[med-svn] [Git][med-team/meme][master] 12 commits: routine-update: Standards-Version: 4.5.1
Andreas Tille
gitlab at salsa.debian.org
Wed Mar 24 10:05:46 GMT 2021
Andreas Tille pushed to branch master at Debian Med / meme
Commits:
872818e0 by Andreas Tille at 2021-03-24T10:43:49+01:00
routine-update: Standards-Version: 4.5.1
- - - - -
06e6e8f0 by Andreas Tille at 2021-03-24T10:43:49+01:00
routine-update: debhelper-compat 13
- - - - -
c0f9cf83 by Andreas Tille at 2021-03-24T10:43:53+01:00
routine-update: Drop useless get-orig-source target
- - - - -
ca3f1cd9 by Andreas Tille at 2021-03-24T10:45:05+01:00
routine-update: Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
- - - - -
2839e956 by Andreas Tille at 2021-03-24T10:45:05+01:00
routine-update: Remove trailing whitespace in debian/changelog
- - - - -
b5c4308f by Andreas Tille at 2021-03-24T10:50:05+01:00
routine-update: Do not parse d/changelog
- - - - -
b27261a0 by Andreas Tille at 2021-03-24T10:50:05+01:00
routine-update: Add salsa-ci file
- - - - -
e949815e by Andreas Tille at 2021-03-24T10:50:05+01:00
routine-update: Rules-Requires-Root: no
- - - - -
8e22e3a3 by Andreas Tille at 2021-03-24T10:50:05+01:00
routine-update: No tab in license text
- - - - -
9e8907af by Andreas Tille at 2021-03-24T10:55:14+01:00
Cleanup changelog, use Python3
- - - - -
f365ba17 by Andreas Tille at 2021-03-24T10:56:34+01:00
There are no such files that are attempted to be saved here
- - - - -
e70d8a46 by Andreas Tille at 2021-03-24T11:02:35+01:00
Trust dh_autoreconf to do the right thing
- - - - -
5 changed files:
- debian/changelog
- debian/control
- debian/copyright
- debian/rules
- + debian/salsa-ci.yml
Changes:
=====================================
debian/changelog
=====================================
@@ -1,13 +1,10 @@
meme (5.0.1.1-1) UNRELEASED; urgency=low
* Initial release (Closes: #xxxxxx)
-
- [ Andreas Tille ]
- * debian/control: Depends: ghostscript, imagemagick | graphicsmagick
- * TODO:
+ TODO:
- debian/copyright
- several manpages
- language extensions
- csh dependency
- -- Andreas Tille <tille at debian.org> Thu, 16 Apr 2020 16:49:43 +0200
+ -- Andreas Tille <tille at debian.org> Wed, 24 Mar 2021 10:50:08 +0100
=====================================
debian/control
=====================================
@@ -1,22 +1,22 @@
Source: meme
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Andreas Tille <tille at debian.org>,
- H. Soon Gweon <soonio at gmail.com>,
- Thorsten Alteholz <debian at alteholz.de>
Section: non-free/science
XS-Autobuild: no
Priority: optional
-Build-Depends: debhelper-compat (= 12),
+Build-Depends: debhelper-compat (= 13),
+ dh-python,
libxslt1-dev,
python-all,
zlib1g-dev,
elinks,
help2man,
ghostscript
-Standards-Version: 4.5.0
+Standards-Version: 4.5.1
Vcs-Browser: https://salsa.debian.org/med-team/meme
Vcs-Git: https://salsa.debian.org/med-team/meme.git
Homepage: http://meme-suite.org/tools/meme
+Rules-Requires-Root: no
Package: meme
Architecture: any
=====================================
debian/copyright
=====================================
@@ -6,33 +6,33 @@ Source: http://meme-suite.org/doc/download.html?man_type=web
Files: *
Copyright: © 1994-2010 The Regents of the University of California. All Rights Reserved.
