[med-svn] r4930 - in trunk/packages: . R/r-other-mott-happy/trunk/debian python-cogent python-cogent/trunk python-cogent/trunk/debian

Fri Jun 25 16:19:26 UTC 2010

Author: moeller
Date: 2010-06-25 16:19:19 +0000 (Fri, 25 Jun 2010)
New Revision: 4930

Added:
   trunk/packages/python-cogent/
   trunk/packages/python-cogent/trunk/
   trunk/packages/python-cogent/trunk/debian/
   trunk/packages/python-cogent/trunk/debian/README.Debian
   trunk/packages/python-cogent/trunk/debian/README.source
   trunk/packages/python-cogent/trunk/debian/changelog
   trunk/packages/python-cogent/trunk/debian/compat
   trunk/packages/python-cogent/trunk/debian/control
   trunk/packages/python-cogent/trunk/debian/copyright
   trunk/packages/python-cogent/trunk/debian/docs
   trunk/packages/python-cogent/trunk/debian/python-cogent.doc-base.EX
   trunk/packages/python-cogent/trunk/debian/python-cogent.prerm.debhelper
   trunk/packages/python-cogent/trunk/debian/python-cogent.substvars
   trunk/packages/python-cogent/trunk/debian/pyversions
   trunk/packages/python-cogent/trunk/debian/rules
   trunk/packages/python-cogent/trunk/debian/watch
Modified:
   trunk/packages/R/r-other-mott-happy/trunk/debian/changelog
Log:
Initial attempt to package pycogent.


Modified: trunk/packages/R/r-other-mott-happy/trunk/debian/changelog
===================================================================

--- trunk/packages/R/r-other-mott-happy/trunk/debian/changelog	2010-06-25 15:34:12 UTC (rev 4929)
+++ trunk/packages/R/r-other-mott-happy/trunk/debian/changelog	2010-06-25 16:19:19 UTC (rev 4930)
@@ -1,3 +1,9 @@
+r-other-mott-happy (2.2.hbrem~beta-2) unstable; urgency=low
+
+  * patch to happyplot
+
+ -- Steffen Moeller <moeller at debian.org>  Wed, 28 Apr 2010 18:24:05 +0200
+
 r-other-mott-happy (2.2.hbrem~beta-1) unstable; urgency=low
 
   * New upstream release.  


Property changes on: trunk/packages/python-cogent/trunk/debian
___________________________________________________________________
Added: mergeWithUpstream
   + 1

Added: trunk/packages/python-cogent/trunk/debian/README.Debian
===================================================================
--- trunk/packages/python-cogent/trunk/debian/README.Debian	                        (rev 0)
+++ trunk/packages/python-cogent/trunk/debian/README.Debian	2010-06-25 16:19:19 UTC (rev 4930)
@@ -0,0 +1,6 @@
+python-pycogent for Debian
+--------------------------
+
+<possible notes regarding this package - if none, delete this file>
+
+ -- root <root at unknown>  Fri, 25 Jun 2010 17:23:58 +0200

Added: trunk/packages/python-cogent/trunk/debian/README.source
===================================================================
--- trunk/packages/python-cogent/trunk/debian/README.source	                        (rev 0)
+++ trunk/packages/python-cogent/trunk/debian/README.source	2010-06-25 16:19:19 UTC (rev 4930)
@@ -0,0 +1,9 @@
+python-pycogent for Debian
+--------------------------
+
+<this file describes information about the source package, see Debian policy
+manual section 4.14. You WILL either need to modify or delete this file>
+
+
+
+

Added: trunk/packages/python-cogent/trunk/debian/changelog
===================================================================
--- trunk/packages/python-cogent/trunk/debian/changelog	                        (rev 0)
+++ trunk/packages/python-cogent/trunk/debian/changelog	2010-06-25 16:19:19 UTC (rev 4930)
@@ -0,0 +1,6 @@
+python-cogent (1.4.1-1) unstable; urgency=low
+
+  * Initial release (Closes: #nnnn)
+
+ -- Sri Girish Srinivasa Murthy <srigirish at evolbio.mpg.de>  Fri, 25 Jun 2010 17:23:58 +0200
+

