[med-svn] [Git][med-team/q2-diversity-lib][upstream] New upstream version 2021.8.0

Steffen Möller (@moeller) gitlab at salsa.debian.org
Tue Sep 21 15:08:24 BST 2021 


Steffen Möller pushed to branch upstream at Debian Med / q2-diversity-lib


Commits:
06c25edf by Steffen at 2021-09-19T00:48:59+02:00
New upstream version 2021.8.0
- - - - -


16 changed files:

- .github/workflows/lint-build-test.yml → .github/workflows/ci.yml
- LICENSE
- README.md
- − ci/recipe/conda_build_config.yaml
- ci/recipe/meta.yaml
- q2_diversity_lib/__init__.py
- q2_diversity_lib/_util.py
- q2_diversity_lib/_version.py
- q2_diversity_lib/alpha.py
- q2_diversity_lib/beta.py
- q2_diversity_lib/plugin_setup.py
- q2_diversity_lib/tests/__init__.py
- q2_diversity_lib/tests/test_alpha.py
- q2_diversity_lib/tests/test_beta.py
- q2_diversity_lib/tests/test_util.py
- setup.py


Changes:

=====================================
.github/workflows/lint-build-test.yml → .github/workflows/ci.yml
=====================================
@@ -1,5 +1,9 @@
-name: lint-build-test
-# build on every PR and commit to master
+# 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:
@@ -10,13 +14,17 @@ jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout at v2
-    - name: set up python 3.6
+    - name: checkout source
+      uses: actions/checkout at v2
+
+    - name: set up python 3.8
       uses: actions/setup-python at v1
       with:
-        python-version: 3.6
+        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
@@ -31,13 +39,17 @@ jobs:
         os: [ubuntu-latest, macos-latest]
     runs-on: ${{ matrix.os }}
     steps:
-    - uses: actions/checkout at v2
+    - name: checkout source
+      uses: actions/checkout at v2
       with:
         fetch-depth: 0
-    # for versioneer
-    - run: git fetch --depth=1 origin +refs/tags/*:refs/tags/*
+
+    - 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-diversity-lib
-        build-target: staging
-        additional-tests: pytest --pyargs q2_diversity_lib --capture=tee-sys
+        build-target: dev
+        additional-tests: py.test --pyargs q2_diversity_lib
+        library-token: ${{ secrets.LIBRARY_TOKEN }}


=====================================
LICENSE
=====================================
@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2018-2020, QIIME 2 development team.
+Copyright (c) 2018-2021, 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-diversity-lib
 
-![](https://github.com/qiime2/q2-diversity-lib/workflows/lint-build-test/badge.svg)
-[![Coverage Status](https://coveralls.io/repos/github/qiime2/q2-diversity-lib/badge.svg?branch=master)](https://coveralls.io/github/qiime2/q2-diversity-lib?branch=master)
+![](https://github.com/qiime2/q2-diversity-lib/workflows/ci/badge.svg)
 
-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-diversity-lib
@@ -18,18 +17,26 @@ requirements:
     - setuptools
 
   run:
+    - python {{ python }}
     - biom-format >=2.1.5,<2.2.0
     - decorator
+    # Inherit global hard pin
+    - hdf5 {{ hdf5 }}
     - numpy
     - pandas
     - psutil
-    - qiime2 {{ release }}.*
-    - q2-types {{ release }}.*
+    - qiime2 {{ qiime2_epoch }}.*
+    - q2-types {{ qiime2_epoch }}.*
     - scikit-bio
     - scipy
     - unifrac >=0.20.0
 
 test:
+  requires:
+    - qiime2 >={{ qiime2 }}
+    - q2-types >={{ q2_types }}
+    - pytest
+
   imports:
     - q2_diversity_lib
     - qiime2.plugins.diversity_lib


=====================================
q2_diversity_lib/__init__.py
=====================================
@@ -1,5 +1,5 @@
 # ----------------------------------------------------------------------------
-# Copyright (c) 2018-2020, QIIME 2 development team.
+# Copyright (c) 2018-2021, QIIME 2 development team.
 #
 # Distributed under the terms of the Modified BSD License.
 #


