[med-svn] [Git][med-team/q2-composition][master] 4 commits: Completed copyright - prior to upload!
Steffen Möller (@moeller)
gitlab at salsa.debian.org
Sat Dec 4 21:33:37 GMT 2021
Steffen Möller pushed to branch master at Debian Med / q2-composition
Commits:
481adc6c by Steffen at 2021-12-04T22:22:31+01:00
Completed copyright - prior to upload!
- - - - -
e9595cbb by Steffen at 2021-12-04T22:23:45+01:00
New upstream version 2021.8.0
- - - - -
350badf5 by Steffen at 2021-12-04T22:23:47+01:00
Update upstream source from tag 'upstream/2021.8.0'
Update to upstream version '2021.8.0'
with Debian dir 7c6a4b3797fc9c7a62d12fbc5125bd8233446339
- - - - -
4be7cf49 by Steffen at 2021-12-04T22:32:46+01:00
Need a solution for vega as for q2-longitudinal
- - - - -
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/copyright
- q2_composition/__init__.py
- q2_composition/_ancom.py
- q2_composition/_impute.py
- q2_composition/_version.py
- q2_composition/plugin_setup.py
- q2_composition/tests/__init__.py
- q2_composition/tests/test_ancom.py
- q2_composition/tests/test_impute.py
- q2_composition/tests/test_plugin_setup.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-composition
+ build-target: dev
+ additional-tests: py.test --pyargs q2_composition
+ library-token: ${{ secrets.LIBRARY_TOKEN }}
=====================================
.travis.yml deleted
=====================================
@@ -1,29 +0,0 @@
-dist: trusty
-sudo: false
-language: python
-before_install:
- - export MPLBACKEND='Agg'
- - wget -q https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
- - export MINICONDA_PREFIX="$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
-notifications:
- webhooks:
- on_success: change
- on_failure: always
=====================================
LICENSE
=====================================
@@ -1,6 +1,6 @@
BSD 3-Clause License
-Copyright (c) 2016-2020, QIIME 2 development team.
+Copyright (c) 2016-2021, 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_composition
+# q2-composition
-[](https://travis-ci.org/qiime2/q2-composition)
-[](https://coveralls.io/github/qiime2/q2-composition?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-composition
@@ -22,12 +21,18 @@ requirements:
- scikit-bio
- biom-format >=2.1.5,<2.2.0
- scipy
- - pandas >=0.23.0
- - qiime2 {{ release }}.*
- - q2templates {{ release }}.*
- - q2-types {{ release }}.*
+ - pandas >=1
+ - qiime2 {{ qiime2_epoch }}.*
+ - q2templates {{ qiime2_epoch }}.*
+ - q2-types {{ qiime2_epoch }}.*
test:
+ requires:
+ - qiime2 >={{ qiime2 }}
+ - q2templates >={{ q2templates }}
+ - q2-types >={{ q2_types }}
+ - pytest
+
imports:
- q2_composition
- qiime2.plugins.composition
=====================================
debian/changelog
=====================================
@@ -1,5 +1,16 @@
-q2-composition (2020.11.1-1) UNRELEASED; urgency=medium
+q2-composition (2021.8.0-1) UNRELEASED; urgency=medium
* Initial release (Closes: #991992).
+ * TODO:
+ $ lintian q2-composition_2020.11.1-1_amd64.changes
+ E: q2-composition source: source-is-missing q2_composition/assets/ancom/js/vega-embed.min.js
+ E: q2-composition source: source-is-missing q2_composition/assets/ancom/js/vega.min.js
+
+ -- Steffen Moeller <moeller at debian.org> Sat, 04 Dec 2021 22:24:14 +0100
+
+q2-composition (2020.11.1-1) UNRELEASED; urgency=medium
+
+ * Initial packaging.
