python-pauvre (0.2.3-1) unstable; urgency=medium

  [ Nilesh Patra ]
  * Team Upload.
  * New upstream version 0.2.3
  * Declare compliance with policy 4.5.1

  [ Etienne Mollier ]
  * d/control: updated my uploader address

[dgit import unpatched python-pauvre 0.2.3-1]

26 files changed, 505 insertions, 0 deletions

diff --git a/debian/README.test b/debian/README.test
new file mode 100644
index 0000000..ae9535f
--- /dev/null
+++ b/debian/README.test
@@ -0,0 +1,20 @@
+Notes on how this package can be tested.
+────────────────────────────────────────
+
+This package can be tested by running the provided test:
+
+    sh run-unit-test
+
+in order to confirm its integrity.
+
+
+Build time tests
+────────────────
+
+Test data are not readily available in upstream repository, but can be
+retrieved from another repository, from the same author, seemingly dedicated to
+test data:
+
+	https://github.com/conchoecia/beroe_forskalii_mitogenome/tree/master/gff_files
+
+Those are made available inside debian/tests/gff_files.
diff --git a/debian/bin/pauvre b/debian/bin/pauvre
new file mode 100755
index 0000000..069038f
--- /dev/null
+++ b/debian/bin/pauvre
@@ -0,0 +1,6 @@
+#! /bin/bash
+# pauvre reimplementation in shell: the test suite expects its availability in
+# the PATH.
+set -ex
+export PYTHONPATH="$BUILDDIR"
+exec python3 "$BUILDDIR/pauvre/pauvre_main.py" "$@"
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..e9c5393
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,35 @@
+python-pauvre (0.2.3-1) unstable; urgency=medium
+
+  [ Nilesh Patra ]
+  * Team Upload.
+  * New upstream version 0.2.3
+  * Declare compliance with policy 4.5.1
+
+  [ Etienne Mollier ]
+  * d/control: updated my uploader address
+
+ -- Nilesh Patra <nilesh@debian.org>  Sun, 15 Aug 2021 18:47:57 +0530
+
+python-pauvre (0.2.2-2) unstable; urgency=medium
+
+  * Added myself as uploader.
+  * Added (build-)dependency on python3-tk (Closes: #962698)
+  * Cleanup test data after build time tests; this reduces the weight of the
+    python3-pauvre package, and improve reproducible builds.
+  * Added ref to bioconda (Steffen Moeller)
+
+ -- Étienne Mollier <etienne.mollier@mailoo.org>  Wed, 08 Jul 2020 18:40:39 +0200
+
+python-pauvre (0.2.2-1) unstable; urgency=medium
+
+  * New upstream version
+  * debhelper-compat 13 (routine-update)
+  * Rules-Requires-Root: no (routine-update)
+
+ -- Andreas Tille <tille@debian.org>  Thu, 11 Jun 2020 22:36:46 +0200
+
+python-pauvre (0.2.1-1) unstable; urgency=medium
+
+  * Initial release (Closes: #958951)
+
+ -- Andreas Tille <tille@debian.org>  Sat, 02 May 2020 10:08:54 +0200
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..ea46713
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,58 @@
+Source: python-pauvre
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille@debian.org>,
+           Étienne Mollier <emollier@debian.org>
+Build-Depends: debhelper-compat (= 13),
+               dh-python,
+               python3,
+               python3-setuptools,
+               python3-matplotlib <!nocheck>,
+               python3-biopython <!nocheck>,
+               python3-pandas <!nocheck>,
+               python3-numpy <!nocheck>,
+               python3-scipy <!nocheck>,
+               python3-sklearn <!nocheck>,
+               python3-tk <!nocheck>,
+               python3-progressbar <!nocheck>
+Standards-Version: 4.5.1
+Vcs-Browser: https://salsa.debian.org/med-team/python-pauvre
+Vcs-Git: https://salsa.debian.org/med-team/python-pauvre.git
+Homepage: https://github.com/conchoecia/pauvre
+Rules-Requires-Root: no
+
+Package: python3-pauvre
+Architecture: all
+Section: python
+Depends: ${python3:Depends},
+         ${misc:Depends},
+         python3-tk,
+         python3-matplotlib,
+         python3-biopython,
+         python3-pandas,
+         python3-numpy,
+         python3-scipy,
+         python3-sklearn
+Description: QC and genome browser plotting Oxford Nanopore and PacBio long reads
+ Pauvre is a plotting package designed for nanopore and PacBio long reads.
+ .
