[med-svn] [Git][med-team/q2-metadata][master] 6 commits: routine-update: New upstream version
Steffen Möller (@moeller)
gitlab at salsa.debian.org
Sat Sep 18 18:49:44 BST 2021
Steffen Möller pushed to branch master at Debian Med / q2-metadata
Commits:
f69abaa0 by Steffen Moeller at 2021-09-18T19:45:30+02:00
routine-update: New upstream version
- - - - -
d41c29e7 by Steffen Moeller at 2021-09-18T19:45:31+02:00
New upstream version 2021.8.0
- - - - -
9c31681c by Steffen Moeller at 2021-09-18T19:45:33+02:00
Update upstream source from tag 'upstream/2021.8.0'
Update to upstream version '2021.8.0'
with Debian dir d4d22828160b49749adf81b4edcc1eee2760c0e0
- - - - -
e867d2e9 by Steffen Moeller at 2021-09-18T19:45:33+02:00
routine-update: Standards-Version: 4.6.0
- - - - -
09812b62 by Steffen Moeller at 2021-09-18T19:46:13+02:00
routine-update: Ready to upload to unstable
- - - - -
6148d2ba by Steffen Moeller at 2021-09-18T19:49:31+02:00
New upstream version.
- - - - -
19 changed files:
- + .github/workflows/ci.yml
- − .travis.yml
- LICENSE
- README.md
- − ci/recipe/conda_build_config.yaml
- ci/recipe/meta.yaml
- debian/changelog
- debian/control
- debian/upstream/metadata
- q2_metadata/__init__.py
- q2_metadata/_distance.py
- q2_metadata/_tabulate.py
- q2_metadata/_version.py
- q2_metadata/plugin_setup.py
- q2_metadata/tests/__init__.py
- q2_metadata/tests/test_distance.py
- q2_metadata/tests/test_plugin_setup.py
- q2_metadata/tests/test_tabulate.py
- setup.py
Changes:
=====================================
.github/workflows/ci.yml
=====================================
@@ -0,0 +1,55 @@
+# This file is automatically generated by busywork.qiime2.org and
+# template-repos - any manual edits made to this file will be erased when
+# busywork performs maintenance updates.
+
+name: ci
+
+on:
+ pull_request:
+ push:
+ branches:
+ - master
+
+jobs:
+ lint:
+ runs-on: ubuntu-latest
+ steps:
+ - name: checkout source
+ uses: actions/checkout at v2
+
+ - name: set up python 3.8
+ uses: actions/setup-python at v1
+ with:
+ python-version: 3.8
+
+ - name: install dependencies
+ run: python -m pip install --upgrade pip
+
+ - name: lint
+ run: |
+ pip install -q https://github.com/qiime2/q2lint/archive/master.zip
+ q2lint
+ pip install -q flake8
+ flake8
+
+ build-and-test:
+ needs: lint
+ strategy:
+ matrix:
+ os: [ubuntu-latest, macos-latest]
+ runs-on: ${{ matrix.os }}
+ steps:
+ - name: checkout source
+ uses: actions/checkout at v2
+ with:
+ fetch-depth: 0
+
+ - name: set up git repo for versioneer
+ run: git fetch --depth=1 origin +refs/tags/*:refs/tags/*
+
+ - uses: qiime2/action-library-packaging at alpha1
+ with:
+ package-name: q2-metadata
+ build-target: dev
+ additional-tests: py.test --pyargs q2_metadata
+ library-token: ${{ secrets.LIBRARY_TOKEN }}
=====================================
.travis.yml deleted
=====================================
@@ -1,25 +0,0 @@
-dist: trusty
-sudo: false
-language: python
-before_install:
- - export MPLBACKEND='Agg'
- - wget -q https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
- - export MINICONDA_PREFIX="$HOME/miniconda"
- - bash miniconda.sh -b -p $MINICONDA_PREFIX
- - export PATH="$MINICONDA_PREFIX/bin:$PATH"
- - conda config --set always_yes yes
- - conda update -q conda
- - conda info -a
-install:
- - wget -q https://raw.githubusercontent.com/qiime2/environment-files/master/latest/staging/qiime2-latest-py36-linux-conda.yml
- - conda env create -q -n test-env --file qiime2-latest-py36-linux-conda.yml
- - source activate test-env
- - conda install -q pytest-cov
- - pip install -q flake8 coveralls
- - pip install -q https://github.com/qiime2/q2lint/archive/master.zip
- - make install
-script:
- - make lint
- - make test-cov
-after_success:
- - coveralls
=====================================
LICENSE
=====================================
@@ -1,6 +1,6 @@
BSD 3-Clause License
-Copyright (c) 2017-2020, QIIME 2 development team.
