Add history section and article for previous versions

.github/workflows/common.yml

@@ -35,7 +35,7 @@ concurrency:
 
 env:
   R_VERSION: "4.1"
-  
+
 jobs:
   get_r_version:
     name: Get R version
@@ -91,7 +91,7 @@ jobs:
       # Whether to skip multiversion docs
       # Note that if you have multiple versions of docs,
       # your URL links are likely to break due to path changes
-      skip-multiversion-docs: false
+      skip-multiversion-docs: true
   linter:
     name: Lint
     uses: pharmaverse/admiralci/.github/workflows/lintr.yml@main

README.Rmd

@@ -4,39 +4,7 @@ output: md_document
 date: '2022-08-06'
 ---
 
-```{r setup, include=FALSE}
-knitr::opts_chunk$set(echo = TRUE)
-link <- function(text, url) {
-  return(
-    paste0(
-      "[", text, "]",
-      "(", url, ")"
-    )
-  )
-}
-dyn_link <- function(text,
-                     base_url,
-                     relative_url = "",
-                     # Change to TRUE when admiral adopts multiversion docs
-                     is_multiversion = TRUE,
-                     multiversion_default_ref = "main") {
-  url <- paste(base_url, relative_url, "", sep = "/")
-  if (is_multiversion) {
-    url <- paste(
-      base_url,
-      Sys.getenv("BRANCH_NAME", multiversion_default_ref),
-      "",
-      sep = "/"
-    )
-  }
-  return(link(text, url))
-}
-# Other variables
-admiral_homepage <- "https://pharmaverse.github.io/admiral"
-```
-
 <!-- Please do not edit the README.md file as it is auto-generated after PR merges. Only edit the README.Rmd file -->
-<!-- The purpose of this is to enable dynamic links using dyn_link function above to access devel/main admiral homepage respectively -->
 <!-- To test this in your feature branch use code: rmarkdown::render("README.Rmd", output_format ="md_document") -->
 
 # Admiral Extension for Ophthalmology <img src="man/figures/logo.png" align="right" width="200" style="margin-left:50px;"/>
@@ -68,7 +36,7 @@ remotes::install_github("pharmaverse/admiralophtha", ref = "devel")
 
 ## References and Documentation
 
-* Please refer to the `r dyn_link("{admiral} References and Documentation", admiral_homepage, "index.html#references-and-documentation")`.
+* Please refer to the [the `{admiral}` References & Documentation page](https://pharmaverse.github.io/admiral/index.html#references-and-documentation).
 
 ## R Versions
 

README.md

@@ -1,7 +1,4 @@
 <!-- Please do not edit the README.md file as it is auto-generated after PR merges. Only edit the README.Rmd file -->
-
-<!-- The purpose of this is to enable dynamic links using dyn_link function above to access devel/main admiral homepage respectively -->
-
 <!-- To test this in your feature branch use code: rmarkdown::render("README.Rmd", output_format ="md_document") -->
 
 # Admiral Extension for Ophthalmology <img src="man/figures/logo.png" align="right" width="200" style="margin-left:50px;"/>

_pkgdown.yml

@@ -12,6 +12,10 @@ repo:
     source: https://github.com/pharmaverse/admiralophtha/blob/main/
     issue: https://github.com/pharmaverse/admiralophtha/issues/
     user: https://github.com/
+
+development:
+  mode: auto
+
 news:
   cran_dates: false
 reference:
@@ -90,8 +94,8 @@ reference:
 
 navbar:
   structure:
-    left: [getstarted, reference, articles, news]
-    right: [search, slack, newissue, github]
+    left: [getstarted, reference, articles, news, versions]
+    right: [search, slack, history, newissue, github]
   components:
     getstarted:
       text: Get Started
@@ -110,6 +114,10 @@ navbar:
         href: articles/adbcva.html
       - text: Creating ADVFQ
         href: articles/advfq.html
+    history:
+      icon: fa-history
+      href: articles/website-versions.html
+      aria-label: Previous Release Websites
     slack:
       icon: fa-slack
       href: https://app.slack.com/client/T028PB489D3/C02M8KN8269

