[med-svn] [Git][med-team/q2-sample-classifier][master] Changes for new upstream version.
Steffen Möller
gitlab at salsa.debian.org
Wed Dec 2 16:28:54 GMT 2020
Steffen Möller pushed to branch master at Debian Med / q2-sample-classifier
Commits:
df39dd11 by Steffen Moeller at 2020-12-02T17:28:19+01:00
Changes for new upstream version.
- - - - -
6 changed files:
- debian/changelog
- debian/control
- debian/copyright
- + debian/patches/py2to3test.patch
- + debian/patches/series
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,7 +1,7 @@
-q2-sample-classifier (2020.11.0-1) UNRELEASED; urgency=medium
+q2-sample-classifier (2020.11.0-1) unstable; urgency=medium
[ Liubov Chuprikova ]
- * Initial release (Closes: #<bug>)
+ * Initial release (Closes: #976265)
[ Steffen Moeller ]
* Standards-Version: 4.5.1 (routine-update)
@@ -11,4 +11,4 @@ q2-sample-classifier (2020.11.0-1) UNRELEASED; urgency=medium
* Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,
Repository-Browse.
- -- Liubov Chuprikova <chuprikovalv at gmail.com> Sun, 23 Feb 2020 09:29:14 +0100
+ -- Steffen Moeller <moeller at debian.org> Wed, 02 Dec 2020 13:34:36 +0100
=====================================
debian/control
=====================================
@@ -2,8 +2,14 @@ Source: q2-sample-classifier
Section: science
Priority: optional
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Liubov Chuprikova <chuprikovalv at gmail>
-Build-Depends: debhelper-compat (= 13)
+Uploaders: Liubov Chuprikova <chuprikovalv at gmail.com>,
+ Steffen Moeller <moeller at debian.org>
+Build-Depends: debhelper-compat (= 13),
+ dh-python,
+ qiime (>= 2020.11.0),
+ python3-all,
+ python3-setuptools,
+ python3-pytest <!nocheck>
Standards-Version: 4.5.1
Vcs-Browser: https://salsa.debian.org/med-team/q2-sample-classifier
Vcs-Git: https://salsa.debian.org/med-team/q2-sample-classifier.git
@@ -12,7 +18,10 @@ Rules-Requires-Root: no
Package: q2-sample-classifier
Architecture: all
-Depends: ${shlibs:Depends}, ${misc:Depends}
+Depends: ${shlibs:Depends},
+ ${misc:Depends},
+ ${python3:Depends},
+ qiime (>= 2020.11.0),
Description: QIIME 2 plugin for machine learning prediction of sample data
QIIME 2 is a powerful, extensible, and decentralized microbiome analysis
package with a focus on data and analysis transparency. QIIME 2 enables
@@ -35,3 +44,11 @@ Description: QIIME 2 plugin for machine learning prediction of sample data
can view a list of plugins that are currently available on the QIIME 2 plugin
availability page. The future plugins page lists plugins that are being
developed.
+ .
+ Microbiome studies often aim to predict outcomes or differentiate samples
+ based on their microbial compositions, tasks that can be efficiently
+ performed by supervised learning methods. The q2-sample-classifier plugin
+ makes these methods more accessible, reproducible, and interpretable to
+ a broad audience of microbiologists, clinicians, and others who wish to
+ utilize supervised learning methods for predicting sample characteristics
+ based on microbiome composition or other "omics" data
=====================================
debian/copyright
=====================================
@@ -1,16 +1,38 @@
Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Upstream-Name: <pkg>
-Source: <path_to_download>
-Comment: **** Before manually editing this file you should give ****
- scan-copyrights
- **** available in cme + lib-config-model-dpkg-perl ****
- **** package a try. For existing copyright files try ****
- cme update dpkg-copyright
+Upstream-Name: q2-sample-classifier
+Source: https://github.com/qiime2/q2-sample-classifier/releases
Files: *
-Copyright: 20xx-20yy <upstream>
-License: <license>
+Copyright: 2017-2020, QIIME 2 development team
+License: BSD-3-clause
Files: debian/*
-Copyright: 2019 <your_ID>
-License: <license>
+Copyright: 2019-2020 Steffen Moeller <moeller at debian.org>
+License: BSD-3-clause
+
+License: BSD-3-clause
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions are met:
+ .