=====================================
q2_diversity_lib/_util.py
=====================================
@@ -1,5 +1,5 @@
 # ----------------------------------------------------------------------------
-# Copyright (c) 2018-2020, QIIME 2 development team.
+# Copyright (c) 2018-2021, QIIME 2 development team.
 #
 # Distributed under the terms of the Modified BSD License.
 #


=====================================
q2_diversity_lib/_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 = "1867d88619465a0c9501477ab2c43d640bab55df"
-    git_date = "2020-12-05 20:44:45 +0000"
+    git_refnames = " (tag: 2021.8.0)"
+    git_full = "9c30351a4ce12d4eccb94158cd808faced68fe0d"
+    git_date = "2021-09-09 18:35:28 +0000"
     keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}
     return keywords
 


=====================================
q2_diversity_lib/alpha.py
=====================================
@@ -1,5 +1,5 @@
 # ----------------------------------------------------------------------------
-# Copyright (c) 2018-2020, QIIME 2 development team.
+# Copyright (c) 2018-2021, QIIME 2 development team.
 #
 # Distributed under the terms of the Modified BSD License.
 #


=====================================
q2_diversity_lib/beta.py
=====================================
@@ -1,5 +1,5 @@
 # ----------------------------------------------------------------------------
-# Copyright (c) 2018-2020, QIIME 2 development team.
+# Copyright (c) 2018-2021, QIIME 2 development team.
 #
 # Distributed under the terms of the Modified BSD License.
 #


=====================================
q2_diversity_lib/plugin_setup.py
=====================================
@@ -1,5 +1,5 @@
 # ----------------------------------------------------------------------------
-# Copyright (c) 2018-2020, QIIME 2 development team.
+# Copyright (c) 2018-2021, QIIME 2 development team.
 #
 # Distributed under the terms of the Modified BSD License.
 #


=====================================
q2_diversity_lib/tests/__init__.py
=====================================
@@ -1,5 +1,5 @@
 # ----------------------------------------------------------------------------
-# Copyright (c) 2018-2020, QIIME 2 development team.
+# Copyright (c) 2018-2021, QIIME 2 development team.
 #
 # Distributed under the terms of the Modified BSD License.
 #


=====================================
q2_diversity_lib/tests/test_alpha.py
=====================================
@@ -1,5 +1,5 @@
 # ----------------------------------------------------------------------------
-# Copyright (c) 2018-2020, QIIME 2 development team.
+# Copyright (c) 2018-2021, QIIME 2 development team.
 #
 # Distributed under the terms of the Modified BSD License.
 #
@@ -8,7 +8,7 @@
 
 import numpy as np
 import pandas as pd
-import pandas.util.testing as pdt
+import pandas.testing as pdt
 import biom
 
 from qiime2.plugin.testing import TestPluginBase


=====================================
q2_diversity_lib/tests/test_beta.py
=====================================
@@ -1,5 +1,5 @@
 # ----------------------------------------------------------------------------
-# Copyright (c) 2018-2020, QIIME 2 development team.
+# Copyright (c) 2018-2021, QIIME 2 development team.
 #
 # Distributed under the terms of the Modified BSD License.
 #


=====================================
q2_diversity_lib/tests/test_util.py
=====================================
@@ -1,5 +1,5 @@
 # ----------------------------------------------------------------------------
-# Copyright (c) 2018-2020, QIIME 2 development team.
+# Copyright (c) 2018-2021, QIIME 2 development team.
 #
 # Distributed under the terms of the Modified BSD License.
 #


=====================================
setup.py
=====================================
@@ -1,5 +1,5 @@
 # ----------------------------------------------------------------------------
-# Copyright (c) 2018-2020, QIIME 2 development team.
+# Copyright (c) 2018-2021, QIIME 2 development team.
 #
 # Distributed under the terms of the Modified BSD License.
 #



View it on GitLab: https://salsa.debian.org/med-team/q2-diversity-lib/-/commit/06c25edf4cac61a4b33a639db29c2382ebab99ac

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View it on GitLab: https://salsa.debian.org/med-team/q2-diversity-lib/-/commit/06c25edf4cac61a4b33a639db29c2382ebab99ac
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