Feat: Add Docs Page via MkDown

.Rbuildignore

@@ -3,3 +3,7 @@
 ^LICENSE\.md$
 ^workflow$
 ^assets$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^\.github$

.github/.gitignore

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

.github/workflows/pkgdown.yaml

@@ -0,0 +1,57 @@
+# 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]  # Add your test branch name here
+  pull_request:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+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: Copy assets to docs
+        run: |
+          if [ -d "assets" ]; then
+            mkdir -p docs/assets
+            cp -r assets/* docs/assets/
+          fi
+        shell: bash
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.gitignore

@@ -5,3 +5,4 @@
 .DS_Store
 .quarto
 permAprox_0.0.1.9000.tar.gz
+docs

DESCRIPTION

@@ -1,40 +1,47 @@
 Package: DGrowthR
 Title: Bacterial Growth Curve Analysis
-Description: A Comprehensive Toolset for Modelling of Bacterial Growth Curves via Gaussian Processes, Differential Testing and Empirical p-value Adjustment.
-Author: Medina Feldl <mail@medinabajramovic.de> [aut, cre], 
-      Roberto Olayo Alarcon <roberto.olayo@lmu.de> [aut]
-Maintainer: Medina Feldl <mail@medinabajramovic.de>
+Description: A Comprehensive Toolset for Modelling of Bacterial Growth 
+    Curves via Gaussian Processes, Differential Testing and Empirical 
+    p-value Adjustment.
+Authors@R: c(
+    person("Medina", "Feldl", email = "mail@medinabajramovic.de", 
+           role = c("aut", "cre")),
+    person("Roberto", "Olayo Alarcon", email = "roberto.olayo@lmu.de", 
+           role = "aut")
+    )
+URL: https://bio-datascience.github.io/DGrowthR/, https://github.com/bio-datascience/DGrowthR/
+BugReports: https://github.com/bio-datascience/DGrowthR/issues
 Version: 1.0
 License: GPL-3 + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.1
 Imports:
-    methods,
-    tidyselect,
-    magrittr,
-    fdapace,
+    dbscan,
     dplyr,
-    tibble,
-    tidyr,
-    pracma,
-    stringr,
-    laGP,
-    ggplot2,
-    tools,
-    foreach,
-    snow,
     doSNOW,
+    fdapace,
+    foreach,
+    ggplot2,
     jsonlite,
-    methods,
-    utils,
-    dbscan,
-    stats,
-    uwot,
+    laGP,
+    magrittr,
     mclust,
+    methods,
     mvtnorm,
+    pracma,
+    purrr,
     readr,
-    purrr
+    snow,
+    stats,
+    stringr,
+    tibble,
+    tidyr,
+    tidyselect,
+    tidyverse,
+    tools,
+    utils,
+    uwot
 Depends: 
     R (>= 2.10)
 LazyData: true

README.md

@@ -1,9 +1,7 @@
-DGrowthR: A comprehensive workflow for growth curve analysis
-================
-Compiled on 2025-03-21 18:53:56
-
 ![](assets/Logo-DGrowthR.png)
 
+# DGrowthR: A comprehensive workflow for growth curve analysis
+
 This repository hosts the `DGrowthR` R package and the workflow for the
 detailed analysis of publicly available datasets mentioned in our
 pre-print. This workflow is designed to showcase the application of the
@@ -12,7 +10,8 @@ growth using Gaussian Process Regression.
 
 ![](assets/dgrowthr_panel.png)
 
-**For more details, check out our [pre-print](https://www.biorxiv.org/content/10.1101/2025.03.25.645164v2):**
+> [!TIP]
+> For more details, check out our pre-print [Statistical end-to-end analysis of large-scale microbial growth data with DGrowthR](https://www.biorxiv.org/content/10.1101/2025.03.25.645164v2) on bioRxiv.
 
 ## Installation Guide
 
@@ -23,8 +22,7 @@ Then you can execute the following commands in R.
 1.  Ensure that you have the `devtools` package installed. If not, you
     can install it using the following command
 
-``` r
-
+```r
 # Install devtools
 install.packages("devtools")
 
@@ -34,8 +32,7 @@ library(devtools)
 
 2.  Use the `install` function to install the `DGrowthR` package:
 
-``` r
-
+```r
 install()
 ```
 

_pkgdown.yml

@@ -0,0 +1,16 @@
+url: https://bio-datascience.github.io/DGrowthR/
+template:
+  bootstrap: 5
+  light-switch: true
+
+navbar:
+  structure:
+    left: [intro, reference, biods]
+    right: [search, github, lightswitch]
+  components:
+    biods:
+      text: "BioDS"
+      href: https://bio-datascience.github.io/
+      target: "_blank"
+      aria-label: "Bio Data Science"
+      icon: fa-arrow-up-right-from-square