+Copyright (c) 2017-2021, QIIME 2 development team.
All rights reserved.
Redistribution and use in source and binary forms, with or without
=====================================
README.md
=====================================
@@ -1,6 +1,5 @@
# q2-metadata
-[](https://travis-ci.org/qiime2/q2-metadata)
-[](https://coveralls.io/github/qiime2/q2-metadata?branch=master)
+
-This is a QIIME 2 plugin. For details on QIIME 2, see https://qiime2.org..
+This is a QIIME 2 plugin. For details on QIIME 2, see https://qiime2.org..
\ No newline at end of file
=====================================
ci/recipe/conda_build_config.yaml deleted
=====================================
@@ -1,2 +0,0 @@
-python:
- - 3.6
=====================================
ci/recipe/meta.yaml
=====================================
@@ -1,6 +1,5 @@
{% set data = load_setup_py_data() %}
{% set version = data.get('version') or 'placehold' %}
-{% set release = '.'.join(version.split('.')[:2]) %}
package:
name: q2-metadata
@@ -23,11 +22,17 @@ requirements:
- scipy
- pandas
- scikit-bio
- - qiime2 {{ release }}.*
- - q2templates {{ release }}.*
- - q2-types {{ release }}.*
+ - qiime2 {{ qiime2_epoch }}.*
+ - q2templates {{ qiime2_epoch }}.*
+ - q2-types {{ qiime2_epoch }}.*
test:
+ requires:
+ - qiime2 >={{ qiime2 }}
+ - q2templates >={{ q2templates }}
+ - q2-types >={{ q2_types }}
+ - pytest
+
imports:
- q2_metadata
- qiime2.plugins.metadata
=====================================
debian/changelog
=====================================
@@ -1,10 +1,17 @@
-q2-metadata (2020.11.1+dfsg-2) UNRELEASED; urgency=medium
+q2-metadata (2021.8.0-1) unstable; urgency=medium
+ [ Étienne Mollier ]
* d/control: update uploader address
* d/watch: fix broken url to github
* d/salsa-ci.yml: disable build test on i386, due to missing python3-skbio
- -- Étienne Mollier <emollier at debian.org> Mon, 05 Jul 2021 22:59:03 +0200
+ [ Steffen Moeller ]
+ * New upstream version.
+ * Added myself to uploaders
+ * d/u/metadata: cosmetics, added ref to conda
+ * Standards-Version: 4.6.0 (routine-update)
+
+ -- Steffen Moeller <moeller at debian.org> Sat, 18 Sep 2021 19:45:41 +0200
q2-metadata (2020.11.1+dfsg-1) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -1,7 +1,8 @@
Source: q2-metadata
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Liubov Chuprikova <chuprikovalv at gmail.com>,
- Étienne Mollier <emollier at debian.org>
+ Étienne Mollier <emollier at debian.org>,
+ Steffen Moeller <moeller at debian.org>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
@@ -13,9 +14,9 @@ Build-Depends: debhelper-compat (= 13),
python3-skbio,
libjs-jquery-datatables,
qiime (>= 2020.11.1),
- q2templates (>= 2020.11.1),
- q2-types (>= 2020.11.1)
-Standards-Version: 4.5.1
+ q2templates,
+ q2-types
+Standards-Version: 4.6.0
Vcs-Browser: https://salsa.debian.org/med-team/q2-metadata
Vcs-Git: https://salsa.debian.org/med-team/q2-metadata.git
Homepage: https://qiime2.org/
@@ -32,8 +33,8 @@ Depends: ${shlibs:Depends},
python3-skbio,
libjs-jquery-datatables,
qiime (>= 2020.11.1),
- q2templates (>= 2020.11.1),
- q2-types (>= 2020.11.1)
+ q2templates,
+ q2-types
Description: QIIME 2 plugin for working with and visualizing Metadata
QIIME 2 is a powerful, extensible, and decentralized microbiome analysis
package with a focus on data and analysis transparency. QIIME 2 enables
=====================================
debian/upstream/metadata
=====================================
@@ -1,7 +1,10 @@
+---
Bug-Database: https://github.com/qiime2/q2-metadata/issues
Bug-Submit: https://github.com/qiime2/q2-metadata/issues/new
+Repository: https://github.com/qiime2/q2-metadata.git
+Repository-Browse: https://github.com/qiime2/q2-metadata
Reference:
-- Author: >
+ - Author: >
Evan Bolyen and Jai Ram Rideout and Matthew R Dillon and Nicholas A
