beatrina 0.8.6 → 0.9.43

package/kernel/workspace-keep.R

@@ -0,0 +1,188 @@
+# workspace-keep.R — "Restart, keep variables": the global environment carried
+# across a restart, the way RStudio carries it.
+#
+# Sourced into the WORKER's private scope (worker.R's import_sources), and
+# testable without a worker: spike/test-workspace-keep.R sources this file
+# alone.
+#
+# This replaces a removed design, and the difference is the point. Until 7.59
+# a restart ran save.image() inside a handoff with a deadline and load()ed one
+# file back; large sessions missed the deadline, one unreadable object sank the
+# whole file, and nothing said what was lost. The owner removed it ("restore
+# work has been abysmally bad"). What is here instead:
+#
+#   * NO DEADLINE. The save is a worker command like any other: progress frames
+#     while it runs, Interrupt (Stop) cancels it, and the restart only happens
+#     once the save has answered.
+#   * ONE FILE PER OBJECT. An object that fails to save or to load is that
+#     object, named in the report — never the whole workspace.
+#   * PACKAGES ARE NOT RECORDED. A notebook's library() calls live in its setup
+#     chunk, and the page runs setup before the first chunk of a fresh R
+#     (lib/document-execution.js) — RStudio's own answer, and the reason this
+#     file keeps variables only.
+#   * WHAT CANNOT TRAVEL IS SAID. A connection or an external pointer
+#     serialises to a dead handle; it is skipped at save time and listed.
+#
+# Known limit, stated rather than hidden: objects are saved separately, so two
+# objects that SHARE an environment (R6 objects pointing at one another) come
+# back as copies that no longer share it.
+#
+# The token names a directory under the keep root and is the only thing that
+# travels: the page and the supervisor never pass a path, so a resume can only
+# ever read a directory this code wrote.
+
+#' Where kept workspaces live: 0700, per user. `BEATRINA_KEEP_DIR` relocates it
+#' for tests.
+#' @return A directory path (not created).
+keep_root <- function() {
+  env <- Sys.getenv("BEATRINA_KEEP_DIR", "")
+  if (nzchar(env)) env else file.path(tools::R_user_dir("beatrina", "data"), "kept-workspace")
+}
+
+KEEP_TOKEN_RE <- "^[0-9]{14}-[0-9a-f]{16}$"
+
+#' Is `x` a token this file could have minted?
+#' @param x Anything the wire delivered.
+#' @return TRUE for one well-formed token.
+keep_token_ok <- function(x) {
+  is.character(x) && length(x) == 1L && !is.na(x) && grepl(KEEP_TOKEN_RE, x)
+}
+
+#' A fresh token: a timestamp (sorts, and ages out) plus 64 random bits.
+#' @return A token matching KEEP_TOKEN_RE.
+keep_token_new <- function() {
+  bytes <- tryCatch({
+    con <- file("/dev/urandom", "rb", raw = TRUE)
+    on.exit(close(con), add = TRUE)
+    readBin(con, "raw", n = 8L)
+  }, error = function(e) as.raw(sample.int(256L, 8L, replace = TRUE) - 1L))
+  paste0(format(Sys.time(), "%Y%m%d%H%M%S"), "-", paste(format(bytes), collapse = ""))
+}
+
+#' Why an object cannot travel, or NULL when it can.
+#'
+#' A connection is an integer index into THIS process's connection table, and
+#' an external pointer is an address in this process's memory: both serialise
+#' without complaint and come back as something that looks right and is dead.
+#' @param x The object.
+#' @return NULL, or a short phrase for the report.
+keep_unsaveable <- function(x) {
+  if (inherits(x, "connection")) return("a connection (a file or URL handle)")
+  if (inherits(x, "DBIConnection")) return("a database connection")
+  if (typeof(x) == "externalptr") return("an external pointer")
+  NULL
+}
+
+#' Delete kept workspaces older than `max_age_s` — a restart that never
+#' resumed (a crash, a closed laptop) must not keep a copy of someone's data
+#' forever.
+#' @param root The keep root.
+#' @param max_age_s Age in seconds.
+#' @return Invisibly, the tokens removed.
+keep_prune <- function(root = keep_root(), max_age_s = 86400) {
+  if (!dir.exists(root)) return(invisible(character(0)))
+  tokens <- Filter(keep_token_ok, list.files(root))
+  old <- Filter(function(t) {
+    age <- as.numeric(difftime(Sys.time(), file.info(file.path(root, t))$mtime, units = "secs"))
+    isTRUE(age > max_age_s)
+  }, tokens)
+  invisible(vapply(old, function(t) { unlink(file.path(root, t), recursive = TRUE); t }, character(1)))
+}
+
+#' Save every object of `env` into a new kept workspace.
+#'
+#' @param env The environment to keep (the worker passes globalenv()).
+#' @param progress function(done, total, bytes, name) called after each object.
+#' @param root The keep root.
+#' @return list(token, saved, bytes, skipped = list of {name, why}).