+ This package currently hosts four scripts for plotting and/or printing stats.
+ .
+  pauvre marginplot
+     Takes a fastq file as input and outputs a marginal histogram with a
+     heatmap.
+  pauvre stats
+     Takes a fastq file as input and prints out a table of stats, including
+     how many basepairs/reads there are for a length/mean quality cutoff.
+     This is also automagically called when using pauvre marginplot
+  pauvre redwood
+     Method of representing circular genomes. A redwood plot contains long
+     reads as "rings" on the inside, a gene annotation "cambrium/phloem",
+     and a RNAseq "bark". The input is .bam files for the long reads and
+     RNAseq data, and a .gff file for the annotation.
+  pauvre synteny
+     Makes a synteny plot of circular genomes. Finds the most parsimonius
+     rotation to display the synteny of all the input genomes with the
+     fewest crossings-over. Input is one .gff file per circular genome
+     and one directory of gene alignments.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..1cd0453
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,25 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: pauvre
+Source: https://pypi.org/project/pauvre/#files
+
+Files: *
+Copyright: 2016-2020 Darrin T. Schultz
+License: GPL-3+
+
+Files: debian/*
+Copyright: 2020 Andreas Tille <tille@debian.org>
+License: GPL-3+
+
+License: GPL-3+
+ pauvre is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+ .
+ pauvre is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ GNU General Public License for more details.
+ .
+ On Debian systems you can find the full text of the GNU General Public
+ License version 3 at /usr/share/common-licenses/GPL-3.
diff --git a/debian/createmanpages b/debian/createmanpages
new file mode 100755
index 0000000..c000f8e
--- /dev/null
+++ b/debian/createmanpages
@@ -0,0 +1,28 @@
+#!/bin/sh
+MANDIR=debian
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+NAME=`grep "^Description:" debian/control | sed 's/^Description: *//' | head -n1`
+PROGNAME=`grep "^Package:" debian/control | sed 's/^Package: *//' | head -n1`
+
+AUTHOR=".SH AUTHOR\n \
+This manpage was written by $DEBFULLNAME for the Debian distribution and\n \
+can be used for any other usage of the program.\
+"
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=pauvre
+help2man --no-info --no-discard-stderr --help-option=" " \
+         --name="$NAME" \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+echo "$MANDIR/*.1" > debian/manpages
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+    http://liw.fi/manpages/
+EOT
diff --git a/debian/docs b/debian/docs
new file mode 100644
index 0000000..9a4f4f8
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1,2 @@
+debian/README.test
+debian/tests/run-unit-test
diff --git a/debian/examples b/debian/examples
new file mode 100644
index 0000000..2ae09a5
--- /dev/null
+++ b/debian/examples
@@ -0,0 +1 @@
+scripts/test.sh
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..0f65186
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/*.1
diff --git a/debian/patches/2to3.patch b/debian/patches/2to3.patch
new file mode 100644
index 0000000..32abb24
--- /dev/null
+++ b/debian/patches/2to3.patch
@@ -0,0 +1,92 @@
+Author: Andreas Tille <tille@debian.org>
+Last-Update: Fri, 24 Apr 2020 12:49:17 +0200
+Description: Test script somehow remained at Python2 -> fix this using 2to3
+
+--- a/pauvre/lsi/test.py
++++ b/pauvre/lsi/test.py
+@@ -3,10 +3,10 @@
+ # Email: splichte@princeton.edu
+ # Date: 09/02/2013
+ 
+-from lsi import intersection
++from .lsi import intersection
+ import random
+ import time, sys
+-from helper import *
++from .helper import *
+ 
+ ev = 0.00000001
+ 
+@@ -42,20 +42,20 @@ es = False
+ now = time.time()
+ for seg1 in S:
+ 	if approx_equal(seg1[0][0], seg1[1][0], ev):
+-		print 'VERTICAL SEG'
+-		print ''
+-		print ''
++		print('VERTICAL SEG')
