Closes #2034 use functions to standardize roxygen text

.Rbuildignore

@@ -28,3 +28,4 @@
 ^\.lycheeignore$
 ^staged_dependencies.yaml$
 ^inst/dev_dependencies.R$
+^\.devcontainer$

.Rprofile

@@ -1,15 +1,48 @@
 # Set renv profile base on R version.
-if ((Sys.getenv("GITHUB_ACTIONS") == "") && (Sys.getenv("DOCKER_CONTAINER_CONTEXT") == "")) {
-  renv_profile <- paste(R.version$major, substr(R.version$minor, 1, 1), sep = ".")
-  if (file.exists("./renv/profile")) {
-    message("Using renv profile from `renv/profile` file.")
-  } else if (renv_profile %in% c("4.1", "4.2", "4.3")) {
-    message("Set renv profile to `", renv_profile, "`")
-    Sys.setenv("RENV_PROFILE" = renv_profile)
+.get_dependencies <- function(project_dir) {
+
+  admdev_loc <- find.package("admiraldev", lib.loc = .libPaths(), quiet = TRUE)
+  adm_dev_suggests <- if(length(admdev_loc) != 0) {
+    renv:::renv_dependencies_discover_description(admdev_loc, fields = c("Depends", "Imports", "LinkingTo", "Suggests"))
+  } else {
+    data.frame(Packages = character(0))
+  }
+  suggests_packages <- renv:::renv_dependencies_discover_description(project_dir, fields = "Suggests")
+
+  packages <- names(
+    renv:::renv_package_dependencies(
+      unique(c(
+        project_dir,
+        adm_dev_suggests[["Package"]],
+        suggests_packages[["Package"]],
+        c("staged.dependencies", "renv", "styler")
+      ))
+    )
+  )
+  packages[!(packages %in% c("admiral", "admiraldev", "admiralci", "admiral.test", "pharmaversesdtm", getwd()))]
+}
+
+options(renv.snapshot.filter = .get_dependencies)
+
+.renv_profile <- paste(R.version$major, substr(R.version$minor, 1, 1), sep = ".")
+if (!file.exists("./renv/profile")) {
+  if (.renv_profile %in% c("4.1", "4.2", "4.3")) {
+    message("Set renv profile to `", .renv_profile, "`")
+    Sys.setenv("RENV_PROFILE" = .renv_profile)
   } else {
     message("This repository do not contains the renv profile for your R version.")
   }
-  source("renv/activate.R")
 } else {
-  options(repos = c(CRAN = "https://cran.rstudio.com"))
+  message(
+    "Using renv profile from `renv/profile` file.\n",
+    "The `", readLines("./renv/profile"), "` profile will be used."
+  )
+}
+
+if (Sys.getenv("GITHUB_ACTIONS") != "") {
+  options(repos = c(CRAN = "https://packagemanager.posit.co/cran/latest"))
+  Sys.setenv("RENV_AUTOLOADER_ENABLED" = FALSE)
 }
+Sys.setenv("RENV_CONFIG_SANDBOX_ENABLED" = FALSE)
+Sys.setenv("RENV_CONFIG_AUTO_SNAPSHOT" = FALSE)
+source("renv/activate.R")

