edit pkgdown template; fix #85

.github/CONTRIBUTING.md

@@ -8,26 +8,26 @@
 
 * Fork this repository to your Github account
 
-* Clone your version on your account down to your machine from your account
+* Clone your version on your account down to your machine from your account 
 
 ```
 git clone https://github.com/<yourgithubusername>/squeacr.git
 ```
 
-* Make sure to track progress upstream i.e., on our version of `intergrowth`
-at `nutriverse/squeacr`, by doing
+* Make sure to track progress upstream i.e., on our version of `squeacr` 
+at `nutriverse/squeacr`, by doing 
 
 ```
 git remote add upstream https://github.com/nutriverse/squeacr.git
 ```
 
-* Before making changes make sure to pull changes in from `upstream` by doing
-either `git fetch upstream` then merge later or `git pull upstream` to fetch
+* Before making changes make sure to pull changes in from `upstream` by doing 
+either `git fetch upstream` then merge later or `git pull upstream` to fetch 
 and merge in one step
 
 * Make your changes on a new feature branch
 
-* Please write a test or tests for your changes if they affect code and not just
+* Please write a test or tests for your changes if they affect code and not just 
 documentation
 
 * Push up changes to your account

.github/workflows/rhub.yaml

@@ -0,0 +1,95 @@
+# R-hub's generic GitHub Actions workflow file. It's canonical location is at
+# https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml
+# You can update this file to a newer version using the rhub2 package:
+#
+# rhub::rhub_setup()
+#
+# It is unlikely that you need to modify this file manually.
+
+name: R-hub
+run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"
+
+on:
+  workflow_dispatch:
+    inputs:
+      config:
+        description: 'A comma separated list of R-hub platforms to use.'
+        type: string
+        default: 'linux,windows,macos'
+      name:
+        description: 'Run name. You can leave this empty now.'
+        type: string
+      id:
+        description: 'Unique ID. You can leave this empty now.'
+        type: string
+
+jobs:
+
+  setup:
+    runs-on: ubuntu-latest
+    outputs:
+      containers: ${{ steps.rhub-setup.outputs.containers }}
+      platforms: ${{ steps.rhub-setup.outputs.platforms }}
+
+    steps:
+    # NO NEED TO CHECKOUT HERE
+    - uses: r-hub/actions/setup@v1
+      with:
+        config: ${{ github.event.inputs.config }}
+      id: rhub-setup
+
+  linux-containers:
+    needs: setup
+    if: ${{ needs.setup.outputs.containers != '[]' }}
+    runs-on: ubuntu-latest
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.containers) }}
+    container:
+      image: ${{ matrix.config.container }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+
+  other-platforms:
+    needs: setup
+    if: ${{ needs.setup.outputs.platforms != '[]' }}
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.platforms) }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/setup-r@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}

DESCRIPTION

@@ -28,7 +28,7 @@ Imports:
 Suggests: 
     knitr,
     rmarkdown,
-    testthat,
+    testthat (>= 3.0.0),
     covr,
     spelling,
     readxl,
@@ -37,7 +37,8 @@ Encoding: UTF-8
 Language: en-GB
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 VignetteBuilder: knitr
 URL: https://nutriverse.io/squeacr/, https://github.com/nutriverse/squeacr
 BugReports: https://github.com/nutriverse/squeacr/issues
+Config/testthat/edition: 3

inst/CITATION

@@ -1,9 +1,9 @@
 bibentry(
   bibtype  = "Manual",
   header   = "To cite squeacr in publications use:",
-  title    = "squeacr: Semi-Quantitative Evaluation of Access and Coverage (SQUEAC) Tools  in R",
+  title    = "squeacr: Semi-Quantitative Evaluation of Access and Coverage ('SQUEAC') Tools in R",
   author   = person("Ernest Guevarra"),
-  year     = "2023",
+  year     = "2024",
   note     = "R package version 0.0.0.9000",
   url      = "https://nutriverse.io/squeacr/",
   doi      = "10.5281/zenodo.7509665"

inst/WORDLIST

@@ -27,7 +27,6 @@ Medani
 MoH
 Myatt
 Naher
-Nutriverse
 ORCID
 RUTF
 SLEAC
@@ -52,6 +51,7 @@ kgs
 kwashiorkor
 lifecycle
 muac
+nutriverse
 singlecoverage
 sudan
 tibble

pkgdown/_pkgdown.yml

@@ -7,16 +7,18 @@ development:
 
 template:
   bootstrap: 5
-  bootswatch: cosmo
-  theme: haddock
-  ganalytics: UA-102485058-6
+  bootswatch: pulse
+  theme: breeze-light
+  ganalytics: G-C6TYX2E6RD
+  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:
@@ -32,10 +34,7 @@ navbar:
     #     href: articles/iodine-deficiency.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://fosstodon.org/@nutriverse
 
 home:
   links:

tests/testthat.R

@@ -1,3 +1,11 @@
+# This file is part of the standard setup for testthat.
+# It is recommended that you do not modify it.
+#
+# Where should you do additional test configuration?
+# Learn more about the roles of various files in:
+# * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
+# * https://testthat.r-lib.org/articles/special-files.html
+
 library(testthat)
 library(squeacr)