beatrina 0.8.6

package/kernel/plugins/csl/modern-language-association/plugin.json

@@ -0,0 +1,19 @@
+{
+  "id": "modern-language-association",
+  "kind": "csl",
+  "name": "MLA Handbook 9th edition (in-text citations)",
+  "version": "2026-02-03",
+  "file": "modern-language-association.csl",
+  "files": [
+    "modern-language-association.csl"
+  ],
+  "requires": [],
+  "license": "CC BY-SA 3.0",
+  "source": "https://www.zotero.org/styles/modern-language-association",
+  "digest": "sha256",
+  "sha256": {
+    "modern-language-association.csl": "e1432698ef28938d044b06bd45ddcc57d6b974cec25f71007075646a11f99484"
+  },
+  "bytes": 44381,
+  "installed": ""
+}

package/kernel/plugins/csl/nature/nature.csl

@@ -0,0 +1,189 @@
+<?xml version="1.0" encoding="utf-8"?>
+<style xmlns="http://purl.org/net/xbiblio/csl" class="in-text" version="1.0" demote-non-dropping-particle="sort-only" default-locale="en-GB">
+  <info>
+    <title>Nature</title>
+    <id>http://www.zotero.org/styles/nature</id>
+    <link href="http://www.zotero.org/styles/nature" rel="self"/>
+    <link href="https://www.nature.com/nature/for-authors/formatting-guide" rel="documentation"/>
+    <author>
+      <name>Michael Berkowitz</name>
+      <email>mberkowi@gmu.edu</email>
+    </author>
+    <contributor>
+      <name>Patrick O'Brien</name>
+      <email>citationstyler@gmail.com</email>
+    </contributor>
+    <category citation-format="numeric"/>
+    <category field="science"/>
+    <category field="generic-base"/>
+    <issn>0028-0836</issn>
+    <eissn>1476-4687</eissn>
+    <updated>2026-08-07T18:26:21+00:00</updated>
+    <rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
+  </info>
+  <macro name="title">
+    <choose>
+      <if type="bill book graphic legal_case legislation motion_picture report song" match="any">
+        <text variable="title" font-style="italic" text-case="title"/>
+      </if>
+      <else>
+        <text variable="title"/>
+      </else>
+    </choose>
+  </macro>
+  <macro name="author">
+    <names variable="author">
+      <name sort-separator=", " delimiter=", " and="symbol" initialize-with=". " delimiter-precedes-last="never" name-as-sort-order="all"/>
+      <label form="short" prefix=", "/>
+      <et-al font-style="italic"/>
+    </names>
+  </macro>
+  <macro name="access">
+    <choose>
+      <if variable="volume" type="article dataset software" match="any"/>
+      <else-if variable="DOI">
+        <text variable="DOI" prefix="doi:"/>
+      </else-if>
+    </choose>
+  </macro>
+  <macro name="access-data">
+    <choose>
+      <if type="dataset software" match="any">
+        <text variable="DOI" prefix="https://doi.org/"/>
+      </if>
+    </choose>
+  </macro>
+  <macro name="issuance">
+    <choose>
+      <if type="bill book graphic legal_case legislation motion_picture song thesis chapter paper-conference" match="any">
+        <group delimiter="; " suffix=".">
+          <group delimiter=", " prefix="(" suffix=")">
+            <text variable="publisher" form="long"/>
+            <text variable="publisher-place"/>
+            <date variable="issued">
+              <date-part name="year"/>
+            </date>
+          </group>
+        </group>
+      </if>
+      <else-if type="article">
+        <group delimiter=" ">
+          <choose>
+            <if variable="genre" match="any">
+              <text variable="genre" text-case="capitalize-first"/>
+            </if>
+            <else>
+              <text term="preprint" text-case="capitalize-first"/>
+            </else>
+          </choose>
+          <text term="at"/>
+          <choose>
+            <if variable="DOI" match="any">
+              <text variable="DOI" prefix="https://doi.org/"/>
+            </if>
+            <else>
+              <text variable="URL"/>
+            </else>
+          </choose>
+          <date date-parts="year" form="text" variable="issued" prefix="(" suffix=")"/>
+        </group>
+      </else-if>
+      <else-if type="dataset software" match="any">
+        <group delimiter=" ">
+          <text variable="publisher"/>
+          <text macro="access-data"/>
+          <date date-parts="year" form="text" variable="issued" prefix="(" suffix=")"/>
+        </group>
+      </else-if>
+      <else-if type="report webpage post post-weblog" match="any">
+        <group delimiter=" ">
+          <text variable="URL"/>
+          <date date-parts="year" form="text" variable="issued" prefix="(" suffix=")"/>
+        </group>
+      </else-if>
+      <else-if type="article-journal" match="any">
+        <group delimiter=" ">
+          <choose>
+            <if match="none" variable="volume page">
+              <choose>
+                <if match="any" variable="DOI">
+                  <text variable="DOI" prefix="https://doi.org/"/>
+                </if>
+                <else>
+                  <text variable="URL"/>
+                </else>
+              </choose>
+            </if>
+          </choose>
+          <date date-parts="year" form="text" variable="issued" prefix="(" suffix=")"/>
+        </group>
+      </else-if>
+      <else>
+        <date variable="issued" prefix="(" suffix=")">
+          <date-part name="year"/>
+        </date>
+      </else>
+    </choose>
+  </macro>
+  <macro name="container-title">
+    <choose>
+      <if type="article-journal">
+        <text variable="container-title" font-style="italic" form="short"/>
+      </if>
+      <else>
+        <text variable="container-title" font-style="italic"/>
+      </else>
+    </choose>
+  </macro>
+  <macro name="editor">
+    <choose>
+      <if type="chapter paper-conference" match="any">
+        <names variable="editor" prefix="(" suffix=")">
+          <label form="short" suffix=" "/>
+          <name and="symbol" delimiter-precedes-last="never" initialize-with=". " name-as-sort-order="all"/>
+        </names>
+      </if>
+    </choose>
+  </macro>
+  <macro name="volume">
+    <choose>
+      <if type="article-journal" match="any">
+        <text variable="volume" font-weight="bold" suffix=","/>
+      </if>
+      <else>
+        <group delimiter=" ">
+          <label variable="volume" form="short"/>
+          <text variable="volume"/>
+        </group>
+      </else>
+    </choose>
+  </macro>
+  <citation collapse="citation-number">
+    <sort>
+      <key variable="citation-number"/>
+    </sort>
+    <layout vertical-align="sup" delimiter=",">
+      <text variable="citation-number"/>
+    </layout>
+  </citation>
+  <bibliography et-al-min="6" et-al-use-first="1" second-field-align="flush" entry-spacing="0" line-spacing="2">
+    <layout suffix=".">
+      <text variable="citation-number" suffix=". "/>
+      <group delimiter=" ">
+        <text macro="author" suffix="."/>
+        <text macro="title" suffix="."/>
+        <choose>
+          <if type="chapter paper-conference" match="any">
+            <text term="in"/>
+          </if>
+        </choose>
+        <text macro="container-title"/>
+        <text macro="editor"/>
+        <text macro="volume"/>
+        <text variable="page"/>
+        <text macro="issuance"/>
+        <text macro="access"/>
+      </group>
+    </layout>
+  </bibliography>
+</style>