Added: trunk/packages/python-cogent/trunk/debian/compat
===================================================================
--- trunk/packages/python-cogent/trunk/debian/compat	                        (rev 0)
+++ trunk/packages/python-cogent/trunk/debian/compat	2010-06-25 16:19:19 UTC (rev 4930)
@@ -0,0 +1 @@
+7

Added: trunk/packages/python-cogent/trunk/debian/control
===================================================================
--- trunk/packages/python-cogent/trunk/debian/control	                        (rev 0)
+++ trunk/packages/python-cogent/trunk/debian/control	2010-06-25 16:19:19 UTC (rev 4930)
@@ -0,0 +1,19 @@
+Source: python-cogent
+Section: science
+Priority: extra
+Maintainer: Sri Girish Srinivasa Murthy <srigirish at evolbio.mpg.de>
+Build-Depends: debhelper (>= 7), cdbs, python, python-central, python-numpy (>= 1.3.0)
+Standards-Version: 3.8.4
+Homepage: http://pycogent.sourceforge.net/
+
+Package: python-cogent
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${misc:Depends}, ${python:Depends}
+Description: framework for genomic biology
+ PyCogent is a software library for genomic biology. It is a fully
+ integrated and thoroughly tested framework for: controlling third-party
+ applications; devising workflows; querying databases; conducting novel
+ probabilistic analyses of biological sequence evolution; and generating
+ publication quality graphics. It is distinguished by many unique built-in
+ capabilities (such as true codon alignment) and the frequent addition
+ of entirely new methods for the analysis of genomic data.

Added: trunk/packages/python-cogent/trunk/debian/copyright
===================================================================
--- trunk/packages/python-cogent/trunk/debian/copyright	                        (rev 0)
+++ trunk/packages/python-cogent/trunk/debian/copyright	2010-06-25 16:19:19 UTC (rev 4930)
@@ -0,0 +1,27 @@
+This work was packaged for Debian by:
+
+    root <root at unknown> on Fri, 25 Jun 2010 17:23:58 +0200
+
+It was downloaded from <http://pycogent.sorceforge.net>
+
+Upstream Authors:
+
+    Gavin Huttley <gavin.huttley at anu.edu.au>
+    Andrew Butterfield
+    Peter Maxwell
+    Rob Knight
+
+Copyright:
+
+    Copyright 2007-2009, The Cogent Project"
+
+License:
+
+    GPL-2+
+
+The Debian packaging is:
+
+    Copyright (C) 2010 root <root at unknown>
+
+and is licensed under the same copyright,
+see `/usr/share/common-licenses/GPL-2'.

Added: trunk/packages/python-cogent/trunk/debian/docs
===================================================================
--- trunk/packages/python-cogent/trunk/debian/docs	                        (rev 0)
+++ trunk/packages/python-cogent/trunk/debian/docs	2010-06-25 16:19:19 UTC (rev 4930)
@@ -0,0 +1,3 @@
+cogent-requirements.txt
+NumpyPortingNotes.txt
+README

Added: trunk/packages/python-cogent/trunk/debian/python-cogent.doc-base.EX
===================================================================
--- trunk/packages/python-cogent/trunk/debian/python-cogent.doc-base.EX	                        (rev 0)
+++ trunk/packages/python-cogent/trunk/debian/python-cogent.doc-base.EX	2010-06-25 16:19:19 UTC (rev 4930)
@@ -0,0 +1,20 @@
+Document: python-pycogent
+Title: Debian python-pycogent Manual
+Author: <insert document author here>
+Abstract: This manual describes what python-pycogent is
+ and how it can be used to
+ manage online manuals on Debian systems.
+Section: unknown
+
+Format: debiandoc-sgml
+Files: /usr/share/doc/python-pycogent/python-pycogent.sgml.gz
+
+Format: postscript
+Files: /usr/share/doc/python-pycogent/python-pycogent.ps.gz
+
+Format: text
+Files: /usr/share/doc/python-pycogent/python-pycogent.text.gz
+
+Format: HTML
+Index: /usr/share/doc/python-pycogent/html/index.html
+Files: /usr/share/doc/python-pycogent/html/*.html

