[med-svn] r7547 - trunk/packages/python-pynast/trunk/debian

Steffen Möller moeller at alioth.debian.org
Thu Aug 25 21:56:01 UTC 2011 

Author: moeller
Date: 2011-08-25 21:56:01 +0000 (Thu, 25 Aug 2011)
New Revision: 7547

Added:
   trunk/packages/python-pynast/trunk/debian/compat
   trunk/packages/python-pynast/trunk/debian/manpages
   trunk/packages/python-pynast/trunk/debian/pynast.1
Removed:
   trunk/packages/python-pynast/trunk/debian/pyversions
Modified:
   trunk/packages/python-pynast/trunk/debian/README.Debian
   trunk/packages/python-pynast/trunk/debian/changelog
   trunk/packages/python-pynast/trunk/debian/control
   trunk/packages/python-pynast/trunk/debian/docs
   trunk/packages/python-pynast/trunk/debian/rules
Log:
Giving python-pynast a spin, getting it
out of experimental while doing so 
 (added man page, moving to dh_python2)
Once it is in, also qiime can get from
experimental to contrib.


Modified: trunk/packages/python-pynast/trunk/debian/README.Debian
===================================================================
--- trunk/packages/python-pynast/trunk/debian/README.Debian	2011-08-25 21:09:33 UTC (rev 7546)
+++ trunk/packages/python-pynast/trunk/debian/README.Debian	2011-08-25 21:56:01 UTC (rev 7547)
@@ -3,6 +3,8 @@
 
 Many many thanks got to Jonas from the CDBS team for indicating
 that I indeed need to set the XB and XS flags for python packages.
+A recent update move this all to dh_python2, which does not seem
+to need those any more.
 
 The package is named -pynast, not -nast, since that is the name
 of the python module.
@@ -12,8 +14,8 @@
 a contribtion to upstream and this Debian package by a rudimentary
 man page would be appreciated.
 
-The documentation is somehow built with the new fancy Free
-environment spinx. The packaging should reflect this by adding
-spinx as a build-indep dependency, but the packagers have not
-yet found the time to address this. Help would be appreciated.
- 
+The package is in need of someone truly loving it. You will be
+helped, just raise your hand.
+
+ -- 
+   Steffen Moeller <moeller at debian.org>  Thu, 25 Aug 2011 23:31:25 +0200

Modified: trunk/packages/python-pynast/trunk/debian/changelog
===================================================================
--- trunk/packages/python-pynast/trunk/debian/changelog	2011-08-25 21:09:33 UTC (rev 7546)
+++ trunk/packages/python-pynast/trunk/debian/changelog	2011-08-25 21:56:01 UTC (rev 7547)
@@ -1,3 +1,12 @@
+python-pynast (1.1-2) unstable; urgency=low
+
+  * Transition to dh7 and dh_python2
+  * Adjusted uploaders, first upload to unstable
+  * Documentation built with sphinx
+  * Added man page
+
+ -- Steffen Moeller <moeller at debian.org>  Thu, 25 Aug 2011 23:19:06 +0200
+
 python-pynast (1.1-1) experimental; urgency=low
 
   * Initial release (Closes: #587189)

Added: trunk/packages/python-pynast/trunk/debian/compat
===================================================================
--- trunk/packages/python-pynast/trunk/debian/compat	                        (rev 0)
+++ trunk/packages/python-pynast/trunk/debian/compat	2011-08-25 21:56:01 UTC (rev 7547)
@@ -0,0 +1 @@
+7

Modified: trunk/packages/python-pynast/trunk/debian/control
===================================================================
--- trunk/packages/python-pynast/trunk/debian/control	2011-08-25 21:09:33 UTC (rev 7546)
+++ trunk/packages/python-pynast/trunk/debian/control	2011-08-25 21:56:01 UTC (rev 7547)
@@ -2,19 +2,18 @@
 Section: contrib/python
 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>
-Build-Depends: debhelper (>= 7), cdbs, python (>= 2.5), python-central, python-cogent
+Uploaders: Steffen Moeller <moeller at debian.org>
+Build-Depends: debhelper (>= 7), python (>= 2.6.6-3~), python-central, python-cogent, python-sphinx
 XS-Autobuild: yes
-Standards-Version: 3.9.0
+Standards-Version: 3.9.2
 Homepage: http://pynast.sourceforge.net/
 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/python-nast/trunk/?rev=0&sc=0
 Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/python-nast/trunk/
-XS-Python-Version: >= 2.5
+X-Python-Version: >= 2.5
 
 Package: python-pynast
 Architecture: all
 Depends: ${shlibs:Depends}, ${misc:Depends}, ${misc:Depends}, ${python:Depends}
-XB-Python-Version: ${python:Versions}
 Description: alignment of short DNA sequences
  The package provices a reimplementation of the Nearest Alignment 
  Space Termination tool in python. It was prepared for next generation