+
-- Steffen Moeller <moeller at debian.org> Sat, 07 Aug 2021 18:09:31 +0200
=====================================
debian/control
=====================================
@@ -9,7 +9,9 @@ Build-Depends: debhelper-compat (= 13),
python3-setuptools,
python3-nose <!nocheck>,
qiime (>= 2019.10.0) <!nocheck>,
-Standards-Version: 4.5.1
+ python3-pytest <!nocheck>,
+ python3-pytest-cov <!nocheck>
+Standards-Version: 4.6.0
Vcs-Browser: https://salsa.debian.org/med-team/q2-composition
Vcs-Git: https://salsa.debian.org/med-team/q2-composition.git
Homepage: https://qiime2.org/
=====================================
debian/copyright
=====================================
@@ -6,6 +6,14 @@ Files: *
Copyright: 2016-2019 QIIME 2 development team
License: BSD-3-clause
+Files: q2_composition/assets/ancom
+Copyright: 2015, University of Washington Interactive Data Lab
+License: BSD-3-clause
+
+Files: versioneer.py q2_composition/_version.py
+Copyright: Brian Warner
+License: CC0-1.0
+
Files: debian/*
Copyright: 2019 Liubov Chuprikova <chuprikovalv at gmail.com>
Andreas Tille <tille at debian.org>,
@@ -57,3 +65,124 @@ License: GPL-2+
.
On a Debian system, the GNU GPL license version 2 is distributed in the
file /usr/share/common-licenses/GPL-2.
+
+License: CC0-1.0
+ From https://creativecommons.org/publicdomain/zero/1.0/
+ .
+ CREATIVE COMMONS CORPORATION IS NOT A LAW FIRM AND DOES NOT PROVIDE
+ LEGAL SERVICES. DISTRIBUTION OF THIS DOCUMENT DOES NOT CREATE AN
+ ATTORNEY-CLIENT RELATIONSHIP. CREATIVE COMMONS PROVIDES THIS INFORMATION
+ ON AN "AS-IS" BASIS. CREATIVE COMMONS MAKES NO WARRANTIES REGARDING THE
+ USE OF THIS DOCUMENT OR THE INFORMATION OR WORKS PROVIDED HEREUNDER,
+ AND DISCLAIMS LIABILITY FOR DAMAGES RESULTING FROM THE USE OF THIS
+ DOCUMENT OR THE INFORMATION OR WORKS PROVIDED HEREUNDER.
+ .
+ Statement of Purpose
+ .
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=====================================
q2_composition/__init__.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2020, QIIME 2 development team.
+# Copyright (c) 2016-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_composition/_ancom.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2020, QIIME 2 development team.
+# Copyright (c) 2016-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_composition/_impute.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2020, QIIME 2 development team.
+# Copyright (c) 2016-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_composition/_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 = "3c99b8b2e2d94a7be6e4ce85e2f9b7f48c493202"
- git_date = "2020-12-05 20:44:48 +0000"
+ git_refnames = " (tag: 2021.8.0)"
+ git_full = "af8070faa7ec68d9527f19f504d258e4be9e4830"
+ git_date = "2021-09-09 18:35:29 +0000"
keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}
return keywords
=====================================
q2_composition/plugin_setup.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2020, QIIME 2 development team.
+# Copyright (c) 2016-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_composition/tests/__init__.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2020, QIIME 2 development team.
+# Copyright (c) 2016-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_composition/tests/test_ancom.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2020, QIIME 2 development team.
+# Copyright (c) 2016-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
@@ -9,7 +9,7 @@
import unittest
import os
-import pandas.util.testing as pdt
+import pandas.testing as pdt
import numpy as np
import pandas as pd
=====================================
q2_composition/tests/test_impute.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2020, QIIME 2 development team.
+# Copyright (c) 2016-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_composition/tests/test_plugin_setup.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2020, QIIME 2 development team.
+# Copyright (c) 2016-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
setup.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2020, QIIME 2 development team.
+# Copyright (c) 2016-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
View it on GitLab: https://salsa.debian.org/med-team/q2-composition/-/compare/99d57a26f3a1b72facb3c62db99d8d65dd716955...4be7cf49d390e9363ef4d442b82a9f3055339ca2
--
View it on GitLab: https://salsa.debian.org/med-team/q2-composition/-/compare/99d57a26f3a1b72facb3c62db99d8d65dd716955...4be7cf49d390e9363ef4d442b82a9f3055339ca2
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