[med-svn] [Git][med-team/kmer][master] 9 commits: Added patch to replace distutils with stdlib usage. Closes: #1080608
Michael R. Crusoe (@crusoe)
gitlab at salsa.debian.org
Tue Sep 10 10:28:46 BST 2024
Michael R. Crusoe pushed to branch master at Debian Med / kmer
Commits:
ad354796 by Michael R. Crusoe at 2024-09-10T10:33:55+02:00
Added patch to replace distutils with stdlib usage. Closes: #1080608
- - - - -
d6942a8c by Michael R. Crusoe at 2024-09-10T10:34:09+02:00
routine-update: Standards-Version: 4.6.2
- - - - -
60fdd236 by Michael R. Crusoe at 2024-09-10T10:34:10+02:00
routine-update: debhelper-compat 13
- - - - -
81848c44 by Michael R. Crusoe at 2024-09-10T10:34:16+02:00
routine-update: Build-Depends: s/dh-python/dh-sequence-python3/
- - - - -
76d0ba95 by Michael R. Crusoe at 2024-09-10T10:34:16+02:00
routine-update: No tab in license text
- - - - -
c93cc9fb by Michael R. Crusoe at 2024-09-10T10:34:22+02:00
Add missing build dependency on dh-python | dh-sequence-python3 for command dh_python3.
Changes-By: lintian-brush
Fixes: lintian: missing-build-dependency-for-dh_-command
See-also: https://lintian.debian.org/tags/missing-build-dependency-for-dh_-command.html
- - - - -
4c93e2ad by Michael R. Crusoe at 2024-09-10T10:39:39+02:00
small formatting tweaks
- - - - -
482bd230 by Michael R. Crusoe at 2024-09-10T11:20:54+02:00
d/rules: set -std=c++03 to reduce warnings
- - - - -
5afd1e89 by Michael R. Crusoe at 2024-09-10T11:20:55+02:00
routine-update: Ready to upload to unstable
- - - - -
6 changed files:
- debian/changelog
- debian/control
- debian/copyright
- + debian/patches/drop_distutils
- debian/patches/series
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,16 @@
+kmer (0~20150903+r2013-9) unstable; urgency=medium
+
+ * Team upload.
+ * Added patch to replace distutils with stdlib usage. Closes: #1080608
+ * Standards-Version: 4.6.2 (routine-update)
+ * debhelper-compat 13 (routine-update)
+ * Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update)
+ * No tab in license text (routine-update)
+ * Add missing build dependency on dh-python | dh-sequence-python3 for command dh_python3.
+ * d/rules: set -std=c++03 to reduce warnings
+
+ -- Michael R. Crusoe <crusoe at debian.org> Tue, 10 Sep 2024 10:35:03 +0200
+
kmer (0~20150903+r2013-8) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -3,12 +3,13 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Afif Elghraoui <afif at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper-compat (= 12),
+Build-Depends: debhelper-compat (= 13),
dh-exec,
# For ATAC
- dh-python,
- python3-dev
-Standards-Version: 4.5.0
+ dh-sequence-python3,
+ python3-dev,
+ dh-python | dh-sequence-python3
+Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/kmer
Vcs-Git: https://salsa.debian.org/med-team/kmer.git
Homepage: http://kmer.sourceforge.net
=====================================
debian/copyright
=====================================
@@ -19,8 +19,8 @@ License: RSA
Files: libutil/qsort_mt.c
Copyright:
- 1992-1993 Regents of the University of California
- 2006-2007 Diomidis Spinellis
+ 1992-1993 Regents of the University of California
+ 2006-2007 Diomidis Spinellis
License: BSD-3-Clause
Files: libutil/kazlib/*
