[med-svn] [Git][med-team/htscodecs][master] 8 commits: d/watch: Use Dist in Github template

Andreas Tille (@tille) gitlab at salsa.debian.org
Wed Sep 16 13:16:14 BST 2026 


Andreas Tille pushed to branch master at Debian Med / htscodecs


Commits:
2e7589f5 by Andreas Tille at 2026-09-16T14:00:47+02:00
d/watch: Use Dist in Github template

- - - - -
47eca48b by Andreas Tille at 2026-09-16T14:11:02+02:00
Update Homepage and Source

- - - - -
8ebedcf1 by Andreas Tille at 2026-09-16T14:11:17+02:00
New upstream version 1.6.7
- - - - -
4453eabc by Andreas Tille at 2026-09-16T14:11:17+02:00
New upstream version

- - - - -
d0e6a21f by Andreas Tille at 2026-09-16T14:11:24+02:00
Update upstream source from tag 'upstream/1.6.7'

Update to upstream version '1.6.7'
with Debian dir 25f0348c8d4baf87c3881876d71cd7105c96de3b
- - - - -
4c2fad0b by Andreas Tille at 2026-09-16T14:11:49+02:00
Changes made by cme

- - - - -
3cabda17 by Andreas Tille at 2026-09-16T14:13:14+02:00
routine-update: Ready to upload to unstable

- - - - -
4dd55277 by Andreas Tille at 2026-09-16T14:15:23+02:00
Add lrc.config

- - - - -


9 changed files:

- NEWS.md
- configure.ac
- debian/changelog
- debian/control
- debian/copyright
- + debian/lrc.config
- debian/watch
- htscodecs/htscodecs.h
- htscodecs/tokenise_name3.c


Changes:

=====================================
NEWS.md
=====================================
@@ -1,3 +1,16 @@
+Release 1.6.7: 24th June 2026
+-----------------------------
+
+This is a trivial release containing a single new commit removing a
+harmless compiler warning.  (The primary purpose of a release is to
+ensure htslib is using a released and tagged htscodecs submodule.)
+
+Bug fixes
+
+- Remove an unused variable detected by gcc 16.
+  (PR #148: James Bonfield)
+
+
 Release 1.6.6: 11th January 2026
 --------------------------------
 


=====================================
configure.ac
=====================================
@@ -1,5 +1,5 @@
 dnl Process this file with autoconf to produce a configure script.
-AC_INIT(htscodecs, 1.6.6)
+AC_INIT(htscodecs, 1.6.7)
 
 # Some functions benefit from -O3 optimisation, so if the user didn't
 # explicitly set any compiler flags, we'll plump for O3.
@@ -61,7 +61,7 @@ AM_EXTRA_RECURSIVE_TARGETS([fuzz])
 #       libhtscodecs.so.1.1.0
 
 VERS_CURRENT=3
-VERS_REVISION=11
+VERS_REVISION=12
 VERS_AGE=1
 AC_SUBST(VERS_CURRENT)
 AC_SUBST(VERS_REVISION)


=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+htscodecs (1.6.7-1) unstable; urgency=medium
+
+  * Team upload.
+  * d/watch: Use Dist in Github template
+  * Update Homepage and Source
+  * New upstream version
+  * Reflow Uploaders field (cme)
+
+ -- Andreas Tille <tille at debian.org>  Wed, 16 Sep 2026 14:12:01 +0200
+
 htscodecs (1.6.6-1) unstable; urgency=medium
 
   * New upstream version 1.6.6


=====================================
debian/control
=====================================
@@ -1,21 +1,25 @@
 Source: htscodecs
-Section: science
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Michael R. Crusoe <crusoe at debian.org>,
-           Étienne Mollier <emollier at debian.org>
-Build-Depends: debhelper-compat (= 13),
-               d-shlibs,
-               libbz2-dev
 Standards-Version: 4.7.4
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders:
+ Michael R. Crusoe <crusoe at debian.org>,
+ Étienne Mollier <emollier at debian.org>,
+Section: science
+Build-Depends:
+ debhelper-compat (= 14),
+ d-shlibs,
+ libbz2-dev,
 Vcs-Browser: https://salsa.debian.org/med-team/htscodecs
 Vcs-Git: https://salsa.debian.org/med-team/htscodecs.git
-Homepage: https://github.com/jkbonfield/htscodecs/
+Homepage: https://github.com/samtools/htscodecs
 
