interrup...t

Author: ms609

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: TreeTools
 Title: Create, Modify and Analyse Phylogenetic Trees
-Version: 2.2.0.9001
+Version: 2.2.0.9002
 Authors@R: c(
   person("Martin R.", 'Smith', role = c("aut", "cre", "cph"), 
          email = "martin.smith@durham.ac.uk",

NEWS.md

@@ -1,10 +1,15 @@
-# TreeTools 2.2.0.9001 #
+# TreeTools 2.2.0.9002 #
 
 ## New functionality
 
 - `Paste0()` provides a fast Rcpp-backed drop-in for `paste0()` / `stri_paste()`
   with `NA` propagation. Exported for use by downstream packages.
 
+## Usability
+
+- `Consensus()` and `SplitFrequency()` now respond to user interrupts during
+  long-running computations.
+
 ## Performance
 
 - Drop `stringi` dependency.

src/consensus.cpp

@@ -1,11 +1,13 @@
 #include <Rcpp/Lightest>
+#include <Rcpp/Interrupt.h> /* for Rcpp::checkUserInterrupt() */
 using namespace Rcpp;
 
 #include "../inst/include/TreeTools/assert.h" /* for ASSERT */
 #include "../inst/include/TreeTools/ClusterTable.h" /* for ClusterTable */
 
 #include <algorithm> /* for fill */
 #include <array> /* for array */
+#include <chrono> /* for steady_clock (interrupt timing) */
 #include <string> /* for string (hash key) */
 #include <unordered_map> /* for unordered_map */
 
@@ -57,8 +59,18 @@ RawMatrix calc_consensus_tree(
 
   int32 i = 0;
   int32 splits_found = 0;
+  auto lastInterrupt = std::chrono::steady_clock::now();
 
   do {
+    // ~1 s user-interrupt check
+    {
+      const auto now = std::chrono::steady_clock::now();
+      if (std::chrono::duration_cast<std::chrono::seconds>(
+            now - lastInterrupt).count() >= 1) {
+        lastInterrupt = now;
+        Rcpp::checkUserInterrupt();
+      }
+    }
     if (tables[i].NOSWX(ntip_3)) {
       continue;
     }
@@ -187,8 +199,18 @@ List calc_split_frequencies(
 
   // Reusable key buffer — avoids per-split heap allocation
   std::string key(nbin, '\0');
+  auto lastInterrupt = std::chrono::steady_clock::now();
 
   for (int32 i = 0; i < n_trees; ++i) {
+    // ~1 s user-interrupt check
+    {
+      const auto now = std::chrono::steady_clock::now();
+      if (std::chrono::duration_cast<std::chrono::seconds>(
+            now - lastInterrupt).count() >= 1) {
+        lastInterrupt = now;
+        Rcpp::checkUserInterrupt();
+      }
+    }
     if (tables[i].NOSWX(ntip_3)) {
       continue;
     }