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pkgdown.yml
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on:
workflow_dispatch:
inputs:
r-version:
description: 'The version of R to use'
default: 'release'
required: false
type: choice
options:
- devel
- latest
skip-multiversion-docs:
description: 'Skip creation of multi-version docs'
default: false
required: false
type: boolean
multiversion-docs-landing-page:
description: 'Ref to use for the multiversion docs landing page'
default: main
required: false
type: string
latest-tag-alt-name:
description: "An alternate name to use for 'latest-tag' for multiversion pkgdown docs"
default: ""
required: false
type: string
branches-or-tags-to-list:
description: |
Which branches or tags should be listed under the
'Versions' dropdown menu on the landing page?
This input should be a regular expression in R.
required: false
default: >-
^main$|^devel$|^pre-release$|^latest-tag$|^cran-release$|^develop$|^v([0-9]+\\.)?([0-9]+\\.)?([0-9]+)$
type: string
workflow_call:
inputs:
r-version:
description: 'The version of R to use'
default: 'release'
required: false
type: string
skip-multiversion-docs:
description: 'Skip creation of multi-version docs'
default: false
required: false
type: boolean
multiversion-docs-landing-page:
description: 'Ref to use for the multiversion docs landing page'
default: main
required: false
type: string
latest-tag-alt-name:
description: "An alternate name to use for 'latest-tag' for multiversion pkgdown docs"
default: ""
required: false
type: string
branches-or-tags-to-list:
description: |
Which branches or tags should be listed under the
'Versions' dropdown menu on the landing page?
This input should be a regular expression in R.
required: false
default: >-
^main$|^devel$|^pre-release$|^latest-tag$|^cran-release$|^develop$|^v([0-9]+\\.)?([0-9]+\\.)?([0-9]+)$
type: string
secrets:
GITHUB_PAT:
required: false
description: GitHub API access token, which might be needed for downstream ops or rendering.
name: Documentation
concurrency:
group: pkgdown-${{ github.event.pull_request.number || github.ref }}
cancel-in-progress: true
jobs:
pkgdown:
name: pkgdown
runs-on: ubuntu-latest
container:
image: "ghcr.io/pharmaverse/admiralci-${{ inputs.r-version }}:latest"
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
if: >
!contains(github.event.commits[0].message, '[skip docs]')
steps:
##################### BEGIN boilerplate steps #####################
- name: Get branch names
id: branch-name
uses: tj-actions/[email protected]
- name: Checkout repo (PR) 🛎
uses: actions/checkout@v3
if: github.event_name == 'pull_request'
with:
ref: ${{ steps.branch-name.outputs.head_ref_branch }}
repository: ${{ github.event.pull_request.head.repo.full_name }}
- name: Checkout repository
uses: actions/checkout@v3
if: github.event_name != 'pull_request'
with:
ref: ${{ steps.branch-name.outputs.head_ref_branch }}
# https://github.com/actions/runner/issues/2033
- name: Set-up safe dir
run: |
echo "${PWD}"
git config --global --add safe.directory "${GITHUB_WORKSPACE}"
shell: bash
- name: Normalize inputs
id: normalizer
run: |
function normalize() {
local var=$1
if [ "$var" == "" ]
then {
var=$2
}
fi
echo ${var}
}
R_VERSION=$(normalize ${{ inputs.r-version }} 4.1)
DOCS_LANDING_PAGE=$(normalize ${{ inputs.multiversion-docs-landing-page }} main)
echo "R_VERSION=$R_VERSION" >> $GITHUB_OUTPUT
echo "DOCS_LANDING_PAGE=$DOCS_LANDING_PAGE" >> $GITHUB_OUTPUT
shell: bash
- name: Restore cache
uses: actions/cache@v3
with:
path: |
~/.staged.dependencies
key: staged-deps
- name: Setup pandoc
uses: r-lib/actions/setup-pandoc@v2
- name: Run Staged dependencies
