files changed, 14 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index b1a326d..017d7fb 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -37,6 +37,14 @@ jobs:
           arch: ${{ matrix.arch }}
       - uses: julia-actions/cache@v2
       - run: sudo apt-get update && sudo apt-get install -y xorg-dev mesa-utils xvfb libgl1 freeglut3-dev libxrandr-dev libxinerama-dev libxcursor-dev libxi-dev libxext-dev xsettingsd x11-xserver-utils
+      - uses: r-lib/actions/setup-r@v2
+        with:
+            r-version: "4.3.1"
+      - name: Install BGLR
+        run: |
+          install.packages("BGLR")
+        shell: Rscript {0}
+      - run: echo "LD_LIBRARY_PATH=$(R RHOME)/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV
       # - uses: julia-actions/julia-buildpkg@v1
       # - uses: julia-actions/julia-runtest@v1
       - run: DISPLAY=:0 xvfb-run -s '-screen 0 1024x768x24' julia --project -e 'using Pkg; Pkg.instantiate(); using GenomicBreeding; include("test/runtests.jl")'
diff --git a/docs/make.jl b/docs/make.jl
index aab99a3..a7d848f 100644
--- a/docs/make.jl
+++ b/docs/make.jl
@@ -8,12 +8,11 @@ makedocs(;
     authors = "jeffersonparil@gmail.com",
     sitename = "GenomicBreeding.jl",
     format = Documenter.HTML(;
-        canonical = "https://jeffersonfparil.github.io/GenomicBreeding.jl",
+        canonical = "https://GenomicBreeding.github.io/GenomicBreeding.jl",
         edit_link = "main",
         assets = String[],
     ),
-    # pages = ["Home" => "index.md"],
-    pages = ["index.md", "simulations.md", "models.md"],
+    pages = ["Home" => "index.md"],
 )
 
-deploydocs(; repo = "github.com/jeffersonfparil/GenomicBreeding.jl", devbranch = "main")
+deploydocs(; repo = "github.com/GenomicBreeding/GenomicBreeding.jl", devbranch = "main")
diff --git a/test/runtests.jl b/test/runtests.jl
index 4443a2d..38510fa 100644
--- a/test/runtests.jl
+++ b/test/runtests.jl
@@ -1,9 +1,9 @@
-using GBCore
+using GenomicBreeding
 using Test
 using Documenter
 
-Documenter.doctest(GBCore)
+Documenter.doctest(GenomicBreeding)
 
-@testset "GBCore.jl" begin
+@testset "GenomicBreeding.jl" begin
     @test 1 == 1
 end