++		print('')
++		print('')
+ 		vs = True
+ 	if approx_equal(seg1[0][1], seg1[1][1], ev):
+-		print 'HORIZONTAL SEG'
+-		print ''
+-		print ''
++		print('HORIZONTAL SEG')
++		print('')
++		print('')
+ 		hs = True
+ 	for seg2 in S:
+ 		if seg1 is not seg2 and segs_equal(seg1, seg2):
+-			print 'EQUAL SEGS'
+-			print ''
+-			print ''
++			print('EQUAL SEGS')
++			print('')
++			print('')
+ 			es = True
+ 		if seg1 is not seg2 and (seg2, seg1) not in seen:
+ 			i = intersect(seg1, seg2)
+@@ -68,17 +68,17 @@ for seg1 in S:
+ 				seen.append((seg1, seg2))
+ later = time.time()
+ n2time = later-now
+-print "Line sweep results:"
++print("Line sweep results:")
+ now = time.time()
+ lsinters = intersection(S)
+ inters = []
+-for k, v in lsinters.iteritems():
++for k, v in lsinters.items():
+ 	#print '{0}: {1}'.format(k, v)
+ 	inters.append(k)
+ #	inters.append(v)
+ later = time.time()
+-print 'TIME ELAPSED: {0}'.format(later-now)
+-print "N^2 comparison results:"
++print('TIME ELAPSED: {0}'.format(later-now))
++print("N^2 comparison results:")
+ pts_seen = []
+ highestseen = 0
+ for i in intersections:
+@@ -97,14 +97,14 @@ for i in intersections:
+ 		if approx_equal(k[0], i[0][0], ev) and approx_equal(k[1], i[0][1], ev):
+ 			in_k = True
+ 	if in_k == False:
+-		print 'Not in K: {0}: {1}'.format(i[0], i[1])
++		print('Not in K: {0}: {1}'.format(i[0], i[1]))
+ #	print i
+-print highestseen
+-print 'TIME ELAPSED: {0}'.format(n2time)
++print(highestseen)
++print('TIME ELAPSED: {0}'.format(n2time))
+ #print 'Missing from line sweep but in N^2:'
+ #for i in seen:
+ #	matched = False
+-print len(lsinters)
+-print len(pts_seen)
++print(len(lsinters))
++print(len(pts_seen))
+ if len(lsinters) != len(pts_seen):
+-	print 'uh oh!'
++	print('uh oh!')
diff --git a/debian/patches/lsi-test-args.patch b/debian/patches/lsi-test-args.patch
new file mode 100644
index 0000000..ef219b7
--- /dev/null
+++ b/debian/patches/lsi-test-args.patch
@@ -0,0 +1,21 @@
+Description: inject arguments in test script
+ The script expects a few arguments which are not passed by the testing
+ infrastructure.  This breaks the test.  The integer value in sys.argv[1] is
+ picked at random, but could be subject to discussion.
+Author: Étienne Mollier <etienne.mollier@mailoo.org>
+Forwarded: not-needed
+Last-Update: 2020-04-26
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- python-pauvre.orig/pauvre/lsi/test.py
++++ python-pauvre/pauvre/lsi/test.py
+@@ -10,6 +10,9 @@
+ 
+ ev = 0.00000001
+ 
++sys.argv[1] = '10'
++sys.argv[2] = None
++
+ def scale(i):
+ 	return float(i)
+ 
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..c1f6c9b
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,2 @@
+2to3.patch
+lsi-test-args.patch
diff --git a/debian/pauvre.1 b/debian/pauvre.1
new file mode 100644
index 0000000..c4a49eb
--- /dev/null
+++ b/debian/pauvre.1
@@ -0,0 +1,40 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.13.
+.TH PAUVRE "1" "April 2020" "pauvre 0.1924" "User Commands"
+.SH NAME
+pauvre \- QC and genome browser plotting Oxford Nanopore and PacBio long reads
+.SH DESCRIPTION
+usage: pauvre [\-h] [\-v]
+.IP
+{browser,custommargin,marginplot,redwood,stats,synplot} ...
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-v\fR, \fB\-\-version\fR
+Installed pauvre version
+.SS "[sub-commands]:"
+.IP
+{browser,custommargin,marginplot,redwood,stats,synplot}
+.TP
+browser
+an adaptable genome browser with various track types
+.TP
+custommargin
+plot custom marginal histograms of tab\-delimited files
+.TP
+marginplot
+plot a marginal histogram of a fastq file
+.TP
+redwood
+make a redwood plot from a bam file
+.TP
+stats
+outputs stats from a fastq file
+.TP
+synplot
+make a synteny plot from a gff file, protein
+alignment, and partition file
+.SH AUTHOR
+ This manpage was written by Andreas Tille for the Debian distribution and
+ can be used for any other usage of the program.
