swarm version 3.1.4

Author: torognes

CITATION.cff

@@ -23,8 +23,8 @@ authors:
   given-names: "Torbjørn"
   orcid: "https://orcid.org/0000-0002-9329-9974"
 title: "SWARM: A robust and fast clustering method for amplicon-based studies"
-version: 3.1.3
-date-released: 2022-12-05
+version: 3.1.4
+date-released: 2023-09-20
 url: "https://github.com/torognes/swarm"
 preferred-citation:
   type: article
@@ -59,4 +59,4 @@ preferred-citation:
   title: "Swarm v3: towards tera-scale amplicon clustering"
   volume: 38
   issue: 1
-  year: 2022
+  year: 2022

man/swarm.1

@@ -1,5 +1,5 @@
 .\" ============================================================================
-.TH swarm 1 "December 5, 2022" "version 3.1.3" "USER COMMANDS"
+.TH swarm 1 "September 20, 2023" "version 3.1.4" "USER COMMANDS"
 .\" ============================================================================
 .SH NAME
 swarm \(em find clusters of nearly-identical nucleotide amplicons
@@ -531,17 +531,41 @@ New features and important modifications of \fBswarm\fR (short lived
 or minor bug releases are not mentioned):
 .RS
 .TP
+.BR v3.1.4\~ "released September 20, 2023"
+Version 3.1.4 fixes a minor bug, eliminates compilation warnings and
+static analysis warnings, and improves code:
+
+- fix: add checks to prevent silent overflow of short unsigned integers,
+
+- fix: compilation warnings with GCC 13 and clang 18,
+
+- fix: 1,040 clang-tidy warnings (from 3,669 warnings, down to 2,629),
+
+- improve: code modernization for long-term maintenance,
+
+- improve: double the maximal number of threads (from 256 threads to 512),
+
+- improve: make `-DNDEBUG` the default compilation behavior,
+performance: stable for all modes, except a 6 to 10% increase in memory footprint when d > 2.
+.TP
 .BR v3.1.3\~ "released December 5, 2022"
 Version 3.1.3 fixes a few minor bugs, removes warnings, and improves code and documentation:
-fix: bug introduced in version 3.1.1, that caused swarm to allocate way too much memory when d > 1 (bug had no impact on clustering results),
-fix: off-by-one error when allocating memory for a Bloom filter (bug had no impact on clustering results),
-fix: compilation warning with GCC 12 (and more recent) when using link-time optimization,
-fix: compilation warning with clang 13 (and more recent): unused set variable,
-fix: five clang-tidy warnings (readability-braces-around-statements),
-fix: minor code refactoring,
-improve: more uniform vocabulary throughout swarm's documentation (code, help, manpage, README, companion scripts and wiki),
-improve: code coverage of our test suite (swarm-tests).
 
+- fix: bug introduced in version 3.1.1, that caused swarm to allocate way too much memory when d > 1 (bug had no impact on clustering results),
+
+- fix: off-by-one error when allocating memory for a Bloom filter (bug had no impact on clustering results),
+
+- fix: compilation warning with GCC 12 (and more recent) when using link-time optimization,
+
+- fix: compilation warning with clang 13 (and more recent): unused set variable,
+
+- fix: five clang-tidy warnings (readability-braces-around-statements),
+
+- fix: minor code refactoring,
+
+- improve: more uniform vocabulary throughout swarm's documentation (code, help, manpage, README, companion scripts and wiki),
+
+- improve: code coverage of our test suite (swarm-tests).
 .TP
 .BR v3.1.2\~ "released November 10, 2022"
 Fix a bug with fastidious mode introduced in version 3.1.1, that could

src/swarm.h

@@ -37,7 +37,7 @@
 // will be de-duplicated by the linker.
 // (source: https://www.youtube.com/watch?v=QVHwOOrSh3w)
 
-const std::string swarm_version {"3.1.3"};
+const std::string swarm_version {"3.1.4"};
 constexpr char sepchar {' '};
 constexpr char dash_filename {'-'};
 constexpr unsigned int opt_differences_default {1};