Documentation updates and review

.Rbuildignore

@@ -18,3 +18,4 @@
 ^vignettes/src$
 ^\.positai$
 ^\.claude$
+^CITATION\.cff$

CITATION.cff

@@ -0,0 +1,263 @@
+# --------------------------------------------
+# CITATION file created with {cffr} R package
+# See also: https://docs.ropensci.org/cffr/
+# --------------------------------------------
+
+cff-version: 1.2.0
+message: 'To cite package "storr.tiledb" in publications use:'
+type: software
+license: MIT
+title: 'storr.tiledb: A TileDB Storage Driver for Storr'
+version: 0.0.41
+abstract: Provides a TileDB driver for 'storr' interface. A 'storr' is a content addressed
+  key value store with an optional caching layer and this package contributes a new
+  driver using TileDB Embedded storage engine as a backend. In addition, storr.tiledb
+  comes with a subclass of 'storr' in order to improve speed and efficiency but also
+  enhances the 'storr' with additional features, such as adding notes and expiration
+  timestamps as well as support for asynchronous and in parallel writes.
+authors:
+- family-names: Giachalis
+  given-names: Constantinos
+  email: 26255858+cgiachalis@users.noreply.github.com
+repository-code: https://github.com/cgiachalis/storr.tiledb
+url: https://cgiachalis.github.io/storr.tiledb/
+date-released: '2026-05-23'
+contact:
+- family-names: Giachalis
+  given-names: Constantinos
+  email: 26255858+cgiachalis@users.noreply.github.com
+keywords:
+- key-value-store
+- r
+- storr
+- tiledb
+references:
+- type: software
+  title: 'R: A Language and Environment for Statistical Computing'
+  notes: Depends
+  url: https://www.R-project.org/
+  authors:
+  - name: R Core Team
+  institution:
+    name: R Foundation for Statistical Computing
+    address: Vienna, Austria
+  year: '2026'
+  version: '>= 4.4.0'
+- type: software
+  title: arrow
+  abstract: 'arrow: Integration to ''Apache'' ''Arrow'''
+  notes: Imports
+  url: https://github.com/apache/arrow/
+  repository: https://CRAN.R-project.org/package=arrow
+  authors:
+  - family-names: Richardson
+    given-names: Neal
+    email: neal.p.richardson@gmail.com
+  - family-names: Cook
+    given-names: Ian
+    email: ianmcook@gmail.com
+  - family-names: Crane
+    given-names: Nic
+    email: thisisnic@gmail.com
+  - family-names: Dunnington
+    given-names: Dewey
+    email: dewey@fishandwhistle.net
+    orcid: https://orcid.org/0000-0002-9415-4582
+  - family-names: François
+    given-names: Romain
+    orcid: https://orcid.org/0000-0002-2444-4226
+  - family-names: Keane
+    given-names: Jonathan
+    email: jkeane@gmail.com
+  - family-names: Mecum
+    given-names: Bryce
+    email: brycemecum@gmail.com
+  - family-names: Moldovan-Grünfeld
+    given-names: Dragoș
+    email: dragos.mold@gmail.com
+  - family-names: Ooms
+    given-names: Jeroen
+    email: jeroen@berkeley.edu
+  - family-names: Wujciak-Jens
+    given-names: Jacob
+    email: jacob@wujciak.de
+  - name: Apache Arrow
+    email: dev@arrow.apache.org
+  year: '2026'
+  doi: 10.32614/CRAN.package.arrow
+- type: software
+  title: cli
+  abstract: 'cli: Helpers for Developing Command Line Interfaces'
+  notes: Imports
+  url: https://cli.r-lib.org
+  repository: https://CRAN.R-project.org/package=cli
+  authors:
+  - family-names: Csárdi
+    given-names: Gábor
+    email: gabor@posit.co
+  year: '2026'
+  doi: 10.32614/CRAN.package.cli
+- type: software
+  title: data.table
+  abstract: 'data.table: Extension of `data.frame`'
+  notes: Imports
+  url: https://r-datatable.com
+  repository: https://CRAN.R-project.org/package=data.table
+  authors:
+  - family-names: Barrett
+    given-names: Tyson
+    email: t.barrett88@gmail.com
+    orcid: https://orcid.org/0000-0002-2137-1391
+  - family-names: Dowle
+    given-names: Matt
+    email: mattjdowle@gmail.com
+  - family-names: Srinivasan
+    given-names: Arun
+    email: asrini@pm.me
+  - family-names: Gorecki
+    given-names: Jan
+    email: j.gorecki@wit.edu.pl
+  - family-names: Chirico
+    given-names: Michael
+    email: michaelchirico4@gmail.com
+    orcid: https://orcid.org/0000-0003-0787-087X
+  - family-names: Hocking