Modified: trunk/packages/python-pynast/trunk/debian/docs
===================================================================
--- trunk/packages/python-pynast/trunk/debian/docs	2011-08-25 21:09:33 UTC (rev 7546)
+++ trunk/packages/python-pynast/trunk/debian/docs	2011-08-25 21:56:01 UTC (rev 7547)
@@ -1,2 +1,2 @@
 README
-doc/*
+doc/_build/html

Added: trunk/packages/python-pynast/trunk/debian/manpages
===================================================================
--- trunk/packages/python-pynast/trunk/debian/manpages	                        (rev 0)
+++ trunk/packages/python-pynast/trunk/debian/manpages	2011-08-25 21:56:01 UTC (rev 7547)
@@ -0,0 +1 @@
+debian/pynast.1

Added: trunk/packages/python-pynast/trunk/debian/pynast.1
===================================================================
--- trunk/packages/python-pynast/trunk/debian/pynast.1	                        (rev 0)
+++ trunk/packages/python-pynast/trunk/debian/pynast.1	2011-08-25 21:56:01 UTC (rev 7547)
@@ -0,0 +1,62 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.40.4. .. and only minimally edited
+.TH VERSION: "1" "August 2011" "Version: pynast 1.1" "User Commands"
+.SH NAME
+PyNAST \- alignment of short DNA sequences
+.SH SYNOPSIS
+.B pynast
+[\fIoptions\fR] \fI{-i input_fp -t template_fp}\fR
+.SH DESCRIPTION
+[] indicates optional input (order unimportant)
+{} indicates required input (order unimportant)
+.SS "Example usage:"
+.IP
+pynast \fB\-i\fR my_input.fasta \fB\-t\fR my_template.fasta
+.SH OPTIONS
+.TP
+\fB\-\-version\fR
+show program's version number and exit
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-t\fR TEMPLATE_FP, \fB\-\-template_fp\fR=\fITEMPLATE_FP\fR
+path to template alignment file [REQUIRED]
+.TP
+\fB\-i\fR INPUT_FP, \fB\-\-input_fp\fR=\fIINPUT_FP\fR
+path to input fasta file [REQUIRED]
+.TP
+\fB\-v\fR, \fB\-\-verbose\fR
+Print status and other information during execution
+[default: False]
+.TP
+\fB\-p\fR MIN_PCT_ID, \fB\-\-min_pct_id\fR=\fIMIN_PCT_ID\fR
+minimum percent sequence  identity to consider a
+sequence a match [default: 75.0]
+.TP
+\fB\-l\fR MIN_LEN, \fB\-\-min_len\fR=\fIMIN_LEN\fR
+minimum sequence length to include in NAST alignment
+[default: 1000]
+.TP
+\fB\-m\fR PAIRWISE_ALIGNMENT_METHOD, \fB\-\-pairwise_alignment_method\fR=\fIPAIRWISE_ALIGNMENT_METHOD\fR
+method for performing pairwise alignment [default:
+uclust]
+.TP
+\fB\-a\fR FASTA_OUT_FP, \fB\-\-fasta_out_fp\fR=\fIFASTA_OUT_FP\fR
+path to store resulting alignment file [default:
+derived from input filepath]
+.TP
+\fB\-g\fR LOG_FP, \fB\-\-log_fp\fR=\fILOG_FP\fR
+path to store log file [default: derived from input
+filepath]
+.TP
+\fB\-f\fR FAILURE_FP, \fB\-\-failure_fp\fR=\fIFAILURE_FP\fR
+path to store file of seqs which fail to align
+[default: derived from input filepath]
+.TP
+\fB\-e\fR MAX_E_VALUE, \fB\-\-max_e_value\fR=\fIMAX_E_VALUE\fR
+Depreciated. Will be removed in PyNAST 1.2
+.TP
+\fB\-d\fR BLAST_DB, \fB\-\-blast_db\fR=\fIBLAST_DB\fR
+Depreciated. Will be removed in PyNAST 1.2
+.SH "SEE ALSO"
+http://pynast.sourceforge.net

Deleted: trunk/packages/python-pynast/trunk/debian/pyversions
===================================================================
--- trunk/packages/python-pynast/trunk/debian/pyversions	2011-08-25 21:09:33 UTC (rev 7546)
+++ trunk/packages/python-pynast/trunk/debian/pyversions	2011-08-25 21:56:01 UTC (rev 7547)
@@ -1 +0,0 @@
-all

Modified: trunk/packages/python-pynast/trunk/debian/rules
===================================================================
--- trunk/packages/python-pynast/trunk/debian/rules	2011-08-25 21:09:33 UTC (rev 7546)
+++ trunk/packages/python-pynast/trunk/debian/rules	2011-08-25 21:56:01 UTC (rev 7547)
@@ -4,9 +4,14 @@
 # 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/debhelper.mk
+#include /usr/share/cdbs/1/class/python-distutils.mk
 
+%:
+	dh $@ --with python2
+
+build-indep:
+	$(MAKE) -C doc html
+
 clean::
 	rm -rf build build-stamp

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