[med-svn] [Git][med-team/sibelia][master] 6 commits: Added patch for the explicit seqan2 namespace.
Michael R. Crusoe (@crusoe)
gitlab at salsa.debian.org
Sat Jan 24 18:51:00 GMT 2026
Michael R. Crusoe pushed to branch master at Debian Med / sibelia
Commits:
575c7471 by Michael R. Crusoe at 2026-01-24T19:21:32+01:00
Added patch for the explicit seqan2 namespace.
Closes: #1125659
- - - - -
373f1e8e by Michael R. Crusoe at 2026-01-24T19:24:44+01:00
Lintian tag adjustment
- - - - -
6adc7501 by Michael R. Crusoe at 2026-01-24T19:24:47+01:00
Standards-Version: 4.7.3 (routine-update)
- - - - -
44614f9d by Michael R. Crusoe at 2026-01-24T19:25:02+01:00
Use secure URI in Homepage field.
Changes-By: lintian-brush
Fixes: lintian: homepage-field-uses-insecure-uri
See-also: https://lintian.debian.org/tags/homepage-field-uses-insecure-uri.html
- - - - -
06718818 by Michael R. Crusoe at 2026-01-24T19:25:37+01:00
Apply multi-arch hints.
+ sibelia-examples: Add Multi-Arch: foreign.
Changes-By: apply-multiarch-hints
- - - - -
5b0dfb97 by Michael R. Crusoe at 2026-01-24T19:28:15+01:00
routine-update: Ready to upload to unstable
- - - - -
11 changed files:
- debian/changelog
- debian/control
- + debian/patches/0005-Upgrade-to-SeqAn-2.5.0.patch
- debian/patches/2to3.patch
- debian/patches/series
- debian/patches/snpeff_is_removed.patch
- debian/patches/use_debian_packaged_lagan.patch
- debian/patches/use_debian_packaged_libdivsufsort.patch
- debian/sibelia-annotate.lintian-overrides
- debian/sibelia.lintian-overrides
- − debian/source/lintian-overrides
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,15 @@
+sibelia (3.0.7+dfsg-6) unstable; urgency=medium
+
+ * Team upload.
+ * Added patch for SeqAn2 2.5.0 support. Closes: #1125659
+ * Lintian tag adjustment
+ * Standards-Version: 4.7.3 (routine-update)
+ * Use secure URI in Homepage field.
+ * Apply multi-arch hints:
+ sibelia-examples: Add Multi-Arch: foreign.
+
+ -- Michael R. Crusoe <crusoe at debian.org> Sat, 24 Jan 2026 19:23:22 +0100
+
sibelia (3.0.7+dfsg-5) unstable; urgency=medium
* Fix build with CMake 4
=====================================
debian/control
=====================================
@@ -1,5 +1,5 @@
Source: sibelia
-Standards-Version: 4.7.2
+Standards-Version: 4.7.3
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders:
Andreas Tille <tille at debian.org>,
@@ -15,7 +15,7 @@ Build-Depends:
libhts-dev,
Vcs-Browser: https://salsa.debian.org/med-team/sibelia
Vcs-Git: https://salsa.debian.org/med-team/sibelia.git
-Homepage: http://bioinf.spbau.ru/sibelia
+Homepage: https://bioinf.spbau.ru/sibelia
Rules-Requires-Root: no
Package: sibelia
@@ -60,3 +60,4 @@ Description: comparative genomics tool (example data)
3) rearrangements that transform one genome to other genomes.
.
This package contains example data for sibelia.
+Multi-Arch: foreign
=====================================
debian/patches/0005-Upgrade-to-SeqAn-2.5.0.patch
=====================================
@@ -0,0 +1,21 @@
+From: "Michael R. Crusoe" <crusoe at debian.org>
+Date: Mon, 25 Nov 2024 15:16:31 +0100
+Subject: Upgrade to SeqAn 2.5.0.
