maintainance badge link updated

AlphaPrime7 · Aug 22, 2023 · 9e367b7 · 9e367b7
1 parent b37be9c
commit 9e367b7
Show file tree

Hide file tree

Showing 5 changed files with 104 additions and 110 deletions.
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -0,0 +1,48 @@
+# 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
+
+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: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4.4.1
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -23,6 +23,6 @@ Imports:
 Depends: 
     R (>= 2.10)
 LazyData: true
-URL: https://github.com/AlphaPrime7/normfluodbf
+URL: https://github.com/AlphaPrime7/normfluodbf, https://alphaprime7.github.io/normfluodbf/
 BugReports: https://github.com/AlphaPrime7/normfluodbf/issues
 VignetteBuilder: knitr
diff --git a/README.Rmd b/README.Rmd
@@ -25,7 +25,7 @@ knitr::opts_chunk$set(
 [![saythanks](https://img.shields.io/badge/say-thanks-ff69b4.svg)](https://saythanks.io/to/GuangchuangYu)
 [![test-coverage](https://github.com/AlphaPrime7/normfluodbf/actions/workflows/test-coverage.yaml/badge.svg)](https://github.com/AlphaPrime7/normfluodbf/actions/workflows/test-coverage.yaml)
 [![license](https://img.shields.io/badge/license-GPL--3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0.en.html)
-[![Maintenance](https://img.shields.io/badge/Maintained%3F-yes-green.svg)](https://GitHub.com/Nelson-Gon/mde/graphs/commit-activity)
+[![Maintenance](https://img.shields.io/badge/Maintained%3F-yes-green.svg)](https://github.com/AlphaPrime7/normfluodbf/graphs/commit-activity)
 
 
 The goal of [`{normfluodbf}`](https://github.com/AlphaPrime7/normfluodbf) is to normalize fluorescence data obtained from liposome flux assay experiments via the FLUOstar microplate reader. Input or source file is a .dbf file that is not ready for analysis without processing through {normfluodbf}. There is a ShinyApp for this as well.

diff --git a/README.md b/README.md
@@ -1,33 +1,16 @@
-Tingwei Adeck
-August 21, 2023
+Tingwei Adeck August 21, 2023
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
-# normfluodbf <img src="man/figures/logo.png" align="right" width="180" />
-
-[![Project
-status](https://www.repostatus.org/badges/latest/concept.svg)](https://github.com/AlphaPrime7/normfluodbf/commits)
-[![Project
-Status](https://www.repostatus.org/badges/latest/active.svg)](https://github.com/AlphaPrime7/normfluodbf/commits)
-[![Project
-Status](https://www.repostatus.org/badges/latest/wip.svg)](https://github.com/AlphaPrime7/normfluodbf/commits)
-[![lifecycle](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://lifecycle.r-lib.org/articles/stages.html)
-[![saythanks](https://img.shields.io/badge/say-thanks-ff69b4.svg)](https://saythanks.io/to/GuangchuangYu)
-[![test-coverage](https://github.com/AlphaPrime7/normfluodbf/actions/workflows/test-coverage.yaml/badge.svg)](https://github.com/AlphaPrime7/normfluodbf/actions/workflows/test-coverage.yaml)
-[![license](https://img.shields.io/badge/license-GPL--3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0.en.html)
-[![Maintenance](https://img.shields.io/badge/Maintained%3F-yes-green.svg)](https://GitHub.com/Nelson-Gon/mde/graphs/commit-activity)
-
-The goal of
-[`{normfluodbf}`](https://github.com/AlphaPrime7/normfluodbf) is to
-normalize fluorescence data obtained from liposome flux assay
-experiments via the FLUOstar microplate reader. Input or source file is
-a .dbf file that is not ready for analysis without processing through
-{normfluodbf}. There is a ShinyApp for this as well.
+# normfluodbf <img src="man/figures/logo.png" align="right" width="180"/>
+
+[![Project status](https://www.repostatus.org/badges/latest/concept.svg)](https://github.com/AlphaPrime7/normfluodbf/commits) [![Project Status](https://www.repostatus.org/badges/latest/active.svg)](https://github.com/AlphaPrime7/normfluodbf/commits) [![Project Status](https://www.repostatus.org/badges/latest/wip.svg)](https://github.com/AlphaPrime7/normfluodbf/commits) [![lifecycle](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://lifecycle.r-lib.org/articles/stages.html) [![saythanks](https://img.shields.io/badge/say-thanks-ff69b4.svg)](https://saythanks.io/to/GuangchuangYu) [![test-coverage](https://github.com/AlphaPrime7/normfluodbf/actions/workflows/test-coverage.yaml/badge.svg)](https://github.com/AlphaPrime7/normfluodbf/actions/workflows/test-coverage.yaml) [![license](https://img.shields.io/badge/license-GPL--3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0.en.html) [![Maintenance](https://img.shields.io/badge/Maintained%3F-yes-green.svg)](https://GitHub.com/Nelson-Gon/mde/graphs/commit-activity)
+
+The goal of [`{normfluodbf}`](https://github.com/AlphaPrime7/normfluodbf) is to normalize fluorescence data obtained from liposome flux assay experiments via the FLUOstar microplate reader. Input or source file is a .dbf file that is not ready for analysis without processing through {normfluodbf}. There is a ShinyApp for this as well.
 
