Prepping for release

README.md

@@ -2,12 +2,13 @@
 
 ## Overview
 
-Tskit enables performant storage, manipulation, and analysis of ancestral
+`Tskit` enables performant storage, manipulation, and analysis of ancestral
 recombination graphs (ARGs) using succinct tree sequence encoding.
 See https://tskit.dev for project news, documentation, and tutorials.
-Tskit provides Python, C, and Rust APIs. The Python API can be called from R
-via the `reticulate` R package to seamlessly load and analyse a tree sequence,
-as described at https://tskit.dev/tutorials/RcppTskit.html.
+`Tskit` provides Python, C, and Rust application programming interfaces (APIs).
+The Python API can be called from R via the `reticulate` R package to
+seamlessly load and analyse a tree sequence, as described at
+https://tskit.dev/tutorials/RcppTskit.html.
 `RcppTskit` provides R access to the `tskit` C API for use cases where the
 `reticulate` option is not optimal. For example, for high-performance and
 low-level work with tree sequences. Currently, `RcppTskit` provides a limited
@@ -91,10 +92,11 @@ By contributing to this project, you agree to abide by its terms.
 
 ### Clone
 
-First clone the repository:
+First clone the repository and step into the directory:
 
 ```
 git clone https://github.com/HighlanderLab/RcppTskit.git
+cd RcppTskit
 ```
 
 ### Pre-commit install

RcppTskit/.Rbuildignore

@@ -10,8 +10,10 @@
 ^\.covrignore$
 ^\.github$
 ^codecov\.yaml$
+^cran-comments\.md$
 ^inst/examples/create_test\.trees\.R$
 ^inst/examples/create_test\.trees\.py$
+^LICENSE.md$
 ^notes_pkg_dev\.Rmd$
 ^pkg_dev_notes\.md$
 ^tests/testthat/_snaps$

RcppTskit/DESCRIPTION

@@ -1,23 +1,27 @@
 Type: Package
 Package: RcppTskit
-Title: R access to the tskit C API
+Title: R Access to the Tskit C API
 Version: 0.1.0
-Date: 2026-01-2607
-Authors@R:
-    person("Gregor", "Gorjanc", , "gregor.gorjanc@gmail.com", role = c("aut", "cre"),
-           comment = c(ORCID = "0000-0001-8008-2787"))
-Description: Tskit enables performant storage, manipulation, and analysis
-    of ancestral recombination graphs (ARGs) using succinct tree sequence
-    encoding.  See https://tskit.dev for project news, documentation, and
-    tutorials.  Tskit provides Python, C, and Rust APIs. The Python API
-    can be called from R via the `reticulate` R package to seamlessly load
-    and analyse a tree sequence as described at
-    https://tskit.dev/tutorials/RcppTskit.html. `RcppTskit` provides R
-    access to the `tskit` C API for use cases where the `reticulate`
+Date: 2026-01-27
+Authors@R: c(
+    person("Gregor", "Gorjanc", , "gregor.gorjanc@gmail.com", role = c("aut", "cre", "cph"),
+           comment = c(ORCID = "0000-0001-8008-2787")),
+    person("Tskit Developers", role = "cph",
+           comment = "Authors of included tskit C library")
+  )
+Description: 'Tskit' enables performant storage, manipulation, and
+    analysis of ancestral recombination graphs (ARGs) using succinct tree
+    sequence encoding. See <https://tskit.dev> for project news,
+    documentation, and tutorials. 'Tskit' provides Python, C, and Rust
+    application programming interfaces (APIs). The Python API can be
+    called from R via the 'reticulate' R package to seamlessly load and
+    analyse a tree sequence as described at
+    <https://tskit.dev/tutorials/tskitr.html>. 'RcppTskit' provides R
+    access to the 'tskit' C API for use cases where the 'reticulate'
     option is not optimal. For example, for high-performance and low-level
-    work with tree sequences. Currently, `RcppTskit` provides a limited
+    work with tree sequences. Currently, 'RcppTskit' provides a limited
     number of R functions due to the availability of extensive Python API
-    and the `reticulate` option.
+    and the 'reticulate' option.
 License: MIT + file LICENSE
 URL: https://github.com/HighlanderLab/RcppTskit
 BugReports: https://github.com/HighlanderLab/RcppTskit/issues
@@ -26,16 +30,16 @@ Depends:
 Imports:
     methods,
     R6,
-    Rcpp (>= 1.1.0),
-    reticulate
+    Rcpp (>= 0.12.10),
+    reticulate (>= 1.41.0)
 Suggests:
     covr,
     knitr,
     quarto,
     spelling,
     testthat (>= 3.0.0)
 LinkingTo:
-    Rcpp
+    Rcpp (>= 0.12.10)
 VignetteBuilder:
     quarto
 Config/testthat/edition: 3

RcppTskit/LICENSE

@@ -1,2 +1,2 @@
-YEAR: 2025
+YEAR: 2026
 COPYRIGHT HOLDER: Gregor Gorjanc

RcppTskit/LICENSE.md

@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2026 Gregor Gorjanc
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

RcppTskit/LICENSE.note

@@ -0,0 +1,2 @@
+The tskit C library is distributed under the MIT license.
+Full copies of the license are included in `inst/include/tskit/LICENSE` and `src/tskit/LICENSE.

