website

.Rbuildignore

@@ -2,3 +2,7 @@
 ^\.Rproj\.user$
 ^LICENSE\.md$
 ^README\.Rmd$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^\.github$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/pkgdown.yaml

@@ -0,0 +1,50 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown.yaml
+
+permissions: read-all
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.gitignore

@@ -5,3 +5,4 @@
 .DS_Store
 .quarto
 inst/doc
+docs

DESCRIPTION

@@ -30,7 +30,7 @@ Collate: class.R AllGenerics.R getset.R
         methods.R annotate.R distance.R formatConverter.R linkSet-package.R
 Author: Gilbert Han [aut]
 Maintainer: Gilbert Han <[email protected]>
-URL: https://github.com/GilbertHan1011/linkSet
+URL: https://github.com/GilbertHan1011/linkSet, https://gilberthan1011.github.io/linkSet, https://gilberthan1011.github.io/linkSet/
 BugReports: https://github.com/GilbertHan1011/linkSet/issues/new
 LazyData: true
 VignetteBuilder: knitr

R/getset.R

@@ -118,11 +118,11 @@ setReplaceMethod("$", "linkSet", function(x, name, value) {
 ###############################################################
 # Name getting and setting.
 
-setMethod("names", "GInteractions", function(x) { 
+setMethod("names", "linkSet", function(x) { 
     x@NAMES 
 })
 
-setReplaceMethod("names", "GInteractions", function(x, value) {
+setReplaceMethod("names", "linkSet", function(x, value) {
     if (!is.null(value) && !is.character(value)) { value <- as.character(value) }                
     x@NAMES <- value
     validObject(x)

_pkgdown.yml

@@ -0,0 +1,4 @@
+url: https://gilberthan1011.github.io/linkSet/
+template:
+  bootstrap: 5
+

vignettes/linkSet.Rmd

@@ -45,7 +45,7 @@ Built on top of established Bioconductor classes, ensuring compatibility with a
 7. Visualization and analysis:
 The class is designed to support functions for analyzing and visualizing genomic interactions.
 
-```{r out.width = '70%', echo = FALSE}
+```{r out.width = '70%', echo = FALSE, fig.alt="Overview diagram of the linkSet class structure and its components"}
 knitr::include_graphics("img/overview.png")
 ```