 ## ↓ Installation
 
-You can install the development version of normfluodbf from
-[`{normfluodbf}`](https://github.com/AlphaPrime7/normfluodbf) with:
+You can install the development version of normfluodbf from [`{normfluodbf}`](https://github.com/AlphaPrime7/normfluodbf) with:
 
 ``` r
 install.packages("devtools")
@@ -51,42 +34,25 @@ normalized_data <- normfluodbf(liposomes_214)
 
 ## R packages used
 
-- tidyr
-- data.table
-- foreign
-- tibble
+-   tidyr
+-   data.table
+-   foreign
+-   tibble
 
 # References
 
 (Dowle and Srinivasan 2023) (R Core Team 2022) (Wickham et al. 2019)
 
-<div id="refs" class="references csl-bib-body hanging-indent">
-
-<div id="ref-datatable" class="csl-entry">
-
-Dowle, Matt, and Arun Srinivasan. 2023.
-*<span class="nocase">data.table</span>: Extension of
-“<span class="nocase">data.frame</span>”*.
-<https://CRAN.R-project.org/package=data.table>.
-
-</div>
-
-<div id="ref-foreign" class="csl-entry">
-
-R Core Team. 2022. *<span class="nocase">foreign</span>: Read Data
-Stored by “Minitab,” “S,” “SAS,” “SPSS,” “Stata,” “Systat,” “Weka,”
-“<span class="nocase">dBase</span>,” ...*
-<https://CRAN.R-project.org/package=foreign>.
-
-</div>
-
-<div id="ref-tidyverse" class="csl-entry">
-
-Wickham, Hadley, Mara Averick, Jennifer Bryan, Winston Chang, Lucy
-D’Agostino McGowan, Romain François, Garrett Grolemund, et al. 2019.
-“Welcome to the <span class="nocase">tidyverse</span>.” *Journal of Open
-Source Software* 4 (43): 1686. <https://doi.org/10.21105/joss.01686>.
+::: {#refs .references .csl-bib-body .hanging-indent}
+::: {#ref-datatable .csl-entry}
+Dowle, Matt, and Arun Srinivasan. 2023. [*data.table*]{.nocase}*: Extension of "[data.frame]{.nocase}"*. <https://CRAN.R-project.org/package=data.table>.
+:::
 
-</div>
+::: {#ref-foreign .csl-entry}
+R Core Team. 2022. [*foreign*]{.nocase}*: Read Data Stored by "Minitab," "S," "SAS," "SPSS," "Stata," "Systat," "Weka," "[dBase]{.nocase}," ...* <https://CRAN.R-project.org/package=foreign>.
+:::
 
-</div>
+::: {#ref-tidyverse .csl-entry}
+Wickham, Hadley, Mara Averick, Jennifer Bryan, Winston Chang, Lucy D'Agostino McGowan, Romain François, Garrett Grolemund, et al. 2019. "Welcome to the [tidyverse]{.nocase}." *Journal of Open Source Software* 4 (43): 1686. <https://doi.org/10.21105/joss.01686>.
+:::
+:::
diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -1,56 +1,41 @@
-#title: normfluodbf #title here no need to title navbar
-url: https://alphaprime7.github.io/
+url: https://alphaprime7.github.io/normfluodbf/
 development:
-  #destination: docs #its all going into the doc folder
-  version_label: danger #gives syntax highlights to the version number
+  version_label: danger
 template:
- bootstrap: 5
- #bootswatch: cyborg #others are materia, flatly etc
- theme: arrow-dark
- #theme: breeze-light
- bslib:
-  code-bg: "#2b2b2b"
-  pkgdown-nav-height: 75px
-  bg: "#202123"
-  fg: "#B8BCC2"
-  primary: "#306cc9"
-  #base_font: {google: "Roboto"}
-  #heading_font: {google: "Roboto Slab"}
-  #code_font: {google: "JetBrains Mono"}
-
-  #bootstrap: 5
-  #bootswatch: flatly
-  #bslib:
-    #pkgdown-nav-height: 100px
-
-#navbar:
-  #structure:
-    #left:  [intro, reference, articles, news]
-    #right: [search, github]
-
+  bootstrap: 5
+  theme: arrow-dark
+  bslib:
+    code-bg: '#2b2b2b'
+    pkgdown-nav-height: 75px
+    bg: '#202123'
+    fg: '#B8BCC2'
+    primary: '#306cc9'
 navbar:
-  title: "normfluodbf 1.1" #dummy title, pkgdown determines the page title based on the pre-release
+  title: normfluodbf 1.1
   type: inverse
   left:
-    - icon: fa-home
-      href: articles/landing_redirect.html
-      text: "Get Started"
-    - icon: fa-question
-      text: "How To"
-      menu:
-      -  icon: fa-code
-         text: "Installation"
-         href: articles/install_redirect.html
-
-      -  icon: fa-code
-         text:  "Input"
-         href: articles/input_redirect.html
-
-      -  icon: fa-code
-         text: "Output and Analysis"
-         href: articles/example_redirect.html
+  - icon: fa-home
+    href: articles/landing_redirect.html
+    text: Get Started
+  - icon: fa-question
+    text: How To
+    menu:
+    - icon: fa-code
+      text: Installation
+      href: articles/install_redirect.html
+    - icon: fa-code
+      text: Input
+      href: articles/input_redirect.html
+    - icon: fa-code
+      text: Output and Analysis
+      href: articles/example_redirect.html
   structure:
-    right: [reference,NEWS, github, email, Linkedin]
+    right:
+    - reference
+    - NEWS
+    - github
+    - email
+    - Linkedin
   components:
     email:
       icon: fa-envelope
@@ -59,8 +44,3 @@ navbar:
       icon: fa-linkedin
       href: https://www.linkedin.com/in/tingwei-adeck-52b963164/
 
-
-
-
-
-