@@ -33,7 +33,7 @@ License: BSD-3-Clause-Generic
Files: debian/*
Copyright:
- 2015-2016 Afif Elghraoui <afif at debian.org>
+ 2015-2016 Afif Elghraoui <afif at debian.org>
License: GPL-2+
Files: debian/tests/test-data/test_data.tar.gz
=====================================
debian/patches/drop_distutils
=====================================
@@ -0,0 +1,31 @@
+From: Michael R. Crusoe <crusoe at debian.org>
+Subject: Replace distutils.sysconfig with the stdlib sysconfig
+
+sysconfig has been available since Python 3.2
+https://docs.python.org/3/library/sysconfig.html#module-sysconfig
+
+--- kmer.orig/atac-driver/config.py
++++ kmer/atac-driver/config.py
+@@ -3,9 +3,9 @@
+ import sys
+ import os
+ import getopt
+-from distutils import sysconfig
++import sysconfig
+
+-print(sysconfig.get_python_inc())
++print(sysconfig.get_config_var("CONFINCLUDEPY"))
+
+ # flags = ['-I' + ,
+ # '-I' + sysconfig.get_python_inc(plat_specific=True)]
+--- kmer.orig/configure.sh
++++ kmer/configure.sh
+@@ -87,7 +87,7 @@
+ WITHOUT_ATAC="atac-driver/ seatac/"
+ else
+ echo "Python executable found in '$PYTHON'"
+- CFLAGS_PYTHON=`$PYTHON -c "from distutils import sysconfig; print(sysconfig.get_python_inc())"`
++ CFLAGS_PYTHON=`$PYTHON -c "import sysconfig; print(sysconfig.get_config_var('CONFINCLUDEPY'))"`
+
+ if [ -z "$CFLAGS_PYTHON" -o ! -d "$CFLAGS_PYTHON" ] ; then
+ echo "WARNING: Python development environment not found."
=====================================
debian/patches/series
=====================================
@@ -5,3 +5,4 @@ spelling.patch
linux-cflags.patch
fix_wrong_evaluation_order.patch
2to3.patch
+drop_distutils
=====================================
debian/rules
=====================================
@@ -7,7 +7,7 @@ include /usr/share/dpkg/default.mk
# The custom build system doesn't support CPPFLAGS
CFLAGS:=$(CPPFLAGS) $(CFLAGS)
-CXXFLAGS:=$(CPPFLAGS) $(CXXFLAGS)
+CXXFLAGS:=$(CPPFLAGS) $(CXXFLAGS) -std=c++03
# The trailing slashes are very important to the build system
subdirectories:= $(filter-out debian/, $(shell ls -d */))
@@ -18,12 +18,12 @@ unusable:= tapper/ trie/
# Note: Parallel build is not reliable
%:
- dh $@ --with python3
+ dh $@
override_dh_auto_build:
- # The Makefile apparently doesn't use regular LDFLAGS.
- # It defines CLDFLAGS and CXXLDFLAGS as empty strings, so let's
- # use them here.
+ # The Makefile apparently doesn't use regular LDFLAGS.
+ # It defines CLDFLAGS and CXXLDFLAGS as empty strings, so let's
+ # use them here.
$(MAKE) install \
CLDFLAGS="$(LDFLAGS)" \
CXXLDFLAGS="$(LDFLAGS)"
@@ -36,8 +36,7 @@ override_dh_auto_clean:
$(MAKE) real-clean
rm -rf installdir
-override_dh_install:
- dh_install
+execute_after_dh_install:
for perlscript in `grep -l '#!/usr/bin/env \+perl' debian/*/usr/bin/*` `grep -l '#!/usr/bin/env \+perl' debian/*/usr/lib/atac/bin/*` ; do \
sed -i '1s+#!/usr/bin/env perl+#!/usr/bin/perl+' $${perlscript} ; \
done
View it on GitLab: https://salsa.debian.org/med-team/kmer/-/compare/b6c298160056b9227a452cff7ae857e5c64d9070...5afd1e89428a974b53450d3dd4406d0638b39f72
--
View it on GitLab: https://salsa.debian.org/med-team/kmer/-/compare/b6c298160056b9227a452cff7ae857e5c64d9070...5afd1e89428a974b53450d3dd4406d0638b39f72
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