[med-svn] [Git][med-team/jellyfish][master] 5 commits: d/source/lintian-overrides: quiet false-positive from the t64 transition.

[Michael R. Crusoe (@crusoe)]

Michael R. Crusoe pushed to branch master at Debian Med / jellyfish


Commits:
8159ae52 by Michael R. Crusoe at 2024-03-07T12:37:16+01:00
d/source/lintian-overrides: quiet false-positive from the t64 transition.

- - - - -
d144ffbb by Michael R. Crusoe at 2024-03-07T12:43:31+01:00
d/patches/fix-32-bit.patch: forward upstream.

- - - - -
14a7089e by Michael R. Crusoe at 2024-03-07T12:54:48+01:00
d/patches/drop_distutils: upgrade to setuptools.

- - - - -
0a79eac0 by Michael R. Crusoe at 2024-03-07T12:54:48+01:00
d/control: s/pkg-config/pkgconf/g

- - - - -
f0d0f8cd by Michael R. Crusoe at 2024-03-07T13:05:46+01:00
debian/libjellyfish-2.0-2t64.lintian-overrides: silence another false-positive.

- - - - -


8 changed files:

- debian/changelog
- debian/control
- debian/libjellyfish-2.0-2t64.lintian-overrides
- + debian/patches/drop_distutils
- debian/patches/fix-32-bit.patch
- debian/patches/series
- + debian/source/lintian-overrides
- − swig/python/jellyfish.py


Changes:

=====================================
debian/changelog
=====================================
@@ -5,6 +5,13 @@ jellyfish (2.3.1-3) UNRELEASED; urgency=medium
   * Point to the Jellyfish 2.0 homepage
   * d/control: simplify architecture specifications by build-dep'ing on
     architecture-is-little-endian.
+  * d/source/lintian-overrides: quiet false-positive from the t64
+    transition.
+  * d/patches/fix-32-bit.patch: forward upstream.
+  * d/patches/drop_distutils: upgrade to setuptools.
+  * d/control: s/pkg-config/pkgconf/g
+  * debian/libjellyfish-2.0-2t64.lintian-overrides: silence another
+    false-positive.
 
  -- Michael R. Crusoe <crusoe at debian.org>  Wed, 28 Feb 2024 14:57:36 +0100
 


=====================================
debian/control
=====================================
@@ -11,13 +11,14 @@ Build-Depends: dpkg-dev (>= 1.22.5), debhelper-compat (= 13),
                d-shlibs (>= 0.106~),
                autoconf-archive,
                yaggo,
-               pkg-config,
+               pkgconf,
                bc,
                time,
                procps,
                swig,
                python3-all-dev,
                dh-sequence-python3,
+               python3-setuptools,
                perl,
                chrpath,
                libhts-dev,


=====================================
debian/libjellyfish-2.0-2t64.lintian-overrides
=====================================
@@ -1,3 +1,4 @@
 # Upstream decided to use a dynamic library without really intending to make this a development package
 libjellyfish-2.0-2t64: no-symbols-control-file usr/lib/*/libjellyfish-*.so.*
 libjellyfish-2.0-2t64: package-name-doesnt-match-sonames libjellyfish-2.0-2
+libjellyfish-2.0-2t64: conflicts-with-version libjellyfish-2.0-2 (<< 2.3.1-3)


=====================================
debian/patches/drop_distutils
=====================================
@@ -0,0 +1,14 @@
+From: Michael R. Crusoe <crusoe at debian.org>
+Subject: Convert another usage of distutils to setuptools
+Forwarded: https://github.com/gmarcais/Jellyfish/pull/203
+--- jellyfish.orig/swig/python/setup.py
++++ jellyfish/swig/python/setup.py
+@@ -9,7 +9,7 @@
+ import os
+ import sys
+ import re
+-from distutils.core import setup, Extension
++from setuptools import setup, Extension
+ 
+ def pkgconfig(s):
+     pipe = os.popen("pkg-config {}".format(s))


=====================================
debian/patches/fix-32-bit.patch
=====================================
@@ -1,6 +1,7 @@
 Date: Thu, 3 Dec 2020 04:05:11 +0530
 From: Nilesh Patra <npatra974 at gmail.com>
 Bug-Debian: https://bugs.debian.org/962184
+Forwarded: https://github.com/gmarcais/Jellyfish/pull/202
 Description: Enable build on 32bit architectures
 
 --- a/include/jellyfish/rectangular_binary_matrix.hpp


=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
+drop_distutils
 manpage_whatis_entry.patch
 portability.patch
 test_needs_bash


=====================================
debian/source/lintian-overrides
=====================================
@@ -0,0 +1,2 @@
+# this is fine, that "external" package used to come from this package
+jellyfish source: version-substvar-for-external-package Conflicts ${source:Version} libjellyfish-2.0-2t64 -> libjellyfish-2.0-2 [debian/control:56]


=====================================
swig/python/jellyfish.py deleted
=====================================
@@ -1,11 +0,0 @@
-#  This file is part of Jellyfish.
-#
-#  This work is dual-licensed under 3-Clause BSD License or GPL 3.0.
-#  You can choose between one of them if you use this work.
-#
-#  `SPDX-License-Identifier: BSD-3-Clause OR  GPL-3.0`
-
-import warnings
-
-warnings.warn("Module 'jellyfish' is deprecated. Use 'dna_jellyfish'", DeprecationWarning)
-import dna_jellyfish as jellyfish



View it on GitLab: https://salsa.debian.org/med-team/jellyfish/-/compare/2a1b898813195b6d387b2f51f73f3f48fa7c284c...f0d0f8cd740ba13aa933ccc5cea9471b5e08f130

-- 
View it on GitLab: https://salsa.debian.org/med-team/jellyfish/-/compare/2a1b898813195b6d387b2f51f73f3f48fa7c284c...f0d0f8cd740ba13aa933ccc5cea9471b5e08f130
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