+    given-names: Toby
+    email: toby.hocking@r-project.org
+    orcid: https://orcid.org/0000-0002-3146-0865
+  - family-names: Schwendinger
+    given-names: Benjamin
+    orcid: https://orcid.org/0000-0003-3315-8114
+  - family-names: Krylov
+    given-names: Ivan
+    email: ikrylov@disroot.org
+    orcid: https://orcid.org/0000-0002-0172-3812
+  year: '2026'
+  doi: 10.32614/CRAN.package.data.table
+- type: software
+  title: digest
+  abstract: 'digest: Create Compact Hash Digests of R Objects'
+  notes: Imports
+  url: https://eddelbuettel.github.io/digest/
+  repository: https://CRAN.R-project.org/package=digest
+  authors:
+  - family-names: Eddelbuettel
+    given-names: Dirk
+    email: edd@debian.org
+    orcid: https://orcid.org/0000-0001-6419-907X
+  year: '2026'
+  doi: 10.32614/CRAN.package.digest
+- type: software
+  title: mirai
+  abstract: 'mirai: Minimalist Async Evaluation Framework for R'
+  notes: Imports
+  url: https://mirai.r-lib.org
+  repository: https://CRAN.R-project.org/package=mirai
+  authors:
+  - family-names: Gao
+    given-names: Charlie
+    email: charlie.gao@posit.co
+    orcid: https://orcid.org/0000-0002-0750-061X
+  year: '2026'
+  doi: 10.32614/CRAN.package.mirai
+  version: '>= 2.6.0'
+- type: software
+  title: R6
+  abstract: 'R6: Encapsulated Classes with Reference Semantics'
+  notes: Imports
+  url: https://r6.r-lib.org
+  repository: https://CRAN.R-project.org/package=R6
+  authors:
+  - family-names: Chang
+    given-names: Winston
+    email: winston@posit.co
+  year: '2026'
+  doi: 10.32614/CRAN.package.R6
+  version: '>= 2.4.0'
+- type: software
+  title: R6.tiledb
+  abstract: 'R6.tiledb: R6 Classes for TileDB Arrays and Groups'
+  notes: Imports
+  url: https://cgiachalis.github.io/R6.tiledb/
+  authors:
+  - family-names: Giachalis
+    given-names: Constantinos
+    email: 26255858+cgiachalis@users.noreply.github.com
+  year: '2026'
+  version: '>= 0.3.0'
+- type: software
+  title: storr
+  abstract: 'storr: Simple Key Value Stores'
+  notes: Imports
+  url: https://richfitz.github.io/storr/
+  repository: https://CRAN.R-project.org/package=storr
+  authors:
+  - family-names: FitzJohn
+    given-names: Rich
+    email: rich.fitzjohn@gmail.com
+  year: '2026'
+  doi: 10.32614/CRAN.package.storr
+- type: software
+  title: tiledb
+  abstract: 'tiledb: Modern Database Engine for Complex Data Based on Multi-Dimensional
+    Arrays'
+  notes: Imports
+  url: https://tiledb-inc.github.io/TileDB-R/
+  repository: https://CRAN.R-project.org/package=tiledb
+  authors:
+  - name: TileDB, Inc.
+  year: '2026'
+  doi: 10.32614/CRAN.package.tiledb
+  version: '>= 0.33.0'
+- type: software
+  title: litedown
+  abstract: 'litedown: A Lightweight Version of R Markdown'
+  notes: Suggests
+  url: https://github.com/yihui/litedown
+  repository: https://CRAN.R-project.org/package=litedown
+  authors:
+  - family-names: Xie
+    given-names: Yihui
+    email: xie@yihui.name
+    orcid: https://orcid.org/0000-0003-0645-5666
+  year: '2026'
+  doi: 10.32614/CRAN.package.litedown
+- type: software
+  title: testthat
+  abstract: 'testthat: Unit Testing for R'
+  notes: Suggests
+  url: https://testthat.r-lib.org
+  repository: https://CRAN.R-project.org/package=testthat
+  authors:
+  - family-names: Wickham
+    given-names: Hadley
+    email: hadley@posit.co
+  year: '2026'
+  doi: 10.32614/CRAN.package.testthat
+  version: '>= 3.0.0'
+- type: software
+  title: withr
+  abstract: 'withr: Run Code ''With'' Temporarily Modified Global State'
+  notes: Suggests
+  url: https://withr.r-lib.org
+  repository: https://CRAN.R-project.org/package=withr
+  authors:
+  - family-names: Hester
+    given-names: Jim
+  - family-names: Henry
+    given-names: Lionel
+    email: lionel@posit.co
+  - family-names: Müller
+    given-names: Kirill
+    email: krlmlr+r@mailbox.org
+  - family-names: Ushey
+    given-names: Kevin
+    email: kevinushey@gmail.com
+  - family-names: Wickham
+    given-names: Hadley
+    email: hadley@posit.co
+  - family-names: Chang
+    given-names: Winston
+  year: '2026'
+  doi: 10.32614/CRAN.package.withr
+

