[med-svn] [Git][med-team/q2-fragment-insertion][upstream] New upstream version 2023.7.0
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Sun Aug 20 15:10:01 BST 2023
Étienne Mollier pushed to branch upstream at Debian Med / q2-fragment-insertion
Commits:
539e135b by Étienne Mollier at 2023-08-20T16:03:46+02:00
New upstream version 2023.7.0
- - - - -
20 changed files:
- + .github/workflows/ci-dev.yaml
- − .github/workflows/ci.yml
- + .github/workflows/join-release.yaml
- + .github/workflows/tag-release.yaml
- LICENSE
- bin/import_references.py
- ci/recipe/meta.yaml
- 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-dev.yaml
=====================================
@@ -0,0 +1,12 @@
+# Example of workflow trigger for calling workflow (the client).
+name: ci-dev
+on:
+ pull_request:
+ branches: ["dev"]
+ push:
+ branches: ["dev"]
+jobs:
+ ci:
+ uses: qiime2/distributions/.github/workflows/lib-ci-dev.yaml at dev
+ with:
+ distro: core
\ No newline at end of file
=====================================
.github/workflows/ci.yml deleted
=====================================
@@ -1,55 +0,0 @@
-# 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 }}
=====================================
.github/workflows/join-release.yaml
=====================================
@@ -0,0 +1,6 @@
+name: join-release
+on:
+ workflow_dispatch: {}
+jobs:
+ release:
+ uses: qiime2/distributions/.github/workflows/lib-join-release.yaml at dev
\ No newline at end of file
=====================================
.github/workflows/tag-release.yaml
=====================================
@@ -0,0 +1,7 @@
+name: tag-release
+on:
+ push:
+ branches: ["Release-*"]
+jobs:
+ tag:
+ uses: qiime2/distributions/.github/workflows/lib-tag-release.yaml at dev
\ No newline at end of file
=====================================
LICENSE
=====================================
@@ -1,6 +1,6 @@
BSD 3-Clause License
-Copyright (c) 2016-2022, QIIME 2 development team.
+Copyright (c) 2016-2023, QIIME 2 development team.
All rights reserved.
Redistribution and use in source and binary forms, with or without
=====================================
bin/import_references.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2022, QIIME 2 development team.
+# Copyright (c) 2016-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
ci/recipe/meta.yaml
=====================================
@@ -25,6 +25,9 @@ requirements:
- q2-types {{ qiime2_epoch }}.*
- sepp
- ijson
+ # they imported a private function which doesn't exist anymore...
+ # https://github.com/smirarab/sepp/blob/66cf22cfb9ca22ed9e9074984018d099617b3c6a/sepp/tree.py#L25
+ - dendropy 4.5.2
test:
requires:
@@ -36,6 +39,9 @@ test:
- q2_fragment_insertion
- qiime2.plugins.fragment_insertion
+ commands:
+ - py.test --pyargs q2_fragment_insertion
+
about:
home: https://qiime2.org
license: BSD-3-Clause
=====================================
q2_fragment_insertion/__init__.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2022, QIIME 2 development team.
+# Copyright (c) 2016-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_fragment_insertion/_format.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2022, QIIME 2 development team.
+# Copyright (c) 2016-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_fragment_insertion/_insertion.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2022, QIIME 2 development team.
+# Copyright (c) 2016-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_fragment_insertion/_transformer.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2022, QIIME 2 development team.
+# Copyright (c) 2016-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
q2_fragment_insertion/_type.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2022, QIIME 2 development team.
+# Copyright (c) 2016-2023, 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: 2022.11.1)"
- git_full = "ce513ef02c8bdbbae872968080c6fa0af3111c3c"
- git_date = "2022-12-21 22:17:44 +0000"
+ git_refnames = " (tag: 2023.7.0, Release-2023.7)"
+ git_full = "f9117bae1742c47d7b96e6b2c4a385dca8d133c1"
+ git_date = "2023-08-17 18:44:05 +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) 2016-2022, QIIME 2 development team.
+# Copyright (c) 2016-2023, 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) 2016-2022, QIIME 2 development team.
+# Copyright (c) 2016-2023, 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) 2016-2022, QIIME 2 development team.
+# Copyright (c) 2016-2023, 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) 2016-2022, QIIME 2 development team.
+# Copyright (c) 2016-2023, 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) 2016-2022, QIIME 2 development team.
+# Copyright (c) 2016-2023, 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) 2016-2022, QIIME 2 development team.
+# Copyright (c) 2016-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
=====================================
setup.py
=====================================
@@ -1,5 +1,5 @@
# ----------------------------------------------------------------------------
-# Copyright (c) 2016-2022, QIIME 2 development team.
+# Copyright (c) 2016-2023, 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/-/commit/539e135bead553a7960953ee68a780397e2ff57b
--
View it on GitLab: https://salsa.debian.org/med-team/q2-fragment-insertion/-/commit/539e135bead553a7960953ee68a780397e2ff57b
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