+#'   An interrupt removes the partial directory and propagates, so the caller
+#'   reports "cancelled" and nothing half-written is ever resumed.
+keep_save <- function(env = globalenv(), progress = function(...) NULL, root = keep_root()) {
+  stopifnot("`env` must be an environment" = is.environment(env))
+  dir.create(root, recursive = TRUE, showWarnings = FALSE, mode = "0700")
+  Sys.chmod(root, mode = "0700")
+  keep_prune(root)
+  token <- keep_token_new()
+  dir <- file.path(root, token)
+  dir.create(dir, mode = "0700")
+  names_ <- sort(ls(env, all.names = TRUE))
+  total <- length(names_)
+  bytes <- 0
+  done <- FALSE
+  on.exit(if (!done) unlink(dir, recursive = TRUE), add = TRUE)
+  # Objects are indexed, never named, on disk: an object name may hold any
+  # character, and a file name must not.
+  entries <- lapply(seq_along(names_), function(i) {
+    name <- names_[[i]]
+    value <- get(name, envir = env, inherits = FALSE)
+    why <- keep_unsaveable(value)
+    entry <- if (!is.null(why)) list(name = name, status = "skipped", why = why)
+    else {
+      file <- sprintf("%06d.rds", i)
+      failed <- tryCatch({ saveRDS(value, file.path(dir, file), compress = FALSE); NULL },
+                         error = function(e) conditionMessage(e))
+      if (is.null(failed)) {
+        bytes <<- bytes + file.size(file.path(dir, file))
+        list(name = name, status = "saved", file = file, class = class(value)[1L])
+      } else {
+        unlink(file.path(dir, file))
+        list(name = name, status = "skipped", why = paste("could not be saved:", failed))
+      }
+    }
+    progress(i, total, bytes, name)
+    entry
+  })
+  manifest <- list(version = 1L, created = format(Sys.time(), "%Y-%m-%dT%H:%M:%S"),
+                   wd = getwd(), entries = entries)
+  writeLines(jsonlite::toJSON(manifest, auto_unbox = TRUE), file.path(dir, "manifest.json"))
+  Sys.chmod(list.files(dir, full.names = TRUE), mode = "0600")
+  done <- TRUE
+  status <- vapply(entries, `[[`, "", "status")
+  list(token = token, saved = sum(status == "saved"), bytes = bytes,
+       skipped = lapply(entries[status == "skipped"], function(e) list(name = e$name, why = e$why)))
+}
+
+#' Load a kept workspace into `env`, then delete it.
+#'
+#' Each object is read on its own; one that fails is reported and the rest
+#' still arrive. The directory is removed afterwards whatever happened — a
+#' kept workspace is used once.
+#' @param token A token from keep_save().
+#' @param env Where the objects go (the worker passes globalenv()).
+#' @param progress function(done, total, bytes, name) called after each object
+#'   (the same shape keep_save() calls, so one callback serves both; bytes is 0).
+#' @param root The keep root.
+#' @return list(restored, failed = list of {name, why}, skipped = the save's
+#'   skips, carried so the one report says everything), or list(error).
+keep_resume <- function(token, env = globalenv(), progress = function(...) NULL, root = keep_root()) {
+  if (!keep_token_ok(token)) return(list(error = "That is not a kept workspace."))
+  dir <- file.path(root, token)
+  manifest_file <- file.path(dir, "manifest.json")
+  if (!file.exists(manifest_file)) {
+    return(list(error = "The kept workspace is gone — it was already restored or removed."))
+  }
+  on.exit(unlink(dir, recursive = TRUE), add = TRUE)
+  manifest <- tryCatch(jsonlite::fromJSON(manifest_file, simplifyVector = FALSE),
+                       error = function(e) NULL)
+  if (is.null(manifest) || !is.list(manifest$entries)) {
+    return(list(error = "The kept workspace's record could not be read."))
+  }
+  saved <- Filter(function(e) identical(e$status, "saved"), manifest$entries)
+  total <- length(saved)
+  outcomes <- lapply(seq_along(saved), function(i) {
+    e <- saved[[i]]
+    # The file name is re-checked, never trusted: only NNNNNN.rds inside dir.
+    why <- if (!is.character(e$file) || !grepl("^[0-9]{6}\\.rds$", e$file)) "its record is malformed"
+    else tryCatch({
+      assign(e$name, readRDS(file.path(dir, e$file)), envir = env)
+      NULL
+    }, error = function(err) conditionMessage(err))
+    progress(i, total, 0, e$name)
+    if (is.null(why)) NULL else list(name = e$name, why = paste("could not be restored:", why))
+  })
+  failed <- Filter(Negate(is.null), outcomes)
+  skipped <- lapply(Filter(function(e) identical(e$status, "skipped"), manifest$entries),
+                    function(e) list(name = e$name, why = e$why))
+  list(restored = total - length(failed), failed = failed, skipped = skipped,
+       wd = if (is.character(manifest$wd)) manifest$wd else "")
+}