package/kernel/plugins/csl/nature/plugin.json

@@ -0,0 +1,19 @@
+{
+  "id": "nature",
+  "kind": "csl",
+  "name": "Nature",
+  "version": "2026-08-07",
+  "file": "nature.csl",
+  "files": [
+    "nature.csl"
+  ],
+  "requires": [],
+  "license": "CC BY-SA 3.0",
+  "source": "https://www.zotero.org/styles/nature",
+  "digest": "sha256",
+  "sha256": {
+    "nature.csl": "cb69522b83d8eee0eab9a06d1255ea40fe2cc1bbd85b22bbf94097129119dc0e"
+  },
+  "bytes": 6445,
+  "installed": ""
+}

package/kernel/plugins/latex/apa7/apa7.json

@@ -0,0 +1,14 @@
+{
+  "label": "APA 7th edition",
+  "description": "apa7 journal manuscript. biblatex's commands, loaded with APA's own style.",
+  "documentclass": "apa7",
+  "classOptions": [
+    "man",
+    "11pt"
+  ],
+  "citeStyle": "biblatex",
+  "citePackage": "\\usepackage[style=apa]{biblatex}",
+  "topLevel": "section",
+  "preamble": [],
+  "version": "1.0"
+}

package/kernel/plugins/latex/apa7/plugin.json

@@ -0,0 +1,19 @@
+{
+  "id": "apa7",
+  "kind": "latex",
+  "name": "APA 7th edition",
+  "version": "1.0",
+  "file": "apa7.json",
+  "files": [
+    "apa7.json"
+  ],
+  "requires": [],
+  "license": "",
+  "source": "",
+  "digest": "sha256",
+  "sha256": {
+    "apa7.json": "ac40dcaad103fba6e01bfbd9b61c2a7c5c13b8a7988860c5daefefff2abcc264"
+  },
+  "bytes": 345,
+  "installed": ""
+}

