Merge pull request #42 from hkim89/master

add ci.yml and remove travis,  appveyor

.github/workflows/ci.yml

@@ -0,0 +1,72 @@
+name: CI
+on:
+  pull_request:
+    branches:
+      - master
+  push:
+    branches:
+      - master
+    tags: '*'
+jobs:
+  test:
+    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+          - '1.6' # Replace this with the minimum Julia version that your package supports. E.g. if your package requires Julia 1.5 or higher, change this to '1.5'.
+          - '1' # Leave this line unchanged. '1' will automatically expand to the latest stable 1.x release of Julia.
+          - 'nightly'
+        os:
+          - ubuntu-latest
+        arch:
+          - x64
+        include:
+          - os: windows-latest
+            version: '1'
+            arch: x64
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+      - uses: actions/cache@v1
+        env:
+          cache-name: cache-artifacts
+        with:
+          path: ~/.julia/artifacts
+          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
+          restore-keys: |
+            ${{ runner.os }}-test-${{ env.cache-name }}-
+            ${{ runner.os }}-test-
+            ${{ runner.os }}-
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-runtest@v1
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v1
+        with:
+          file: lcov.info
+  docs:
+    name: Documentation
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: '1'
+      - run: |
+          julia --project=docs -e '
+            using Pkg
+            Pkg.develop(PackageSpec(path=pwd()))
+            Pkg.instantiate()'
+      - run: |
+          julia --project=docs -e '
+            using Documenter: doctest
+            using FlxQTL
+            doctest(FlxQTL)' 
+      - run: julia --project=docs docs/make.jl
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}

Project.toml

@@ -18,13 +18,16 @@ Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 
 [compat]
+Conda = "1"
+DelimitedFiles = "1"
 Distributions = "^0.23, 0.24, 0.25"
-LossFunctions = "~0.7"
-PyPlot = "~2.10"
-Revise = "3.3"
-StaticArrays = "1.4"
-StatsBase = "~0.33"
-julia = "~1.6, ~1.7"
+LossFunctions = "~0.11"
+PyPlot = "~2.11"
+Revise = "3.5"
+StaticArrays = "1.7"
+Statistics = "1"
+StatsBase = "0.33"
+julia = "~1.9"
 
 [extras]
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

README.md

@@ -3,8 +3,7 @@
 ## *Fl*e*x*ible Multivariate Linear Mixed Model based *QTL* Analysis for Structured Multiple Traits
 
 [![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://senresearch.github.io/FlxQTL.jl/stable)
-[![Build Status](https://travis-ci.com/senresearch/FlxQTL.jl.svg?branch=master)](https://travis-ci.com/github/senresearch/FlxQTL.jl)
-[![Build Status](https://ci.appveyor.com/api/projects/status/github/senresearch/FlxQTL.jl?svg=true)](https://ci.appveyor.com/project/sens/flxqtl-jl)
+[![CI](https://github.com/senresearch/FlxQTL.jl/actions/workflows/ci.yml/badge.svg)](https://github.com/senresearch/FlxQTL.jl/actions/workflows/ci.yml)
 [![codecov](https://codecov.io/gh/senresearch/FlxQTL.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/senresearch/FlxQTL.jl)
 <!-- [![codecov](https://codecov.io/gh/hkim89/FlxQTL.jl/branch/master/graph/badge.svg?token=wNYkIkfRx1)](https://codecov.io/gh/hkim89/FlxQTL.jl) -->
 

src/FlxQTL.jl

@@ -12,7 +12,7 @@ module FlxQTL
 
 
 include("MLM.jl")
-include("QTLplot.jl")
+# include("QTLplot.jl")
 include("Miscellanea.jl")
 include("GRM.jl")
 include("EcmNestrv.jl")
@@ -25,8 +25,8 @@ using .GRM:kinshipMan,kinship4way,kinshipGs,kinshipLin,kinshipCtr,kinshipStd,shr
 export kinshipMan,kinship4way,kinshipGs,kinshipLin,kinshipCtr,kinshipStd
 export shrinkg,shrinkgLoco,kinshipLoco
 
-using .QTLplot:layers, plot1d, plot2d, subplot2d
-export layers, plot1d, plot2d, subplot2d
+# using .QTLplot:layers, plot1d, plot2d, subplot2d
+# export layers, plot1d, plot2d, subplot2d
 
 using .flxMLMM: geneScan,gene2Scan,envScan,permTest,K2eig, K2Eig, obtainKc,gene1Scan,updateKc
 #selectQTL

src/Miscellanea.jl

@@ -10,7 +10,7 @@ module Util
 
 using Random
 using Distributed
-import LossFunctions: HuberLoss, value
+import LossFunctions: HuberLoss
 import Distributions: Chisq,ccdf
 import StatsBase: mad, sample
 import Statistics: mean, var, median
@@ -341,7 +341,7 @@ function huberize(y::Vector{Float64})
 m = median(y)
 s = mad(y,normalize=true)
 z = (y.-m)./s
-l = value.(HuberLoss(1),z)
+l = HuberLoss().(z)
 x = sign.(z).* sqrt.(2*l)
 return m .+ s.*x
 end

src/QTLplot.jl

@@ -8,7 +8,7 @@ A module for generating PyPlot-based 1D-, 2D-plots for LOD scores (or effects).
 """
 module QTLplot
 
-using PyPlot
+using PyPlot, LinearAlgebra
 import Statistics:median
 
 
@@ -237,7 +237,7 @@ Chr=unique(S.chr);
           subplot(position)
           imshow(Chrom,cmap="jet",interpolation="bicubic",extent=[minimum(x),maximum(x),maximum(y),minimum(y)],vmin=0.0,vmax=maximum(S.lod));
 #          eval(Meta.parse(string("""title(string("Chromsome ", """,Chr[i+inner_num*(j-1)],""")) """)))
-           title(string("Chromosome ",Chromosome[i+inner_num*(j-1)]),fontsize=title_font)
+           title(string("Chromosome ",Chr[i+inner_num*(j-1)]),fontsize=title_font)
             xticks(fontsize=fontsize);yticks(fontsize=fontsize)
            cbar=colorbar()
             cbar.ax.tick_params(labelsize=fontsize)