[med-svn] [Git][med-team/python-pbcore][master] 10 commits: Ignore some tests needing pbtestdata which is not packaged
Andreas Tille
gitlab at salsa.debian.org
Thu Dec 5 10:30:22 GMT 2019
Andreas Tille pushed to branch master at Debian Med / python-pbcore
Commits:
cede0ed3 by Andreas Tille at 2019-12-04T19:36:42Z
Ignore some tests needing pbtestdata which is not packaged
- - - - -
bd9849d2 by Andreas Tille at 2019-12-04T19:42:06Z
Fix AFTER_INSTALL
- - - - -
1203f788 by Andreas Tille at 2019-12-04T19:49:57Z
Adjust installation and tests
- - - - -
9a07ce85 by Andreas Tille at 2019-12-04T19:59:00Z
Add myself to Uploaders, close bug
- - - - -
025043ff by Andreas Tille at 2019-12-04T20:46:11Z
Update copyright
- - - - -
22f228ec by Andreas Tille at 2019-12-05T09:08:52Z
Breaks/Provides/Replaces: python-pbcore (<= (1.7)
- - - - -
33e82f5a by Andreas Tille at 2019-12-05T10:21:47Z
Rewrite autopkgtest
- - - - -
baa7b371 by Andreas Tille at 2019-12-05T10:22:03Z
Adapt docbase control file
- - - - -
32595e5d by Andreas Tille at 2019-12-05T10:23:40Z
Polish changelog
- - - - -
268872da by Andreas Tille at 2019-12-05T10:27:18Z
Upload to unstable
- - - - -
8 changed files:
- debian/changelog
- debian/control
- debian/copyright
- debian/python-pbcore-doc.doc-base
- debian/python-pbcore-doc.install
- debian/rules
- debian/tests/control
- + debian/tests/run-unit-test
Changes:
=====================================
debian/changelog
=====================================
@@ -1,15 +1,17 @@
-python-pbcore (1.7.1+git20191121.7947eb7+dfsg-1) UNRELEASED; urgency=medium
+python-pbcore (1.7.1+git20191121.7947eb7+dfsg-1) unstable; urgency=medium
- * Team upload.
+ * Afif removed himself from Uploaders
+ * Add myself to Uploaders
* New upstream version Git checkout
+ Drop Python2 support and switch to Python3
+ Closes: #938009
* debhelper-compat 12
- * Drop Python2 support and switch to Python3
- --> discussed at https://github.com/PacificBiosciences/pbcore/issues/121
* Standards-Version: 4.4.1
* (Build-)Depends: python3-biopython (>= 1.74)
- TODO: #944242 (Needs biopython 1.74)
+ * Rewrite autopkgtest
+ * Breaks/Provides/Replaces: python-pbcore (<= (1.7)
- -- Andreas Tille <tille at debian.org> Wed, 04 Sep 2019 10:29:56 +0200
+ -- Andreas Tille <tille at debian.org> Thu, 05 Dec 2019 11:23:55 +0100
python-pbcore (1.6.5+dfsg-1) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -1,5 +1,6 @@
Source: python-pbcore
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
Section: python
Priority: optional
Build-Depends: debhelper-compat (= 12),
@@ -33,6 +34,9 @@ Depends: ${misc:Depends},
python3-biopython (>= 1.74)
Recommends: python3-h5py
Suggests: python-pbcore-doc (= ${source:Version})
+Breaks: python-pbcore (<= 1.7)
+Provides: python-pbcore
+Replaces: python-pbcore
Description: Python 3 library for processing PacBio data files
The pbcore package provides Python modules for processing Pacific Biosciences
data files and building PacBio bioinformatics applications. These modules
=====================================
debian/copyright
=====================================
@@ -4,32 +4,12 @@ Source: https://github.com/PacificBiosciences/pbcore
Files-Excluded: doc/pacbio-theme/*
Files: *
-Copyright: 2011-2015 Pacific Biosciences of California, Inc.
+Copyright: 2011-2019 Pacific Biosciences of California, Inc.
License: PacBio-BSD-3-Clause
-Files: pbcore/io/align/_bgzf.py
-Copyright: 2010-2013 Peter Cock
-License: Biopython-License-Agreement
- Permission to use, copy, modify, and distribute this software and its
- documentation with or without modifications and for any purpose and
- without fee is hereby granted, provided that any copyright notices
- appear in all copies and that both those copyright notices and this
- permission notice appear in supporting documentation, and that the
- names of the contributors or copyright holders not be used in
- advertising or publicity pertaining to distribution of the software
- without specific prior permission.