package/kernel/plugins/latex/elsarticle/elsarticle.json

@@ -0,0 +1,14 @@
+{
+  "label": "Elsevier article",
+  "description": "elsarticle, the class Elsevier journals ask for. Line numbers on, for review.",
+  "documentclass": "elsarticle",
+  "classOptions": ["review", "3p", "times"],
+  "citeStyle": "natbib",
+  "topLevel": "section",
+  "preamble": [
+    "\\usepackage{lineno}",
+    "\\modulolinenumbers[5]",
+    "\\linenumbers"
+  ],
+  "version": "1.0"
+}

package/kernel/plugins/latex/elsarticle/plugin.json

@@ -0,0 +1,19 @@
+{
+  "id": "elsarticle",
+  "kind": "latex",
+  "name": "Elsevier article",
+  "version": "1.0",
+  "file": "elsarticle.json",
+  "files": [
+    "elsarticle.json"
+  ],
+  "requires": [],
+  "license": "",
+  "source": "",
+  "digest": "sha256",
+  "sha256": {
+    "elsarticle.json": "26735bb4cec577a105ff801f471592818b9e455f7ec3135f4348627323f1b548"
+  },
+  "bytes": 379,
+  "installed": ""
+}

package/kernel/plugins/latex/ieeetran/ieeetran.json

@@ -0,0 +1,10 @@
+{
+  "label": "IEEE conference or journal",
+  "description": "IEEEtran, two-column. IEEE's own bibliography macros, so plain \\cite.",
+  "documentclass": "IEEEtran",
+  "classOptions": ["conference"],
+  "citeStyle": "plain",
+  "topLevel": "section",
+  "preamble": [],
+  "version": "1.0"
+}

package/kernel/plugins/latex/ieeetran/plugin.json

@@ -0,0 +1,19 @@
+{
+  "id": "ieeetran",
+  "kind": "latex",
+  "name": "IEEE conference or journal",
+  "version": "1.0",
+  "file": "ieeetran.json",
+  "files": [
+    "ieeetran.json"
+  ],
+  "requires": [],
+  "license": "",
+  "source": "",
+  "digest": "sha256",
+  "sha256": {
+    "ieeetran.json": "d8c7db78e804fac0abd98c0ec41c8b55e1478e140ee56436acd983f22692868d"
+  },
+  "bytes": 287,
+  "installed": ""
+}