RcppTskit/NAMESPACE

@@ -1,6 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
 export(TreeSequence)
+export(check_tskit_py)
 export(get_tskit_py)
 export(kastore_version)
 export(ts_load)

RcppTskit/R/Class-TreeSequence.R

@@ -71,8 +71,8 @@ TreeSequence <- R6Class(
     },
 
     #' @description Alias for \code{\link[=TreeSequence]{TreeSequence$dump}}.
-    #' @param file see
-    #' @param options see
+    #' @param file see \code{\link[=TreeSequence]{TreeSequence$dump}}.
+    #' @param options see \code{\link[=TreeSequence]{TreeSequence$dump}}.
     write = function(file, options = 0L) {
       self$dump(file = file, options = options)
     },
@@ -106,11 +106,14 @@ TreeSequence <- R6Class(
     #' ts_r$num_samples() # 160
     #'
     #' # Transfer the tree sequence to reticulate Python and use tskit Python API
-    #' ts_py <- ts_r$r_to_py()
-    #' is(ts_py)
-    #' ts_py$num_samples # 160
-    #' ts2_py <- ts_py$simplify(samples = c(0L, 1L, 2L, 3L))
-    #' ts2_py$num_samples # 4
+    #' tskit <- get_tskit_py()
+    #' if (check_tskit_py(tskit)) {
+    #'   ts_py <- ts_r$r_to_py()
+    #'   is(ts_py)
+    #'   ts_py$num_samples # 160
+    #'   ts2_py <- ts_py$simplify(samples = c(0L, 1L, 2L, 3L))
+    #'   ts2_py$num_samples # 4
+    #' }
     r_to_py = function(tskit_module = get_tskit_py(), cleanup = TRUE) {
       ts_r_to_py_ptr(
         self$pointer,
@@ -120,107 +123,137 @@ TreeSequence <- R6Class(
     },
 
     #' @description Get the number of provenances in a tree sequence.
+    #' @examples
     #' ts_file <- system.file("examples/test.trees", package = "RcppTskit")
     #' ts <- ts_load(ts_file)
-    #' ts_num_provenances(ts)
+    #' ts$num_provenances()
     num_provenances = function() {
       ts_num_provenances_ptr(self$pointer)
     },
 
     #' @description Get the number of populations in a tree sequence.
+    #' @examples
     #' ts_file <- system.file("examples/test.trees", package = "RcppTskit")
     #' ts <- ts_load(ts_file)
-    #' ts_num_populations(ts)
+    #' ts$num_populations()
     num_populations = function() {
       ts_num_populations_ptr(self$pointer)
     },
 
     #' @description Get the number of migrations in a tree sequence.
+    #' @examples
     #' ts_file <- system.file("examples/test.trees", package = "RcppTskit")
     #' ts <- ts_load(ts_file)
-    #' ts_num_migrations(ts)
+    #' ts$num_migrations()
     num_migrations = function() {
       ts_num_migrations_ptr(self$pointer)
     },
 
     #' @description Get the number of individuals in a tree sequence.
+    #' @examples
     #' ts_file <- system.file("examples/test.trees", package = "RcppTskit")
     #' ts <- ts_load(ts_file)
-    #' ts_num_individuals(ts)
+    #' ts$num_individuals()
     num_individuals = function() {
       ts_num_individuals_ptr(self$pointer)
     },
 
     #' @description Get the number of samples (of nodes) in a tree sequence.
+    #' @examples
     #' ts_file <- system.file("examples/test.trees", package = "RcppTskit")
     #' ts <- ts_load(ts_file)
-    #' ts_num_samples(ts)
+    #' ts$num_samples()
     num_samples = function() {
       ts_num_samples_ptr(self$pointer)
     },
 
     #' @description Get the number of nodes in a tree sequence.
+    #' @examples
     #' ts_file <- system.file("examples/test.trees", package = "RcppTskit")
     #' ts <- ts_load(ts_file)
-    #' ts_num_nodes(ts)
+    #' ts$num_nodes()
     num_nodes = function() {
       ts_num_nodes_ptr(self$pointer)
     },
 
