[med-svn] [Git][med-team/q2-alignment][master] 8 commits: Versioned (Build-)Depends qiime and q2 modules (>= 2021.8.0)
Andreas Tille (@tille)
gitlab at salsa.debian.org
Wed Sep 29 17:01:06 BST 2021
Andreas Tille pushed to branch master at Debian Med / q2-alignment
Commits:
ecafd760 by Andreas Tille at 2021-09-29T17:47:50+02:00
Versioned (Build-)Depends qiime and q2 modules (>= 2021.8.0)
- - - - -
a2daf1c9 by Andreas Tille at 2021-09-29T17:48:00+02:00
routine-update: Fix watchfile to detect new versions on github
- - - - -
c018f703 by Andreas Tille at 2021-09-29T17:48:03+02:00
routine-update: Standards-Version: 4.6.0
- - - - -
88cf0ad0 by Andreas Tille at 2021-09-29T17:57:03+02:00
Really fix watch file
- - - - -
c0333a92 by Andreas Tille at 2021-09-29T17:57:22+02:00
routine-update: New upstream version
- - - - -
a4da4a09 by Andreas Tille at 2021-09-29T17:57:23+02:00
New upstream version 2021.8.0
- - - - -
7ede36b9 by Andreas Tille at 2021-09-29T17:57:23+02:00
Update upstream source from tag 'upstream/2021.8.0'
Update to upstream version '2021.8.0'
with Debian dir 06cfc0d62df3dd1f7cead9aae228e1a3b095669e
- - - - -
2eded836 by Andreas Tille at 2021-09-29T17:59:27+02:00
routine-update: Ready to upload to unstable
- - - - -
18 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/watch
- q2_alignment/__init__.py
- q2_alignment/_filter.py
- q2_alignment/_mafft.py
- q2_alignment/_version.py
- q2_alignment/plugin_setup.py
- q2_alignment/tests/__init__.py
- q2_alignment/tests/test_filter.py
- q2_alignment/tests/test_mafft.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-alignment
+ build-target: dev
+ additional-tests: py.test --pyargs q2_alignment
+ 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) 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-alignment
-[](https://travis-ci.org/qiime2/q2-alignment)
-[](https://coveralls.io/github/qiime2/q2-alignment?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-alignment
@@ -19,13 +18,17 @@ requirements:
run:
- python {{ python }}
- - scikit-bio
- - qiime2 {{ release }}.*
- - q2-types {{ release }}.*
+ - scikit-bio >=0.5.5
+ - qiime2 {{ qiime2_epoch }}.*
+ - q2-types {{ qiime2_epoch }}.*
- mafft >=7.394
- - sina >=1.3.5,<=2
test:
+ requires:
+ - qiime2 >={{ qiime2 }}
+ - q2-types >={{ q2_types }}
+ - pytest
+
imports:
- q2_alignment
- qiime2.plugins.alignment
=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+q2-alignment (2021.8.0-1) unstable; urgency=medium
+
+ * Team upload.
+ * Versioned (Build-)Depends qiime and q2 modules (>= 2021.8.0)
+ * Fix watchfile to detect new versions on github (routine-update)
+ * Standards-Version: 4.6.0 (routine-update)
+
+ -- Andreas Tille <tille at debian.org> Wed, 29 Sep 2021 17:57:32 +0200
+
q2-alignment (2020.11.1-2) unstable; urgency=high
* Team Upload.
=====================================
debian/control
=====================================
@@ -9,10 +9,10 @@ Build-Depends: debhelper-compat (= 13),
python3-setuptools,
python3-skbio,
python3-pytest-cov,
- qiime,
- q2-types,
+ qiime (>= 2021.8.0),
+ q2-types (>= 2021.8.0),
mafft
-Standards-Version: 4.5.1
+Standards-Version: 4.6.0
Vcs-Browser: https://salsa.debian.org/med-team/q2-alignment
Vcs-Git: https://salsa.debian.org/med-team/q2-alignment.git
Homepage: https://qiime2.org/
@@ -25,9 +25,9 @@ Depends: ${shlibs:Depends},
${python3:Depends},
python3-setuptools,
python3-skbio,
- qiime,
+ qiime (>= 2021.8.0),
mafft,
- q2-types
+ q2-types (>= 2021.8.0)
Suggests: sina
Description: QIIME 2 plugin for generating and manipulating alignments
QIIME 2 is a powerful, extensible, and decentralized microbiome analysis
=====================================
debian/watch
=====================================
@@ -1,4 +1,3 @@
version=4
-
-opts="filenamemangle=s/.*\/archive\/(\d[\d.]+ at ARCHIVE_EXT@)/@PACKAGE at -$1/" \
- https://github.com/qiime2/q2-alignment/releases/latest .*/archive/(\d[.\d]+)@ARCHIVE_EXT@
+opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar.gz%@PACKAGE at -$1.tar.gz%" \
+ https://github.com/qiime2/q2-alignment/tags (?:.*?/)?v?(\d[\d.]*)\.tar\.gz
=====================================
q2_alignment/__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_alignment/_filter.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_alignment/_mafft.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_alignment/_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 = "5993d9e09b96ba63fd9bc07e063398cfd18f94d5"
- git_date = "2020-12-05 20:44:49 +0000"
+ git_refnames = " (tag: 2021.8.0)"
+ git_full = "1abd1be756284f20cd172cf9e9b1e713527febfb"
+ git_date = "2021-09-09 18:35:30 +0000"
keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}
return keywords
=====================================
q2_alignment/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_alignment/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_alignment/tests/test_filter.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_alignment/tests/test_mafft.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-alignment/-/compare/ff29c57586f4506b1e82245a6f5a8957e4063ac6...2eded836f69db7d7c44e2035b9ced56acb1c7db1
--
View it on GitLab: https://salsa.debian.org/med-team/q2-alignment/-/compare/ff29c57586f4506b1e82245a6f5a8957e4063ac6...2eded836f69db7d7c44e2035b9ced56acb1c7db1
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