Added: trunk/packages/python-cogent/trunk/debian/python-cogent.prerm.debhelper
===================================================================
--- trunk/packages/python-cogent/trunk/debian/python-cogent.prerm.debhelper	                        (rev 0)
+++ trunk/packages/python-cogent/trunk/debian/python-cogent.prerm.debhelper	2010-06-25 16:19:19 UTC (rev 4930)
@@ -0,0 +1,45 @@
+# Automatically added by dh_pycentral
+case "$1" in remove|upgrade)
+	pkgremove=y
+esac
+if [ -f /var/lib/pycentral/python-cogent.pkgremove ] || [ -f /var/lib/pycentral/pkgremove ]; then
+	pkgremove=y
+fi
+if [ "$pkgremove" = y ]; then
+if which python >/dev/null 2>&1 && which pycentral >/dev/null 2>&1; then
+	pycentral pkgremove python-cogent
+else
+	flist=$(tempfile)
+	slist=$(tempfile)
+	dpkg -L python-cogent | tee $flist | \
+	while read n; do
+	  case "$n" in
+	    /usr/share/pyshared/*)
+	      n2=${n#/usr/share/pyshared/*}
+	      case "$n" in
+		*.py) echo "p $n";;
+		*) [ -d "$n" ] && echo "d $n2" || echo "f $n2"
+	      esac
+	      ;;
+	    *) continue
+	  esac
+	done > $slist
+	if [ -s $slist ]; then
+	    for d in /usr/lib/python[0-9].[0-9]/????-packages; do
+		case "$d" in */python2.1/*|*/python2.2/*) continue; esac
+		while read t n; do
+		    case "$t" in
+			p) rm -f $d/$n $d/${n}[co];;
+			d) rmdir $d/$n 2>/dev/null || true;;
+			*) rm -f $d/$n
+		    esac
+		done < $slist
+	    done
+	fi
+        awk '/\/usr\/share\/pyshared/ {next} /\.py$/ {print $0"c\n" $0"o"}' $flist \
+	    | xargs -r rm -f >&2
+	rm -f $flist $slist
+fi
+rm -f /var/lib/pycentral/python-cogent.pkgremove
+fi
+# End automatically added section

Added: trunk/packages/python-cogent/trunk/debian/python-cogent.substvars
===================================================================
--- trunk/packages/python-cogent/trunk/debian/python-cogent.substvars	                        (rev 0)
+++ trunk/packages/python-cogent/trunk/debian/python-cogent.substvars	2010-06-25 16:19:19 UTC (rev 4930)
@@ -0,0 +1,5 @@
+python:Versions=2.6
+python:Provides=python2.6-cogent
+python:Depends=python (<< 2.7), python (>= 2.6), python-central (>= 0.6.11)
+shlibs:Depends=libc6 (>= 2.3.4)
+misc:Depends=

Added: trunk/packages/python-cogent/trunk/debian/pyversions
===================================================================
--- trunk/packages/python-cogent/trunk/debian/pyversions	                        (rev 0)
+++ trunk/packages/python-cogent/trunk/debian/pyversions	2010-06-25 16:19:19 UTC (rev 4930)
@@ -0,0 +1 @@
+2.6

Added: trunk/packages/python-cogent/trunk/debian/rules
===================================================================
--- trunk/packages/python-cogent/trunk/debian/rules	                        (rev 0)
+++ trunk/packages/python-cogent/trunk/debian/rules	2010-06-25 16:19:19 UTC (rev 4930)
@@ -0,0 +1,19 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+export DEB_PYTHON_SYSTEM=pycentral
+
+include /usr/share/cdbs/1/rules/debhelper.mk
+include /usr/share/cdbs/1/class/python-distutils.mk
+#include /usr/share/cdbs/1/rules/patchsys-quilt.mk
+
+install::
+	find . -name runAdt | xargs -r chmod +x 
+
+clean::
+	find . -name CVS -a -type d | xargs -r rm -r
+	find . -name runAdt | xargs -r chmod +x 
+	rm -rf build build-stamp


Property changes on: trunk/packages/python-cogent/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
   + *

Added: trunk/packages/python-cogent/trunk/debian/watch
===================================================================
--- trunk/packages/python-cogent/trunk/debian/watch	                        (rev 0)
+++ trunk/packages/python-cogent/trunk/debian/watch	2010-06-25 16:19:19 UTC (rev 4930)
@@ -0,0 +1,2 @@
+version=3
+http://sf.net/pycogent/PyCogent-(.*)\.tar\.gz