+
+---
+ src/postprocessor.cpp | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/src/postprocessor.cpp b/src/postprocessor.cpp
+index fa52a7c..11b605a 100644
+--- a/src/postprocessor.cpp
++++ b/src/postprocessor.cpp
+@@ -256,7 +256,7 @@ namespace SyntenyFinder
+
+ void Postprocessor::LocalAlignment(const std::string & sequence1, const std::string & sequence2, std::pair<size_t, size_t> & coord1, std::pair<size_t, size_t> & coord2)
+ {
+- using namespace seqan;
++ using namespace seqan2;
+ typedef String<char> TSequence; // sequence type
+ typedef Align<TSequence, ArrayGaps> TAlign; // align type
+ typedef Row<TAlign>::Type TRow;
=====================================
debian/patches/2to3.patch
=====================================
@@ -1,7 +1,15 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Sun, 26 Jan 2020 20:50:21 +0100
-Description: Use 2to3 to port to Python3
+From: Andreas Tille <tille at debian.org>
+Date: Sun, 26 Jan 2020 20:51:50 +0100
+Subject: Use 2to3 to port to Python3
+Last-Update: 2024-11-25
+---
+ src/annotation/snpEffAnnotate.py | 10 +++----
+ src/csibelia/C-Sibelia.py | 58 ++++++++++++++++++++--------------------
+ 2 files changed, 34 insertions(+), 34 deletions(-)
+
+diff --git a/src/annotation/snpEffAnnotate.py b/src/annotation/snpEffAnnotate.py
+index 0d1b646..a98e3e1 100644
--- a/src/annotation/snpEffAnnotate.py
+++ b/src/annotation/snpEffAnnotate.py
@@ -1,4 +1,4 @@
@@ -39,6 +47,8 @@ Description: Use 2to3 to port to Python3
sys.exit(-1)
dest_file = open(FILENAME, "w")
+diff --git a/src/csibelia/C-Sibelia.py b/src/csibelia/C-Sibelia.py
+index ebf1db5..7a3369d 100644
--- a/src/csibelia/C-Sibelia.py
+++ b/src/csibelia/C-Sibelia.py
@@ -1,4 +1,4 @@
@@ -74,7 +84,7 @@ Description: Use 2to3 to port to Python3
if (not reference_instance is None) and (not assembly_instance is None):
reference_size = get_size(reference_instance)
assembly_size = get_size(assembly_instance)
-@@ -326,9 +326,9 @@ def depict_coverage(block_seq, reference
+@@ -326,9 +326,9 @@ def depict_coverage(block_seq, reference_seq, assembly_seq, base_cover):
if base_cover is None:
base_cover = dict()
for seq_group in (reference_seq, assembly_seq):
@@ -86,7 +96,7 @@ Description: Use 2to3 to port to Python3
reference = [instance for instance in instance_list if instance.chr_id in reference_seq]
if reference and len(reference) < len(instance_list):
for instance in instance_list:
-@@ -348,7 +348,7 @@ def call_variants(directory, genomes, re
+@@ -348,7 +348,7 @@ def call_variants(directory, genomes, reference_seq, assembly_seq, min_block_siz
blocks_coords = [parse_blocks_coords(file_name, genomes) for file_name in coords_file_list]
pool = multiprocessing.Pool(proc_num)
annotated_block = []
@@ -95,7 +105,7 @@ Description: Use 2to3 to port to Python3
unique = False
if len(instance_list) == 2:
reference_instance, assembly_instance = determine_unique_block(instance_list, reference_seq, min_block_size)
-@@ -377,7 +377,7 @@ def call_variants(directory, genomes, re
+@@ -377,7 +377,7 @@ def call_variants(directory, genomes, reference_seq, assembly_seq, min_block_siz
main_cover = depict_coverage(block_seq, reference_seq, assembly_seq, None)
insertion = []
os.chdir('..')
