[med-svn] [Git][med-team/porechop][master] 15 commits: Team upload.
Andreas Tille (@tille)
gitlab at salsa.debian.org
Tue May 5 06:57:38 BST 2026
Andreas Tille pushed to branch master at Debian Med / porechop
Commits:
06d9a5a4 by Enrico Seiler at 2024-11-27T14:28:41+01:00
Team upload.
* Team upload.
* d/control: Experimental rebuild using the 3rd release candidate of
SeqAn 2.5.0
- - - - -
9bc33181 by Enrico Seiler at 2024-11-27T14:31:52+01:00
Added patch for the explicit seqan2 namespace.
- - - - -
c89889eb by Enrico Seiler at 2024-11-27T14:52:55+01:00
ready for uploading to experimental
- - - - -
7751992c by Michael R. Crusoe at 2024-11-27T17:05:07+01:00
Added patch for CPPFLAGS & LDFLAGS
- - - - -
2f53db8f by Andreas Tille at 2024-12-08T21:05:58+01:00
Fix Python3.12 string syntax Closes: #1085786
- - - - -
7bb467bd by Andreas Tille at 2024-12-08T21:07:16+01:00
Build-Depends: s/dh-python/dh-sequence-python3/
- - - - -
d6a8bc53 by Andreas Tille at 2024-12-08T21:08:09+01:00
Upload to exprimental
- - - - -
89e4da36 by Andreas Tille at 2026-05-05T07:35:28+02:00
Standards-Version: 4.7.4 (routine-update)
- - - - -
6c3fc025 by Andreas Tille at 2026-05-05T07:40:24+02:00
Changes made by cme
- - - - -
4e17ace3 by Andreas Tille at 2026-05-05T07:40:25+02:00
Drop default 'Rules-Requires-Root: no' from d/control (routine- update)
- - - - -
6c413dcc by Andreas Tille at 2026-05-05T07:43:35+02:00
No versioned Build-Depends
- - - - -
f3b0eb6f by Andreas Tille at 2026-05-05T07:51:17+02:00
SeqAn-2.5.0 patch from experimental Closes #1126095
- - - - -
c8bce2b5 by Andreas Tille at 2026-05-05T07:52:55+02:00
DEP3 dates
- - - - -
5e44456e by Andreas Tille at 2026-05-05T07:55:38+02:00
d/watch: version=5
- - - - -
03a1e696 by Andreas Tille at 2026-05-05T07:56:25+02:00
Upload to unstable
- - - - -
11 changed files:
- debian/changelog
- debian/control
- + debian/patches/0004-Upgrade-to-SeqAn-2.5.0.patch
- debian/patches/add_python_interpreter_line.patch
- debian/patches/define-all-attribute-in-clean.patch
- + debian/patches/hardening
- debian/patches/no_soname.patch
- + debian/patches/python3.12-syntax.patch
- debian/patches/series
- debian/rules
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,37 @@
+porechop (0.2.4+dfsg-9) unstable; urgency=medium
+
+ * Standards-Version: 4.7.4 (routine-update)
+ * Reflow Uploaders field (cme)
+ * Remove Priority field (cme)
+ * Drop default 'Rules-Requires-Root: no' from d/control (routine-
+ update)
+ * SeqAn-2.5.0 patch from experimental Closes: #1126095
+ * DEP3 dates
+ * d/watch: version=5
+
+ -- Andreas Tille <tille at debian.org> Tue, 05 May 2026 07:55:42 +0200
+
+porechop (0.2.4+dfsg-8) experimental; urgency=medium
+
+ * Fix Python3.12 string syntax
+ Closes: #1085786
+ * Build-Depends: s/dh-python/dh-sequence-python3/
+
+ -- Andreas Tille <tille at debian.org> Sun, 08 Dec 2024 21:07:46 +0100
+
+porechop (0.2.4+dfsg-7) experimental; urgency=medium
+
+ [ Enrico Seiler ]
+ * Team upload.
+ * d/control: Experimental rebuild using the 3rd release candidate of
+ SeqAn 2.5.0
+ * Added patch for the explicit seqan2 namespace.
