admiraldev v.0.5.0 (#327)

* docs: #283 update description and news * closes #286 commit messaging, new r-cmd vignette (#291) * docs: #286 commit messaging, new r-cmd vignette * chore: #286 spelling * docs: #286 squash and merge blurb * Update vignettes/git_usage.Rmd Co-authored-by: Zelos Zhu <[email protected]> * chore: #286 news update --------- Co-authored-by: Zelos Zhu <[email protected]> * Closes #271, #213, #260, #240 Documentation Update of get_datasets(); keep_source_vars argument; @family tag; compute_ functions (#287) * docs: #271 #213 clarify get_datasets and add keep_source_vars to prog strat * docs: #260 cleanup @family mentions * docs: #240 add blurb about compute functions * docs: #271 #213 #240 #260 add news blurb * adopt suggestion for family/keywords Co-authored-by: Ben Straub <[email protected]> * docs #271 adopt get_dataset feedback * docs: #213 #240 adopt recommendations from PR * chore: #240 add BMI to WORDLIST for spellcheck * chore: #271 #213 #260 adopt feedback --------- Co-authored-by: Zelos Zhu <[email protected]> Co-authored-by: Ben Straub <[email protected]> * Closes #264, #288 cleanup assertions and continue deprecation process (#289) * feat: #288 cleanup deprecation process * feat: #264 deprecate assert_function * test: #264 cleanup some tests in assert_function, confused how others would go * test: #264 rewrite tests in a more logical way * chore: #264 run styler/lintr * chore: #288 revert back to devel test file * chore: #288 properly fix assert_order_vars again * feat: #264 begin deprecation of redundant assertions * feat: #288 deprecate assert_named_exprs * deprecate assert_has_variables properly #264 * chore: #264 run styler * docs: #264 add blurb in news for the deprecated assertions * chore: #264 fix description version and remove deprecated examples --------- Co-authored-by: Zelos Zhu <[email protected]> * Propagate renv.lock from pharmaverse/admiralci (#294) renv update from pharmaverse/admiralci Co-authored-by: dgrassellyb <[email protected]> * Closes #22 #181 #201 #292 #298 Variety of small-scale general documentation updates (#303) * feat: #22 add documentation to friendly_type_of * feat: #181 add the appropriate URL * feat: #201 #292 add documentation about PR guidance and codeowners * chore: update wordlist for codeowners * chore: add NEWS --------- Co-authored-by: Zelos Zhu <[email protected]> * Closes #302 Adding Snapshot testing guidance to unit testing vignette (#308) * Update unit_test_guidance.Rmd * Update NEWS.md * Update NEWS.md * Closes #301: (#307) * #301: edoardo added as author, and author/contributor distinction implemented as in core admiral package * #301 chore: document * Propagate renv.lock from pharmaverse/admiralci (#310) * renv / codespaces update from pharmaverse/admiralci --------- Co-authored-by: galachad <[email protected]> Co-authored-by: Adam Foryś <[email protected]> * Closes #295 template documentation@devel (#300) * #295 set up package extension guidance page * #295 fix vignetteindexentry * #295 chore: spellcheck * #295 chore: fix encoding issues in vignettes that prevented package from being built * #295: updates following review * #295 Chore: spellcheck * Update vignettes/package_extensions.Rmd Co-authored-by: Ross Farrugia <[email protected]> * #295 update to refer to admiraldev devel site * #295 Chore: spellcheck --------- Co-authored-by: Ross Farrugia <[email protected]> * Closes #296 document_missing_value_s@devel (#311) * #296 - `missing_value` and `missing_values` added to the table of common arguments. * #296 - add in discussion of when to use singular vs plural arguments to programming strategy. * #296 - run checks required for PR and update NEWS.md. * #296 - Update according to requested changes. * #296 - revert the 'wrapped' changes in the programming strategy vignette * #296 - re-insert the new text into the programming strategy vignette, altered according to changes requested. * #296 - update NEWS.md with changes requested and run the required checks for PR. * Closes #282: Test Data Guidance vignette (#293) * #282: add test_data_guidance.Rmd, copy from admiraldata README devel * #282: update .yml * #282: add link for packages, remove SDTM, add naming conventions for program name * #282 spelling * #282: link to two data packages * #282: updated wordlist * #282: update pharmaverseadam description --------- Co-authored-by: Edoardo Mancini <[email protected]> * Propagate renv.lock from pharmaverse/admiralci (#314) renv / codespaces