[pull] develop from solgenomics:master

.eslintignore

@@ -0,0 +1 @@
+/docs/*

.github/linters/.htmlhintrc

@@ -0,0 +1,5 @@
+{
+    "head-script-disabled": false,
+    "alt-require": false,
+    "id-class-value": false
+}

.github/workflows/.htmlhintrc

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+{
+  "head-script-disabled": false
+}

.github/workflows/linter.yml

@@ -0,0 +1,50 @@
+---
+name: Lint
+
+on: # yamllint disable-line rule:truthy
+  push:
+    branches:
+      - 'master'
+  pull_request:
+    branches:
+      - 'master'
+
+permissions: {}
+
+env:
+  FILTER_REGEX_EXCLUDE: "docs/.*"
+
+jobs:
+  build:
+    name: Lint
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: read
+      packages: read
+      # To report GitHub Actions status checks
+      statuses: write
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+        with:
+          # super-linter needs the full git history to get the
+          # list of files that changed across commits
+          fetch-depth: 0
+
+      - name: Super-linter
+        uses: super-linter/super-linter@v7.1.0 # x-release-please-version
+        env:
+          # To report GitHub Actions status checks
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          HTMLHINT_CONFIG_FILE: .github/linters/.htmlhintrc
+          VALIDATE_ALL_CODEBASE: false
+          VALIDATE_ANSIBLE: false
+          VALIDATE_CHECKOV: false
+          VALIDATE_JSCPD: false
+          VALIDATE_LATEX: false
+          FIX_YAML_PRETTIER: true
+          VALIDATE_JAVASCRIPT_PRETTIER: false
+          VALIDATE_JAVASCRIPT_STANDARD: false
+          VALIDATE_SQLFLUFF: false

.github/workflows/static.yml

@@ -0,0 +1,47 @@
+# Simple workflow for deploying static content to GitHub Pages
+name: Deploy static content to Pages
+
+on:
+  # Runs on pushes/marge targeting the default branch
+  push:
+    branches: ["master"]
+    paths:
+      - 'docs/**'
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
+# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  # Single deploy job since we're just deploying
+  deploy_static_pages:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Setup Pages
+        uses: actions/configure-pages@v4
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          # Upload docs only
+          path: './docs'
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4
+
+

.github/workflows/test.yml

@@ -42,7 +42,7 @@ jobs:
 
     steps:
       - name: Checkout sgn
-        uses: actions/checkout@v2
+        uses: actions/checkout@v5
 
       - name: Run unit tests
         run: prove --recurse t/unit 2>/dev/null

.github/workflows/test_static.yml

@@ -0,0 +1,45 @@
+# Simple workflow for deploying static content to GitHub Pages
+name: Build documentation with R bookmark
+
+on:
+  # Runs on pushes/marge targeting the default branch
+  pull_request:    
+    paths:
+      - 'docs/r_markdown_docs/**'
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: write 
+  id-token: write
+
+jobs:
+  # Single deploy job since we're just deploying
+  build_and_deploy_static_pages_for_manual:          
+    runs-on: ubuntu-latest
+    container: 
+      image: bienkowskid/fedora40-r-bookdown
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:          
+          fetch-depth: 0
+          ref: ${{ github.event.pull_request.head.ref }}        
+      - name: Save directory for checkout
+        run: git config --global --add safe.directory "$GITHUB_WORKSPACE"
+      - name: Create gitbook         
+        working-directory: ./docs/r_markdown_docs
+        run: R -q -e 'bookdown::render_book("index.Rmd", "bookdown::gitbook")'        
+      - name: Create manual pdf         
+        working-directory: ./docs/r_markdown_docs
+        run: R -q -e 'bookdown::render_book("index.Rmd", "bookdown::pdf_book")'        
+      - name: Commit and push documentation        
+        run: |          
+          date > generated.txt
+          git config user.name github-actions
+          git config user.email github-actions@github.com
+          git add --force --all docs/
+          git commit -m "update bookdown docs"
+          git push

.gitignore

@@ -47,4 +47,7 @@ typescript
 docs/Gemfile.lock
 docs/_site/
 .DS_Store
-sgn.iml
+sgn.iml
+docs/*
+!docs/r_markdown_docs
+.idea/

