python-pymummer (0.11.0-2) unstable; urgency=medium

  * Team Upload.
  * Add autopkgtests

[dgit import unpatched python-pymummer 0.11.0-2]

11 files changed, 202 insertions, 0 deletions

diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..18d63d5
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,93 @@
+python-pymummer (0.11.0-2) unstable; urgency=medium
+
+  * Team Upload.
+  * Add autopkgtests
+
+ -- Nilesh Patra <npatra974@gmail.com>  Fri, 28 Aug 2020 20:28:54 +0530
+
+python-pymummer (0.11.0-1) unstable; urgency=medium
+
+  * New upstream version
+  * Standards-Version: 4.5.0 (routine-update)
+  * debhelper-compat 13 (routine-update)
+  * Add salsa-ci file (routine-update)
+  * Rules-Requires-Root: no (routine-update)
+  * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,
+    Repository-Browse. (routine-update)
+  * lintian complained about missing maintainer, added Andreas and myself
+  * removed egg.info files
+
+ -- Steffen Moeller <moeller@debian.org>  Wed, 10 Jun 2020 02:13:58 +0200
+
+python-pymummer (0.10.3-2) unstable; urgency=medium
+
+  * debhelper 11
+  * Point Vcs fields to salsa.debian.org
+  * Standards-Version: 4.3.0
+  * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
+
+ -- Andreas Tille <tille@debian.org>  Mon, 07 Jan 2019 09:37:20 +0100
+
+python-pymummer (0.10.3-1) unstable; urgency=medium
+
+  * Team upload.
+  * New upstream release.
+
+ -- Sascha Steinbiss <satta@debian.org>  Mon, 29 Jan 2018 15:46:12 +0100
+
+python-pymummer (0.10.2-1) unstable; urgency=medium
+
+  * Team upload.
+  * New upstream release.
+
+ -- Sascha Steinbiss <satta@debian.org>  Thu, 02 Feb 2017 14:30:00 +0100
+
+python-pymummer (0.10.1-1) unstable; urgency=medium
+
+  * Team upload.
+  * New upstream release.
+
+ -- Sascha Steinbiss <satta@debian.org>  Fri, 18 Nov 2016 19:58:54 +0000
+
+python-pymummer (0.10.0-1) unstable; urgency=medium
+
+  * Team upload.
+  * New upstream release.
+
+ -- Sascha Steinbiss <satta@debian.org>  Tue, 15 Nov 2016 11:18:13 +0000
+
+python-pymummer (0.9.0-1) unstable; urgency=medium
+
+  * Team upload.
+  * New upstream release.
+
+ -- Sascha Steinbiss <satta@debian.org>  Tue, 18 Oct 2016 18:37:05 +0000
+
+python-pymummer (0.8.1-1) unstable; urgency=medium
+
+  * Team upload.
+  * New upstream release.
+  * Bump Standards-Version.
+
+ -- Sascha Steinbiss <satta@debian.org>  Wed, 24 Aug 2016 13:45:50 +0000
+
+python-pymummer (0.7.1-1) unstable; urgency=low
+
+  * Update Standards-Version
+  * Imported Upstream version 0.7.1
+
+ -- Afif Elghraoui <afif@debian.org>  Sat, 23 Apr 2016 20:25:13 -0700
+
+python-pymummer (0.7.0-1) unstable; urgency=medium
+
+  * Imported Upstream version 0.7.0
+  * Use secure VCS URLs
+  * Bump copyright year
+
+ -- Afif Elghraoui <afif@ghraoui.name>  Fri, 12 Feb 2016 01:09:47 -0800
+
+python-pymummer (0.6.1-1) unstable; urgency=low
+
+  * Initial release (Closes: #805230)
+
+ -- Afif Elghraoui <afif@ghraoui.name>  Sun, 15 Nov 2015 15:00:31 -0800
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..a6f2d7f
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,29 @@
+Source: python-pymummer
+Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+Uploaders: Steffen Moeller <moeller@debian.org>,
+           Andreas Tille <tille@debian.org>
+Section: python
+Testsuite: autopkgtest-pkg-python
+Priority: optional
+Build-Depends: debhelper-compat (= 13),
+               dh-python,
+               python3-all,
+               python3-setuptools,
+               fastaq (>=3.10.0),
+               mummer,