vignettes/adbcva.Rmd

@@ -13,33 +13,6 @@ knitr::opts_chunk$set(
   collapse = TRUE,
   comment = "#>"
 )
-link <- function(text, url) {
-  return(
-    paste0(
-      "[", text, "]",
-      "(", url, ")"
-    )
-  )
-}
-dyn_link <- function(text,
-                     base_url,
-                     relative_url = "",
-                     # Change to TRUE when admiral adopts multiversion docs
-                     is_multiversion = FALSE,
-                     multiversion_default_ref = "main") {
-  url <- paste(base_url, relative_url, sep = "/")
-  if (is_multiversion) {
-    url <- paste(
-      base_url,
-      Sys.getenv("BRANCH_NAME", multiversion_default_ref),
-      relative_url,
-      sep = "/"
-    )
-  }
-  return(link(text, url))
-}
-# Other variables
-admiral_homepage <- "https://pharmaverse.github.io/admiral"
 library(admiraldev)
 ```
 
@@ -371,6 +344,4 @@ adbcva <- adbcva %>%
 
   ADaM | Sample Code 
   ---- | -------------- 
-  ADBCVA | `r dyn_link("ad_adbcva.R", "https://github.com/pharmaverse/admiralophtha/blob", "inst/templates/ad_adbcva.R", is_multiversion = TRUE)`
-
-
+  ADBCVA | [ad_adbcva.R](https://github.com/pharmaverse/admiralophtha/blob/main/inst/templates/ad_adbcva.R)

vignettes/admiralophtha.Rmd

@@ -12,39 +12,12 @@ knitr::opts_chunk$set(
   collapse = TRUE,
   comment = "#>"
 )
-link <- function(text, url) {
-  return(
-    paste0(
-      "[", text, "]",
-      "(", url, ")"
-    )
-  )
-}
-dyn_link <- function(text,
-                     base_url,
-                     relative_url = "",
-                     # Change to TRUE when admiral adopts multiversion docs
-                     is_multiversion = FALSE,
-                     multiversion_default_ref = "main") {
-  url <- paste(base_url, relative_url, sep = "/")
-  if (is_multiversion) {
-    url <- paste(
-      base_url,
-      Sys.getenv("BRANCH_NAME", multiversion_default_ref),
-      relative_url,
-      sep = "/"
-    )
-  }
-  return(link(text, url))
-}
-# Other variables
-admiral_homepage <- "https://pharmaverse.github.io/admiral/cran-release"
 ```
 
 # Introduction
 
 As this is a package extension, if you are new to `{admiral}` then the best place to first start
-reading would be this `r dyn_link("Get Started", admiral_homepage, "articles/admiral.html")`
+reading would be this [Get Started](https://pharmaverse.github.io/admiral/articles/admiral.html)
 guide. This extension package follows the same main idea and conventions, and re-uses many
 functions from `{admiral}`, so it is important to thoroughly understand these to be able to
 use `{admiralophtha}`.

vignettes/adoe.Rmd

@@ -13,33 +13,6 @@ knitr::opts_chunk$set(
   collapse = TRUE,
   comment = "#>"
 )
-link <- function(text, url) {
-  return(
-    paste0(
-      "[", text, "]",
-      "(", url, ")"
-    )
-  )
-}
-dyn_link <- function(text,
-                     base_url,
-                     relative_url = "",
-                     # Change to TRUE when admiral adopts multiversion docs
-                     is_multiversion = FALSE,
-                     multiversion_default_ref = "main") {
-  url <- paste(base_url, relative_url, sep = "/")
-  if (is_multiversion) {
-    url <- paste(
-      base_url,
-      Sys.getenv("BRANCH_NAME", multiversion_default_ref),
-      relative_url,
-      sep = "/"
-    )
-  }
-  return(link(text, url))
-}
-# Other variables
-admiral_homepage <- "https://pharmaverse.github.io/admiral"
 library(admiraldev)
 ```
 
@@ -143,5 +116,5 @@ The user is invited to consult the article on [creating a BDS dataset from SDTM]
 
 ADaM | Sample Code 
  ---- | -------------- 
-ADOE | `r dyn_link("ad_adoe.R", "https://github.com/pharmaverse/admiralophtha/blob", "inst/templates/ad_adoe.R", is_multiversion = TRUE)`
+ADOE | [ad_adoe.R](https://github.com/pharmaverse/admiralophtha/blob/main/inst/templates/ad_adoe.R)
 

vignettes/advfq.Rmd

@@ -13,33 +13,6 @@ knitr::opts_chunk$set(
   collapse = TRUE,
   comment = "#>"
 )
-link <- function(text, url) {
-  return(
-    paste0(
-      "[", text, "]",
-      "(", url, ")"
-    )
-  )
-}
-dyn_link <- function(text,
-                     base_url,
-                     relative_url = "",
-                     # Change to TRUE when admiral adopts multiversion docs
-                     is_multiversion = FALSE,
-                     multiversion_default_ref = "main") {
-  url <- paste(base_url, relative_url, sep = "/")
-  if (is_multiversion) {
-    url <- paste(
-      base_url,
-      Sys.getenv("BRANCH_NAME", multiversion_default_ref),
-      relative_url,
-      sep = "/"
-    )
-  }
-  return(link(text, url))
-}
-# Other variables
-admiral_homepage <- "https://pharmaverse.github.io/admiral"
 ```
 
