From 8a8839ace0479915be8e119c078b06a5795ab592 Mon Sep 17 00:00:00 2001
From: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: Tue, 24 Sep 2024 11:35:27 +0200
Subject: [PATCH] ran with pckgdown

---
 .Rbuildignore                       |  4 +++
 .github/.gitignore                  |  1 +
 .github/workflows/build_deploy.yaml |  2 --
 .github/workflows/pkgdown.yaml      | 50 +++++++++++++++++++++++++++++
 .gitignore                          |  1 +
 DESCRIPTION                         | 18 +++++------
 NAMESPACE                           |  2 ++
 README.md                           |  8 -----
 _pkgdown.yml                        |  4 +++
 9 files changed, 70 insertions(+), 20 deletions(-)
 create mode 100644 .Rbuildignore
 create mode 100644 .github/.gitignore
 create mode 100644 .github/workflows/pkgdown.yaml
 create mode 100644 NAMESPACE
 create mode 100644 _pkgdown.yml

diff --git a/.Rbuildignore b/.Rbuildignore
new file mode 100644
index 0000000..531e115
--- /dev/null
+++ b/.Rbuildignore
@@ -0,0 +1,4 @@
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^\.github$
diff --git a/.github/.gitignore b/.github/.gitignore
new file mode 100644
index 0000000..2d19fc7
--- /dev/null
+++ b/.github/.gitignore
@@ -0,0 +1 @@
+*.html
diff --git a/.github/workflows/build_deploy.yaml b/.github/workflows/build_deploy.yaml
index 0ec21a7..2899440 100644
--- a/.github/workflows/build_deploy.yaml
+++ b/.github/workflows/build_deploy.yaml
@@ -47,8 +47,6 @@ jobs:
 
       - name: Deploy package
         if: github.ref == 'refs/heads/main'
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
           git config --global user.email "action@github.com"
           git config --global user.name "GitHub Action"
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
new file mode 100644
index 0000000..4bbce75
--- /dev/null
+++ b/.github/workflows/pkgdown.yaml
@@ -0,0 +1,50 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown.yaml
+
+permissions: read-all
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ 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/github-pages-deploy-action@v4.5.0
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs
diff --git a/.gitignore b/.gitignore
index 26064e4..47b94b6 100644
--- a/.gitignore
+++ b/.gitignore
@@ -6,3 +6,4 @@ hidden_file_ext = c(
     ".gitattributes", ".gitmodules", ".hgtags", ".project", ".seed",
     ".settings", ".tm_properties"
 )
+docs
diff --git a/DESCRIPTION b/DESCRIPTION
index 3acdf88..2de9498 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,19 +1,18 @@
 Package: metabonaut
 Title: Exploring and Analyzing LC-MS data
 Version: 0.0.1
-Authors@R: c(
-         person(given = "Philippine", family = "Louail",
+Authors@R: 
+    c(person(given = "Philippine", family = "Louail",
             email = "philippine.louail@eurac.edu",
             role = c("aut", "cre"),
             comment = c(ORCID = "0009-0007-5429-6846")),
-
-            person(given = "Johannes", family = "Rainer",
+     person(given = "Johannes", family = "Rainer",
             email = "Johannes.Rainer@eurac.edu",
-            role = c("aut", "cre"),
+            role = c("aut"),
             comment = c(ORCID = "0000-0002-6977-7147")))
 Description: This resource hosts tutorials and end-to-end workflows 
-describing how to analyse LC-MS/MS data from raw files to annotation
-using biocoductor softwares.
+             describing how to analyse LC-MS/MS data from raw files to
+             annotation using biocoductor softwares.
 License: Artistic-2.0
 Encoding: UTF-8
 LazyData: false
@@ -43,9 +42,8 @@ Suggests:
     RColorBrewer,
     SummarizedExperiment,
     pheatmap
-URL: https://github.com/rformassspectrometry/metabonaut/
+URL: https://github.com/rformassspectrometry/metabonaut/, https://rformassspectrometry.github.io/metabonaut/
 BugReports: https://github.com/rformassspectrometry/metabonaut/issues/new
 VignetteBuilder: knitr
 BiocType: Workflow
-biocViews: ?
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
diff --git a/NAMESPACE b/NAMESPACE
new file mode 100644
index 0000000..6ae9268
--- /dev/null
+++ b/NAMESPACE
@@ -0,0 +1,2 @@
+# Generated by roxygen2: do not edit by hand
+
diff --git a/README.md b/README.md
index 8112721..f9a41d9 100644
--- a/README.md
+++ b/README.md
@@ -40,14 +40,6 @@ and analyzing LC-MS data with Spectra and xcms. Zenodo, May
 
 ## Installation
 
-```r
-install.packages("BiocManager")
-BiocManager::install("RforMassSpectrometry/metabonaut",
-    dependencies = TRUE, ask = FALSE, update = TRUE)
-```
-
-
-
 
 ## Contribution
 
diff --git a/_pkgdown.yml b/_pkgdown.yml
new file mode 100644
index 0000000..12ae509
--- /dev/null
+++ b/_pkgdown.yml
@@ -0,0 +1,4 @@
+url: https://rformassspectrometry.github.io/metabonaut/
+template:
+  bootstrap: 5
+