.devcontainer/4.1/devcontainer.json

@@ -0,0 +1,76 @@
+{
+	// https://containers.dev/implementors/json_reference/
+	"name": "Admiral R-4.1 (RStudio) container",
+	"image": "ghcr.io/pharmaverse/admiralci-4.1:latest",
+	// Install Dev Container Features. More info: https://containers.dev/features
+	"containerEnv": {
+		"ROOT": "true",
+		"PASSWORD": "rstudio",
+		"DISABLE_AUTH": "true",
+		"RENV_AUTOLOADER_ENABLED": "false"
+	},
+	"features": {
+		"ghcr.io/rocker-org/devcontainer-features/r-rig:1": {
+			"version": "none",
+			"vscodeRSupport": "full",
+			"installRadian": true,
+			"installVscDebugger": true
+		},
+		"ghcr.io/rocker-org/devcontainer-features/renv-cache:latest": {},
+		"ghcr.io/devcontainers/features/common-utils:2": {
+			"installZsh": true,
+			"configureZshAsDefaultShell": false,
+			"installOhMyZsh": true,
+			"username": "rstudio",
+			"upgradePackages": false
+		},
+		"ghcr.io/mikaello/devcontainer-features/modern-shell-utils:1": {}
+	},
+	"init": true,
+	"overrideCommand": false,
+
+	"postCreateCommand": "bash ./.devcontainer/postCreateCommand.sh",
+
+	"postAttachCommand": "$BROWSER \"https://${CODESPACE_NAME}-8787.${GITHUB_CODESPACES_PORT_FORWARDING_DOMAIN}/\"",
+
+	"customizations": {
+		"vscode": {
+			"settings": {
+				"r.rterm.linux": "/usr/local/bin/radian",
+				"r.bracketedPaste": true,
+				"editor.bracketPairColorization.enabled": true, 
+				"editor.guides.bracketPairs": "active"
+			},
+			"extensions": [
+				"vsls-contrib.codetour",
+				"GitHub.copilot",
+				"GitHub.copilot-chat",
+				// R extensions
+				"ikuyadeu.r",
+				"REditorSupport.r-lsp",
+				// Extra extension
+				"streetsidesoftware.code-spell-checker",
+				"eamodio.gitlens",
+				"cweijan.vscode-office",
+				"donjayamanne.githistory",
+				"GitHub.vscode-github-actions",
+				"GitHub.vscode-pull-request-github",
+				"GitHub.remotehub",
+				"alefragnani.Bookmarks",
+				"vscode-icons-team.vscode-icons"
+			]
+		}
+	},
+
+	// RStudio ports
+	"forwardPorts": [8787],
+	"portsAttributes": {
+		"8787": {
+			"label": "Rstudio",
+			"requireLocalPort": true,
+			"onAutoForward": "openBrowser"
+		}
+	},
+	// Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root
+	"remoteUser": "rstudio"
+}

.devcontainer/4.2/devcontainer.json

@@ -0,0 +1,76 @@
+{
+	// https://containers.dev/implementors/json_reference/
+	"name": "Admiral R-4.2 (RStudio) container",
+	"image": "ghcr.io/pharmaverse/admiralci-4.2:latest",
+	// Install Dev Container Features. More info: https://containers.dev/features
+	"containerEnv": {
+		"ROOT": "true",
+		"PASSWORD": "rstudio",
+		"DISABLE_AUTH": "true",
+		"RENV_AUTOLOADER_ENABLED": "false"
+	},
+	"features": {
+		"ghcr.io/rocker-org/devcontainer-features/r-rig:1": {
+			"version": "none",
+			"vscodeRSupport": "full",
+			"installRadian": true,
+			"installVscDebugger": true
+		},
+		"ghcr.io/rocker-org/devcontainer-features/renv-cache:latest": {},
+		"ghcr.io/devcontainers/features/common-utils:2": {
+			"installZsh": true,
+			"configureZshAsDefaultShell": false,
+			"installOhMyZsh": true,
+			"username": "rstudio",
+			"upgradePackages": false
+		},
+		"ghcr.io/mikaello/devcontainer-features/modern-shell-utils:1": {}
+	},
+	"init": true,
+	"overrideCommand": false,
+
+	"postCreateCommand": "bash ./.devcontainer/postCreateCommand.sh",
+
+	"postAttachCommand": "$BROWSER \"https://${CODESPACE_NAME}-8787.${GITHUB_CODESPACES_PORT_FORWARDING_DOMAIN}/\"",
+
+	"customizations": {
+		"vscode": {
+			"settings": {
+				"r.rterm.linux": "/usr/local/bin/radian",
+				"r.bracketedPaste": true,
+				"editor.bracketPairColorization.enabled": true, 
+				"editor.guides.bracketPairs": "active"
+			},
+			"extensions": [
+				"vsls-contrib.codetour",
+				"GitHub.copilot",
+				"GitHub.copilot-chat",
+				// R extensions
+				"ikuyadeu.r",
+				"REditorSupport.r-lsp",
+				// Extra extension
+				"streetsidesoftware.code-spell-checker",
+				"eamodio.gitlens",
+				"cweijan.vscode-office",
+				"donjayamanne.githistory",
+				"GitHub.vscode-github-actions",
+				"GitHub.vscode-pull-request-github",
+				"GitHub.remotehub",
+				"alefragnani.Bookmarks",
+				"vscode-icons-team.vscode-icons"
+			]
+		}
+	},
+
+	// RStudio ports
+	"forwardPorts": [8787],
+	"portsAttributes": {
+		"8787": {
+			"label": "Rstudio",
+			"requireLocalPort": true,
+			"onAutoForward": "openBrowser"
+		}
+	},
+	// Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root
+	"remoteUser": "rstudio"
+}

