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Merge branch 'main' into 204_admiral_updates
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manciniedoardo authored Nov 16, 2023
2 parents 33a4c54 + 3db19a5 commit b52e13f
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4 changes: 2 additions & 2 deletions .github/workflows/common.yml
Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,7 @@ concurrency:

env:
R_VERSION: "4.1"

jobs:
get_r_version:
name: Get R version
Expand Down Expand Up @@ -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
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34 changes: 1 addition & 33 deletions README.Rmd
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Expand Up @@ -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;"/>
Expand Down Expand Up @@ -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

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3 changes: 0 additions & 3 deletions README.md
Original file line number Diff line number Diff line change
@@ -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;"/>
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12 changes: 10 additions & 2 deletions _pkgdown.yml
Original file line number Diff line number Diff line change
Expand Up @@ -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:
Expand Down Expand Up @@ -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
Expand All @@ -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
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31 changes: 1 addition & 30 deletions vignettes/adbcva.Rmd
Original file line number Diff line number Diff line change
Expand Up @@ -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)
```

Expand Down Expand Up @@ -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)
29 changes: 1 addition & 28 deletions vignettes/admiralophtha.Rmd
Original file line number Diff line number Diff line change
Expand Up @@ -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}`.
Expand Down
29 changes: 1 addition & 28 deletions vignettes/adoe.Rmd
Original file line number Diff line number Diff line change
Expand Up @@ -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)
```

Expand Down Expand Up @@ -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)

30 changes: 2 additions & 28 deletions vignettes/advfq.Rmd
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -245,4 +218,5 @@ 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)

82 changes: 82 additions & 0 deletions vignettes/articles/website-versions.Rmd
Original file line number Diff line number Diff line change
@@ -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`
27 changes: 0 additions & 27 deletions vignettes/standards.Rmd
Original file line number Diff line number Diff line change
Expand Up @@ -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)
```

Expand Down

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