[med-svn] [Git][med-team/q2-phylogeny][upstream] New upstream version 2023.7.0
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Sun Aug 20 15:37:54 BST 2023
Étienne Mollier pushed to branch upstream at Debian Med / q2-phylogeny
Commits:
7032c52d by Étienne Mollier at 2023-08-20T16:11:07+02:00
New upstream version 2023.7.0
- - - - -
29 changed files:
- + .github/workflows/ci-dev.yaml
- − .github/workflows/ci.yml
- + .github/workflows/join-release.yaml
- + .github/workflows/tag-release.yaml
- LICENSE
- ci/recipe/meta.yaml
- q2_phylogeny/__init__.py
- q2_phylogeny/_align_to_tree_mafft_fasttree.py
- q2_phylogeny/_align_to_tree_mafft_iqtree.py
- q2_phylogeny/_align_to_tree_mafft_raxml.py
- q2_phylogeny/_examples.py
- q2_phylogeny/_fasttree.py
- q2_phylogeny/_filter.py
- q2_phylogeny/_iqtree.py
- q2_phylogeny/_raxml.py
- q2_phylogeny/_util.py
- q2_phylogeny/_version.py
- q2_phylogeny/plugin_setup.py
- q2_phylogeny/tests/__init__.py
- q2_phylogeny/tests/test_align_to_tree_mafft_fasttree.py
- q2_phylogeny/tests/test_align_to_tree_mafft_iqtree.py
- q2_phylogeny/tests/test_align_to_tree_mafft_raxml.py
- q2_phylogeny/tests/test_examples.py
- q2_phylogeny/tests/test_fasttree.py
- q2_phylogeny/tests/test_filter.py
- q2_phylogeny/tests/test_iqtree.py
- q2_phylogeny/tests/test_raxml.py
- q2_phylogeny/tests/test_util.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-phylogeny
- build-target: dev
- additional-tests: py.test --pyargs q2_phylogeny
- 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
=====================================
ci/recipe/meta.yaml
=====================================
@@ -29,6 +29,9 @@ requirements:
- h5py
test:
+ commands:
+ - py.test --pyargs q2_phylogeny
+
requires:
- qiime2 >={{ qiime2 }}
- q2-types >={{ q2_types }}
=====================================
q2_phylogeny/__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_phylogeny/_align_to_tree_mafft_fasttree.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_phylogeny/_align_to_tree_mafft_iqtree.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_phylogeny/_align_to_tree_mafft_raxml.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_phylogeny/_examples.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_phylogeny/_fasttree.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_phylogeny/_filter.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_phylogeny/_iqtree.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_phylogeny/_raxml.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_phylogeny/_util.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_phylogeny/_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 = "85dc5265c9b5f9bb45da0ba95b2b053d5211aa90"
- git_date = "2022-12-21 22:07:16 +0000"
+ git_refnames = " (tag: 2023.7.0, Release-2023.7)"
+ git_full = "bad0b4d321df13288be23fe6317351a095b84a8c"
+ git_date = "2023-08-17 19:35:00 +0000"
keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}
return keywords
=====================================
q2_phylogeny/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.
#
@@ -272,7 +272,7 @@ plugin.methods.register_function(
'allnni': ('Perform more thorough NNI search.'),
'alrt': ('Single branch test method. Number of bootstrap replicates '
'to perform an SH-like approximate likelihood ratio test '
- '(SH-aLRT). Minimum of 1000 replicates is recomended. Can '
+ '(SH-aLRT). Minimum of 1000 replicates is required. Can '
'be used with other \'single branch test methods\'. Values '
'reported in the order of: alrt, lbp, abayes.'),
'abayes': ('Single branch test method. Approximate Bayes test. '
@@ -280,7 +280,7 @@ plugin.methods.register_function(
'Values reported in the order of: alrt, lbp, abayes.'),
'lbp': ('Single branch test method. Number of bootstrap replicates '
'to perform a fast local bootstrap probability method. '
- 'Minimum of 1000 replicates is recomended. Can be used with '
+ 'Minimum of 1000 replicates is required. Can be used with '
'other \'single branch test methods\'. Values reported in '
'the order of: alrt, lbp, abayes.'),
'safe': ('Safe likelihood kernel to avoid numerical underflow.')},
@@ -375,7 +375,7 @@ plugin.methods.register_function(
'allnni': ('Perform more thorough NNI search.'),
'alrt': ('Single branch test method. Number of bootstrap replicates '
'to perform an SH-like approximate likelihood ratio test '
- '(SH-aLRT). Minimum of 1000 replicates is recomended. Can '
+ '(SH-aLRT). Minimum of 1000 replicates is required. Can '
'be used with other \'single branch test methods\'. Values '
'reported in the order of: alrt, lbp, abayes.'),
'abayes': ('Single branch test method. Performs an '
@@ -385,7 +385,7 @@ plugin.methods.register_function(
'ufboot.'),
'lbp': ('Single branch test method. Number of bootstrap replicates '
'to perform a fast local bootstrap probability method. '
- 'Minimum of 1000 replicates is recomended. Can be used with '
+ 'Minimum of 1000 replicates is required. Can be used with '
'other \'single branch test methods\'. Values reported in '
'the order of: alrt, lbp, abayes, ufboot.'),
'safe': ('Safe likelihood kernel to avoid numerical underflow.')},
@@ -629,7 +629,7 @@ plugin.pipelines.register_function(
'fast': 'Fast search to resemble FastTree.',
'alrt': 'Single branch test method. Number of bootstrap replicates '
'to perform an SH-like approximate likelihood ratio test '
- '(SH-aLRT). Minimum of 1000 replicates is recomended.'
+ '(SH-aLRT). Minimum of 1000 replicates is required.'
},
output_descriptions={
'alignment': 'The aligned sequences.',
=====================================
q2_phylogeny/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_phylogeny/tests/test_align_to_tree_mafft_fasttree.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_phylogeny/tests/test_align_to_tree_mafft_iqtree.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_phylogeny/tests/test_align_to_tree_mafft_raxml.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_phylogeny/tests/test_examples.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_phylogeny/tests/test_fasttree.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_phylogeny/tests/test_filter.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_phylogeny/tests/test_iqtree.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_phylogeny/tests/test_raxml.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_phylogeny/tests/test_util.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-phylogeny/-/commit/7032c52d459cfc88e9ea0e7541e6407261b62b51
--
View it on GitLab: https://salsa.debian.org/med-team/q2-phylogeny/-/commit/7032c52d459cfc88e9ea0e7541e6407261b62b51
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