License: non-free_for_commercial
- * Permission to use, copy, modify, and distribute any part of *
- * this software for educational, research and non-profit purposes,*
- * without fee, and without a written agreement is hereby granted, *
- * provided that the above copyright notice, this paragraph and *
- * the following three paragraphs appear in all copies. *
- * *
- * Those desiring to incorporate this software into commercial *
- * products or use for commercial purposes should contact the *
- * Technology Transfer Office, University of California, San Diego,*
- * 9500 Gilman Drive, La Jolla, California, 92093-0910, *
- * Ph: (858) 534 5815. *
- * *
- * IN NO EVENT SHALL THE UNIVERSITY OF CALIFORNIA BE LIABLE TO *
- * ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR *
- * CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF *
- * THE USE OF THIS SOFTWARE, EVEN IF THE UNIVERSITY OF CALIFORNIA *
- * HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. *
- * *
- * THE SOFTWARE PROVIDED HEREUNDER IS ON AN "AS IS" BASIS, AND THE *
- * UNIVERSITY OF CALIFORNIA HAS NO OBLIGATIONS TO PROVIDE *
- * MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS. *
- * THE UNIVERSITY OF CALIFORNIA MAKES NO REPRESENTATIONS AND *
- * EXTENDS NO WARRANTIES OF ANY KIND, EITHER EXPRESSED OR IMPLIED, *
- * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF *
- * MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE, OR THAT *
- * THE USE OF THE MATERIAL WILL NOT INFRINGE ANY PATENT, *
- * TRADEMARK OR OTHER RIGHTS. *
+ * Permission to use, copy, modify, and distribute any part of *
+ * this software for educational, research and non-profit purposes,*
+ * without fee, and without a written agreement is hereby granted, *
+ * provided that the above copyright notice, this paragraph and *
+ * the following three paragraphs appear in all copies. *
+ * *
+ * Those desiring to incorporate this software into commercial *
+ * products or use for commercial purposes should contact the *
+ * Technology Transfer Office, University of California, San Diego,*
+ * 9500 Gilman Drive, La Jolla, California, 92093-0910, *
+ * Ph: (858) 534 5815. *
+ * *
+ * IN NO EVENT SHALL THE UNIVERSITY OF CALIFORNIA BE LIABLE TO *
+ * ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR *
+ * CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF *
+ * THE USE OF THIS SOFTWARE, EVEN IF THE UNIVERSITY OF CALIFORNIA *
+ * HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. *
+ * *
+ * THE SOFTWARE PROVIDED HEREUNDER IS ON AN "AS IS" BASIS, AND THE *
+ * UNIVERSITY OF CALIFORNIA HAS NO OBLIGATIONS TO PROVIDE *
+ * MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS. *
+ * THE UNIVERSITY OF CALIFORNIA MAKES NO REPRESENTATIONS AND *
+ * EXTENDS NO WARRANTIES OF ANY KIND, EITHER EXPRESSED OR IMPLIED, *
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF *
+ * MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE, OR THAT *
+ * THE USE OF THE MATERIAL WILL NOT INFRINGE ANY PATENT, *
+ * TRADEMARK OR OTHER RIGHTS. *
Files: src/readseq src/ureadseq.[ch]
Copyright: 1990 D. G. Gilbert, Biology Dept., Indiana University, Bloomington, in 47405
=====================================
debian/rules
=====================================
@@ -1,51 +1,27 @@
#!/usr/bin/make -f