- .
- THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
- WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
- WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
- CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
- OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
- OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
- OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
- OR PERFORMANCE OF THIS SOFTWARE.
-
Files: debian/*
-Copyright: 2015 Afif Elghraoui <afif at ghraoui.name>
+Copyright: 2015-2018 Afif Elghraoui <afif at ghraoui.name>
+ 2018-2019 Andreas Tille <tille at debian.org>
License: PacBio-BSD-3-Clause
License: PacBio-BSD-3-Clause
=====================================
debian/python-pbcore-doc.doc-base
=====================================
@@ -4,5 +4,5 @@ Author: Pacific Biosciences
Section: Programming/Python
Format: HTML
-Index: /usr/share/doc/python-pbcore/html/index.html
-Files: /usr/share/doc/python-pbcore/html/*.html
+Index: /usr/share/doc/python3-pbcore/html/index.html
+Files: /usr/share/doc/python3-pbcore/html/*.html
=====================================
debian/python-pbcore-doc.install
=====================================
@@ -1 +1,2 @@
-doc/_build/html usr/share/doc/python-pbcore
+doc/_build/html usr/share/doc/python3-pbcore
+_tmp/usr/share/doc/python3-pbcore/tests usr/share/doc/python3-pbcore
=====================================
debian/rules
=====================================
@@ -5,10 +5,9 @@ include /usr/share/dpkg/default.mk
export PYBUILD_NAME = pbcore
export PYBUILD_AFTER_INSTALL = \
- chmod -x {destdir}/{install_dir}/pbcore/data/*.h5 \
- {destdir}/{install_dir}/pbcore/data/datasets/*.xml
+ chmod -x {destdir}/{install_dir}/pbcore/data/datasets/*.xml
-DESTDIR = $(CURDIR)/debian/$(DEB_SOURCE)
+DESTDIR = $(CURDIR)/debian/python3-$(PYBUILD_NAME)
%:
LC_ALL=C.UTF-8 dh $@ --with python3 --buildsystem=pybuild
@@ -27,12 +26,25 @@ override_dh_installdocs:
override_dh_auto_clean:
dh_auto_clean
$(MAKE) clean
+ rm -rf _tmp
override_dh_auto_test:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
+ # we need to exclude tests requiring pbtestdata which is not packaged
+ mkdir -p /tmp/tests_avoid
+ mv `grep -l pbtestdata tests/*.py` /tmp/tests_avoid
+ # for whatever reason this test is failing as well - just skip it for the moment
+ mv tests/test_pbdataset_filters.py /tmp/tests_avoid
PYBUILD_SYSTEM=custom \
PYBUILD_TEST_ARGS="{interpreter} setup.py test" \
dh_auto_test
+ # copy working test data into doc dir as user examples
+ mkdir -p _tmp/usr/share/doc/python3-$(PYBUILD_NAME)
+ cp -a tests _tmp/usr/share/doc/python3-$(PYBUILD_NAME)
+ find _tmp -type d -name __pycache__ | xargs rm -rf
+ # move back ignored tests
+ mv /tmp/tests_avoid/* tests
+ rmdir /tmp/tests_avoid
endif
override_dh_installchangelogs:
=====================================
debian/tests/control
=====================================
@@ -1,8 +1,3 @@
-Test-Command: nosetests -v
-Depends:
- python-pbcore,
- python-nose,
- python-pyxb,
- python-coverage,
- python-h5py,
+Tests: run-unit-test
+Depends: @, python3-pytest, python3-pyxb, python3-pyxb, python3-pytest-runner, python3-pytest-xdist, python3-pytest-cov
Restrictions: allow-stderr
=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,18 @@
+#!/bin/bash
+set -e
+
+pkg=python3-pbcore
+
+export LC_ALL=C.UTF-8
+if [ "${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}/tests "${AUTOPKGTEST_TMP}"
+
+cd "${AUTOPKGTEST_TMP}"
+
+gunzip -r *
+
+pytest-3
View it on GitLab: https://salsa.debian.org/med-team/python-pbcore/compare/15e355ba956d807cf7c47e8821c911f35ab0823c...268872da5d634f88858b5d186d73b0954a6943c9
--
View it on GitLab: https://salsa.debian.org/med-team/python-pbcore/compare/15e355ba956d807cf7c47e8821c911f35ab0823c...268872da5d634f88858b5d186d73b0954a6943c9
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