From e6027fda08358c5d6cbdd58fbb8e89f54792c5ef Mon Sep 17 00:00:00 2001
From: Ernest Guevarra <ernest@guevarra.io>
Date: Tue, 29 Oct 2024 16:40:29 +0000
Subject: [PATCH 1/3] edit pkgdown.yml; fix #89; fix #90; fix #88

---
 .github/workflows/test-coverage.yaml |  1 +
 DESCRIPTION                          |  2 +-
 pkgdown/_pkgdown.yml                 | 22 +++++++++-------------
 3 files changed, 11 insertions(+), 14 deletions(-)

diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index 21b8a93..4e0ec42 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -13,6 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
     steps:
       - uses: actions/checkout@v4
diff --git a/DESCRIPTION b/DESCRIPTION
index dadf6c4..cddba3e 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -35,7 +35,7 @@ Suggests:
 Encoding: UTF-8
 Language: en-GB
 LazyData: true
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Roxygen: list(markdown = TRUE)
 URL: https://nutriverse.io/nipnTK/, https://github.com/nutriverse/nipnTK
 BugReports: https://github.com/nutriverse/nipnTK/issues
diff --git a/pkgdown/_pkgdown.yml b/pkgdown/_pkgdown.yml
index 3cd9969..5e491dd 100644
--- a/pkgdown/_pkgdown.yml
+++ b/pkgdown/_pkgdown.yml
@@ -7,16 +7,18 @@ development:
 
 template:
   bootstrap: 5
-  bootswatch: cosmo
-  theme: pygments #haddock
-  ganalytics: G-HD17FR1JE1
+  bootswatch: pulse
+  theme: breeze-light
+  ganalytics: G-51ZQ0EXXM4
+  bslib:
+    pkgdown-nav-height: 100px
 
 navbar:
   bg: success
   type: light
   structure:
     left:  [home, intro, reference, articles, news]
-    right: [mastodon, linkedin, github]
+    right: [search, mastodon, github]
 
   components:
     articles:
@@ -24,7 +26,7 @@ navbar:
       menu:
       - text: Check ranges and legal values
         href: articles/rl.html
-      - text: Identify outliers using scatterplots
+      - text: Identify outliers using scatter plots
         href: articles/sp.html
       - text: Identify outliers using flags
         href: articles/flagging.html
@@ -40,15 +42,9 @@ navbar:
         href: articles/as.html
     mastodon:
       icon: fab fa-mastodon fa-lg
-      href: https://fosstodon.org/@katilingban
-    linkedin:
-      icon: fab fa-linkedin fa-lg
-      href: https://www.linkedin.com/company/katilingban/
+      href: https://mastodon.social/@nutriverse
 
 home:
-  sidebar:
-    structure: [links, license, community, citation, authors, dev]
-
   links:
   - text: Read more about NiPN
     href: https://www.nipn-nutrition-platforms.org
@@ -63,7 +59,7 @@ reference:
     - outliersUV
     - rl.ex01
 
-  - title: Using scatterplots to identify outliers
+  - title: Using scatter plots to identify outliers
     contents:
     - outliersMD
     - sp.ex01

From d87dfd874b583b596cc7fc551f8bd38757ab99cf Mon Sep 17 00:00:00 2001
From: Ernest Guevarra <ernest@guevarra.io>
Date: Tue, 29 Oct 2024 16:59:15 +0000
Subject: [PATCH 2/3] remove dependency to bbw

---
 vignettes/sr.Rmd | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/vignettes/sr.Rmd b/vignettes/sr.Rmd
index de8672a..4287ae5 100644
--- a/vignettes/sr.Rmd
+++ b/vignettes/sr.Rmd
@@ -12,7 +12,7 @@ knitr::opts_chunk$set(
 
 ```{r setup, echo = FALSE}
 library(nipnTK)
-library(bbw)
+#library(bbw)
 library(knitr)
 library(kableExtra)
 ```

From 3a27a1000e7e1e10d0e628408788c9704b2b8cbb Mon Sep 17 00:00:00 2001
From: Ernest Guevarra <ernest@guevarra.io>
Date: Tue, 29 Oct 2024 17:05:06 +0000
Subject: [PATCH 3/3] return dependency to bbw

---
 DESCRIPTION      | 3 ++-
 vignettes/sr.Rmd | 2 +-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index cddba3e..dcfc3e0 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -31,7 +31,8 @@ Suggests:
     tufte,
     spelling,
     covr,
-    kableExtra
+    kableExtra,
+    bbw
 Encoding: UTF-8
 Language: en-GB
 LazyData: true
diff --git a/vignettes/sr.Rmd b/vignettes/sr.Rmd
index 4287ae5..de8672a 100644
--- a/vignettes/sr.Rmd
+++ b/vignettes/sr.Rmd
@@ -12,7 +12,7 @@ knitr::opts_chunk$set(
 
 ```{r setup, echo = FALSE}
 library(nipnTK)
-#library(bbw)
+library(bbw)
 library(knitr)
 library(kableExtra)
 ```