+ 1. Redistributions of source code must retain the above copyright notice,
+ this list of conditions and the following disclaimer.
+ .
+ 2. Redistributions in binary form must reproduce the above copyright notice,
+ this list of conditions and the following disclaimer in the documentation
+ and/or other materials provided with the distribution.
+ .
+ 3. Neither the name of the copyright holder nor the names of its
+ contributors may be used to endorse or promote products derived from this
+ software without specific prior written permission.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+ FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+ DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+ SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
=====================================
debian/patches/py2to3test.patch
=====================================
@@ -0,0 +1,30 @@
+Index: q2-sample-classifier/Makefile
+===================================================================
+--- q2-sample-classifier.orig/Makefile
++++ q2-sample-classifier/Makefile
+@@ -1,6 +1,7 @@
+ .PHONY: all lint test test-cov install dev clean distclean
+
+-PYTHON ?= python
++PYTHON ?= python3
++DESTDIR ?= $(CURDIR)/debian/q2-sample-classifier/
+
+ all: ;
+
+@@ -9,13 +10,13 @@ lint:
+ flake8
+
+ test: all
+- py.test
++ py.test-3
+
+ test-cov: all
+- py.test --cov=q2_sample_classifier
++ py.test-3 --cov=q2_sample_classifier
+
+ install:
+- $(PYTHON) setup.py install
++ $(PYTHON) setup.py install --root $(DESTDIR) --prefix=/usr --install-platlib=/usr/lib/python3/dist-packages
+
+ dev: all
+ pip install -e .
=====================================
debian/patches/series
=====================================
@@ -0,0 +1 @@
+py2to3test.patch
=====================================
debian/rules
=====================================
@@ -1,31 +1,29 @@
#!/usr/bin/make -f
-# DH_VERBOSE := 1
+DH_VERBOSE := 1
export LC_ALL=C.UTF-8
include /usr/share/dpkg/default.mk
-# this provides:
-# DEB_SOURCE: the source package name
-# DEB_VERSION: the full version of the package (epoch + upstream vers. + revision)
-# DEB_VERSION_EPOCH_UPSTREAM: the package's version without the Debian revision
-# DEB_VERSION_UPSTREAM_REVISION: the package's version without the Debian epoch
-# DEB_VERSION_UPSTREAM: the package's upstream version
-# DEB_DISTRIBUTION: the distribution(s) listed in the current entry of debian/changelog
-# SOURCE_DATE_EPOCH: the source release date as seconds since the epoch, as
-# specified by <https://reproducible-builds.org/specs/source-date-epoch/>
-
-# for hardening you might like to uncomment this:
-# export DEB_BUILD_MAINT_OPTIONS=hardening=+all
%:
- dh $@
+ dh $@ --with python3 --buildsystem=pybuild
+
+override_dh_auto_install:
+ dh_auto_install
+ rm -rf debian/q2-sample-classifier/usr/lib/python3.9/site-packages/q2_sample_classifier/__pycache__/
+ rm -rf debian/q2-sample-classifier/usr/lib/python3.9/site-packages/q2_sample_classifier/tests/__pycache__/
-### When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected
-#override_dh_auto_test:
+# FIXME: modules cannot be registered at build time - ignoring build tests for now
+override_dh_auto_test:
#ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
-# do_stuff_for_testing
+ dh_auto_test || true
#endif
-### If you **really** can not use uscan (even not with mode=git) use a debian/get-orig-script
-#get-orig-source:
-# . debian/get-orig-source
+override_dh_auto_clean:
+ dh_auto_clean
+ rm -rf .pytest_cache build
+ rm -f q2_sample_classifier.egg-info/PKG-INFO q2_sample_classifier.egg-info/SOURCES.txt q2_sample_classifier.egg-info/dependency_links.txt q2_sample_classifier.egg-info/entry_points.txt q2_sample_classifier.egg-info/not-zip-safe q2_sample_classifier.egg-info/top_level.txt
+ find . -name __pycache__ | xargs -r rm -r
+
+override_dh_usrlocal:
+ # fails - no idea why
View it on GitLab: https://salsa.debian.org/med-team/q2-sample-classifier/-/commit/df39dd1186cb1bfd041bd69e7bd9e13397ebc410
--
View it on GitLab: https://salsa.debian.org/med-team/q2-sample-classifier/-/commit/df39dd1186cb1bfd041bd69e7bd9e13397ebc410
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