[Debian-med-packaging] Qiime changes

Thu Mar 24 21:54:03 UTC 2011

Hi Tim,

I'd suggest working on these two lintian warnings:

W: qiime: binary-without-manpage usr/bin/qiime
W: qiime: embedded-javascript-library usr/share/pyshared/qiime/support_files/js/jquery.js

The first is writing a (simple?) manpage the second would be to make the
package depend libjs-jquery and use debian/links to adjust symlinks
accordingly.

Fell free to ask any question which might raise out of my work.

Kind regards

    Andreas.

----- Forwarded message from Andreas Tille <tille at alioth.debian.org> -----

Date: Thu, 24 Mar 2011 21:48:42 +0000
To: debian-med-commit at lists.alioth.debian.org
From: Andreas Tille <tille at alioth.debian.org>
X-Spam_score: -4.1
Subject: r6382 - trunk/packages/qiime/trunk/debian

Author: tille
Date: 2011-03-24 21:48:42 +0000 (Thu, 24 Mar 2011)
New Revision: 6382

Added:
   trunk/packages/qiime/trunk/debian/dirs
   trunk/packages/qiime/trunk/debian/docs
   trunk/packages/qiime/trunk/debian/install
Removed:
   trunk/packages/qiime/trunk/debian/pyversions
   trunk/packages/qiime/trunk/debian/qiime.docs
Modified:
   trunk/packages/qiime/trunk/debian/changelog
   trunk/packages/qiime/trunk/debian/compat
   trunk/packages/qiime/trunk/debian/control
   trunk/packages/qiime/trunk/debian/rules
Log:
  * Dropped cdbs in favour of dh
  * Debhelper 8 (compat+control)
  * Use debian/{install,dirs) to enable better readable debian/rules
  * debian/rules:
    - override_dh_compress
    - override_dh_installchangelogs
Hope this simplifies maintaining the debian/rules file


Modified: trunk/packages/qiime/trunk/debian/changelog
===================================================================

--- trunk/packages/qiime/trunk/debian/changelog	2011-03-24 17:45:15 UTC (rev 6381)
+++ trunk/packages/qiime/trunk/debian/changelog	2011-03-24 21:48:42 UTC (rev 6382)
@@ -1,3 +1,14 @@
+qiime (1.2.1-1) UNRELEASED; urgency=low
+
+  * Dropped cdbs in favour of dh
+  * Debhelper 8 (compat+control)
+  * Use debian/{install,dirs) to enable better readable debian/rules
+  * debian/rules:
+    - override_dh_compress
+    - override_dh_installchangelogs
+
+ -- Andreas Tille <tille at debian.org>  Thu, 24 Mar 2011 22:39:55 +0100
+
 qiime (1.2.1-ubuntu5) lucid; urgency=low
 
   * Fixed silly error in qiime wrapper script

Modified: trunk/packages/qiime/trunk/debian/compat
===================================================================
--- trunk/packages/qiime/trunk/debian/compat	2011-03-24 17:45:15 UTC (rev 6381)
+++ trunk/packages/qiime/trunk/debian/compat	2011-03-24 21:48:42 UTC (rev 6382)
@@ -1 +1 @@
-5
+8

Modified: trunk/packages/qiime/trunk/debian/control
===================================================================
--- trunk/packages/qiime/trunk/debian/control	2011-03-24 17:45:15 UTC (rev 6381)
+++ trunk/packages/qiime/trunk/debian/control	2011-03-24 21:48:42 UTC (rev 6382)
@@ -3,7 +3,7 @@
 Priority: extra
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 Uploaders: Sri Girish Srinivasa Murthy <srigirish at evolbio.mpg.de>, Steffen Moeller <moeller at debian.org>, Tim Booth <tbooth at ceh.ac.uk>
-Build-Depends: debhelper (>= 7), cdbs, python, python-central, python-cogent, python-numpy, python-matplotlib
+Build-Depends: debhelper (>= 8), python, python-central, python-cogent, python-numpy, python-matplotlib
 Standards-Version: 3.9.1
 Homepage: http://qiime.sourceforge.net/
 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/qiime/trunk/?rev=0&sc=0

Added: trunk/packages/qiime/trunk/debian/dirs
===================================================================
--- trunk/packages/qiime/trunk/debian/dirs	                        (rev 0)
+++ trunk/packages/qiime/trunk/debian/dirs	2011-03-24 21:48:42 UTC (rev 6382)
@@ -0,0 +1,2 @@
+usr/lib/qiime/bin
+etc/qiime

Added: trunk/packages/qiime/trunk/debian/docs
===================================================================
--- trunk/packages/qiime/trunk/debian/docs	                        (rev 0)
+++ trunk/packages/qiime/trunk/debian/docs	2011-03-24 21:48:42 UTC (rev 6382)
@@ -0,0 +1,5 @@
+README
+qiime_parameters.txt
+qiime_tutorial/
+doc/_build/*
+doc/vb_files

