diff --git a/.Rbuildignore b/.Rbuildignore index c7366abf79..c39a8a6839 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -28,7 +28,6 @@ ^\.lycheeignore$ ^staged_dependencies.yaml$ ^inst/dev_dependencies.R$ -^\.devcontainer$ ^vignettes/articles$ ^inst/cheatsheet$ ^data-raw$ diff --git a/.devcontainer/4.1/devcontainer.json b/.devcontainer/4.1/devcontainer.json deleted file mode 100644 index ab6ddfeeae..0000000000 --- a/.devcontainer/4.1/devcontainer.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - // 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}/\"; echo 'To open rstudio in your browser, just type rstudio in the terminal'", - - "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 deleted file mode 100644 index decbcca545..0000000000 --- a/.devcontainer/4.2/devcontainer.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - // 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}/\"; echo 'To open rstudio in your browser, just type rstudio in the terminal'", - - "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 deleted file mode 100644 index 3f47589f32..0000000000 --- a/.devcontainer/devcontainer.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - // 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.${GITHUB_CODESPACES_PORT_FORWARDING_DOMAIN}/\"; echo 'To open rstudio in your browser, just type rstudio in the terminal'", - - "customizations": { - "vscode": { - "settings": { - "r.rterm.linux": "/usr/local/bin/radian", - "r.bracketedPaste": true, - "editor.bracketPairColorization.enabled": true, - "editor.guides.bracketPairs": "active" - }, - "extensions": [ - "vsls-contrib.codetour", - "GitHub.copilot", - "GitHub.copilot-chat", - // R extensions - "ikuyadeu.r", - "REditorSupport.r-lsp", - // Extra extension - "streetsidesoftware.code-spell-checker", - "eamodio.gitlens", - "cweijan.vscode-office", - "donjayamanne.githistory", - "GitHub.vscode-github-actions", - "GitHub.vscode-pull-request-github", - "GitHub.remotehub", - "alefragnani.Bookmarks", - "vscode-icons-team.vscode-icons" - ] - } - }, - - // RStudio ports - "forwardPorts": [8787], - "portsAttributes": { - "8787": { - "label": "Rstudio", - "requireLocalPort": true, - "onAutoForward": "openBrowser" - } - }, - // Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root - "remoteUser": "rstudio" -} diff --git a/.devcontainer/postCreateCommand.sh b/.devcontainer/postCreateCommand.sh deleted file mode 100644 index 8dfe4e236e..0000000000 --- a/.devcontainer/postCreateCommand.sh +++ /dev/null @@ -1,11 +0,0 @@ -#!/bin/bash - -# move script rstudio into /usr/bin -sudo cp "$(pwd)/.devcontainer/rstudio.sh" /usr/bin/rstudio -sudo chmod +x /usr/bin/rstudio - -# Restore renv and install staged dependencies -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);' - -# Define rstudio default working directory -jq --arg folder "$(pwd)/" '. + { "initial_working_directory": $folder }' .devcontainer/rstudio-prefs.json > ~/.config/rstudio/rstudio-prefs.json diff --git a/.devcontainer/rstudio-prefs.json b/.devcontainer/rstudio-prefs.json deleted file mode 100644 index 2d5cce8464..0000000000 --- a/.devcontainer/rstudio-prefs.json +++ /dev/null @@ -1,8 +0,0 @@ -{ - "save_workspace": "never", - "always_save_history": false, - "reuse_sessions_for_project_links": true, - "posix_terminal_shell": "bash", - "initial_working_directory": "/workspaces", - "show_hidden_files": true -} diff --git a/.devcontainer/rstudio.sh b/.devcontainer/rstudio.sh deleted file mode 100644 index 053a247b5b..0000000000 --- a/.devcontainer/rstudio.sh +++ /dev/null @@ -1,5 +0,0 @@ -#!/bin/bash - -$BROWSER "https://${CODESPACE_NAME}-8787.${GITHUB_CODESPACES_PORT_FORWARDING_DOMAIN}" - -exit 1 diff --git a/NEWS.md b/NEWS.md index 91fb0405c8..a52fb8c6da 100644 --- a/NEWS.md +++ b/NEWS.md @@ -6,7 +6,6 @@ `AVALCATx` & `AVALCAxN`. (#2480) - New function `derive_vars_crit_flag()` for deriving criterion flag variables (`CRITy`, `CRITyFL`, `CRITyFLN`). (#2468) - - Replace use of `data("sdtm")` with `sdtm <- pharmaverse::sdtm` in templates and vignettes. (#2498) ## Updates of Existing Functions @@ -43,6 +42,7 @@ Developer Notes - Adopted `data-raw/data` R Package Convention (#2427) +- Removed `.devcontainer` file (codespace) (#2524) diff --git a/inst/WORDLIST b/inst/WORDLIST index e3a009b79f..bdee907508 100644 --- a/inst/WORDLIST +++ b/inst/WORDLIST @@ -265,6 +265,7 @@ bds censorings chk codebase +codespace constructible creatinine cyclomatic