+               python3-nose <!nocheck>
+Standards-Version: 4.5.0
+Vcs-Browser: https://salsa.debian.org/med-team/python-pymummer
+Vcs-Git: https://salsa.debian.org/med-team/python-pymummer.git
+Homepage: https://github.com/sanger-pathogens/pymummer
+Rules-Requires-Root: no
+
+Package: python3-pymummer
+Architecture: all
+Depends: ${misc:Depends},
+         ${python3:Depends},
+         fastaq (>=3.10.0),
+         mummer
+Description: Python 3 interface to MUMmer
+ pymummer is a Python wrapper for running the programs of the MUMmer
+ sequence alignment suite and parsing their output.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..450527f
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,29 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: pymummer
+Upstream-Contact: Martin Hunt <path-help@sanger.ac.uk>
+Source: https://github.com/sanger-pathogens/pymummer
+
+Files: *
+Copyright: 2015-2016 Martin Hunt <path-help@sanger.ac.uk>
+                     Nishadi De Silva
+License: GPL-3.0
+
+Files: debian/*
+Copyright: 2015-2016 Afif Elghraoui <afif@debian.org>
+License: GPL-3.0
+
+License: GPL-3.0
+ This program 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.
+ .
+ This package 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.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 3 can be found in "/usr/share/common-licenses/GPL-3".
diff --git a/debian/docs b/debian/docs
new file mode 100644
index 0000000..b43bf86
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1 @@
+README.md
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..e19ff93
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,21 @@
+#!/usr/bin/make -f
+
+#DH_VERBOSE = 1
+
+include /usr/share/dpkg/default.mk
+
+export PYBUILD_NAME=pymummer
+
+%:
+	LC_ALL=C.UTF-8 dh $@ --with python3 --buildsystem=pybuild
+
+override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
+	PYBUILD_SYSTEM=custom \
+	PYBUILD_TEST_ARGS="{interpreter} setup.py test" \
+	  dh_auto_test
+endif
+
+override_dh_auto_clean:
+	rm -f pymummer.egg-info/PKG-INFO pymummer.egg-info/SOURCES.txt pymummer.egg-info/dependency_links.txt pymummer.egg-info/requires.txt pymummer.egg-info/top_level.txt
+	rm -rf .pybuild pymummer/tests/__pycache__ pymummer/__pycache__
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..4b450a8
--- /dev/null
+++ b/debian/tests/control
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @, python3-all, python3-pytest
+Restrictions: allow-stderr
diff --git a/debian/tests/run-unit-test b/debian/tests/run-unit-test
new file mode 100644
index 0000000..0b19e00
--- /dev/null
+++ b/debian/tests/run-unit-test
@@ -0,0 +1,8 @@
+#!/bin/bash
+set -e
+
+for py in $(py3versions -r 2> /dev/null)
+do
+	$py -m pytest -v
+done
+
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..8f4c0dc
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,9 @@
+Bug-Database: https://github.com/sanger-pathogens/pymummer/issues
+Bug-Submit: https://github.com/sanger-pathogens/pymummer/issues/new
+Registry:
+ - Name: conda:bioconda
+   Entry: pymummer
+ - Name: OMICtools
+   Entry: NA
+Repository: https://github.com/sanger-pathogens/pymummer.git
+Repository-Browse: https://github.com/sanger-pathogens/pymummer
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..a586a89
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,4 @@
+version=3
+
+opts="filenamemangle=s/(?:.*?)?v?(\d[\d.]*)\.tar\.gz/python-pymummer-$1.tar.gz/" \
+  https://github.com/sanger-pathogens/pymummer/tags (?:.*?/)?v?(\d[\d.]*)\.tar\.gz