Bokulich and Christian Abnet and Gabriel A Al-Ghalith and Harriet
Alexander and Eric J Alm and Manimozhiyan Arumugam and Francesco
@@ -35,14 +38,17 @@ Reference:
Wang and Jonathan Warren and Kyle C Weber and Chase HD Williamson
and Amy D Willis and Zhenjiang Zech Xu and Jesse R Zaneveld and
Yilong Zhang and Qiyun Zhu and Rob Knight and J Gregory Caporaso
- Title: >
+ Title: >
Reproducible, interactive, scalable and extensible microbiome data
science using QIIME 2
- Journal: Nature Biotechnology
- Year: 2019
- Volume: 37
- DOI: 10.1038/s41587-019-0209-9
- URL: https://www.nature.com/articles/s41587-019-0209-9
- eprint: https://www.nature.com/articles/s41587-019-0209-9.pdf
-Repository: https://github.com/qiime2/q2-metadata.git
-Repository-Browse: https://github.com/qiime2/q2-metadata
+ Journal: Nature Biotechnology
+ Year: 2019
+ Volume: 37
+ DOI: 10.1038/s41587-019-0209-9
+ URL: https://www.nature.com/articles/s41587-019-0209-9
+ eprint: https://www.nature.com/articles/s41587-019-0209-9.pdf
+Registry:
+ - Name: conda:qiime2
+ Entry: q2-metadata
+ - Name: bio.tools
+ Entry: NA
=====================================
q2_metadata/__init__.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2017-2020, QIIME 2 development team.
+# Copyright (c) 2017-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_metadata/_distance.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2017-2020, QIIME 2 development team.
+# Copyright (c) 2017-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_metadata/_tabulate.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2017-2020, QIIME 2 development team.
+# Copyright (c) 2017-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_metadata/_version.py
=====================================
@@ -23,9 +23,9 @@ def get_keywords():
# setup.py/versioneer.py will grep for the variable names, so they must
# each be defined on a line of their own. _version.py will just call
# get_keywords().
- git_refnames = " (tag: 2020.11.1)"
- git_full = "6ab5b4a9e543f6c8deeae26e4b5f0be004a8ee21"
- git_date = "2020-12-05 20:44:48 +0000"
+ git_refnames = " (tag: 2021.8.0)"
+ git_full = "1ba2cc31a9e49ab8db82e172d62088dbc0c2fc61"
+ git_date = "2021-09-09 18:35:29 +0000"
keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}
return keywords
=====================================
q2_metadata/plugin_setup.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2017-2020, QIIME 2 development team.
+# Copyright (c) 2017-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_metadata/tests/__init__.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2017-2020, QIIME 2 development team.
+# Copyright (c) 2017-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_metadata/tests/test_distance.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2017-2020, QIIME 2 development team.
+# Copyright (c) 2017-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_metadata/tests/test_plugin_setup.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2017-2020, QIIME 2 development team.
+# Copyright (c) 2017-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_metadata/tests/test_tabulate.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2017-2020, QIIME 2 development team.
+# Copyright (c) 2017-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
setup.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2017-2020, QIIME 2 development team.
+# Copyright (c) 2017-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
View it on GitLab: https://salsa.debian.org/med-team/q2-metadata/-/compare/ca7c05c2b4352fc7f5cea8d102bf7be01179d089...6148d2ba75562923edd0b46831d9d1dbf68ace13
--
View it on GitLab: https://salsa.debian.org/med-team/q2-metadata/-/compare/ca7c05c2b4352fc7f5cea8d102bf7be01179d089...6148d2ba75562923edd0b46831d9d1dbf68ace13
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