 # Introduction
@@ -241,4 +214,5 @@ advfq <- advfq %>%
 
 ADaM | Sample Code 
  ---- | -------------- 
-ADVFQ | `r dyn_link("ad_advfq.R", "https://github.com/pharmaverse/admiralophtha/blob", "inst/templates/ad_advfq.R", is_multiversion = TRUE)`
+ADVFQ | [ad_advfq.R](https://github.com/pharmaverse/admiralophtha/blob/main/inst/templates/ad_advfq.R)
+

vignettes/articles/website-versions.Rmd

@@ -0,0 +1,82 @@
+---
+title: "Previous Versions of Website"
+---
+
+```{r, include = FALSE}
+# TO USE THIS ARTICLE, THE DESCRIPTION FILE MUST INCLUDE
+# Config/Needs/website: gert
+# Make sure to copy the gh-pages branch to your local git
+
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>"
+)
+```
+
+```{r setup, include=FALSE}
+base_url <-
+  "https://pharmaverse.github.io/admiralophtha/" # include the trailing backslash!
+
+# get list of all files in the `gh-pages` branch
+df_all_files <- tryCatch(gert::git_ls(ref = "gh-pages"), error = function(x) FALSE)
+
+# if a local user (not on CI) does not have a copy of the `gh-pages` branch, exit silently
+if (!isTRUE(as.logical(Sys.getenv("CI"))) && isFALSE(df_all_files)) {
+  knitr::knit_exit()
+}
+```
+
+```{r include=FALSE}
+# extract all folders in the root of the branch
+all_folders <-
+  sub("/.*", "", df_all_files$path)[grepl(
+    x = df_all_files$path,
+    pattern = "/",
+    fixed = TRUE
+  )] |>
+  unique()
+
+# subset to all version folders
+all_version_folders <-
+  all_folders[grep("^v[0-9]+|dev", x = all_folders)] |>
+  rev()
+# more dev first if it appears
+if ("dev" %in% all_version_folders) {
+  all_version_folders <- c("dev", all_version_folders) |> unique()
+}
+
+# release dates of prior tags
+df_tags <- gert::git_tag_list()
+df_tags <- df_tags[df_tags$name %in% all_version_folders, ]
+df_tags$date <-
+  lapply(
+    df_tags$commit,
+    FUN = function(x) {
+      tryCatch(
+        gert::git_commit_info(ref = x)$time |> as.Date() |> as.character(),
+        error = function(x) NA
+      )
+    }
+  ) |>
+  unlist()
+df_tags <- df_tags[!is.na(df_tags$date), ]
+
+lst_tag_dates <-
+  paste0(" (", df_tags$date, ")") |>
+  as.list() |>
+  setNames(df_tags$name)
+
+# string with all markdown links
+str_website_links <-
+  lapply(
+    X = all_version_folders,
+    FUN = function(x) {
+      x_label <- ifelse(x %in% "dev", "Development Site", x)
+      paste0("[", x_label, lst_tag_dates[[x]], "](", paste0(base_url, x), ")")
+    }
+  ) |>
+  unlist() |>
+  paste(collapse = "\n\n")
+```
+
+`r str_website_links`

vignettes/standards.Rmd

@@ -13,33 +13,6 @@ knitr::opts_chunk$set(
   collapse = TRUE,
   comment = "#>"
 )
-link <- function(text, url) {
-  return(
-    paste0(
-      "[", text, "]",
-      "(", url, ")"
-    )
-  )
-}
-dyn_link <- function(text,
-                     base_url,
-                     relative_url = "",
-                     # Change to TRUE when admiral adopts multiversion docs
-                     is_multiversion = FALSE,
-                     multiversion_default_ref = "main") {
-  url <- paste(base_url, relative_url, sep = "/")
-  if (is_multiversion) {
-    url <- paste(
-      base_url,
-      Sys.getenv("BRANCH_NAME", multiversion_default_ref),
-      relative_url,
-      sep = "/"
-    )
-  }
-  return(link(text, url))
-}
-# Other variables
-admiral_homepage <- "https://pharmaverse.github.io/admiral"
 library(admiraldev)
 ```