     #' @description Get the number of edges in a tree sequence.
+    #' @examples
     #' ts_file <- system.file("examples/test.trees", package = "RcppTskit")
     #' ts <- ts_load(ts_file)
-    #' ts_num_edges(ts)
+    #' ts$num_edges()
     num_edges = function() {
       ts_num_edges_ptr(self$pointer)
     },
 
     #' @description Get the number of trees in a tree sequence.
+    #' @examples
     #' ts_file <- system.file("examples/test.trees", package = "RcppTskit")
     #' ts <- ts_load(ts_file)
-    #' ts_num_trees(ts)
+    #' ts$num_trees()
     num_trees = function() {
       ts_num_trees_ptr(self$pointer)
     },
 
     #' @description Get the number of sites in a tree sequence.
+    #' @examples
     #' ts_file <- system.file("examples/test.trees", package = "RcppTskit")
     #' ts <- ts_load(ts_file)
-    #' ts_num_sites(ts)
+    #' ts$num_sites()
     num_sites = function() {
       ts_num_sites_ptr(self$pointer)
     },
 
     #' @description Get the number of mutations in a tree sequence.
+    #' @examples
     #' ts_file <- system.file("examples/test.trees", package = "RcppTskit")
     #' ts <- ts_load(ts_file)
-    #' ts_num_mutations(ts)
+    #' ts$num_mutations()
     num_mutations = function() {
       ts_num_mutations_ptr(self$pointer)
     },
 
     #' @description Get the sequence length.
+    #' @examples
     #' ts_file <- system.file("examples/test.trees", package = "RcppTskit")
     #' ts <- ts_load(ts_file)
-    #' ts_sequence_length(ts)
+    #' ts$sequence_length()
     sequence_length = function() {
       ts_sequence_length_ptr(self$pointer)
     },
 
     #' @description Get the time units string.
+    #' @examples
     #' ts_file <- system.file("examples/test.trees", package = "RcppTskit")
     #' ts <- ts_load(ts_file)
-    #' ts_time_units(ts)
+    #' ts$time_units()
     time_units = function() {
       ts_time_units_ptr(self$pointer)
     },
 
+    #' @description Get the min time in node table and mutation table.
+    #' @examples
+    #' ts_file <- system.file("examples/test.trees", package = "RcppTskit")
+    #' ts <- ts_load(ts_file)
+    #' ts$min_time()
+    min_time = function() {
+      ts_min_time_ptr(self$pointer)
+    },
+
+    #' @description Get the max time in node table and mutation table.
+    #' @examples
+    #' ts_file <- system.file("examples/test.trees", package = "RcppTskit")
+    #' ts <- ts_load(ts_file)
+    #' ts$max_time()
+    max_time = function() {
+      ts_max_time_ptr(self$pointer)
+    },
+
     #' @description Get the length of metadata in a tree sequence and its tables.
     #' @return A named list with the length of metadata.
     #' @examples
-    #'ts_file <- system.file("examples/test.trees", package = "RcppTskit")
+    #' ts_file <- system.file("examples/test.trees", package = "RcppTskit")
     #' ts <- ts_load(ts_file)
-    #'ts$metadata_length()
+    #' ts$metadata_length()
     metadata_length = function() {
       ts_metadata_length_ptr(self$pointer)
     }

RcppTskit/R/RcppExports.R

@@ -95,10 +95,6 @@ ts_metadata_length_ptr <- function(ts) {
     .Call(`_RcppTskit_ts_metadata_length_ptr`, ts)
 }
 
-ts_grow <- function(ts) {
-    .Call(`_RcppTskit_ts_grow`, ts)
-}
-
 test_tsk_bug_assert_c <- function() {
     invisible(.Call(`_RcppTskit_test_tsk_bug_assert_c`))
 }

RcppTskit/R/RcppTskit-package.R

@@ -1,12 +1,13 @@
 # Contains the package description and .onLoad() function
 
 #' @description
-#' Tskit enables performant storage, manipulation, and analysis of
+#' `Tskit` enables performant storage, manipulation, and analysis of
 #' ancestral recombination graphs (ARGs) using succinct tree sequence encoding.
 #' See https://tskit.dev for project news, documentation, and tutorials.
-#' Tskit provides Python, C, and Rust APIs. The Python API can be called from R
-#' via the `reticulate` R package to seamlessly load and analyse a tree sequence
-#' as described at https://tskit.dev/tutorials/tskitr.html.
+#' `Tskit` provides Python, C, and Rust application programming interfaces (APIs).
+#' The Python API can be called from R via the `reticulate` R package to
+#' seamlessly load and analyse a tree sequence as described at
+#' https://tskit.dev/tutorials/tskitr.html.
 #' `RcppTskit` provides R access to the `tskit` C API for use cases where the
 #' `reticulate` option is not optimal. For example, for high-performance
 #' and low-level work with tree sequences. Currently, `RcppTskit` provides a