# debian/rules file for meme
-# Andreas Tille <tille at debian.org>
-# Thorsten Alteholz <debian at alteholz.de>
-# GPL
-pkg := $(shell dpkg-parsechangelog | sed -n 's/^Source: //p')
-version=$(shell dpkg-parsechangelog -ldebian/changelog | grep Version: | cut -f2 -d' ' | cut -f1 -d- )
-mandir=$(CURDIR)/debian/$(pkg)/usr/share/man/man1/
+include /usr/share/dpkg/default.mk
+mandir=$(CURDIR)/debian/$(DEB_SOURCE)/usr/share/man/man1/
-DBPATH=/var/lib/$(pkg)
-LOGPATH=/var/log/$(pkg)
+DBPATH=/var/lib/$(DEB_SOURCE)
+LOGPATH=/var/log/$(DEB_SOURCE)
# Only needed for fixing brocken upstream build mechanism
-PYTHON=/usr/bin/python
+PYTHON=/usr/bin/python3
-# PYTHONSUBDIR=$(pkg)/
+# PYTHONSUBDIR=$(DEB_SOURCE)/
# if the Python modules should be put into a separate meme subdirectory you need to patch the following scripts
# scripts/dreme.py.in
# scripts/fasta-hamming-enrich.py.in
PYTHONSUBDIR=
%:
- dh $@,python2
-
-override_dh_autoreconf:
- # save original configuration files to enable building twice in a row
- mkdir -p orig
- cp -a config orig/
- cp -a aclocal.m4 INSTALL configure orig/
- mkdir -p orig/website/html
- cp -a website/html/metameme-help-format.html orig/website/html
- cp -a website/html/metameme-intro.html orig/website/html
- cp -a website/html/cisml.pattern.html.xsl orig/website/html
- mkdir -p orig/src
- cp -a src/projrel.h orig/src
- cp -a src/dir.h orig/src
- #mkdir -p orig/etc
- #cp -a etc/logging.conf orig/etc
- for origfile in `find . -type f -name Makefile.in` ; do \
- mkdir -p orig/`dirname $$origfile` ; \
- cp -a $${origfile} orig/`dirname $$origfile` ; \
- done ;
- dh_autoreconf
+ dh $@ --with python3
override_dh_auto_configure:
./configure --prefix=/usr --mandir=\$${prefix}/share/man --infodir=\$${prefix}/share/info \
--host=$(DEB_HOST_GNU_TYPE) --build=$(DEB_BUILD_GNU_TYPE) \
- --sysconfdir=/etc/$(pkg) \
+ --sysconfdir=/etc/$(DEB_SOURCE) \
--with-logs=$(LOGPATH) \
--with-db=$(DBPATH) \
--with-python=/usr/bin/python
@@ -56,18 +32,18 @@ override_dh_auto_install:
override_dh_install:
#Sort out some funny locations used by upstream
mv debian/tmp/usr/doc/examples debian/tmp || true
- mkdir -p debian/tmp/usr/share/doc/$(pkg) ; mv debian/tmp/usr/doc/* debian/tmp/usr/share/doc/$(pkg)
- mv debian/tmp/etc/$(pkg)/meme.doc debian/tmp/usr/share/doc/$(pkg)
+ mkdir -p debian/tmp/usr/share/doc/$(DEB_SOURCE) ; mv debian/tmp/usr/doc/* debian/tmp/usr/share/doc/$(DEB_SOURCE)
+ mv debian/tmp/etc/$(DEB_SOURCE)/meme.doc debian/tmp/usr/share/doc/$(DEB_SOURCE)
find ./* -print|grep STRGGTCAN.meme|xargs chmod 644
mkdir -p debian/tmp/usr/share/perl5/Meme
cp website/scripts/*.pm debian/tmp/usr/share/perl5/Meme
cp scripts/*.pm debian/tmp/usr/share/perl5/Meme
# *.py files are Python libraries
- mkdir -p $(CURDIR)/debian/$(pkg)/usr/share/pyshared/$(PYTHONSUBDIR)
- mv $(CURDIR)/debian/tmp/usr/bin/*.py $(CURDIR)/debian/$(pkg)/usr/share/pyshared/$(PYTHONSUBDIR)
+ mkdir -p $(CURDIR)/debian/$(DEB_SOURCE)/usr/share/pyshared/$(PYTHONSUBDIR)
+ mv $(CURDIR)/debian/tmp/usr/bin/*.py $(CURDIR)/debian/$(DEB_SOURCE)/usr/share/pyshared/$(PYTHONSUBDIR)
# fix insufficient replacement procedure of @WHICHPYTHON@
for pyfile in sequence.py hypergeometric.py ; do \
- sed -i -e 's% *@WHICHPYTHON@%$(PYTHON)%' $(CURDIR)/debian/$(pkg)/usr/share/pyshared/$(PYTHONSUBDIR)$${pyfile} ; \
+ sed -i -e 's% *@WHICHPYTHON@%$(PYTHON)%' $(CURDIR)/debian/$(DEB_SOURCE)/usr/share/pyshared/$(PYTHONSUBDIR)$${pyfile} ; \
