Initial commit

jeffreyad · Oct 6, 2023 · 8a85b01 · 8a85b01
commit 8a85b01
Show file tree

Hide file tree

Showing 62 changed files with 10,264 additions and 0 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -0,0 +1,21 @@
+^renv$
+^renv\.lock$
+^.*\.Rproj$
+^.*\.lycheeignore$
+^\.Rproj\.user$
+^pkgdown$
+^_pkgdown\.yml$
+^.github$
+^.lintr$
+^docs$
+^Meta$
+^codecov\.yml$
+^man/dev_util_.+\.Rd$
+^LICENSE\.md$
+^\.github$
+^admiraltemplate\.Rcheck$
+^admiraltemplate.*\.tar\.gz$
+^admiraltemplate.*\.tgz$
+^staged_dependencies.yaml$
+^README.Rmd$
+^\.devcontainer$
diff --git a/.Rprofile b/.Rprofile
@@ -0,0 +1,48 @@
+# Set renv profile base on R version.
+.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.")
+  }
+} else {
+  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")
diff --git a/.devcontainer/4.1/devcontainer.json b/.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"
+}
diff --git a/.devcontainer/4.2/devcontainer.json b/.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"
+}
diff --git a/.devcontainer/devcontainer.json b/.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.${GITHUB_CODESPACES_PORT_FORWARDING_DOMAIN}/\"",
+
+	"customizations": {
+		"vscode": {
+			"settings": {
+				"r.rterm.linux": "/usr/local/bin/radian",
+				"r.bracketedPaste": true,
+				"editor.bracketPairColorization.enabled": true, 
+				"editor.guides.bracketPairs": "active"
+			},
+			"extensions": [
+				"vsls-contrib.codetour",
+				"GitHub.copilot",
+				"GitHub.copilot-chat",
+				// R extensions
+				"ikuyadeu.r",
+				"REditorSupport.r-lsp",
+				// Extra extension
+				"streetsidesoftware.code-spell-checker",
+				"eamodio.gitlens",
+				"cweijan.vscode-office",
+				"donjayamanne.githistory",
+				"GitHub.vscode-github-actions",
+				"GitHub.vscode-pull-request-github",
+				"GitHub.remotehub",
+				"alefragnani.Bookmarks",
+				"vscode-icons-team.vscode-icons"
+			]
+		}
+	},
+
+	// RStudio ports
+	"forwardPorts": [8787],
+	"portsAttributes": {
+		"8787": {
+			"label": "Rstudio",
+			"requireLocalPort": true,
+			"onAutoForward": "openBrowser"
+		}
+	},
+	// Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root
+	"remoteUser": "rstudio"
+}
diff --git a/.devcontainer/postCreateCommand.sh b/.devcontainer/postCreateCommand.sh
@@ -0,0 +1,5 @@
+#!/bin/bash
+
+R -q -e 'renv::restore(lockfile = file.path("renv", "profiles", paste(R.version$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
diff --git a/.devcontainer/rstudio-prefs.json b/.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
+}
diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS
@@ -0,0 +1,5 @@
+# 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. In this instance, cicdguy will be notified of any
+# changes made the files inside the .github/workflows directory.
+.github/workflows/* @cicdguy
diff --git a/.github/ISSUE_TEMPLATE/01_bug_report.yml b/.github/ISSUE_TEMPLATE/01_bug_report.yml
@@ -0,0 +1,35 @@
+name: Bug Report
+description: Something is not working correctly or is not working at all!
+title: "Bug: <Insert Issue Title Here>"
+labels: ["bug", "programming"]
+assignees:
+  - octocat
+body:
+  - type: markdown
+    attributes:
+      value: |
+        **Example:** Bug: derive_vars_dtm() is returning NA values when using preserve argument
+  - type: textarea
+    id: what-happened
+    attributes:
+      label: What happened?
+      description: Also tell us what were you expecting to happen before the bug?
+      placeholder: "A bug happened!"
+    validations:
+      required: true
+  - type: textarea
+    id: session-info
+    attributes:
+      label: Session Information
+      description: Use `sessionInfo()` in the R console to gather all the details of your environment when the bug happened.
+      placeholder: "Place the console output here"
+    validations:
+      required: false
+  - type: textarea
+    id: logs
+    attributes:
+      label: Reproducible Example
+      description: We love code that can reproduce the example. Check out [reprex](https://reprex.tidyverse.org/articles/reprex-dos-and-donts.html)
+      placeholder: "Please give us as many details as you can! The faster we can recreate the bug, the faster we can get a fix in the works.  Warning, Error Messages and Screenshots are also great."
+    validations:
+      required: false