biosyntax 0.1.1 → 0.1.2

data/README.md

@@ -147,9 +147,10 @@ bundle exec rake
 
 ## License
 
-`biosyntax` vendors `libbiosyntax`, which is licensed under the GNU General
-Public License version 3 only. This gem is therefore distributed under
-`GPL-3.0-only`. See `LICENSE.md`.
+The Ruby code and native binding are licensed under the [MIT License](LICENSE.md).
+The vendored `libbiosyntax` source is licensed under
+[LGPL-2.1-or-later](LICENSE.libbiosyntax.md), and the compiled extension is
+subject to its terms.
 
 This project is inspired by the original bioSyntax project:
 <https://github.com/bioSyntax/bioSyntax>

data/ext/biosyntax/biosyntax.c

@@ -1,7 +1,7 @@
 
 /*
  * libbiosyntax: dependency-free C tokenizer/highlighter core for biological files.
- * SPDX-License-Identifier: GPL-3.0-only
+ * SPDX-License-Identifier: LGPL-2.1-or-later
  */
 #define BIOSYN_BUILDING_LIBRARY
 #include "biosyntax.h"
@@ -431,25 +431,25 @@ static uint32_t mapq_score(int64_t v) { if (v == 255 || v < 10) return BIOSYN_CL
 
 static void hi_fasta_scheme(writer_t *w, const char *s, size_t n, uint32_t scheme) { n = trim_eol(s, n); if (!n) return; if (s[0] == '>') emit(w, 0, n, BIOSYN_CLASS_HEADER); else if (s[0] == ';' || s[0] == '#') emit(w, 0, n, BIOSYN_CLASS_COMMENT); else seq_runs_scheme(w, s, 0, n, scheme); }
 static int is_start_codon(const char *s, size_t i, size_t n) {
-    unsigned char a, b, c;
+    int a, b, c;
     if (i + 3 > n) return 0;
     a = up((unsigned char)s[i]); b = up((unsigned char)s[i + 1]); c = up((unsigned char)s[i + 2]);
     return a == 'A' && b == 'T' && c == 'G';
 }
 static int is_stop_codon(const char *s, size_t i, size_t n) {
-    unsigned char a, b, c;
+    int a, b, c;
     if (i + 3 > n) return 0;
     a = up((unsigned char)s[i]); b = up((unsigned char)s[i + 1]); c = up((unsigned char)s[i + 2]);
     return a == 'T' && ((b == 'A' && (c == 'A' || c == 'G')) || (b == 'G' && c == 'A'));
 }
 static int is_rna_start_codon(const char *s, size_t i, size_t n) {
-    unsigned char a, b, c;
+    int a, b, c;
     if (i + 3 > n) return 0;
     a = up((unsigned char)s[i]); b = up((unsigned char)s[i + 1]); c = up((unsigned char)s[i + 2]);
     return a == 'A' && b == 'U' && c == 'G';
 }
 static int is_rna_stop_codon(const char *s, size_t i, size_t n) {
-    unsigned char a, b, c;
+    int a, b, c;
     if (i + 3 > n) return 0;
     a = up((unsigned char)s[i]); b = up((unsigned char)s[i + 1]); c = up((unsigned char)s[i + 2]);
     return a == 'U' && ((b == 'A' && (c == 'A' || c == 'G')) || (b == 'G' && c == 'A'));

data/ext/biosyntax/biosyntax.h

@@ -4,7 +4,7 @@
 /*
  * libbiosyntax: dependency-free C tokenizer/highlighter core for biological files.
  * The core performs no IO; callers pass one already-read text line at a time.
- * SPDX-License-Identifier: GPL-3.0-only
+ * SPDX-License-Identifier: LGPL-2.1-or-later
  */
 
 #include <stddef.h>
@@ -32,7 +32,7 @@ extern "C" {
 
 #define BIOSYN_VERSION_MAJOR 0
 #define BIOSYN_VERSION_MINOR 1
-#define BIOSYN_VERSION_PATCH 0
+#define BIOSYN_VERSION_PATCH 1
 #define BIOSYN_ABI_VERSION   1u
 
 #define BIOSYN_STRINGIFY_DETAIL(x) #x

data/ext/biosyntax/biosyntax_ext.c

@@ -1,6 +1,6 @@
 /*
  * Ruby native extension for libbiosyntax.
- * SPDX-License-Identifier: GPL-3.0-only
+ * SPDX-License-Identifier: MIT
  */
 
 #include "ruby.h"

data/lib/biosyntax/version.rb

@@ -1,5 +1,5 @@
 module BioSyntax
   # Ruby gem version.
   # @return [String]
-  VERSION = '0.1.1'
+  VERSION = '0.1.2'
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: biosyntax
 version: !ruby/object:Gem::Version
-  version: 0.1.1
+  version: 0.1.2
 platform: ruby
 authors:
 - kojix2
@@ -16,6 +16,7 @@ extensions:
 - ext/biosyntax/extconf.rb
 extra_rdoc_files: []
 files:
+- LICENSE.libbiosyntax.md
 - LICENSE.md
 - README.md
 - exe/biocat
@@ -25,9 +26,9 @@ files:
 - ext/biosyntax/extconf.rb
 - lib/biosyntax.rb
 - lib/biosyntax/version.rb
-homepage: https://github.com/kojix2/biosyntax
+homepage: https://github.com/kojix2/ruby-biosyntax
 licenses:
-- GPL-3.0-only
+- MIT
 metadata: {}
 rdoc_options: []
 require_paths:
@@ -43,7 +44,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 4.0.10
+rubygems_version: 4.0.16
 specification_version: 4
 summary: Ruby native binding for libbiosyntax
 test_files: []