[med-svn] r15207 - trunk/packages/python-biom-format/trunk/debian

[Andreas Tille]

Author: tille
Date: 2013-11-20 22:00:47 +0000 (Wed, 20 Nov 2013)
New Revision: 15207

Added:
   trunk/packages/python-biom-format/trunk/debian/biom.1
Modified:
   trunk/packages/python-biom-format/trunk/debian/changelog
   trunk/packages/python-biom-format/trunk/debian/control
   trunk/packages/python-biom-format/trunk/debian/rules
Log:
Mass commit for 1.2.0-1


Added: trunk/packages/python-biom-format/trunk/debian/biom.1
===================================================================
--- trunk/packages/python-biom-format/trunk/debian/biom.1	                        (rev 0)
+++ trunk/packages/python-biom-format/trunk/debian/biom.1	2013-11-20 22:00:47 UTC (rev 15207)
@@ -0,0 +1,24 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.43.3.
+.TH BIOM "1" "November 2013" "biom 1.2.0" "User Commands"
+.SH NAME
+biom \- wrapper for Biological Observation Matrix
+.SH SYNOPSIS
+.B biom
+<\fBcommand\fR> [<\fBargs\fR>]
+.SH DESCRIPTION
+.PP
+The BIOM file format (canonically pronounced biome) is designed to be a
+general-use format for representing biological sample by observation
+contingency tables. BIOM is a recognized standard for the Earth
+Microbiome Project and is a Genomics Standards Consortium candidate
+project.
+.PP
+To see a list of all available commands, run the following command:
+.IP
+biom
+.PP
+See
+.IP
+biom help <command>
+.PP
+for more information on a specific command.
\ No newline at end of file

Modified: trunk/packages/python-biom-format/trunk/debian/changelog
===================================================================
--- trunk/packages/python-biom-format/trunk/debian/changelog	2013-11-20 22:00:16 UTC (rev 15206)
+++ trunk/packages/python-biom-format/trunk/debian/changelog	2013-11-20 22:00:47 UTC (rev 15207)
@@ -1,3 +1,17 @@
+python-biom-format (1.2.0-1) unstable; urgency=low
+
+  * New upstream version
+  * debian/control:
+     - (Build-)Depends: pyqi
+     - Build-Depends: python-nose to enable auto_test
+  * debian/biom.1: Add simple manpage
+  * debian/rules:
+     - activate test using python-nose
+     - deactivate get-orig-source script and use plain uscan since
+       upstream tarball is clean now
+
+ -- Andreas Tille <tille at debian.org>  Mon, 11 Nov 2013 09:24:46 +0100
+
 python-biom-format (1.1.2-1) unstable; urgency=low
 
   * debian/watch:

Modified: trunk/packages/python-biom-format/trunk/debian/control
===================================================================
--- trunk/packages/python-biom-format/trunk/debian/control	2013-11-20 22:00:16 UTC (rev 15206)
+++ trunk/packages/python-biom-format/trunk/debian/control	2013-11-20 22:00:47 UTC (rev 15207)
@@ -9,7 +9,9 @@
                cython (>= 0.17),
                help2man,
                python-dateutil,
-               python-cogent
+               python-cogent,
+               pyqi,
+               python-nose
 Standards-Version: 3.9.4
 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/python-biom-format/trunk/
 Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/python-biom-format/trunk/
@@ -22,7 +24,8 @@
          ${python:Depends},
          ${misc:Depends},
          python-dateutil,
-         python-cogent
+         python-cogent,
+         pyqi
 Description: Biological Observation Matrix (BIOM) format
  The BIOM file format (canonically pronounced biome) is designed to be a
  general-use format for representing biological sample by observation

Modified: trunk/packages/python-biom-format/trunk/debian/rules
===================================================================
--- trunk/packages/python-biom-format/trunk/debian/rules	2013-11-20 22:00:16 UTC (rev 15206)
+++ trunk/packages/python-biom-format/trunk/debian/rules	2013-11-20 22:00:47 UTC (rev 15207)
@@ -12,6 +12,9 @@
 #MIN_CYTHONVER := 0.17~beta1-2
 #NO_CYTHON := $(shell if dpkg --compare-versions $(CYTHONVER) lt $(MIN_CYTHONVER) ; then echo 0 ; else echo 1 ; fi)
 
+# linux-x86_64
+pybuilddir := $(shell dpkg-architecture -qDEB_BUILD_ARCH_OS)-$(shell dpkg-architecture -qDEB_BUILD_GNU_CPU)
+
 %:
 	dh $@ --with python2 # ,sphinxdoc
 
@@ -19,6 +22,7 @@
 	debian/create-manpages
 
 override_dh_auto_clean:
+	rm -rf build/tests
 	dh_auto_clean
 	find -name "._*" -exec rm -f '{}' ';'  #Needed if you try to build from pristine tarball
 	rm -rf python-code/support-code/_sparsemat.cpp
@@ -29,6 +33,7 @@
 	rename 's/\.py$$//;' $(bindir)/*
 
 override_dh_installman:
+	dh_installman
 	# try to create man pages whereever possible
 	mkdir -p $(mandir)
 	export PYTHONPATH=$(CURDIR)/python-code ; \
@@ -47,5 +52,17 @@
 		--name='subset a BIOM file, over either the observations or samples' \
 		$(bindir)/subset_biom > $(mandir)/subset_biom.1
 
+override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
+	set -e -x;\
+	for pyv in `pyversions -dv` ; do \
+	    cd build/; \
+	    ln -s ../python-code/tests; \
+	    env PYTHONPATH=lib.$(pybuilddir)-$${pyv} nosetests ; \
+	done
+endif
+
 get-orig-source:
-	. debian/get-orig-source
+	# . debian/get-orig-source
+	mkdir -p ../tarballs
+	uscan --verbose --force-download --destdir=../tarballs