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..155d22a
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,28 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+export PYBUILD_NAME=pauvre
+
+%:
+	dh $@ --with python3 --buildsystem=pybuild
+
+override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
+	PYBUILDDIR="$$(echo "$(CURDIR)"/.pybuild/cpython3_3.*/build)" \
+	&& mkdir -p "$${PYBUILDDIR}/pauvre/tests/testdata/alignments" \
+		"$${PYBUILDDIR}/pauvre/tests/testresults" \
+	&& cp -r "$(CURDIR)/debian/tests/gff_files" \
+		"$${PYBUILDDIR}/pauvre/tests/testdata" \
+	&& BUILDDIR="$${PYBUILDDIR}" PATH="$(CURDIR)/debian/bin:$$PATH" \
+		dh_auto_test \
+	&& rm "$${PYBUILDDIR}/input" \
+	&& rm -r "$${PYBUILDDIR}/pauvre/tests/testdata" \
+		"$${PYBUILDDIR}/pauvre/tests/testresults"
+endif
+
+override_dh_installexamples:
+	# Do not install test script in Python lib
+	find debian -name scripts -type d | xargs rm -rf
+	dh_installexamples
+	sed -i 's/^git clone/#&/' `find debian -name test.sh`
diff --git a/debian/salsa-ci.yml b/debian/salsa-ci.yml
new file mode 100644
index 0000000..33c3a64
--- /dev/null
+++ b/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
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/tests/control b/debian/tests/control
new file mode 100644
index 0000000..109e19f
--- /dev/null
+++ b/debian/tests/control
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @, python3-nanoget-examples
+Restrictions: allow-stderr
diff --git a/debian/tests/gff_files/Bf201706.gff b/debian/tests/gff_files/Bf201706.gff
new file mode 100644
index 0000000..9d6c315
--- /dev/null
+++ b/debian/tests/gff_files/Bf201706.gff
@@ -0,0 +1,18 @@
+##gff-version 3
+##source-version geneious 9.0.2
+Bf201706_circ	Geneious	region	1	13338	.	+	0	Is_circular=true
+Bf201706_circ	Geneious	rRNA	2256	3115	.	+	.	Name=16S
+Bf201706_circ	Geneious	rRNA	1880	2255	.	+	.	Name=12S
+Bf201706_circ	Geneious	gene	1	1524	.	+	.	Name=COX1
+Bf201706_circ	Geneious	gene	5981	7459	.	+	.	Name=ND5
+Bf201706_circ	Geneious	gene	4699	5781	.	+	.	Name=ND4
+Bf201706_circ	Geneious	gene	7608	8672	.	+	.	Name=URF1
+Bf201706_circ	Geneious	gene	10863	11918	.	+	.	Name=CYTB
+Bf201706_circ	Geneious	gene	11837	12751	.	+	.	Name=ND1
+Bf201706_circ	Geneious	gene	3308	4051	.	+	.	Name=COX3
+Bf201706_circ	Geneious	gene	10016	10744	.	+	.	Name=ND2
+Bf201706_circ	Geneious	gene	9200	9868	.	+	.	Name=URF2
+Bf201706_circ	Geneious	gene	12757	13320	.	+	.	Name=COX2
+Bf201706_circ	Geneious	gene	4324	4698	.	+	.	Name=ND3
+Bf201706_circ	Geneious	gene	3099	3302	.	+	.	Name=ND6
+Bf201706_circ	Geneious	gene	5781	5969	.	+	.	Name=ND4L
diff --git a/debian/tests/gff_files/JN392469.gff b/debian/tests/gff_files/JN392469.gff
new file mode 100644
index 0000000..2965641
--- /dev/null
+++ b/debian/tests/gff_files/JN392469.gff
@@ -0,0 +1,17 @@
+##gff-version 3
+##source-version geneious 9.0.2
+JN392469	Geneious	region	1	11017	.	+	0	Is_circular=true
+JN392469	Geneious	source	1	11017	.	+	.	Name=source Pleurobrachia bachei
+JN392469	Geneious	gene	1	1539	.	+	.	Name=COX1 gene
+JN392469	Geneious	gene	1660	2241	.	+	.	Name=COX2 gene
+JN392469	Geneious	rRNA	2518	3460	.	+	.	Name=16S rRNA
+JN392469	Geneious	rRNA	3491	4053	.	+	.	Name=12S rRNA
