[med-svn] [Git][med-team/q2-fragment-insertion][master] 6 commits: routine-update: New upstream version

Étienne Mollier (@emollier) gitlab at salsa.debian.org
Sun Aug 20 15:09:52 BST 2023 


Étienne Mollier pushed to branch master at Debian Med / q2-fragment-insertion


Commits:
8b400104 by Étienne Mollier at 2023-08-20T16:03:45+02:00
routine-update: New upstream version

- - - - -
539e135b by Étienne Mollier at 2023-08-20T16:03:46+02:00
New upstream version 2023.7.0
- - - - -
538f6c80 by Étienne Mollier at 2023-08-20T16:03:46+02:00
Update upstream source from tag 'upstream/2023.7.0'

Update to upstream version '2023.7.0'
with Debian dir 9ca5efaae6504d3b7da1ee26fa1cd4ec8059e3c0
- - - - -
15e1d30a by Étienne Mollier at 2023-08-20T16:08:33+02:00
d/copyright: bump copyright year.

- - - - -
4ecddf43 by Étienne Mollier at 2023-08-20T16:08:47+02:00
d/control: add myself to uploaders.

- - - - -
f219d146 by Étienne Mollier at 2023-08-20T16:09:20+02:00
ready for upload to unstable.

- - - - -


23 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
- debian/changelog
- debian/control
- debian/copyright
- 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


=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+q2-fragment-insertion (2023.7.0-1) unstable; urgency=medium
+
+  * New upstream version 2023.7.0
+  * d/copyright: bump copyright year.
+  * d/control: add myself to uploaders.
+
+ -- Étienne Mollier <emollier at debian.org>  Sun, 20 Aug 2023 16:09:03 +0200
+
 q2-fragment-insertion (2022.11.1-3) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/control
=====================================
@@ -1,6 +1,7 @@
 Source: q2-fragment-insertion
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Steffen Moeller <moeller at debian.org>
+Uploaders: Steffen Moeller <moeller at debian.org>,
+           Étienne Mollier <emollier at debian.org>
 Section: science
 Priority: optional
 Build-Depends: debhelper-compat (= 13),


=====================================
debian/copyright
=====================================
@@ -4,7 +4,7 @@ Source: https://github.com/qiime2/q2-fragment-insertion
 #Files-Excluded: verioneer.py # does not work.
 
 Files: *
-Copyright: 2016-2019 QIIME 2 development team
+Copyright: 2016-2023 QIIME 2 development team
 License: BSD-3-clause
 
 Files: versioneer.py


=====================================
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/-/compare/779a12d98cccbb007337448d049cf1138a0c53f7...f219d1462c66ddc38fcfa2425d78f61ea0fcc1be

-- 
View it on GitLab: https://salsa.debian.org/med-team/q2-fragment-insertion/-/compare/779a12d98cccbb007337448d049cf1138a0c53f7...f219d1462c66ddc38fcfa2425d78f61ea0fcc1be
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