.devcontainer/devcontainer.json

@@ -0,0 +1,76 @@
+{
+	// https://containers.dev/implementors/json_reference/
+	"name": "Admiral R-4.3 (RStudio) container",
+	"image": "ghcr.io/pharmaverse/admiralci-4.3:latest",
+	// Install Dev Container Features. More info: https://containers.dev/features
+	"containerEnv": {
+		"ROOT": "true",
+		"PASSWORD": "rstudio",
+		"DISABLE_AUTH": "true",
+		"RENV_AUTOLOADER_ENABLED": "false"
+	},
+	"features": {
+		"ghcr.io/rocker-org/devcontainer-features/r-rig:1": {
+			"version": "none",
+			"vscodeRSupport": "full",
+			"installRadian": true,
+			"installVscDebugger": true
+		},
+		"ghcr.io/rocker-org/devcontainer-features/renv-cache:latest": {},
+		"ghcr.io/devcontainers/features/common-utils:2": {
+			"installZsh": true,
+			"configureZshAsDefaultShell": false,
+			"installOhMyZsh": true,
+			"username": "rstudio",
+			"upgradePackages": false
+		},
+		"ghcr.io/mikaello/devcontainer-features/modern-shell-utils:1": {}
+	},
+	"init": true,
+	"overrideCommand": false,
+
+	"postCreateCommand": "bash ./.devcontainer/postCreateCommand.sh",
+
+	"postAttachCommand": "$BROWSER \"https://${CODESPACE_NAME}-8787.${GITHUB_CODESPACES_PORT_FORWARDING_DOMAIN}/\"",
+
+	"customizations": {
+		"vscode": {
+			"settings": {
+				"r.rterm.linux": "/usr/local/bin/radian",
+				"r.bracketedPaste": true,
+				"editor.bracketPairColorization.enabled": true, 
+				"editor.guides.bracketPairs": "active"
+			},
+			"extensions": [
+				"vsls-contrib.codetour",
+				"GitHub.copilot",
+				"GitHub.copilot-chat",
+				// R extensions
+				"ikuyadeu.r",
+				"REditorSupport.r-lsp",
+				// Extra extension
+				"streetsidesoftware.code-spell-checker",
+				"eamodio.gitlens",
+				"cweijan.vscode-office",
+				"donjayamanne.githistory",
+				"GitHub.vscode-github-actions",
+				"GitHub.vscode-pull-request-github",
+				"GitHub.remotehub",
+				"alefragnani.Bookmarks",
+				"vscode-icons-team.vscode-icons"
+			]
+		}
+	},
+
+	// RStudio ports
+	"forwardPorts": [8787],
+	"portsAttributes": {
+		"8787": {
+			"label": "Rstudio",
+			"requireLocalPort": true,
+			"onAutoForward": "openBrowser"
+		}
+	},
+	// Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root
+	"remoteUser": "rstudio"
+}