+
+ [ Michael R. Crusoe ]
+ * Added patch for CPPFLAGS & LDFLAGS
+
+ -- Enrico Seiler <enrico.seiler.debian at outlook.com> Wed, 27 Nov 2024 14:52:55 +0100
+
porechop (0.2.4+dfsg-6) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -1,25 +1,26 @@
Source: porechop
+Standards-Version: 4.7.4
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Cédric Lood <cedric.lood at kuleuven.be>,
- Andreas Tille <tille at debian.org>
+Uploaders:
+ Cédric Lood <cedric.lood at kuleuven.be>,
+ Andreas Tille <tille at debian.org>,
Section: science
-Priority: optional
-Build-Depends: debhelper-compat (= 13),
- dh-python,
- libseqan2-dev,
- python3-dev,
- python3-setuptools
-Standards-Version: 4.7.0
-Rules-Requires-Root: no
+Build-Depends:
+ debhelper-compat (= 13),
+ dh-sequence-python3,
+ libseqan2-dev,
+ python3-dev,
+ python3-setuptools,
Vcs-Browser: https://salsa.debian.org/med-team/porechop
Vcs-Git: https://salsa.debian.org/med-team/porechop.git
Homepage: https://rrwick.github.io/Porechop
Package: porechop
Architecture: any
-Depends: ${misc:Depends},
- ${python3:Depends},
- ${shlibs:Depends}
+Depends:
+ ${misc:Depends},
+ ${python3:Depends},
+ ${shlibs:Depends},
Description: adapter trimmer for Oxford Nanopore reads
Porechop is a tool for finding and removing adapters from Oxford
Nanopore reads. Adapters on the ends of reads are trimmed off, and
=====================================
debian/patches/0004-Upgrade-to-SeqAn-2.5.0.patch
=====================================
@@ -0,0 +1,50 @@
+From: Enrico Seiler <enrico.seiler.debian at outlook.com>
+Last-Update: 2024-11-27
+Subject: Upgrade to SeqAn 2.5.0.
+Bug-Debian: https://bugs.debian.org/1126095
+
+---
+ Makefile | 2 +-
+ porechop/include/adapter_align.h | 2 +-
+ porechop/include/alignment.h | 2 +-
+ 3 files changed, 3 insertions(+), 3 deletions(-)
+
+diff --git a/Makefile b/Makefile
+index b1b9e23..a2ebf09 100644
+--- a/Makefile
++++ b/Makefile
+@@ -14,7 +14,7 @@ CXX ?= g++
+ CXXFLAGS ?= -Wall -Wextra -pedantic -mtune=native
+
+ # These flags are required for the build to work.
+-FLAGS = -std=c++14 -Iporechop/include -fPIC
++FLAGS = -std=c++17 -Iporechop/include -fPIC
+ LDFLAGS = -shared
+
+ # Different debug/optimisation levels for debug/release builds.
+diff --git a/porechop/include/adapter_align.h b/porechop/include/adapter_align.h
+index d0f8497..e79c94b 100644
+--- a/porechop/include/adapter_align.h
++++ b/porechop/include/adapter_align.h
+@@ -6,7 +6,7 @@
+ #include <vector>
+ #include "alignment.h"
+
+-using namespace seqan;
++using namespace seqan2;
+
+ // Functions that are called by the Python script must have C linkage, not C++ linkage.
+ extern "C" {
+diff --git a/porechop/include/alignment.h b/porechop/include/alignment.h
+index 90305b5..fb1949b 100644
+--- a/porechop/include/alignment.h
++++ b/porechop/include/alignment.h
+@@ -7,7 +7,7 @@
+ #include <seqan/basic.h>
+ #include <seqan/align.h>
+
+-using namespace seqan;
++using namespace seqan2;
+
+
+ class ScoredAlignment {
=====================================
debian/patches/add_python_interpreter_line.patch
=====================================
@@ -1,7 +1,14 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Sun, 26 Aug 2018 19:57:42 +0200
-Description: Add interpreter line
+From: Andreas Tille <tille at debian.org>
+Date: Sun, 26 Aug 2018 19:59:45 +0200
+Subject: Add interpreter line
+Last-Update: 2018-08-26
+---
+ porechop/porechop.py | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/porechop/porechop.py b/porechop/porechop.py
+index 25febe6..2d79988 100755
--- a/porechop/porechop.py
+++ b/porechop/porechop.py
@@ -1,3 +1,4 @@
=====================================
debian/patches/define-all-attribute-in-clean.patch
=====================================
@@ -1,12 +1,21 @@
-Description: Define that attribute like distutils.command.clean.initialize_options
- Not sure what requires it, but everything is nicer with it...
-Author: Mattia Rizzolo <mattia at debian.org>
+From: Mattia Rizzolo <mattia at debian.org>
+Last-Update: 2018-09-28
+Subject: Define that attribute like
+ distutils.command.clean.initialize_options
+
Bug-Debian: https://bugs.debian.org/909761
Forwarded: no
+Not sure what requires it, but everything is nicer with it...