package/lib/agent-authoring-contract.js

@@ -1,5 +1,5 @@
 // agent-authoring-contract.js — the one place that says how a model may write
-// into a CarmaR document, and the only one that decides whether it did.
+// into a Beatrina document, and the only one that decides whether it did.
 //
 // WHY THIS IS A MODULE AND NOT A PROMPT. The rules below were previously
 // stated in three unsynchronised places — the MCP server's initialize text,
@@ -10,13 +10,13 @@
 // whether a proposal is valid. Only the third one is enforcement.
 //
 // Nothing here touches the DOM, the notebook, or the network, because
-// `tools/mcp/carmar-mcp.mjs` imports it in Node (outside the browser bundle)
+// `tools/mcp/beatrina-mcp.mjs` imports it in Node (outside the browser bundle)
 // and `lib/mcp-bridge.js` imports it in the page. One module, both sides, so
 // the rule an agent is told and the rule it is held to cannot drift apart.
 
 import { CODE_KIND, isCodeKind } from "./cell-kinds.js";
 
-export const CONTRACT = "carmar.authoring/v1";
+export const CONTRACT = "beatrina.authoring/v1";
 export const SCHEMA_VERSION = 1;
 
 /** A browser answer may still be reviewed as one bounded user-requested set. */
@@ -36,7 +36,7 @@ export const AUTHORING_RULES = [
   // document unit at a time. The removed batch tool changed the model's unit
   // of composition from "this notebook block" to "my reply, split into an
   // array", which is how chat scaffolding reached saved documents.
-  "CarmaR is the user's live R notebook. Start with notebook_read. Build the analysis ONE "
+  "Beatrina is the user's live R notebook. Start with notebook_read. Build the analysis ONE "
   + "document block at a time: call chunk_insert once for each finished prose section or runnable "
   + "R step, in reading and execution order. AUTHOR every text block as part of the saved .qmd, "
   + "not as a chat reply. Never paste or divide your chat response into notebook blocks. Keep "
@@ -309,12 +309,19 @@ const PASTED_VALUE = /^\s*\[\d+\]\s+\S/m;
 // a comment, so it is untouched.
 const CONSOLE_TRANSCRIPT = /^\s*(>\s+\S|\[\d+\]\s+\S)/m;
 
