[med-svn] [Git][med-team/jellyfish][master] 3 commits: Forwarded several patches upstream.
Michael R. Crusoe (@crusoe)
gitlab at salsa.debian.org
Wed Feb 28 14:09:39 GMT 2024
Michael R. Crusoe pushed to branch master at Debian Med / jellyfish
Commits:
c4d23a8e by Michael R. Crusoe at 2024-02-28T15:08:39+01:00
Forwarded several patches upstream.
- - - - -
cc13c3ee by Michael R. Crusoe at 2024-02-28T15:08:41+01:00
debian/patches/fix_catch.patch is no longer used, remove it.
- - - - -
00416ec9 by Michael R. Crusoe at 2024-02-28T15:08:41+01:00
Point to the Jellyfish 2.0 homepage
- - - - -
8 changed files:
- debian/changelog
- debian/control
- debian/copyright
- − debian/patches/fix_catch.patch
- debian/patches/manpage_whatis_entry.patch
- debian/patches/python3
- debian/patches/series
- debian/patches/test_needs_bash
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+jellyfish (2.3.1-3) UNRELEASED; urgency=medium
+
+ * Forwarded several patches upstream.
+ * debian/patches/fix_catch.patch is no longer used, remove it.
+ * Point to the Jellyfish 2.0 homepage
+
+ -- Michael R. Crusoe <crusoe at debian.org> Wed, 28 Feb 2024 14:57:36 +0100
+
jellyfish (2.3.1-2.1) unstable; urgency=medium
* Non-maintainer upload.
=====================================
debian/control
=====================================
@@ -25,7 +25,7 @@ Build-Depends: dpkg-dev (>= 1.22.5), debhelper-compat (= 13),
Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/jellyfish
Vcs-Git: https://salsa.debian.org/med-team/jellyfish.git
-Homepage: https://github.com/gmarcais/Jellyfish
+Homepage: https://www.genome.umd.edu/jellyfish.html
Rules-Requires-Root: no
Package: jellyfish
=====================================
debian/copyright
=====================================
@@ -1,7 +1,7 @@
Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: JELLYFISH
Upstream-Contact: Guillaume Marçais <gmarcais at umd.edu>
-Source: http://www.cbcb.umd.edu/software/jellyfish/
+Source: http://www.genome.umd.edu/jellyfish.html
Files: *
Copyright: Copyright 2011-2014 Guillaume Marçais1, Carl Kingsford
=====================================
debian/patches/fix_catch.patch deleted
=====================================
@@ -1,58 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Mon, 03 Sep 2018 08:34:22 +0200
-Description: Catch exceptions by reference
- see https://blog.knatten.org/2010/04/02/always-catch-exceptions-by-referenc
-
---- a/sub_commands/count_main.cc
-+++ b/sub_commands/count_main.cc
-@@ -360,7 +360,7 @@ int count_main(int argc, char *argv[])
- uint64_t max = args.upper_count_given ? args.upper_count_arg : std::numeric_limits<uint64_t>::max();
- try {
- merge_files(files, args.output_arg, header, min, max);
-- } catch(MergeError e) {
-+ } catch(MergeError &e) {
- err::die(err::msg() << e.what());
- }
- if(!args.no_unlink_flag) {
---- a/include/jellyfish/hash_counter.hpp
-+++ b/include/jellyfish/hash_counter.hpp
-@@ -213,7 +213,7 @@ protected:
- new_ary_ = new array(ary_->size(), ary_->key_len(), ary_->val_len() + 1,
- ary_->max_reprobe(), ary_->reprobes());
- }
-- } catch(typename array::ErrorAllocation e) {
-+ } catch(typename array::ErrorAllocation &e) {
- new_ary_ = 0;
- }
- }
---- a/sub_commands/merge_main.cc
-+++ b/sub_commands/merge_main.cc
-@@ -33,7 +33,7 @@ int merge_main(int argc, char *argv[])
-
- try {
- merge_files(args.input_arg, args.output_arg, out_header, min, max);
-- } catch(MergeError e) {
-+ } catch(MergeError &e) {
- err::die(err::msg() << e.what());
- }
-
---- a/sub_commands/query_main.cc
-+++ b/sub_commands/query_main.cc
-@@ -60,7 +60,7 @@ void query_from_cmdline(std::vector<cons
- if(canonical)
- m.canonicalize();
- out << m << " " << db.check(m) << "\n";
-- } catch(std::length_error e) {
-+ } catch(std::length_error &e) {
- std::cerr << "Invalid mer '" << *it << "'\n";
- }
- }
-@@ -77,7 +77,7 @@ void query_from_stdin(const Database& db
- if(canonical)
- m.canonicalize();
- out << db.check(m) << std::endl; // a flush is need for interactive use
-- } catch(std::length_error e) {
-+ } catch(std::length_error &e) {
- std::cerr << "Invalid mer '" << buffer << "'" << std::endl;
- }
- }
=====================================
debian/patches/manpage_whatis_entry.patch
=====================================
@@ -1,6 +1,7 @@
-Author: Andreas Tille <tille at debian.org>
+From: Andreas Tille <tille at debian.org>
Last-Update: Mon, 28 Aug 2017 14:10:27 +0200
-Description: Fix whatis entry in manpage (also fix some spelling issues)
+Subject: Fix whatis entry in manpage (also fix some spelling issues)
+Forwarded: https://github.com/gmarcais/Jellyfish/pull/170
--- jellyfish.orig/doc/jellyfish.man
+++ jellyfish/doc/jellyfish.man
=====================================
debian/patches/python3
=====================================
@@ -1,5 +1,6 @@
-Author: Michael R. Crusoe <michael.crusoe at gmail.com>
+Author: Michael R. Crusoe <crusoe at debian.org>
Description: forcibly avoid the deprecated module name
+Forwarded: not-needed
--- jellyfish.orig/swig/Makefile.am
+++ jellyfish/swig/Makefile.am
@@ -20,11 +20,6 @@
=====================================
debian/patches/series
=====================================
@@ -1,7 +1,5 @@
manpage_whatis_entry.patch
portability.patch
-#Apparently fixed upstream
-#fix_catch.patch
test_needs_bash
python3
fix-32-bit.patch
=====================================
debian/patches/test_needs_bash
=====================================
@@ -1,5 +1,6 @@
-From: Michael R. Crusoe <michael.crusoe at gmail.com>
+From: Michael R. Crusoe <crusoe at debian.org>
Subject: small_mers needs bash
+Forwarded: https://github.com/gmarcais/Jellyfish/pull/172
Due to process substitution. Thanks to https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/jellyfish.html for highlighting this.
--- jellyfish.orig/tests/small_mers.sh
View it on GitLab: https://salsa.debian.org/med-team/jellyfish/-/compare/c323f160cb50390534010c77aa5efd1fdfbc126f...00416ec961a42f895939dd22ee638b9b4258a418
--
View it on GitLab: https://salsa.debian.org/med-team/jellyfish/-/compare/c323f160cb50390534010c77aa5efd1fdfbc126f...00416ec961a42f895939dd22ee638b9b4258a418
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