R/DRRC.r

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+
+args=commandArgs(TRUE)
+
+##args is now a list of character vectors
+## First check to see if arguments are passed.
+## Then cycle through each element of the list and evaluate the expressions.
+
+if(length(args)==0){
+    print("No arguments supplied.")
+    ##supply default values
+    paramfile=''
+} else {
+    for(i in 1:length(args)){
+        print(paste("Processing arg ", args[[i]]));
+        eval(parse(text=args[[i]]))
+    }
+}
+
+library(reshape2)
+library(dplyr)
+library(blocksdesign)
+
+source(paramfile)
+## 1) Preparing dataframe
+all.clones <- treatments
+nTrt <- length(all.clones)
+nRep <- nRep
+nRows <- nRow
+nCols <- nCol
+# nCols <- nTrt*nRep/nRows
+rowsPerBlock <- nTrt/nCols
+colsPerBlock <- nTrt/nRows
+superCols <- nCols/colsPerBlock
+totalPlots <- nTrt*nRep
+
+plot_type <- plot_type 
+plot_start <- plot_start
+
+blocks = data.frame(block_number = gl(nRep,nTrt),
+                    Cols = gl(superCols,colsPerBlock,totalPlots),
+                    row_number = gl(nRows,nCols,totalPlots),
+                    col_number = gl(nCols,1,totalPlots))
+
+## Setting rep number orthogonal to block number
+rep_number = as.numeric(blocks$Cols)
+
+
+# treatments = data.frame(treatments =gl(nTrt,1,totalPlots))
+Z=design(all.clones,blocks, searches = 50, weighting=0.5)
+fieldBook <- Z$Design
+
+trialMatrix <- matrix(0,nRows,nCols)
+
+for(i in 1:nrow(fieldBook)){
+  trialMatrix[fieldBook$subRows[i],fieldBook$subCols[i]]<-fieldBook$treatments[i]
+}
+trialMatrix
+
+## Adding plot number
+colnames(fieldBook)[5] <- "plot_number"
+
+fieldBook$block_number <- as.integer(fieldBook$block_number)
+fieldBook$row_number <- as.integer(fieldBook$row_number)
+fieldBook$col_number <- as.integer(fieldBook$col_number)
+
+# Load dplyr
+library(dplyr)
+
+# Arrange fieldBook by row_number and col_number
+fieldBook <- fieldBook %>% arrange(row_number, col_number)
+fieldBook$plot_number <- c(1:totalPlots)
+fieldBook$plot_id <- c(1:nTrt)
+
+
+
+## Number start
+## 00101 will be added for NCSU
+if(plot_start == "00101"){
+  fieldBook$plot_number = paste0(formatC(fieldBook$block_number,width=3,flag="0"),
+                              formatC(fieldBook$plot_id,width=2,flag="0"))
+}else if (plot_start == 1001){
+  fieldBook$plot_number <- (1000*fieldBook$block_number)+fieldBook$plot_id
+}else if (plot_start == 101) {
+  fieldBook$plot_number <- (100*fieldBook$block_number)+fieldBook$plot_id
+}
+
+cat("plot start is ", plot_start,"\n")
+cat("plot type is ", plot_type,"\n")
+
+plot_type = "serpentine"
+## Plot number format
+if(plot_type == "serpentine"){
+  for(i in 1:nRows){
+    if(i%%2==0){
+      fieldBook[fieldBook$row_number == i, "plot_number"] <- rev(fieldBook[fieldBook$row_number==i,"plot_number"])
+    }
+  }
+}
+
+fieldBook$rep_number <- rep_number
+
+
+#### create is_a_control
+names(fieldBook)[names(fieldBook) == "treatments"] <- "accession_name"
+fieldBook <- transform(fieldBook, is_a_control = ifelse(fieldBook$accession_name %in% controls, 1, 0))
+
+design <- fieldBook %>% dplyr::select(block_number, rep_number, row_number, col_number, plot_number, accession_name, is_a_control)
+
+head(design)
+
+# save result files
+basefile <- tools::file_path_sans_ext(paramfile)
+outfile = paste(basefile, ".design", sep="");
+sink(outfile)
+write.table(design, quote=F, sep='\t', row.names=FALSE)
+sink();