.devcontainer/postCreateCommand.sh

@@ -0,0 +1,5 @@
+#!/bin/bash
+
+R -q -e 'renv::restore(lockfile = file.path("renv", "profiles", paste(R.version$major, substr(R.version$minor, 1, 1), sep = "."), "renv.lock")); staged.dependencies::install_deps(staged.dependencies::dependency_table(project = ".", verbose = 1), verbose = 1);'
+
+jq --arg folder "$(pwd)/" '. + { "initial_working_directory": $folder }' .devcontainer/rstudio-prefs.json > ~/.config/rstudio/rstudio-prefs.json

.devcontainer/rstudio-prefs.json

@@ -0,0 +1,8 @@
+{
+	"save_workspace": "never",
+	"always_save_history": false,
+	"reuse_sessions_for_project_links": true,
+	"posix_terminal_shell": "bash",
+	"initial_working_directory": "/workspaces",
+	"show_hidden_files": true
+}

.github/CODEOWNERS

@@ -0,0 +1,15 @@
+# This a CODEOWNERS file, where you can establish code owners.
+# Code owners are automatically requested for review when someone opens a pull request
+# that modifies code that they own.
+#
+# Lab related files for Gordon Miller
+vignettes/lab_grading.Rmd @millerg23
+inst/adlb_grading/* @millerg23
+R/derive_var_atoxgr.R @millerg23
+data/atoxgr_criteria_ctcv5.rda @millerg23
+
+# PKPD related files for Jeff Dickinson
+inst/templates/ad_adppk.R @jeffreyad
+inst/templates/ad_adpc.R @jeffreyad
+R/compute_kidney.R @jeffreyad
+vignettes/pk_adnca.Rmd @jeffreyad

.github/workflows/cran-status.yml

@@ -17,7 +17,7 @@ jobs:
     with:
       # Whom should the issue be assigned to if errors are encountered
       # in the CRAN status checks?
-      issue-assignees: "bundfussr,esimms999-gsk,thomas-neitmann,bms63"
+      issue-assignees: "bundfussr,esimms999-gsk,manciniedoardo,bms63"
       # Create an issue if one or more of the following
       # statuses are reported on the check report.
       statuses: "WARN,ERROR,NOTE"

.github/workflows/stale-bot.yml

@@ -0,0 +1,25 @@
+# https://github.com/actions/stale
+
+name: Close Inactive Issues and Pull Requests
+on:
+  schedule:
+    - cron: "30 1 * * *"
+
+jobs:
+  close-issues:
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+      pull-requests: write
+    steps:
+      - uses: actions/stale@v8
+        with:
+          days-before-issue-stale: 90
+          days-before-issue-close: -1
+          stale-issue-label: "stale"
+          stale-issue-message: "This issue is stale because it has been open for 90 days with no activity."
+          days-before-pr-stale: 15
+          days-before-pr-close: -1
+          stale-pr-label: "stale"
+          stale-pr-message: "This Pull Request is stale because it has not been worked on in 15 days."
+          repo-token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/templates.yml

@@ -3,13 +3,15 @@ name: Check Templates
 
 on:
   workflow_dispatch:
-  pull_request_review:
-    types: [submitted]
+  pull_request:
+    branches:
+      - main
+      - devel
 
 jobs:
   templates:
     name: Check Templates
     uses: pharmaverse/admiralci/.github/workflows/check-templates.yml@main
-    if: github.event.review.state == 'approved'
+    if: github.event_name == 'pull_request'
     with:
       r-version: "4.1"

.gitignore

@@ -40,7 +40,6 @@ vignettes/*.pdf
 
 # website documents
 /docs/*
-!/docs/pkgdown.yml
 doc
 Meta
 admiral.Rcheck/

.lycheeignore

@@ -3,4 +3,3 @@ https://github.com/pharmaverse/admiral/blob/main/
 https://github.com/pharmaverse/admiral/blob/main/inst/templates/ad_adxx.R
 irongut/CodeCoverageSummary@v1.2.0
 https://packagemanager.rstudio.com/cran/__linux__/focal/latest
-https://pharmaverse.github.io/admiral/articles/higher_order.html