[med-svn] [Git][med-team/q2-fragment-insertion][master] 4 commits: routine-update: New upstream version

Steffen Möller (@moeller) gitlab at salsa.debian.org
Wed Sep 22 13:59:17 BST 2021 


Steffen Möller pushed to branch master at Debian Med / q2-fragment-insertion


Commits:
ba00499c by Steffen Moeller at 2021-09-22T14:54:17+02:00
routine-update: New upstream version

- - - - -
3f6658d2 by Steffen Moeller at 2021-09-22T14:54:18+02:00
New upstream version 2021.8.0
- - - - -
d811b3ee by Steffen Moeller at 2021-09-22T14:54:20+02:00
Update upstream source from tag 'upstream/2021.8.0'

Update to upstream version '2021.8.0'
with Debian dir dfda677ac03d369e6c48724db5934ff66dc9551a
- - - - -
12ebb788 by Steffen Moeller at 2021-09-22T14:58:49+02:00
New upstream version, still initial release.

- - - - -


23 changed files:

- + .github/workflows/ci.yml
- − .travis.yml
- LICENSE
- README.md
- bin/import_references.py
- − ci/recipe/conda_build_config.yaml
- ci/recipe/meta.yaml
- debian/changelog
- debian/control
- debian/upstream/metadata
- q2_fragment_insertion/__init__.py
- q2_fragment_insertion/_format.py
- q2_fragment_insertion/_insertion.py
- q2_fragment_insertion/_transformer.py
- q2_fragment_insertion/_type.py
- q2_fragment_insertion/_version.py
- q2_fragment_insertion/plugin_setup.py
- q2_fragment_insertion/tests/__init__.py
- q2_fragment_insertion/tests/test_formats.py
- q2_fragment_insertion/tests/test_insertion.py
- q2_fragment_insertion/tests/test_transformers.py
- q2_fragment_insertion/tests/test_types.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-fragment-insertion
+        build-target: dev
+        additional-tests: py.test --pyargs q2_fragment_insertion
+        library-token: ${{ secrets.LIBRARY_TOKEN }}


=====================================
.travis.yml deleted
=====================================
@@ -1,24 +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
-  - rm qiime2-latest-py36-linux-conda.yml
-  - source activate test-env
-  - conda install -q pytest
-  - pip install -q https://github.com/qiime2/q2lint/archive/master.zip
-  - conda install -q flake8
-  - python setup.py install
-script:
-  - make lint
-  - make test


=====================================
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
=====================================
@@ -1,10 +1,5 @@
 # q2-fragment-insertion
 
-[![Build Status](https://travis-ci.org/qiime2/q2-fragment-insertion.svg?branch=master)](https://travis-ci.org/qiime2/q2-fragment-insertion)
-[![Coverage Status](https://coveralls.io/repos/github/qiime2/q2-fragment-insertion/badge.svg?branch=master)](https://coveralls.io/github/qiime2/q2-fragment-insertion?branch=master)
+![](https://github.com/qiime2/q2-fragment-insertion/workflows/ci/badge.svg)
 
-
-This is a QIIME 2 plugin. For details on QIIME 2, see https://qiime2.org..
-
-For usage examples and additional details please see this plugin's entry on the
-[QIIME 2 Library](https://library.qiime2.org/plugins/q2-fragment-insertion/16/).
+This is a QIIME 2 plugin. For details on QIIME 2, see https://qiime2.org..
\ No newline at end of file


=====================================
bin/import_references.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.
 #


=====================================
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-fragment-insertion
@@ -22,12 +21,17 @@ requirements:
     - python {{ python }}
     - openjdk
     - biom-format >=2.1.5,<2.2.0
-    - qiime2 {{ release }}.*
-    - q2-types {{ release }}.*
+    - qiime2 {{ qiime2_epoch }}.*
+    - q2-types {{ qiime2_epoch }}.*
     - sepp
     - ijson
 
 test:
+  requires:
+    - qiime2 >={{ qiime2 }}
+    - q2-types >={{ q2_types }}
+    - pytest
+
   imports:
     - q2_fragment_insertion
     - qiime2.plugins.fragment_insertion


=====================================
debian/changelog
=====================================
@@ -1,5 +1,6 @@
-q2-fragment-insertion (2020.11.1-1) UNRELEASED; urgency=medium
+q2-fragment-insertion (2021.8.0-1) UNRELEASED; urgency=medium
 
   * Initial release (Closes: #977115)
+  * New upstream version
 
- -- Steffen Moeller <moeller at debian.org>  Fri, 11 Dec 2020 00:56:08 +0100
+ -- Steffen Moeller <moeller at debian.org>  Wed, 22 Sep 2021 14:54:28 +0200


=====================================
debian/control
=====================================
@@ -27,8 +27,8 @@ Depends: ${shlibs:Depends},
          qiime (>= 2020.11.0),
          python3-biom-format,
          python3-skbio,
-         q2-types (>= 2020.11.1)
-Recommends: sepp (>= 4.3.10+dfsg-4),
+         q2-types
+Recommends: sepp,
             python3-ijson,
             default-jdk
 Description: QIIME 2 plugin for fragment insertion


=====================================
debian/upstream/metadata
=====================================
@@ -1,5 +1,8 @@
+---
 Bug-Database: https://github.com/qiime2/q2-feature-table/issues
 Bug-Submit: https://github.com/qiime2/q2-feature-table/issues/new
+Repository: https://github.com/qiime2/q2-feature-table.git
+Repository-Browse: https://github.com/qiime2/q2-feature-table
 Reference:
  - Author: >
     Evan Bolyen and Jai Ram Rideout and Matthew R Dillon and Nicholas A
@@ -44,8 +47,12 @@ Reference:
    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-feature-table.git
-Repository-Browse: https://github.com/qiime2/q2-feature-table
 Registry:
+ - Name: conda:qiime2
+   Entry: q2-fragment-insertion
  - Name: bio.tools
    Entry: NA
+   Checked: 2021-09-21
+ - Name: guix
+   Entry: NA
+   Checked: 2021-09-21


=====================================
q2_fragment_insertion/__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_fragment_insertion/_format.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_fragment_insertion/_insertion.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_fragment_insertion/_transformer.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_fragment_insertion/_type.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_fragment_insertion/_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 = "37e25ad7ee6a1e611d9e43b15e15af13f4bca18c"
-    git_date = "2020-12-05 20:44:49 +0000"
+    git_refnames = " (tag: 2021.8.0)"
+    git_full = "45be95bdc8cf0183506d9e11e8caf394b11a42da"
+    git_date = "2021-09-09 18:35:31 +0000"
     keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}
     return keywords
 


=====================================
q2_fragment_insertion/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_fragment_insertion/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_fragment_insertion/tests/test_formats.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_fragment_insertion/tests/test_insertion.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_fragment_insertion/tests/test_transformers.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_fragment_insertion/tests/test_types.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-fragment-insertion/-/compare/4e001ec46cd8a888f22f7bec9fa90e4d7be57b05...12ebb788747c2b565b7fbe20032ad091c1efe463

-- 
View it on GitLab: https://salsa.debian.org/med-team/q2-fragment-insertion/-/compare/4e001ec46cd8a888f22f7bec9fa90e4d7be57b05...12ebb788747c2b565b7fbe20032ad091c1efe463
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