@@ -104,7 +114,7 @@ Description: Use 2to3 to port to Python3
i = 0
while i < len(cover):
if cover[i] == UNCOVER:
-@@ -428,20 +428,20 @@ def call_variants(directory, genomes, re
+@@ -428,20 +428,20 @@ def call_variants(directory, genomes, reference_seq, assembly_seq, min_block_siz
def generate_conventional_output(variant_list, handle):
for variant in variant_list:
@@ -132,7 +142,7 @@ Description: Use 2to3 to port to Python3
def write_insertions_vcf(variant_list, reference_organism, handle):
ref_len = str(len(reference_organism.seq))
-@@ -460,35 +460,35 @@ def write_insertions_vcf(variant_list, r
+@@ -460,35 +460,35 @@ def write_insertions_vcf(variant_list, reference_organism, handle):
start_record = [reference_chr, ref_pos, start_bnd, ref_allele, start_alt_allele, '.', '.', info]
end_record = [reference_chr, ref_pos, end_bnd, ref_allele, end_alt_allele, '.', '.', info]
for record in (start_record, end_record):
=====================================
debian/patches/series
=====================================
@@ -2,3 +2,4 @@ use_debian_packaged_libdivsufsort.patch
use_debian_packaged_lagan.patch
snpeff_is_removed.patch
2to3.patch
+0005-Upgrade-to-SeqAn-2.5.0.patch
=====================================
debian/patches/snpeff_is_removed.patch
=====================================
@@ -1,7 +1,16 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Thu, 14 Feb 2019 14:52:05 +0100
-Description: snpEff is removed - see README.Debian
+From: Andreas Tille <tille at debian.org>
+Date: Fri, 15 Feb 2019 09:57:55 +0100
+Subject: snpEff is removed - see README.Debian
+Forwarded: not-needed
+
+Last-Update: 2024-11-25
+---
+ src/CMakeLists.txt | 2 --
+ 1 file changed, 2 deletions(-)
+
+diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
+index f72674d..44edbb3 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -28,8 +28,6 @@ else()
=====================================
debian/patches/use_debian_packaged_lagan.patch
=====================================
@@ -1,7 +1,17 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Thu, 14 Feb 2019 14:52:05 +0100
-Description: Use Debian packaged lagan
+From: Andreas Tille <tille at debian.org>
+Date: Thu, 14 Feb 2019 15:44:16 +0100
+Subject: Use Debian packaged lagan
+Forwarded: not-needed
+
+Last-Update: 2024-11-25
+---
+ src/CMakeLists.txt | 2 --
+ src/csibelia/C-Sibelia.py | 2 +-
+ 2 files changed, 1 insertion(+), 3 deletions(-)
+
+diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
+index bbac8ab..f72674d 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -27,8 +27,6 @@ else()
@@ -13,6 +23,8 @@ Description: Use Debian packaged lagan
install(PROGRAMS csibelia/C-Sibelia.py DESTINATION bin)
install(PROGRAMS annotation/snpEffAnnotate.py DESTINATION bin)
install(DIRECTORY annotation/snpEff DESTINATION ${LIB_DIR})
+diff --git a/src/csibelia/C-Sibelia.py b/src/csibelia/C-Sibelia.py
+index f1beee2..ebf1db5 100644
--- a/src/csibelia/C-Sibelia.py
+++ b/src/csibelia/C-Sibelia.py
@@ -20,7 +20,7 @@ LINE_LENGTH = 60
=====================================
debian/patches/use_debian_packaged_libdivsufsort.patch
=====================================
@@ -1,7 +1,16 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Thu, 14 Feb 2019 14:52:05 +0100
-Description: Use Debian packaged libdivsufsort
+From: Andreas Tille <tille at debian.org>
+Date: Thu, 14 Feb 2019 15:44:16 +0100
+Subject: Use Debian packaged libdivsufsort
+Forwarded: not-needed
+
+Last-Update: 2024-11-25
+---
+ src/CMakeLists.txt | 3 +--
+ 1 file changed, 1 insertion(+), 2 deletions(-)
+
+diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
+index 98f3105..bbac8ab 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -1,13 +1,12 @@
=====================================
debian/sibelia-annotate.lintian-overrides
=====================================
@@ -1,4 +1,4 @@
# see https://lists.debian.org/debian-med/2018/06/msg00043.html
-sibelia-annotate: script-with-language-extension usr/bin/*.*
+sibelia-annotate: script-with-language-extension [usr/bin/*.*]
# this file should not be there in an official package - so just ignore the wrong place for now
-sibelia-annotate: jar-not-in-usr-share usr/lib/Sibelia/snpEff/snpEff.jar
+sibelia-annotate: jar-not-in-usr-share [usr/lib/Sibelia/snpEff/snpEff.jar]
=====================================
debian/sibelia.lintian-overrides
=====================================
@@ -1,2 +1,2 @@
# see https://lists.debian.org/debian-med/2018/06/msg00043.html
-sibelia: script-with-language-extension usr/bin/*.*
+sibelia: script-with-language-extension [usr/bin/*.*]
=====================================
debian/source/lintian-overrides deleted
=====================================
@@ -1,2 +0,0 @@
-# false positive
-sibelia source: source-is-missing examples/Sibelia/Staphylococcus_aureus/d3_blocks_diagram.html line length is *
View it on GitLab: https://salsa.debian.org/med-team/sibelia/-/compare/97b1d4b946b892c7922214bc3fa73fcc2678874c...5b0dfb97453138c74beb8f99de8ccb4601a26ee6
--
View it on GitLab: https://salsa.debian.org/med-team/sibelia/-/compare/97b1d4b946b892c7922214bc3fa73fcc2678874c...5b0dfb97453138c74beb8f99de8ccb4601a26ee6
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