-/** Side effects on the user's machine that a chunk should not quietly carry. */
+/**
+ * Side effects on the user's machine that a chunk should not quietly carry.
+ *
+ * Worded as what the code WOULD do when it runs: this is a reading of the
+ * proposed source, made before anything executes, and an agent that saw
+ * "changes the working directory" beside a run that was restored from the
+ * cache took it for a report of what had happened.
+ */
 const SIDE_EFFECTS = [
-  { re: /\binstall\.packages\s*\(/, what: "installs packages into the user's R library" },
-  { re: /\bsetwd\s*\(/, what: "changes the working directory for the whole session" },
-  { re: /\brm\s*\(\s*list\s*=\s*ls\s*\(/, what: "erases every object in the user's session" },
-  { re: /\bunlink\s*\(|\bfile\.remove\s*\(/, what: "deletes files from disk" },
+  { re: /\binstall\.packages\s*\(/, what: "would install packages into the user's R library" },
+  { re: /\bsetwd\s*\(/, what: "would change the working directory for the whole session" },
+  { re: /\brm\s*\(\s*list\s*=\s*ls\s*\(/, what: "would erase every object in the user's session" },
+  { re: /\bunlink\s*\(|\bfile\.remove\s*\(/, what: "would delete files from disk" },
 ];
 
 // A path out of the project, in a string. `~` alone is not checked: in R it is
@@ -332,9 +339,9 @@ const ENGINE_RULES = {
     transcript: /^\s*>>>\s/m,
     transcriptWhat: "a Python console TRANSCRIPT — lines beginning `>>> `",
     sideEffects: [
-      { re: /(^|\n)\s*[!%]\s*pip\s+install\b|\bpip\.main\s*\(|["']pip["']\s*,\s*["']install["']/, what: "installs packages into the user's Python environment" },
-      { re: /\bos\.chdir\s*\(/, what: "changes the working directory for the whole session" },
-      { re: /\bshutil\.rmtree\s*\(|\bos\.(?:remove|unlink|rmdir)\s*\(/, what: "deletes files from disk" },
+      { re: /(^|\n)\s*[!%]\s*pip\s+install\b|\bpip\.main\s*\(|["']pip["']\s*,\s*["']install["']/, what: "would install packages into the user's Python environment" },
+      { re: /\bos\.chdir\s*\(/, what: "would change the working directory for the whole session" },
+      { re: /\bshutil\.rmtree\s*\(|\bos\.(?:remove|unlink|rmdir)\s*\(/, what: "would delete files from disk" },
     ],
   },
 };
@@ -389,7 +396,7 @@ export function normalizeBlocks(raw, { tool = "This answer", max = MAX_BLOCKS, e
     const isText = declared === "text" || declared === "md";
     if (!isText && declared !== "r" && !isCodeKind(declared)) {
       throw repair(`${ordinal(index)} has kind "${declared}". `
-        + `CarmaR blocks are ${BLOCK_KINDS.map((k) => `"${k}"`).join(" or ")}.`);
+        + `Beatrina blocks are ${BLOCK_KINDS.map((k) => `"${k}"`).join(" or ")}.`);
     }
     const content = String(item && item.content != null ? item.content : "");
     if (!content.trim()) {
@@ -476,9 +483,10 @@ export function normalizeBlocks(raw, { tool = "This answer", max = MAX_BLOCKS, e
       }
       rules.sideEffects.forEach(({ re, what }) => {
         if (re.test(content)) {
-          lints.push(`${ordinal(index)} ${what}. The user reviews this block before it is `
-            + "theirs, but do not include it unless they asked for it — a chunk should compute, "
-            + "not change the machine it runs on.");
+          lints.push(`${ordinal(index)} ${what} when it runs — a note on the code as written, `
+            + "not a report that it ran. The user reviews this block before it is theirs, but do "
+            + "not include it unless they asked for it: a chunk should compute, not change the "
+            + "machine it runs on.");
         }
       });
       if (ABSOLUTE_PATH.test(content)) {
@@ -499,9 +507,10 @@ export function normalizeBlocks(raw, { tool = "This answer", max = MAX_BLOCKS, e
     }
     SIDE_EFFECTS.forEach(({ re, what }) => {
       if (re.test(content)) {
-        lints.push(`${ordinal(index)} ${what}. The user reviews this block before it is `
-          + "theirs, but do not include it unless they asked for it — a chunk should compute, "
-          + "not change the machine it runs on.");
+        lints.push(`${ordinal(index)} ${what} when it runs — a note on the code as written, `
+          + "not a report that it ran. The user reviews this block before it is theirs, but do "
+          + "not include it unless they asked for it: a chunk should compute, not change the "
+          + "machine it runs on.");
       }
     });
     if (ABSOLUTE_PATH.test(content)) {