uses: insightsengineering/staged-dependencies-action@v1
with:
run-system-dependencies: false
renv-restore: false
enable-check: false
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
- name: Install dependencies from DESCRIPTION
run: |
remotes::install_local(force = TRUE, dependencies = TRUE)
shell: Rscript {0}
##################### END boilerplate steps #####################
- name: Install package
run: renv::install(".", dependencies = "no-deps")
shell: Rscript {0}
- name: Add script to fix rdrr.io links for pharmaverse packages
uses: "DamianReeves/[email protected]"
with:
path: ./.Rprofile
write-mode: append
contents: |
tweak_rdrr_url <- function(...) {
html <- ..1
links <- xml2::xml_find_all(html, ".//a")
if (length(links) == 0) {
return(invisible())
}
hrefs <- xml2::xml_attr(links, "href")
needs_tweak <- grepl("^https://rdrr.io/pkg/", hrefs) & xml2::url_parse(hrefs)$scheme == "https"
fix_links <- function(x) {
pattern <- "/pkg/(\\w+)/man/(\\w+)\\.html"
matches <- stringr::str_match(x, pattern)
package_name <- matches[2]
function_name <- matches[3]
if (!(grepl("^admiral", package_name) || package_name %in% c("matatools", "matacore"))) {
return(x)
}
sprintf("https://pharmaverse.github.io/%s/main/reference/%s.html", package_name, function_name)
}
if (any(needs_tweak)) {
purrr::walk2(
links[needs_tweak],
purrr::map(hrefs[needs_tweak], fix_links),
xml2::xml_set_attr,
attr = "href"
)
}
invisible()
}
setHook("UserHook::admiralci::tweak_page", tweak_rdrr_url)
print("Tweak rdrr.io links for admiral pharmaverse packages.")
- name: Publish documentation
run: |
git config --local user.email "[email protected]"
git config --local user.name "GitHub Actions"
SUBDIR_OPTION=""
if [ "${{ inputs.skip-multiversion-docs }}" != "true" ]
then {
SUBDIR_OPTION="subdir = \"${GITHUB_REF##*/}\","
}
fi
Rscript - <<EOF
pkgdown_env <- asNamespace("pkgdown")
rlang::env_unlock(env = pkgdown_env)
rlang::env_binding_unlock(env = pkgdown_env)
pkgdown_env\$call_hook <- function(hook_name, ...) {
hooks <- getHook(paste0("UserHook::admiralci::", hook_name))
if (!is.list(hooks)) {
hooks <- list(hooks)
}
purrr::map(hooks, function(fun) {
fun(...)
}) %>%
invisible()
}
environment(pkgdown_env\$call_hook) <- pkgdown_env
tweak_page <- body(pkgdown_env\$tweak_page)
body(pkgdown_env\$tweak_page) <-
as.call(
append(
as.list(tweak_page),
expression(call_hook("tweak_page", html, name, pkg)),
after=length(tweak_page)
)
)
rlang::env_binding_lock(env = pkgdown_env)
rlang::env_lock(pkgdown_env)
require(desc::desc_get("Package"), character.only = TRUE)
clean = FALSE
if ("${{ inputs.skip-multiversion-docs }}" == "true"){
clean = TRUE
}
pkgdown::deploy_to_branch(
new_process = FALSE,
${SUBDIR_OPTION}
clean = clean
)
EOF
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
multi-version-docs:
name: Multi-version docs
needs: pkgdown
runs-on: ubuntu-latest
if: >
!inputs.skip-multiversion-docs &&
!contains(github.event.commits[0].message, '[skip docs]')
steps:
- name: Checkout repo
uses: actions/checkout@v3
with:
path: ${{ github.event.repository.name }}
ref: "gh-pages"
- name: Normalize inputs
id: normalizer
run: |
function normalize() {
local var=$1
if [ "$var" == "" ]
then {
var=$2
}
fi
echo ${var}
}
DOCS_LANDING_PAGE=$(normalize ${{ inputs.multiversion-docs-landing-page }} main)
echo "DOCS_LANDING_PAGE=$DOCS_LANDING_PAGE" >> $GITHUB_OUTPUT
shell: bash
- name: Create and publish docs
uses: insightsengineering/r-pkgdown-multiversion@v2
with:
path: ${{ github.event.repository.name }}
default-landing-page: "${{ steps.normalizer.outputs.DOCS_LANDING_PAGE }}"
latest-tag-alt-name: "${{ inputs.latest-tag-alt-name }}"
branches-or-tags-to-list: ${{ inputs.branches-or-tags-to-list }}