 Package: libhtscodecs2
 Architecture: any
 Multi-Arch: same
 Section: libs
-Depends: ${shlibs:Depends}, ${misc:Depends}
+Depends:
+ ${shlibs:Depends},
+ ${misc:Depends},
 Description: Custom compression for CRAM and others
  This library implements the custom CRAM codecs used for "EXTERNAL" block
  types. These consist of two variants of the rANS codec (8-bit and 16-bit
@@ -28,9 +32,11 @@ Description: Custom compression for CRAM and others
 
 Package: libhtscodecs-dev
 Architecture: any
-Section: libdevel
-Depends: libhtscodecs2 (= ${binary:Version}), ${misc:Depends}
 Multi-Arch: same
+Section: libdevel
+Depends:
+ libhtscodecs2 (= ${binary:Version}),
+ ${misc:Depends},
 Description: Development headers for custom compression for CRAM and others
  This library implements the custom CRAM codecs used for "EXTERNAL" block
  types. These consist of two variants of the rANS codec (8-bit and 16-bit


=====================================
debian/copyright
=====================================
@@ -1,6 +1,6 @@
 Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: htscodecs
-Source: https://github.com/jkbonfield/htscodecs/
+Source: https://github.com/samtools/htscodecs
 
 Files: *
 Copyright: 2009-2025, Genome Research Ltd.


=====================================
debian/lrc.config
=====================================
@@ -0,0 +1,2 @@
+m4/hts_check_compile_flags_needed.m4
+m4/vl_prog_warnings.m4


=====================================
debian/watch
=====================================
@@ -1,5 +1,4 @@
 Version: 5
 
 Template: Github
-Owner: samtools
-Project: htscodecs
+Dist: https://github.com/samtools/htscodecs


=====================================
htscodecs/htscodecs.h
=====================================
@@ -43,7 +43,7 @@
  * Note currently this needs manually editing as it isn't automatically
  * updated by autoconf.
  */
-#define HTSCODECS_VERSION 100606
+#define HTSCODECS_VERSION 100607
 
 /*
  * A const string form of the HTSCODECS_VERSION define.


=====================================
htscodecs/tokenise_name3.c
=====================================
@@ -475,7 +475,6 @@ static int encode_token_diff(name_context *ctx, uint32_t val) {
 // Trie implementation for tracking common name prefixes.
 static
 int build_trie(name_context *ctx, char *data, size_t len, int n) {
-    int nlines = 0;
     size_t i;
     trie_t *t;
 
@@ -486,7 +485,7 @@ int build_trie(name_context *ctx, char *data, size_t len, int n) {
     }
 
     // Build our trie, also counting input lines
-    for (nlines = i = 0; i < len; i++, nlines++) {
+    for (i = 0; i < len; i++) {
         t = ctx->t_head;
         t->count++;
         while (i < len && (unsigned char)data[i] > '\n') {
@@ -589,7 +588,6 @@ void dump_trie(trie_t *t, int depth) {
 
 static
 int search_trie(name_context *ctx, char *data, size_t len, int n, int *exact, int *is_fixed, int *fixed_len) {
-    int nlines = 0;
     size_t i;
     trie_t *t;
     int from = -1, p3 = -1;
@@ -651,7 +649,7 @@ int search_trie(name_context *ctx, char *data, size_t len, int n, int *exact, in
 
     // Find an item in the trie
     int from_punct = from;
-    for (nlines = i = 0; i < len; i++, nlines++) {
+    for (i = 0; i < len; i++) {
         t = ctx->t_head;
         while (i < len && data[i] > '\n') {
             unsigned char c = data[i++];



View it on GitLab: https://salsa.debian.org/med-team/htscodecs/-/compare/d73c42c13e37d318883345ddf604fb41d53ad8a1...4dd552771addfc806c56df466cfc57dc1c63de99

-- 
View it on GitLab: https://salsa.debian.org/med-team/htscodecs/-/compare/d73c42c13e37d318883345ddf604fb41d53ad8a1...4dd552771addfc806c56df466cfc57dc1c63de99
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