DESCRIPTION

@@ -1,10 +1,11 @@
 Package: storr.tiledb
 Title: A TileDB Storage Driver for Storr
-Version: 0.0.40
-Date: 2026-05-21
+Version: 0.0.41
+Date: 2026-05-26
 Authors@R: 
-    person("Constantinos", "Giachalis", , "xx@github.com", role = c("aut", "cre"))
-Maintainer: Constantinos Giachalis <xx@github.com>
+    person("Constantinos", "Giachalis", , "26255858+cgiachalis@users.noreply.github.com", role = c("aut", "cre"))
+Maintainer: Constantinos Giachalis
+    <26255858+cgiachalis@users.noreply.github.com>
 Description: Provides a TileDB driver for 'storr' interface. A 'storr' is
     a content addressed key value store with an optional caching layer and
     this package contributes a new driver using TileDB Embedded storage
@@ -14,7 +15,8 @@ Description: Provides a TileDB driver for 'storr' interface. A 'storr' is
     expiration timestamps as well as support for asynchronous and in
     parallel writes.
 License: MIT + file LICENSE
-URL: https://github.com/cgiachalis/storr.tiledb, https://cgiachalis.github.io/storr.tiledb/
+URL: https://github.com/cgiachalis/storr.tiledb,
+    https://cgiachalis.github.io/storr.tiledb/
 BugReports: https://github.com/cgiachalis/storr.tiledb/issues
 Depends:
     R (>= 4.4.0)
@@ -36,10 +38,10 @@ VignetteBuilder:
     litedown
 Remotes: 
     cgiachalis/R6.tiledb
+Config/roxygen2/version: 8.0.0
 Config/testthat/edition: 3
 Config/testthat/parallel: true
 Config/testthat/start-first: StorrFragments,auto*
 Encoding: UTF-8
 Language: en-GB
 Roxygen: list(markdown = TRUE, old_usage = TRUE)
-Config/roxygen2/version: 8.0.0

NAMESPACE

@@ -11,6 +11,7 @@ export(driver_tiledb_create)
 export(get_allocation_size_preference)
 export(new_context)
 export(set_allocation_size_preference)
+export(set_tiledb_timestamp)
 export(storr_consolidate)
 export(storr_copy)
 export(storr_fragments)
@@ -25,6 +26,7 @@ importFrom(R6,R6Class)
 importFrom(R6.tiledb,TileDBArray)
 importFrom(R6.tiledb,TileDBGroup)
 importFrom(R6.tiledb,new_context)
+importFrom(R6.tiledb,set_tiledb_timestamp)
 importFrom(arrow,call_function)
 importFrom(data.table,`:=`)
 importFrom(stats,na.omit)

NEWS.md

@@ -1,3 +1,3 @@
-# storr.tiledb 0.0.40
+# storr.tiledb 0.0.41
 
 * Initial GitHub release.

