[med-svn] [Git][med-team/lambda-align2][master] Build with libseqan2 2.5 Closes: #1125645

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / lambda-align2


Commits:
28202989 by Andreas Tille at 2026-04-30T20:57:16+02:00
Build with libseqan2 2.5 Closes: #1125645

- - - - -


3 changed files:

- debian/changelog
- + debian/patches/libseqan2.5.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -6,6 +6,8 @@ lambda-align2 (2.0.1-4) UNRELEASED; urgency=medium
 
   [ Andreas Tille ]
   * d/watch: version=5
+  * Build with libseqan2 2.5
+    Closes: #1125645
 
  -- Andreas Tille <tille at debian.org>  Tue, 28 Apr 2026 22:11:26 +0200
 


=====================================
debian/patches/libseqan2.5.patch
=====================================
@@ -0,0 +1,137 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: 2026-04-30
+Bug-Debian: https://bugs.debian.org/1125645
+Description: Build with libseqan2 2.5
+
+--- a/src/search_algo.hpp
++++ b/src/search_algo.hpp
+@@ -38,6 +38,13 @@
+ 
+ #include <seqan/align_extend.h>
+ 
++// SeqAn 2.5 renamed the namespace from 'seqan' to 'seqan2'.
++// Provide a backward-compatibility alias for older code.
++#include <seqan/version.h>
++#if defined(SEQAN_VERSION_MINOR) && SEQAN_VERSION_MINOR >= 5
++namespace seqan = seqan2;
++#endif
++
+ using namespace seqan;
+ 
+ // ============================================================================
+--- a/src/search_misc.hpp
++++ b/src/search_misc.hpp
+@@ -24,6 +24,13 @@
+ 
+ #include <vector>
+ 
++// SeqAn 2.5 renamed the namespace from 'seqan' to 'seqan2'.
++// Provide a backward-compatibility alias for older code.
++#include <seqan/version.h>
++#if defined(SEQAN_VERSION_MINOR) && SEQAN_VERSION_MINOR >= 5
++namespace seqan = seqan2;
++#endif
++
+ using namespace seqan;
+ 
+ // ============================================================================
+--- a/src/shared_definitions.hpp
++++ b/src/shared_definitions.hpp
+@@ -25,6 +25,13 @@
+ #include <seqan/index.h>
+ #include <seqan/blast.h>
+ 
++// SeqAn 2.5 renamed the namespace from 'seqan' to 'seqan2'.
++// Provide a backward-compatibility alias for older code.
++#include <seqan/version.h>
++#if defined(SEQAN_VERSION_MINOR) && SEQAN_VERSION_MINOR >= 5
++namespace seqan = seqan2;
++#endif
++
+ using namespace seqan;
+ 
+ // ==========================================================================
+@@ -60,7 +67,7 @@ using SizeTypePos_ = typename SizeTypePo
+ 
+ 
+ // suffix array overloads
+-namespace seqan
++namespace seqan2
+ {
+ 
+ template<typename TSpec1, typename TSpec2, typename TSpec3>
+--- a/src/shared_options.hpp
++++ b/src/shared_options.hpp
+@@ -32,6 +32,13 @@
+ #include <seqan/index.h>
+ #include <seqan/blast.h>
+ 
++// SeqAn 2.5 renamed the namespace from 'seqan' to 'seqan2'.
++// Provide a backward-compatibility alias for older code.
++#include <seqan/version.h>
++#if defined(SEQAN_VERSION_MINOR) && SEQAN_VERSION_MINOR >= 5
++namespace seqan = seqan2;
++#endif
++
+ using namespace seqan;
+ 
+ // ==========================================================================
+--- a/src/mkindex_algo.hpp
++++ b/src/mkindex_algo.hpp
+@@ -36,6 +36,13 @@
+ #include "shared_options.hpp"
+ #include "search_output.hpp" //TODO only needed because options are in one file, remove later
+ 
++// SeqAn 2.5 renamed the namespace from 'seqan' to 'seqan2'.
++// Provide a backward-compatibility alias for older code.
++#include <seqan/version.h>
++#if defined(SEQAN_VERSION_MINOR) && SEQAN_VERSION_MINOR >= 5
++namespace seqan = seqan2;
++#endif
++
+ using namespace seqan;
+ 
+ // --------------------------------------------------------------------------
+--- a/src/mkindex_options.hpp
++++ b/src/mkindex_options.hpp
+@@ -33,6 +33,13 @@
+ #include <seqan/index.h>
+ #include <seqan/blast.h>
+ 
++// SeqAn 2.5 renamed the namespace from 'seqan' to 'seqan2'.
++// Provide a backward-compatibility alias for older code.
++#include <seqan/version.h>
++#if defined(SEQAN_VERSION_MINOR) && SEQAN_VERSION_MINOR >= 5
++namespace seqan = seqan2;
++#endif
++
+ using namespace seqan;
+ 
+ // --------------------------------------------------------------------------
+--- a/src/shared_misc.hpp
++++ b/src/shared_misc.hpp
+@@ -37,6 +37,13 @@
+ #include <seqan/align.h>
+ #include <seqan/blast.h>
+ 
++// SeqAn 2.5 renamed the namespace from 'seqan' to 'seqan2'.
++// Provide a backward-compatibility alias for older code.
++#include <seqan/version.h>
++#if defined(SEQAN_VERSION_MINOR) && SEQAN_VERSION_MINOR >= 5
++namespace seqan = seqan2;
++#endif
++
+ using namespace seqan;
+ 
+ // ============================================================================
+--- a/src/mkindex_saca.hpp
++++ b/src/mkindex_saca.hpp
+@@ -49,7 +49,7 @@
+ #endif
+ //TODO(h-2): for clang use std::experimenta::parallel if available
+ 
+-namespace seqan
++namespace seqan2
+ {
+ 
+ // ==========================================================================


=====================================
debian/patches/series
=====================================
@@ -3,3 +3,4 @@ set-seqan-cmake-dir.patch
 force-link-rt-pthread.patch
 0006-Fix-binaries-not-being-installed-on-non-amd64-archs.patch
 cmake-4.patch
+libseqan2.5.patch



View it on GitLab: https://salsa.debian.org/med-team/lambda-align2/-/commit/28202989b96fe5d085485d8b1c83bf120244b48b

-- 
View it on GitLab: https://salsa.debian.org/med-team/lambda-align2/-/commit/28202989b96fe5d085485d8b1c83bf120244b48b
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