Added: trunk/packages/qiime/trunk/debian/install
===================================================================
--- trunk/packages/qiime/trunk/debian/install	                        (rev 0)
+++ trunk/packages/qiime/trunk/debian/install	2011-03-24 21:48:42 UTC (rev 6382)
@@ -0,0 +1,3 @@
+debian/scripts/qiime		usr/bin
+debian/scripts/shell		usr/lib/qiime
+debian/scripts/qiime_config	etc/qiime/qiime_config

Deleted: trunk/packages/qiime/trunk/debian/pyversions
===================================================================
--- trunk/packages/qiime/trunk/debian/pyversions	2011-03-24 17:45:15 UTC (rev 6381)
+++ trunk/packages/qiime/trunk/debian/pyversions	2011-03-24 21:48:42 UTC (rev 6382)
@@ -1 +0,0 @@
-2.6

Deleted: trunk/packages/qiime/trunk/debian/qiime.docs
===================================================================
--- trunk/packages/qiime/trunk/debian/qiime.docs	2011-03-24 17:45:15 UTC (rev 6381)
+++ trunk/packages/qiime/trunk/debian/qiime.docs	2011-03-24 21:48:42 UTC (rev 6382)
@@ -1,6 +0,0 @@
-README
-ChangeLog
-qiime_parameters.txt
-qiime_tutorial/
-doc/_build/*
-doc/vb_files

Modified: trunk/packages/qiime/trunk/debian/rules
===================================================================
--- trunk/packages/qiime/trunk/debian/rules	2011-03-24 17:45:15 UTC (rev 6381)
+++ trunk/packages/qiime/trunk/debian/rules	2011-03-24 21:48:42 UTC (rev 6382)
@@ -1,38 +1,41 @@
 #!/usr/bin/make -f
 # -*- makefile -*-
+# debian/rules for Qiime
+# Tim Booth <tbooth at ceh.ac.uk>, Andreas Tille <tille at debian.org>
+# GPL
 
 # Uncomment this to turn on verbose mode.
 #export DH_VERBOSE=1
 
-export DEB_PYTHON_SYSTEM=pycentral
-export DEB_COMPRESS_EXCLUDE=.js .sff .qual .fna .fna.txt
+%:
+	dh $@ --with python2
 
-include /usr/share/cdbs/1/rules/debhelper.mk
-include /usr/share/cdbs/1/class/python-distutils.mk
+override_dh_compress:
+	dh_compress \
+	    --exclude=.js \
+	    --exclude=.sff \
+	    --exclude=.qual \
+	    --exclude=.fna \
+	    --exclude=.fna.txt
 
+override_dh_clean:
+	dh_clean
+	rm -rf doc/_build
+
 export ROOTDIR=debian/`dh_listpackages`
 
-# Apparently the override_dh_* mechanism doesn't work with the above includes??
-# Yes, see http://lists.debian.org/debian-med/2011/03/msg00211.html
-# TODO - redo this file as Andreas suggested.
-clean::
-	rm -rf doc/_build
-
 #Lots of shuffling to be done...
 # Python scripts go into /usr/lib/qiime/bin (not /usr/bin)
 # Helper script goes into /usr/bin
 # Setup scripts go into /usr/lib/qiime/shell
 # Default configuration goes into /etc/qiime/default_qiime_config
 # ...or maybe it should be copied to $HOME/.qiime_config on 1st run?
-common-binary-fixup-indep::
-	install -m 755 -d $(ROOTDIR)/usr/lib/qiime/bin
-	install -m 755 -d $(ROOTDIR)/etc/qiime
+override_dh_install:
+	dh_install
 	mv $(ROOTDIR)/usr/bin/*.py  $(ROOTDIR)/usr/lib/qiime/bin
-	install -m 755 debian/scripts/qiime $(ROOTDIR)/usr/bin
 	install -m 755 debian/scripts/uclust $(ROOTDIR)/usr/lib/qiime/bin
-	cp -R --no-preserve=all debian/scripts/shell $(ROOTDIR)/usr/lib/qiime
-	rm -r $(ROOTDIR)/usr/lib/qiime/shell/.svn
+	rm -rf $(ROOTDIR)/usr/lib/qiime/shell/.svn
 	chmod -R a+rX $(ROOTDIR)/usr/lib/qiime/shell
-	install -m 644 debian/scripts/qiime_config $(ROOTDIR)/etc/qiime/qiime_config	
-	# Lintian complains about case of ChangeLog.gz
-	( cd $(ROOTDIR)/usr/share/doc/`dh_listpackages` ; mv ChangeLog.gz changelog.gz || true )
+
+override_dh_installchangelogs:
+	dh_installchangelogs ChangeLog


_______________________________________________
debian-med-commit mailing list
debian-med-commit at lists.alioth.debian.org
http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit


----- End forwarded message -----

-- 
http://fam-tille.de

