Prepare release

Author: ms609

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: TreeTools
 Title: Create, Modify and Analyse Phylogenetic Trees
-Version: 2.1.0.9009
+Version: 2.2.0
 Authors@R: c(
   person("Martin R.", 'Smith', role = c("aut", "cre", "cph"), 
          email = "martin.smith@durham.ac.uk",

NEWS.md

@@ -1,53 +1,42 @@
-# TreeTools 2.1.0.9009 (2026-03-18) #
+# TreeTools 2.2.0 (2026-03-18) #
 
-- `RCurl` moved from Imports to Suggests; `ReadMrBayesTrees()` uses
-  `RCurl::url.exists()` when available, falling back to base R `url()` for
-  URL checks.
-
-# TreeTools 2.1.0.9008 (2026-03-17) #
-
-- `PhyDatToMatrix()` no longer crashes on zero-character `phyDat` objects
-  (e.g. from a star tree); returns a 0-column matrix with correct row names.
-- `AddUnconstrained()` handles zero-character `phyDat` input gracefully.
-
-# TreeTools 2.1.0.9007 (2026-03-13) #
-
-- `duplicated.Splits()` uses hash-based O(n) de-duplication, replacing
-  O(n²) pairwise comparison.
-
-# TreeTools 2.1.0.9006 (2026-03-13) #
-  
-- `NodeDepth()` for unrooted trees rewritten as O(n) two-pass C++ algorithm,
-  replacing iterative R while-loop.
-
-# TreeTools 2.1.0.9005 (2026-03-13) #
-
-- `SplitFrequency(reference = NULL)` performance improvements:
-  split normalization moved to C++; internal split de-duplication uses
-  hash map instead of ordered map.
-
-# TreeTools 2.1.0.9003 (2026-03-09) #
+## New functionality
 
-- `inst/include/TreeTools/tree_number.h` added to support downstream packages
-  (e.g. TBRDist) via `LinkingTo: TreeTools`. Provides 256-bit tree number
-  encoding/decoding supporting up to 51 leaves, extended from the 44-leaf
-  limit of the previous `uint64_t`-based implementation.
+- `EdgeRatio()` reports the ratio of external:internal edges.
+- `SplitInformation()` supports `Splits` and `phylo` objects.
+- `sort` and `order` support `Splits` objects.
+- `SplitFrequency(reference = NULL)` returns frequency of all splits.
 - `as.TreeNumber()` now supports trees with up to 51 leaves (previously 19).
   Trees with 20–51 leaves have more than 2^64 distinct topologies, so their
   `TreeNumber` is stored as a decimal character string rather than `integer64`.
   The 19-leaf limit for `integer64`-backed storage (and `as.MixedBase()`
   round-trips) is unchanged.
 - `as.TreeNumber()` no longer warns for trees with 20–44 leaves.
+- `inst/include/TreeTools/tree_number.h` added to support downstream packages
+  (e.g. TBRDist) via `LinkingTo: TreeTools`. Provides 256-bit tree number
+  encoding/decoding supporting up to 51 leaves, extended from the 44-leaf
+  limit of the previous `uint64_t`-based implementation.
 
-# TreeTools 2.1.0.9001 (2026-02-19) #
+## Performance
 
-- `EdgeRatio()` reports the ratio of external:internal edges.
+- `SplitFrequency(reference = NULL)`: split normalization moved to C++;
+  internal split de-duplication uses hash map instead of ordered map.
+- `NodeDepth()` for unrooted trees rewritten as O(n) two-pass C++ algorithm,
+  replacing iterative R while-loop.
+- `duplicated.Splits()` uses hash-based O(n) de-duplication, replacing
+  O(n²) pairwise comparison.
 
-# TreeTools 2.1.0.9000 (2026-02-16) #
+## Fixes
 
-- `SplitInformation()` supports `Splits` and `phylo` objects.
-- `sort` and `order` support `Splits` objects.
-- `SplitFrequency(reference = NULL)` returns frequency of all splits.
+- `PhyDatToMatrix()` no longer crashes on zero-character `phyDat` objects
+  (e.g. from a star tree); returns a 0-column matrix with correct row names.
+- `AddUnconstrained()` handles zero-character `phyDat` input gracefully.
+
+## Dependencies
+
+- `RCurl` moved from Imports to Suggests; `ReadMrBayesTrees()` uses
+  `RCurl::url.exists()` when available, falling back to base R `url()` for
+  URL checks.
 
 
 # TreeTools 2.1.0 (2026-02-10) #

R/zzz.R

@@ -28,7 +28,7 @@ release_questions <- function() {
 # Check valgrind results on Github Actions
 # revdepcheck::revdep_check()
 #
-# codemetar::write_codemeta()
+# codemeta::write_codemeta()
 #
 # tools::resaveRdaFiles("R", compress="auto") - is default bzip2 the optimal?
 # tools::checkRdaFiles("R") - set optimal compression in `data-raw`

codemeta.json

@@ -8,13 +8,13 @@
   "codeRepository": "https://github.com/ms609/TreeTools/",
   "issueTracker": "https://github.com/ms609/TreeTools/issues/",
   "license": "https://spdx.org/licenses/GPL-3.0",
-  "version": "2.1.0.9009",
+  "version": "2.2.0",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
     "url": "https://r-project.org"
   },
-  "runtimePlatform": "R version 4.5.3 (2026-03-11)",
+  "runtimePlatform": "R Under development (unstable) (2025-11-23 r89052 ucrt)",
   "provider": {
     "@id": "https://cran.r-project.org",
     "@type": "Organization",
@@ -275,7 +275,7 @@
     },
     "SystemRequirements": "C++17"
   },
-  "fileSize": "1849.728KB",
+  "fileSize": "1881.301KB",
   "citation": [
     {
       "@type": "SoftwareSourceCode",
@@ -290,7 +290,7 @@
       ],
       "name": "TreeTools: create, modify and analyse phylogenetic trees",
       "identifier": "10.32614/CRAN.package.TreeTools",
-      "description": "R package version 2.1.0.9009",
+      "description": "R package version 2.2.0",
       "@id": "https://doi.org/10.32614/CRAN.package.TreeTools",
       "sameAs": "https://doi.org/10.32614/CRAN.package.TreeTools"
     }

cran-comments.md

@@ -1,7 +1,7 @@
 ## Test environments
 
 * Local PC:
-  - Windows 10, R devel
+  - Windows 11, R devel
 
 * [GitHub Actions](https://github.com/ms609/TreeTools/actions)
   - Ubuntu latest
@@ -19,4 +19,4 @@ There were no ERRORs or WARNINGs or NOTEs.
 ## Downstream dependencies
 
 Reverse dependencies have been checked using "revdepcheck" on
-[GitHub Actions](https://github.com/ms609/TreeTools/actions/workflows/revdep.yml).
+[GitHub Actions](https://github.com/ms609/TreeTools/actions/workflows/R-CMD-check.yml).