R/StorrTimeTravel.R

@@ -1,8 +1,7 @@
 #' @title Generate a `StorrTimeTravel` Object
 #'
-#' @description A [TileDBStorr] is a time-travel variant of `TileDBStorr` designed
-#' to query data at specific points in time and in read-only mode with no write
-#' capabilities.
+#' @description A variant of `TileDBStorr` designed to query data at specific
+#'  points in time and in read-only mode with no write capabilities.
 #'
 #' This class is not intended to be used directly and the preferred
 #' usage is through [storr_timetravel()].

R/TileDBDriver.R

@@ -33,8 +33,8 @@ TileDBDriver <- R6::R6Class(
 
     #' @description Create a new `TileDBDriver` object.
     #'
-    #' @param uri URI path for the `TileDBDriver` object.
-    #' @param ctx Optional [tiledb::tiledb_ctx()] object.
+    #' @param uri URI path to `TileDB` driver.
+    #' @param ctx Optional \link[tiledb:tiledb_ctx]{tiledb_ctx} object.
     #'
     initialize = function(uri, ctx = NULL) {
 

R/TimeTravelDriver.R

@@ -24,15 +24,15 @@ TimeTravelDriver <- R6::R6Class(
 
     #' @description Instantiate a new `TimeTravelDriver` object.
     #'
-    #' @param uri URI path for the `TimeBDriver` object.
-    #' @param ctx Optional [tiledb::tiledb_ctx()] object.
+    #' @param uri URI path to `TileDB` driver.
+    #' @param ctx Optional \link[tiledb:tiledb_ctx]{tiledb_ctx} object.
     #' @param timestamp Set a `TileDB` timestamp range that
     #'  the resource will be opened at. Effective in `"READ"` mode only.
     #'  Valid options:
     #'  - A `NULL` value (default)
     #'  - An `R` object coercible to `POSIXct` with length 1 which is used for end timestamp,
     #'  or length 2 with start, end timestamps
-    #'  - An object of class `tiledb_timestamp`. See [R6.tiledb::set_tiledb_timestamp()]
+    #'  - An object of class `tiledb_timestamp`. See [set_tiledb_timestamp()]
     #'
     initialize = function(uri, ctx = NULL, timestamp = NULL) {
 

R/reexports.R

@@ -2,6 +2,10 @@
 #' @importFrom R6.tiledb new_context
 R6.tiledb::new_context
 
+#' @export
+#' @importFrom R6.tiledb set_tiledb_timestamp
+R6.tiledb::set_tiledb_timestamp
+
 #' @export
 #' @importFrom tiledb tiledb_config
 tiledb::tiledb_config

R/storr_tiledb.R

@@ -30,7 +30,7 @@
 #'  ## Buffer size
 #'
 #'  The buffer allocation size is set to 3 MB per column when fetching data. Use
-#'  [tiledb::set_allocation_size_preference()] to set a different limit.
+#'  [set_allocation_size_preference()] to set a different limit.
 #'
 #' # Class Methods Summary
 #'

R/storr_timetravel.R

@@ -69,7 +69,7 @@
 #'  - A `NULL` value (default)
 #'  - An `R` object coercible to `POSIXct` with length 1 which used for end timestamp,
 #'  or length 2 with start, end timestamps
-#'  - An object of class `tiledb_timestamp`. See [R6.tiledb::set_tiledb_timestamp()]
+#'  - An object of class `tiledb_timestamp`. See [set_tiledb_timestamp()]
 #'
 #' Set a new timestamp with active field `$timestamp`, see examples.
 #'