+JN392469	Geneious	gene	4054	4794	.	+	.	Name=COX3 gene
+JN392469	Geneious	gene	4802	5470	.	+	.	Name=ND2 gene
+JN392469	Geneious	gene	5521	5841	.	+	.	Name=ND3 gene
+JN392469	Geneious	gene	5842	6912	.	+	.	Name=ND4 gene
+JN392469	Geneious	gene	7074	8156	.	+	.	Name=CYTB gene
+JN392469	Geneious	gene	8158	9672	.	+	.	Name=ND5 gene
+JN392469	Geneious	gene	9672	10511	.	+	.	Name=ND1 gene
+JN392469	Geneious	gene	10511	10708	.	+	.	Name=ND6 gene
+JN392469	Geneious	gene	10803	11003	.	+	.	Name=ND4L gene
\ No newline at end of file
diff --git a/debian/tests/gff_files/LN898113.gff b/debian/tests/gff_files/LN898113.gff
new file mode 100644
index 0000000..bf4e335
--- /dev/null
+++ b/debian/tests/gff_files/LN898113.gff
@@ -0,0 +1,17 @@
+##gff-version 3
+##source-version geneious 9.0.2
+LN898113	Geneious	region	1	11574	.	+	0	Is_circular=true
+LN898113	Geneious	source	1	11574	.	+	.	Name=source Coeloplana loyai
+LN898113	Geneious	gene	1	1551	.	+	.	Name=COX1 gene
+LN898113	Geneious	gene	1556	2131	.	+	.	Name=COX2 gene
+LN898113	Geneious	gene	2136	3242	.	+	.	Name=ND4 gene
+LN898113	Geneious	gene	3242	3982	.	+	.	Name=ND2 gene
+LN898113	Geneious	rRNA	4707	5549	.	+	.	Name=16S rRNA
+LN898113	Geneious	rRNA	5550	5962	.	+	.	Name=12S rRNA
+LN898113	Geneious	gene	5963	6190	.	+	.	Name=ND4L gene
+LN898113	Geneious	gene	6192	7484	.	+	.	Name=ND1 gene
+LN898113	Geneious	gene	7488	8555	.	+	.	Name=CYTB gene
+LN898113	Geneious	gene	8556	9314	.	+	.	Name=COX3 gene
+LN898113	Geneious	gene	9314	9655	.	+	.	Name=ND3 gene
+LN898113	Geneious	gene	9790	11307	.	+	.	Name=ND5 gene
+LN898113	Geneious	gene	11309	11515	.	+	.	Name=ND6 gene
diff --git a/debian/tests/gff_files/LN898114.gff b/debian/tests/gff_files/LN898114.gff
new file mode 100644
index 0000000..25430ef
--- /dev/null
+++ b/debian/tests/gff_files/LN898114.gff
@@ -0,0 +1,17 @@
+##gff-version 3
+##source-version geneious 9.0.2
+LN898114	Geneious	region	1	11551	.	+	0	Is_circular=true
+LN898114	Geneious	source	1	11551	.	+	.	Name=source Coeloplana yulianicorum
+LN898114	Geneious	gene	1	1551	.	+	.	Name=COX1 gene
+LN898114	Geneious	gene	1561	2136	.	+	.	Name=COX2 gene
+LN898114	Geneious	gene	2137	3243	.	+	.	Name=ND4 gene
+LN898114	Geneious	gene	3243	3983	.	+	.	Name=ND2 gene
+LN898114	Geneious	rRNA	4694	5540	.	+	.	Name=16S rRNA
+LN898114	Geneious	rRNA	5541	5948	.	+	.	Name=12S rRNA
+LN898114	Geneious	gene	5949	6221	.	+	.	Name=ND4L gene
+LN898114	Geneious	gene	6235	7482	.	+	.	Name=ND1 gene
+LN898114	Geneious	gene	7488	8555	.	+	.	Name=CYTB gene
+LN898114	Geneious	gene	8556	9314	.	+	.	Name=COX3 gene
+LN898114	Geneious	gene	9314	9655	.	+	.	Name=ND3 gene
+LN898114	Geneious	gene	9785	11302	.	+	.	Name=ND5 gene
+LN898114	Geneious	gene	11304	11510	.	+	.	Name=ND6 gene
diff --git a/debian/tests/gff_files/LN898115.gff b/debian/tests/gff_files/LN898115.gff
new file mode 100644
index 0000000..d1ad2ad
--- /dev/null
+++ b/debian/tests/gff_files/LN898115.gff
@@ -0,0 +1,17 @@
+##gff-version 3
+##source-version geneious 9.0.2
+LN898115	Geneious	region	1	9961	.	+	0	Is_circular=true
+LN898115	Geneious	source	1	9961	.	+	.	Name=source Vallicula multiformis
+LN898115	Geneious	gene	1	1533	.	+	.	Name=COX1 gene
+LN898115	Geneious	gene	1523	2080	.	+	.	Name=COX2 gene
+LN898115	Geneious	gene	2074	3126	.	+	.	Name=ND4 gene