package/kernel/project.R

@@ -0,0 +1,131 @@
+# project.R — inspect and restore a project's package environment without
+# requiring terminal commands. Pure status logic is separate from worker.R so
+# lockfile edge cases and organisation-mirror policy can be tested directly.
+
+carmar_project_or <- function(value, fallback) if (is.null(value)) fallback else value
+
+carmar_repository_display <- function(value) {
+  value <- as.character(carmar_project_or(value, ""))[[1L]]
+  value <- sub("^([A-Za-z]+://)[^/@]+@", "\\1", value)
+  sub("[?#].*$", "", value)
+}
+
+carmar_project_status <- function(path = getwd(), env = Sys.getenv,
+                                  installed = NULL, repos = getOption("repos"),
+                                  renv_available = NULL, libraries = .libPaths()) {
+  root <- normalizePath(path, winslash = "/", mustWork = FALSE)
+  lockfile <- file.path(root, "renv.lock")
+  has_lock <- file.exists(lockfile)
+  project_files <- list.files(root, pattern = "[.]Rproj$", ignore.case = TRUE)
+  has_quarto <- any(file.exists(file.path(root, c("_quarto.yml", "_quarto.yaml"))))
+  managed_raw <- trimws(env("CARMAR_CRAN_MIRROR", ""))
+  mirror_error <- if (nzchar(managed_raw) && !grepl("^https://", managed_raw))
+    "The administrator's package mirror must use HTTPS." else ""
+  cran <- if (length(repos) && "CRAN" %in% names(repos)) unname(repos[["CRAN"]]) else ""
+  repository <- if (nzchar(managed_raw)) managed_raw else cran
+  repository <- carmar_repository_display(repository)
+  if (is.null(renv_available)) renv_available <- requireNamespace("renv", quietly = TRUE)
+  active_project <- trimws(env("RENV_PROJECT", ""))
+  active <- nzchar(active_project) && identical(
+    normalizePath(active_project, winslash = "/", mustWork = FALSE), root)
+  if (!active) {
+    prefix <- paste0(root, "/renv/library/")
+    active <- any(startsWith(normalizePath(libraries, winslash = "/", mustWork = FALSE), prefix))
+  }
+
+  locked <- character()
+  wanted <- character()
+  lock_error <- ""
+  if (has_lock) {
+    size <- file.info(lockfile)$size[[1L]]
+    if (is.na(size) || size > 10 * 1024 * 1024) {
+      lock_error <- "renv.lock is too large to inspect safely."
+    } else {
+      parsed <- tryCatch(jsonlite::fromJSON(lockfile, simplifyVector = FALSE),
+                         error = function(e) e)
+      if (inherits(parsed, "error") || !is.list(parsed$Packages)) {
+        lock_error <- "renv.lock is not valid JSON package metadata."
+      } else {
+        locked <- names(parsed$Packages)
+        wanted <- vapply(parsed$Packages, function(record) {
+          value <- carmar_project_or(record$Version, "")
+          if (is.character(value) && length(value) == 1L) value else ""
+        }, character(1))
+      }
+    }
+  }
+
+  if (is.null(installed)) {
+    matrix <- utils::installed.packages()[, c("Package", "Version"), drop = FALSE]
+    installed <- stats::setNames(as.character(matrix[, "Version"]), matrix[, "Package"])
+  }
+  installed <- stats::setNames(as.character(installed), names(installed))
+  missing <- setdiff(locked, names(installed))
+  shared <- intersect(locked, names(installed))
+  different <- shared[nzchar(wanted[shared]) & installed[shared] != wanted[shared]]
+  list(
+    project = length(project_files) > 0L || has_quarto || has_lock,
+    rproj = length(project_files) > 0L,
+    quarto = has_quarto,
+    lockfile = has_lock,
+    lock_error = lock_error,
+    renv_available = isTRUE(renv_available),
+    active = isTRUE(active),
+    packages = length(locked),
+    missing = length(missing),
+    different = length(different),
+    missing_names = I(as.character(utils::head(missing, 12L))),
+    different_names = I(as.character(utils::head(different, 12L))),
+    managed_mirror = nzchar(managed_raw),
+    repository = repository,
+    mirror_error = mirror_error,
+    can_restore = has_lock && !nzchar(lock_error) && !nzchar(mirror_error)
+      && isTRUE(renv_available)
+  )
+}
+
+carmar_project_action <- function(action, path = getwd(), env = Sys.getenv,
+                                  install = NULL, restore = NULL,
+                                  available = function() requireNamespace("renv", quietly = TRUE)) {
+  action <- if (is.character(action) && length(action) == 1L) action else ""
+  if (!action %in% c("bootstrap", "restore")) stop("unknown project environment action")
+  state <- carmar_project_status(path = path, env = env,
+                                 renv_available = isTRUE(available()))
+  if (nzchar(state$mirror_error)) stop(state$mirror_error)
+  managed <- trimws(env("CARMAR_CRAN_MIRROR", ""))
+  repos <- getOption("repos")
+  if (nzchar(managed)) repos <- c(CRAN = managed)
+
+  if (identical(action, "bootstrap")) {
+    if (isTRUE(state$renv_available)) {
+      return(list(ok = TRUE, message = "renv is already installed.", restart = FALSE))
+    }
+    if (is.null(install)) install <- function(repositories) {
+      writable <- .libPaths()[file.access(.libPaths(), 2L) == 0L]
+      if (!length(writable)) stop("This R session has no writable package library.")
+      suppressWarnings(utils::install.packages("renv", lib = writable[[1L]],
+        repos = repositories, dependencies = NA, quiet = TRUE))
+    }
+    install(repos)
+    if (!isTRUE(available())) stop("renv installation did not complete.")
+    return(list(ok = TRUE, message = "renv was installed from the configured package repository.",
+                restart = FALSE))
+  }
+
+  if (!isTRUE(state$lockfile)) stop("This project has no renv.lock to restore.")
+  if (nzchar(state$lock_error)) stop(state$lock_error)
+  if (!isTRUE(state$renv_available)) stop("renv is not installed. Install renv first.")
+  if (is.null(restore)) restore <- function(project) {
+    renv::restore(project = project, prompt = FALSE, clean = FALSE)
+  }
+  old_override <- Sys.getenv("RENV_CONFIG_REPOS_OVERRIDE", unset = NA_character_)
+  on.exit({
+    if (is.na(old_override)) Sys.unsetenv("RENV_CONFIG_REPOS_OVERRIDE")
+    else Sys.setenv(RENV_CONFIG_REPOS_OVERRIDE = old_override)
+  }, add = TRUE)
+  if (nzchar(managed)) Sys.setenv(RENV_CONFIG_REPOS_OVERRIDE = managed)
+  restore(normalizePath(path, winslash = "/", mustWork = TRUE))
+  list(ok = TRUE,
+       message = "The packages recorded in renv.lock were restored from the configured repository.",
+       restart = !isTRUE(state$active))
+}