package/lib/cell-kinds.js

@@ -17,10 +17,10 @@
 //                                   a saved .html. Still ACCEPTED everywhere,
 //                                   and still registered as a (hidden) verb so
 //                                   such a cell mounts. Never emitted.
-//   disk   `rcode` · `md`           the `kind` field of a `<!-- carmar-cell:`
+//   disk   `rcode` · `md`           the `kind` field of a `<!-- beatrina-cell:`
 //                                   annotation in a .carmd/.qmd. THE DOCUMENT
 //                                   FORMAT, and deliberately unchanged: a file
-//                                   written today must still open in CarmaR
+//                                   written today must still open in Beatrina
 //                                   0.8.01, whose reader validates exactly
 //                                   `['rcode','md']`. lib/document-source-cells.js
 //                                   translates at that one boundary and
@@ -82,7 +82,7 @@ export function cellKind(kind) {
 // ── the document-format boundary ────────────────────────────────────────────
 
 /**
- * The `kind` to WRITE into a `<!-- carmar-cell: … -->` annotation.
+ * The `kind` to WRITE into a `<!-- beatrina-cell: … -->` annotation.
  *
  * A code chunk is written as `rcode` whatever this build calls it, because
  * that is the format, and a file CarmaR 0.8.01 refuses to open is a file its

package/lib/engine-labels.js

@@ -245,10 +245,10 @@ export function declaredEngines(info) {
 }
 
 // ── authoring: what an AI may say about a chunk's language ─────────────────
-// The tool schemas (lib/ai-tools.js, lib/mcp-bridge.js, tools/mcp/carmar-mcp.mjs)
+// The tool schemas (lib/ai-tools.js, lib/mcp-bridge.js, tools/mcp/beatrina-mcp.mjs)
 // all name engines from HERE, so the enum a model is shown, the refusal it gets
 // and the header a chunk is written with cannot disagree. Pure and import-free:
-// tools/mcp/carmar-mcp.mjs loads it in Node beside the authoring contract.
+// tools/mcp/beatrina-mcp.mjs loads it in Node beside the authoring contract.
 
 /** The engines a tool schema offers. The SESSION decides which of them run. */
 export const AUTHORING_ENGINES = Object.freeze(KNOWN_ENGINES.map((e) => e.key));
@@ -267,14 +267,14 @@ export function engineArg(value, name = "engine") {
   }
   const key = engineKey(value);
   if (!AUTHORING_ENGINES.includes(key)) {
-    throw new Error(`${name} "${value}" is not an engine CarmaR knows. Use one of ${AUTHORING_ENGINES.join(", ")}.`);
+    throw new Error(`${name} "${value}" is not an engine Beatrina knows. Use one of ${AUTHORING_ENGINES.join(", ")}.`);
   }
   return key;
 }
 
 /**
  * The chunk header a new code chunk carries for `engine` — the SAME shape the
- * `carmar:insert-cell` door writes (src/notebook-entry.js). R gets none, so an
+ * `beatrina:insert-cell` door writes (src/notebook-entry.js). R gets none, so an
  * R insert is byte-identical to one made before engines existed.
  *
  * @returns {object|null}

package/menu/Beatrina Menu.app/Contents/Info.plist

@@ -0,0 +1,14 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
+<plist version="1.0"><dict>
+  <key>CFBundleName</key><string>Beatrina Menu</string>
+  <key>CFBundleDisplayName</key><string>Beatrina Menu</string>
+  <key>CFBundleExecutable</key><string>Beatrina Menu</string>
+  <key>CFBundleIdentifier</key><string>me.saqr.beatrina.menu</string>
+  <key>CFBundlePackageType</key><string>APPL</string>
+  <key>CFBundleShortVersionString</key><string>0.9.43</string>
+  <key>CFBundleVersion</key><string>0.9.43</string>
+  <key>LSMinimumSystemVersion</key><string>13.0</string>
+  <!-- Menu bar only: no Dock tile, no window, nothing to close by accident. -->
+  <key>LSUIElement</key><true/>
+</dict></plist>