+LN898115	Geneious	rRNA	3127	3951	.	+	.	Name=16S rRNA
+LN898115	Geneious	rRNA	3952	4306	.	+	.	Name=12S rRNA
+LN898115	Geneious	gene	4307	5011	.	+	.	Name=ND2 gene
+LN898115	Geneious	gene	5011	6048	.	+	.	Name=CYTB gene
+LN898115	Geneious	gene	6032	6799	.	+	.	Name=COX3 gene
+LN898115	Geneious	gene	6796	7119	.	+	.	Name=ND3 gene
+LN898115	Geneious	gene	7124	8569	.	+	.	Name=ND5 gene
+LN898115	Geneious	gene	8577	8792	.	+	.	Name=ND4L gene
+LN898115	Geneious	gene	8792	9655	.	+	.	Name=ND1 gene
+LN898115	Geneious	CDS	9751	9948	.	+	.	Name=ND6 CDS
diff --git a/debian/tests/gff_files/NC016117.gff b/debian/tests/gff_files/NC016117.gff
new file mode 100644
index 0000000..c179edb
--- /dev/null
+++ b/debian/tests/gff_files/NC016117.gff
@@ -0,0 +1,17 @@
+##gff-version 3
+##source-version geneious 9.0.2
+NC_016117	Geneious	region	1	10326	.	+	0	Is_circular=true
+NC_016117	Geneious	source	1	10326	.	+	.	Name=source Mnemiopsis leidyi
+NC_016117	Geneious	rRNA	3521	4398	.	+	.	Name=16S rRNA
+NC_016117	Geneious	rRNA	3153	3520	.	+	.	Name=12S rRNA
+NC_016117	Geneious	gene	1	1524	.	+	.	Name=COX1 gene
+NC_016117	Geneious	gene	6527	7933	.	+	.	Name=ND5 gene
+NC_016117	Geneious	gene	4399	5493	.	+	.	Name=ND4 gene
+NC_016117	Geneious	gene	8775	9860	.	+	.	Name=CYTB gene
+NC_016117	Geneious	gene	7933	8802	.	+	.	Name=ND1 gene
+NC_016117	Geneious	gene	1525	2250	.	+	.	Name=COX3 gene
+NC_016117	Geneious	gene	5495	6220	.	+	.	Name=ND2 gene
+NC_016117	Geneious	gene	2574	3152	.	+	.	Name=COX2 gene
+NC_016117	Geneious	gene	2247	2573	.	+	.	Name=ND3 gene
+NC_016117	Geneious	gene	9847	10050	.	+	.	Name=ND6 gene
+NC_016117	Geneious	gene	6221	6418	.	+	.	Name=ND4L gene
\ No newline at end of file
diff --git a/debian/tests/run-unit-test b/debian/tests/run-unit-test
new file mode 100644
index 0000000..28306fd
--- /dev/null
+++ b/debian/tests/run-unit-test
@@ -0,0 +1,17 @@
+#!/bin/bash
+set -e
+
+pkg=python3-pauvre
+
+export LC_ALL=C.UTF-8
+if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
+  AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+  trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
+cp -a /usr/share/doc/python3-nanoget/examples/nanotest "${AUTOPKGTEST_TMP}"
+
+cd "${AUTOPKGTEST_TMP}"
+
+sh test.sh
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..00bc0b8
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,9 @@
+---
+Bug-Database: https://github.com/conchoecia/pauvre/issues
+Bug-Submit: https://github.com/conchoecia/pauvre/issues/new
+Repository: https://github.com/conchoecia/pauvre.git
+Registry:
+ - Name: bio.tools
+   Entry: NA
+ - Name: conda:bioconda
+   Entry: pauvre
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..f3483c3
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,9 @@
+version=4
+
+opts="uversionmangle=s/(0\.\d)(\d)/$1.$2/" \
+  https://pypi.python.org/simple/pauvre .*/pauvre-@ANY_VERSION@@ARCHIVE_EXT@#sha256=.*
+
+# The Github tarball contains some more files in dir pauvre/bioawk/ and files/ .  Theses do not seem to be needed.
+# Asked for clarification in https://github.com/conchoecia/pauvre/issues/38
+#opts="uversionmangle=s/(0\.\d)(\d)/$1.$2/,filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE@-$1.tar.gz%" \
+#  https://github.com/conchoecia/pauvre/tags .*/archive/v?@ANY_VERSION@\.tar\.gz