update from pharmaverse/admiralci Co-authored-by: galachad <[email protected]> * Propagate renv.lock from pharmaverse/admiralci (#315) * renv / codespaces update from pharmaverse/admiralci * renv / codespaces update from pharmaverse/admiralci --------- Co-authored-by: galachad <[email protected]> * Closes #306 argument descriptions added to table (#320) argument descriptions added to table Co-authored-by: Zelos Zhu <[email protected]> * Closes #316 remove messaging that includes "-" as year not handled (#317) * feat: #316 remove messaging that includes "-" as year not handled * feat: #316 replace warning message * chore: #316 fix warning message and typos * chore: #316 add news blurb --------- Co-authored-by: Zelos Zhu <[email protected]> * Closes #318 #321 Documentation updates around admiral.test, staged dependencies, and function arguments (#323) * Fix hardcoded URL (#326) Resolves #325 * Closes #312 breakup wall of text (#319) * brick in the wall * remove special characters from image name * remove special characters from image name * replaced iframe with png * fixed image reference --------- Co-authored-by: Zelos Zhu <[email protected]> * Closes #328 add missing news entries (#329) * feat: #295 add missing news entries * feat: #295 add missing news entries * fixed it * feat: add news entry for #306 * chore: #312 missing reference * chore: fix link that pointed to merged branch and use devel * Update NEWS.md --------- Co-authored-by: Zelos Zhu <[email protected]> Co-authored-by: Ben Straub <[email protected]> --------- Co-authored-by: Zelos Zhu <[email protected]> Co-authored-by: Ben Straub <[email protected]> Co-authored-by: pharmaverse-bot <[email protected]> Co-authored-by: dgrassellyb <[email protected]> Co-authored-by: Daniel Sjoberg <[email protected]> Co-authored-by: Edoardo Mancini <[email protected]> Co-authored-by: galachad <[email protected]> Co-authored-by: Adam Foryś <[email protected]> Co-authored-by: Ross Farrugia <[email protected]> Co-authored-by: Sophie Shapcott <[email protected]> Co-authored-by: Kangjie Zhang <[email protected]> Co-authored-by: StefanThoma <[email protected]> Co-authored-by: cicdguy <[email protected]>
pharmaverse · Sep 10, 2023 · 696a0f2 · 696a0f2
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -26,3 +26,4 @@
 ^admiraldev.*\.tgz$
 ^staged_dependencies.yaml$
 ^README.Rmd$
+^\.devcontainer$
diff --git a/.Rprofile b/.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")
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/DESCRIPTION b/DESCRIPTION
@@ -1,19 +1,20 @@
 Package: admiraldev
 Type: Package
 Title: Utility Functions and Development Tools for the Admiral Package Family
-Version: 0.4.0
+Version: 0.5.0
 Authors@R: c(
     person("Ben", "Straub", email = "[email protected]", role = c("aut", "cre")),
     person("Stefan", "Bundfuss", role = "aut"),
-    person("Thomas", "Neitmann", role = "aut"),
-    person("Samia", "Kabi", role = "aut"),
-    person("Pooja", "Kumari", role = "aut"),
-    person("Syed", "Mubasheer", role = "aut"),
+    person("Jeffrey", "Dickinson", role = "aut"),
     person("Ross", "Farrugia", role = "aut"),
+    person("Pooja", "Kumari", role = "aut"),
+    person("Edoardo", "Mancini", role = "aut"),
     person("Sadchla", "Mascary", role = "aut"),
     person("Zelos", "Zhu", role = "aut"),
-    person("Jeffrey", "Dickinson", role = "aut"),
-    person("Ania", "Golab", role = "aut"),
+    person("Ania", "Golab", role = "ctb"),
+    person("Samia", "Kabi", role = "ctb"),
+    person("Syed", "Mubasheer", role = "ctb"),
+    person("Thomas", "Neitmann", role = "ctb"),
     person("Ondrej", "Slama", role = "ctb"),
     person("F. Hoffmann-La Roche AG", role = c("cph", "fnd")),
     person("GlaxoSmithKline LLC", role = c("cph", "fnd"))
@@ -42,7 +43,7 @@ Imports:
     tidyr (>= 1.0.2),
     tidyselect (>= 1.0.0)
 Suggests:
-    admiral.test,
+    pharmaversesdtm,
     devtools,
     diffdf,
     lintr,

diff --git a/NAMESPACE b/NAMESPACE
@@ -43,6 +43,7 @@ export(expect_dfs_equal)
 export(expr_c)
 export(extract_vars)
 export(filter_if)
+export(friendly_type_of)
 export(get_constant_vars)
 export(get_dataset)
 export(get_duplicates)
@@ -55,11 +56,8 @@ export(is_order_vars)
 export(is_valid_dtc)
 export(left_join)
 export(process_set_values_to)
-export(quo_c)
-export(quo_not_missing)
 export(remove_tmp_vars)
 export(replace_symbol_in_expr)
-export(replace_symbol_in_quo)
 export(replace_values_by_names)
 export(squote)
 export(suppress_warning)