package/menu/Beatrina Menu.app/Contents/_CodeSignature/CodeResources

@@ -0,0 +1,115 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
+<plist version="1.0">
+<dict>
+	<key>files</key>
+	<dict/>
+	<key>files2</key>
+	<dict/>
+	<key>rules</key>
+	<dict>
+		<key>^Resources/</key>
+		<true/>
+		<key>^Resources/.*\.lproj/</key>
+		<dict>
+			<key>optional</key>
+			<true/>
+			<key>weight</key>
+			<real>1000</real>
+		</dict>
+		<key>^Resources/.*\.lproj/locversion.plist$</key>
+		<dict>
+			<key>omit</key>
+			<true/>
+			<key>weight</key>
+			<real>1100</real>
+		</dict>
+		<key>^Resources/Base\.lproj/</key>
+		<dict>
+			<key>weight</key>
+			<real>1010</real>
+		</dict>
+		<key>^version.plist$</key>
+		<true/>
+	</dict>
+	<key>rules2</key>
+	<dict>
+		<key>.*\.dSYM($|/)</key>
+		<dict>
+			<key>weight</key>
+			<real>11</real>
+		</dict>
+		<key>^(.*/)?\.DS_Store$</key>
+		<dict>
+			<key>omit</key>
+			<true/>
+			<key>weight</key>
+			<real>2000</real>
+		</dict>
+		<key>^(Frameworks|SharedFrameworks|PlugIns|Plug-ins|XPCServices|Helpers|MacOS|Library/(Automator|Spotlight|LoginItems))/</key>
+		<dict>
+			<key>nested</key>
+			<true/>
+			<key>weight</key>
+			<real>10</real>
+		</dict>
+		<key>^.*</key>
+		<true/>
+		<key>^Info\.plist$</key>
+		<dict>
+			<key>omit</key>
+			<true/>
+			<key>weight</key>
+			<real>20</real>
+		</dict>
+		<key>^PkgInfo$</key>
+		<dict>
+			<key>omit</key>
+			<true/>
+			<key>weight</key>
+			<real>20</real>
+		</dict>
+		<key>^Resources/</key>
+		<dict>
+			<key>weight</key>
+			<real>20</real>
+		</dict>
+		<key>^Resources/.*\.lproj/</key>
+		<dict>
+			<key>optional</key>
+			<true/>
+			<key>weight</key>
+			<real>1000</real>
+		</dict>
+		<key>^Resources/.*\.lproj/locversion.plist$</key>
+		<dict>
+			<key>omit</key>
+			<true/>
+			<key>weight</key>
+			<real>1100</real>
+		</dict>
+		<key>^Resources/Base\.lproj/</key>
+		<dict>
+			<key>weight</key>
+			<real>1010</real>
+		</dict>
+		<key>^[^/]+$</key>
+		<dict>
+			<key>nested</key>
+			<true/>
+			<key>weight</key>
+			<real>10</real>
+		</dict>
+		<key>^embedded\.provisionprofile$</key>
+		<dict>
+			<key>weight</key>
+			<real>20</real>
+		</dict>
+		<key>^version\.plist$</key>
+		<dict>
+			<key>weight</key>
+			<real>20</real>
+		</dict>
+	</dict>
+</dict>
+</plist>

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "beatrina",
-  "version": "0.8.6",
+  "version": "0.9.43",
   "description": "Beatrina is a modern, powerful, feature-rich integrated development environment (IDE) for R, Python, and JavaScript.",
   "type": "module",
   "bin": {
@@ -22,9 +22,10 @@
     "kernel",
     "failsafe",
     "lib",
-    "check",
+    "menu",
     "build-info.json",
-    "carmar_V0.8.6.html",
+    "beatrina_V0.9.43.html",
+    "beatrina_V0.9.43.html.inputs.json",
     "README.md",
     "LICENSE",
     "NOTICES"