done
dh_install -v --sourcedir=debian/tmp
@@ -77,20 +53,20 @@ override_dh_installman:
if head -n 1 $${var} | grep -q '^#!/usr/bin/perl' ; then pod2man $${var} > $(mandir)/`basename $${var}`.1 ; fi ; \
done
help2man --no-info --help-option="''" --no-discard-stderr \
- --name='Average Motif Affinity' --version-string="$(version)" \
- $(CURDIR)/debian/$(pkg)/usr/bin/ama > $(mandir)/ama.1
+ --name='Average Motif Affinity' --version-string="$(DEB_VERSION_UPSTREAM)" \
+ $(CURDIR)/debian/$(DEB_SOURCE)/usr/bin/ama > $(mandir)/ama.1
help2man --no-info --help-option="''" --no-discard-stderr \
- --name='Analysis of Motif Enrichment' --version-string="$(version)" \
- $(CURDIR)/debian/$(pkg)/usr/bin/ame > $(mandir)/ame.1
+ --name='Analysis of Motif Enrichment' --version-string="$(DEB_VERSION_UPSTREAM)" \
+ $(CURDIR)/debian/$(DEB_SOURCE)/usr/bin/ame > $(mandir)/ame.1
help2man --no-info --help-option="''" --no-discard-stderr \
- --name='Build a linear hidden Markov model (HMM) from motif' --version-string="$(version)" \
- $(CURDIR)/debian/$(pkg)/usr/bin/beadstring > $(mandir)/beadstring.1
+ --name='Build a linear hidden Markov model (HMM) from motif' --version-string="$(DEB_VERSION_UPSTREAM)" \
+ $(CURDIR)/debian/$(DEB_SOURCE)/usr/bin/beadstring > $(mandir)/beadstring.1
help2man --no-info --help-option="''" --no-discard-stderr \
- --name='Evaluate if motifs are locally enriched in a set of sequences' --version-string="$(version)" \
- $(CURDIR)/debian/$(pkg)/usr/bin/centrimo > $(mandir)/centrimo.1
+ --name='Evaluate if motifs are locally enriched in a set of sequences' --version-string="$(DEB_VERSION_UPSTREAM)" \
+ $(CURDIR)/debian/$(DEB_SOURCE)/usr/bin/centrimo > $(mandir)/centrimo.1
help2man --no-info --help-option="''" --no-discard-stderr \
- --name='Load all motifs within a MEME motif file and write to eps' --version-string="$(version)" \
- $(CURDIR)/debian/$(pkg)/usr/bin/ceqlogo > $(mandir)/ceqlogo.1
+ --name='Load all motifs within a MEME motif file and write to eps' --version-string="$(DEB_VERSION_UPSTREAM)" \
+ $(CURDIR)/debian/$(DEB_SOURCE)/usr/bin/ceqlogo > $(mandir)/ceqlogo.1
# Very dirty trick to drain information via help2man even if binary outputs to stderr
debian/help2man-wrapper clustalw2fasta 'Converts a multiple alignment in clustalw format into a FASTA file'
debian/help2man-wrapper clustalw2phylip 'Converts a multiple alignment in clustalw format into a Phylip file'
@@ -118,11 +94,9 @@ override_dh_clean:
#XXX Disable testing temporarily to save time
override_dh_auto_test:
- true
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
+ echo "FIXME: Skip build time test for the moment."
+endif
override_dh_compress:
dh_compress -v -X.doc
-
-get-orig-source:
- mkdir -p ../tarballs
- uscan --verbose --force-download --destdir=../tarballs
=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,4 @@
+---
+include:
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
View it on GitLab: https://salsa.debian.org/med-team/meme/-/compare/9e2bea97026962f8a3321130640e70fd4185060f...e70d8a46a91d93b9ecb9c0a115f0deec1fb8c6c1
--
View it on GitLab: https://salsa.debian.org/med-team/meme/-/compare/9e2bea97026962f8a3321130640e70fd4185060f...e70d8a46a91d93b9ecb9c0a115f0deec1fb8c6c1
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