[med-svn] [Git][med-team/q2-cutadapt][master] 6 commits: Versioned (Build-)Depends qiime and q2 modules (>= 2021.8.0)
Andreas Tille (@tille)
gitlab at salsa.debian.org
Wed Sep 29 16:21:24 BST 2021
Andreas Tille pushed to branch master at Debian Med / q2-cutadapt
Commits:
632e408b by Andreas Tille at 2021-09-29T17:17:40+02:00
Versioned (Build-)Depends qiime and q2 modules (>= 2021.8.0)
- - - - -
41f83c1d by Andreas Tille at 2021-09-29T17:17:56+02:00
New upstream version 2021.8.0
- - - - -
6ee4a2aa by Andreas Tille at 2021-09-29T17:17:56+02:00
routine-update: New upstream version
- - - - -
852807e6 by Andreas Tille at 2021-09-29T17:17:59+02:00
Update upstream source from tag 'upstream/2021.8.0'
Update to upstream version '2021.8.0'
with Debian dir ae94ee3c437ae6e8403fafaf39e2c5d41ebff891
- - - - -
188c8367 by Andreas Tille at 2021-09-29T17:18:00+02:00
routine-update: Standards-Version: 4.6.0
- - - - -
8d79104f by Andreas Tille at 2021-09-29T17:19:45+02:00
routine-update: Ready to upload to unstable
- - - - -
17 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
- q2_cutadapt/__init__.py
- q2_cutadapt/_demux.py
- q2_cutadapt/_trim.py
- q2_cutadapt/_version.py
- q2_cutadapt/plugin_setup.py
- q2_cutadapt/tests/__init__.py
- q2_cutadapt/tests/test_demux.py
- q2_cutadapt/tests/test_trim.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-cutadapt
+ build-target: dev
+ additional-tests: py.test --pyargs q2_cutadapt
+ 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 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
=====================================
@@ -1,5 +1,5 @@
# q2-cutadapt
-[](https://travis-ci.org/qiime2/q2-cutadapt) [](https://coveralls.io/github/qiime2/q2-cutadapt?branch=master)
+
-This is a QIIME 2 plugin. For details on QIIME 2 and tutorials demonstrating how to use this plugin, see the [QIIME 2 documentation](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-cutadapt
@@ -23,10 +22,15 @@ requirements:
- pigz
- pandas
- numpy
- - qiime2 {{ release }}.*
- - q2-types {{ release }}.*
+ - qiime2 {{ qiime2_epoch }}.*
+ - q2-types {{ qiime2_epoch }}.*
test:
+ requires:
+ - qiime2 >={{ qiime2 }}
+ - q2-types >={{ q2_types }}
+ - pytest
+
imports:
- q2_cutadapt
- qiime2.plugins.cutadapt
=====================================
debian/changelog
=====================================
@@ -1,4 +1,6 @@
-q2-cutadapt (2020.11.1-2) UNRELEASED; urgency=medium
+q2-cutadapt (2021.8.0-1) unstable; urgency=medium
+
+ * Team upload.
[ Steffen Moeller ]
* Fixed d/watch.
@@ -6,7 +8,11 @@ q2-cutadapt (2020.11.1-2) UNRELEASED; urgency=medium
[ Nilesh Patra ]
* d/salsa-ci.yml: Disable build on i386 due to missing python3-skbio
- -- Steffen Moeller <moeller at debian.org> Mon, 26 Jul 2021 00:34:24 +0530
+ [ Andreas Tille ]
+ * Versioned (Build-)Depends qiime and q2 modules (>= 2021.8.0)
+ * Standards-Version: 4.6.0 (routine-update)
+
+ -- Andreas Tille <tille at debian.org> Wed, 29 Sep 2021 17:18:08 +0200
q2-cutadapt (2020.11.1-1) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -10,9 +10,9 @@ Build-Depends: debhelper-compat (= 13),
python3-pytest-cov,
python3-pandas,
cutadapt (>= 2.3),
- qiime (>= 2020.11.0),
- q2-types (>= 2020.11.0)
-Standards-Version: 4.5.1
+ qiime (>= 2021.8.0),
+ q2-types (>= 2021.8.0)
+Standards-Version: 4.6.0
Vcs-Browser: https://salsa.debian.org/med-team/q2-cutadapt
Vcs-Git: https://salsa.debian.org/med-team/q2-cutadapt.git
Homepage: https://qiime2.org/
@@ -27,8 +27,8 @@ Depends: ${shlibs:Depends},
python3-pandas,
cutadapt,
pigz,
- qiime,
- q2-types
+ qiime (>= 2021.8.0),
+ q2-types (>= 2021.8.0)
Description: QIIME 2 plugin to work with adapters in sequence data
QIIME 2 is a powerful, extensible, and decentralized microbiome analysis
package with a focus on data and analysis transparency. QIIME 2 enables
=====================================
q2_cutadapt/__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_cutadapt/_demux.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_cutadapt/_trim.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_cutadapt/_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 = " (HEAD -> master, tag: 2020.11.1)"
- git_full = "13b69a6fd0be98d8d089cec05612466765dcb0de"
- git_date = "2020-12-05 20:44:46 +0000"
+ git_refnames = " (tag: 2021.8.0)"
+ git_full = "ca9ebf26c396e42120d9e9b8e0f6a1c3905b689d"
+ git_date = "2021-09-09 18:35:28 +0000"
keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}
return keywords
=====================================
q2_cutadapt/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_cutadapt/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_cutadapt/tests/test_demux.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_cutadapt/tests/test_trim.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-cutadapt/-/compare/565d29a405fe645e1fd3ccabae841663a0946732...8d79104fdc270c8809326b1dcb12bff5df112fd0
--
View it on GitLab: https://salsa.debian.org/med-team/q2-cutadapt/-/compare/565d29a405fe645e1fd3ccabae841663a0946732...8d79104fdc270c8809326b1dcb12bff5df112fd0
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