+---
+ setup.py | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/setup.py b/setup.py
+index 0b03c32..044c16b 100755
--- a/setup.py
+++ b/setup.py
-@@ -78,6 +78,7 @@
+@@ -78,6 +78,7 @@ class PorechopClean(Command):
def initialize_options(self):
self.cwd = None
=====================================
debian/patches/hardening
=====================================
@@ -0,0 +1,28 @@
+From: Michael R. Crusoe <crusoe at debian.org>
+Subject: Enable user-supplied LDFLAGS and CPPFLAGS
+--- porechop.orig/Makefile
++++ porechop/Makefile
+@@ -15,7 +15,7 @@
+
+ # These flags are required for the build to work.
+ FLAGS = -std=c++17 -Iporechop/include -fPIC
+-LDFLAGS = -shared
++LDFLAGS += -shared
+
+ # Different debug/optimisation levels for debug/release builds.
+ DEBUGFLAGS = -DSEQAN_ENABLE_DEBUG=1 -g
+@@ -44,7 +44,7 @@
+ debug: $(TARGET)
+
+ $(TARGET): $(OBJECTS)
+- $(CXX) $(FLAGS) $(CXXFLAGS) $(LDFLAGS) -o $(TARGET) $(OBJECTS)
++ $(CXX) $(FLAGS) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $(TARGET) $(OBJECTS)
+
+ clean:
+ $(RM) $(OBJECTS)
+@@ -53,4 +53,4 @@
+ $(RM) $(TARGET)
+
+ %.o: %.cpp $(HEADERS)
+- $(CXX) $(FLAGS) $(CXXFLAGS) -c -o $@ $<
++ $(CXX) $(FLAGS) $(CPPFLAGS) $(CXXFLAGS) -c -o $@ $<
=====================================
debian/patches/no_soname.patch
=====================================
@@ -1,8 +1,15 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Sun, 26 Aug 2018 19:57:42 +0200
+From: Andreas Tille <tille at debian.org>
+Date: Mon, 27 Aug 2018 10:46:57 +0200
+Subject: Do not set soname
+
+Last-Update: 2018-08-26
Origin: https://lists.debian.org/debian-python/2018/08/msg00113.html
-Description: Do not set soname
+---
+ Makefile | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+diff --git a/Makefile b/Makefile
+index 26f0540..b1b9e23 100644
--- a/Makefile
+++ b/Makefile
@@ -44,7 +44,7 @@ debug: FLAGS+=$(DEBUGFLAGS)
=====================================
debian/patches/python3.12-syntax.patch
=====================================
@@ -0,0 +1,16 @@
+Description: Fix Python3.12 string syntax
+Bug-Debian: https://bugs.debian.org/1085786
+Author: Andreas Tille <tille at debian.org>
+Last-Update: 2024-06-08
+
+--- a/porechop/misc.py
++++ b/porechop/misc.py
+@@ -258,7 +258,7 @@ def print_table(table, print_dest, align
+ for text, colour_name in sub_colour.items():
+ row_str = row_str.replace(text, colour(text, colour_name))
+ if j < row_rows - 1 and UNDERLINE in row_str:
+- row_str = re.sub('\033\[4m', '', row_str)
++ row_str = re.sub(r'\033\[4m', '', row_str)
+ if return_str:
+ full_table_str += indenter + row_str + '\n'
+ else:
=====================================
debian/patches/series
=====================================
@@ -1,3 +1,6 @@
add_python_interpreter_line.patch
no_soname.patch
define-all-attribute-in-clean.patch
+0004-Upgrade-to-SeqAn-2.5.0.patch
+hardening
+python3.12-syntax.patch
=====================================
debian/rules
=====================================
@@ -8,7 +8,7 @@ export DEB_BUILD_MAINT_OPTIONS=hardening=+all
export PYBUILD_DISABLE=test
%:
- dh $@ --with python3 --buildsystem pybuild
+ dh $@ --buildsystem pybuild
override_dh_python3:
dh_python3 --no-ext-rename
=====================================
debian/watch
=====================================
@@ -1,6 +1,7 @@
-version=4
-
-# github - new files
-opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
- https://github.com/rrwick/Porechop/tags .*/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
+Version: 5
+Template: Github
+Owner: rrwick
+Project: Porechop
+Dversion-Mangle: auto
+Repack-Suffix: +dfsg
View it on GitLab: https://salsa.debian.org/med-team/porechop/-/compare/4e0873727f113ff6baf8503ceafc11a76cf183dd...03a1e696078cb6266637dea64b7e80f51d3d4271
--
View it on GitLab: https://salsa.debian.org/med-team/porechop/-/compare/4e0873727f113ff6baf8503ceafc11a76cf183dd...03a1e696078cb6266637dea64b7e80f51d3d4271
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