rlabkey CLI deprecated, session init only on R console, impossible on...

rlabkey CLI deprecated, session init only on R console, impossible on terminal. Building CLI as R package

.Rbuildignore

+^renv$
+^renv\.lock$
+^.*\.Rproj$
+^\.Rproj\.user$

.Rprofile

+source("renv/activate.R")

.gitignore

+.Rproj.user

DESCRIPTION

+Package: rlabkeyCLI
+Type: Package
+Title: What the Package Does (Title Case)
+Version: 0.1.0
+Author: Who wrote it
+Maintainer: The package maintainer <yourself@somewhere.net>
+Description: More about what it does (maybe more than one line)
+    Use four spaces when indenting paragraphs within the Description.
+License: What license is it under?
+Encoding: UTF-8
+LazyData: true

NAMESPACE

+exportPattern("^[[:alpha:]]+")

bash/rlabkey

 #!/bin/bash
 
+# DEPRECATED, since use of rlabkey API needs R session ID, not possible from terminal
+
 VERSION="1.0.0"
 RLABKEY_DIR="$HOME/.rlabkey"
 CONFIG_FILE="$RLABKEY_DIR/config/"
@@ -96,7 +98,7 @@ case "$1" in
         PROJECT=""
         FILE=""
         FILTER=""
-        
+
         while [[ $# -gt 0 ]]; do
             case "$1" in
                 --project)
@@ -116,7 +118,7 @@ case "$1" in
                     ;;
             esac
         done
-        
+
         Rscript $RLABKEY_DIR/R/fetch.R "$PROJECT" "$FILE" || error "Failed to execute fetch command."
 
         if [[ -n "$FILTER" ]]; then
@@ -184,7 +186,7 @@ case "$1" in
                     echo "Uploading $(basename "$file") as $word ..."
                     Rscript $RLABKEY_DIR/R/push.R "$PROJECT" "$file" $(basename "$file") "$ASSAY" "$DATASET" || error "Failed to push file: $file"
                 done
-            else 
+            else
                 echo "Abort upload."
                 exit 0
             fi
@@ -213,7 +215,7 @@ case "$1" in
         if [[ -z "$1" ]]; then
             show_help
         else
-            echo "Unknown command: $1"            
+            echo "Unknown command: $1"
         fi
         ;;
 esac

install

 #!/bin/bash
 
+# DEPRECATED, since use of rlabkey API needs R session ID, not possible from terminal
+
 # Installation script for rlabkey-cli
 INSTALL_DIR="$HOME/.rlabkey"
 

renv.lock

+{
+  "R": {
+    "Version": "4.4.0",
+    "Repositories": [
+      {
+        "Name": "CRAN",
+        "URL": "https://p3m.dev/cran/2024-06-13"
+      }
+    ]
+  },
+  "Packages": {
+    "renv": {
+      "Package": "renv",
+      "Version": "1.0.7",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "utils"
+      ],
+      "Hash": "397b7b2a265bc5a7a06852524dabae20"
+    }
+  }
+}

renv/.gitignore

+library/
+local/
+cellar/
+lock/
+python/
+sandbox/
+staging/

renv/settings.json

+{
+  "bioconductor.version": null,
+  "external.libraries": [],
+  "ignored.packages": [],
+  "package.dependency.fields": [
+    "Imports",
+    "Depends",
+    "LinkingTo"
+  ],
+  "ppm.enabled": null,
+  "ppm.ignored.urls": [],
+  "r.version": null,
+  "snapshot.type": "explicit",
+  "use.cache": true,
+  "vcs.ignore.cellar": true,
+  "vcs.ignore.library": true,
+  "vcs.ignore.local": true,
+  "vcs.manage.ignores": true
+}

rlabkeyCLI.Rproj

+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source

uninstall

 #!/bin/bash
 
+# DEPRECATED, since use of rlabkey API needs R session ID, not possible from terminal
+
 if command -v Rscript &> /dev/null; then
     RVERSION="$(Rscript --version)"
     echo "$RVERSION is already installed. Would you like to uninstall it? (Y/n)"