[med-svn] [Git][med-team/q2-feature-classifier][upstream] New upstream version 2021.8.0
Andreas Tille (@tille)
gitlab at salsa.debian.org
Fri Oct 1 12:07:31 BST 2021
Andreas Tille pushed to branch upstream at Debian Med / q2-feature-classifier
Commits:
55ef240e by Andreas Tille at 2021-10-01T12:43:42+02:00
New upstream version 2021.8.0
- - - - -
24 changed files:
- + .github/workflows/ci.yml
- − .travis.yml
- LICENSE
- README.md
- − ci/recipe/conda_build_config.yaml
- ci/recipe/meta.yaml
- q2_feature_classifier/__init__.py
- q2_feature_classifier/_blast.py
- q2_feature_classifier/_consensus_assignment.py
- q2_feature_classifier/_cutter.py
- q2_feature_classifier/_skl.py
- q2_feature_classifier/_taxonomic_classifier.py
- q2_feature_classifier/_version.py
- q2_feature_classifier/_vsearch.py
- q2_feature_classifier/classifier.py
- q2_feature_classifier/custom.py
- q2_feature_classifier/plugin_setup.py
- q2_feature_classifier/tests/__init__.py
- q2_feature_classifier/tests/test_classifier.py
- q2_feature_classifier/tests/test_consensus_assignment.py
- q2_feature_classifier/tests/test_custom.py
- q2_feature_classifier/tests/test_cutter.py
- q2_feature_classifier/tests/test_taxonomic_classifier.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-feature-classifier
+ build-target: dev
+ additional-tests: py.test --pyargs q2_feature_classifier
+ library-token: ${{ secrets.LIBRARY_TOKEN }}
=====================================
.travis.yml deleted
=====================================
@@ -1,25 +0,0 @@
-dist: trusty
-sudo: false
-language: python
-before_install:
- - export MPLBACKEND='Agg'
- - wget -q https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
- - export MINICONDA_PREFIX="$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
- - source activate test-env
- - conda install -q pytest-cov
- - pip install -q flake8 coveralls
- - pip install -q https://github.com/qiime2/q2lint/archive/master.zip
- - make install
-script:
- - make lint
- - make test-cov
-after_success:
- - coveralls
=====================================
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
=====================================
@@ -1,6 +1,5 @@
# q2-feature-classifier
-[](https://travis-ci.org/qiime2/q2-feature-classifier)
-[](https://coveralls.io/github/qiime2/q2-feature-classifier?branch=master)
+
-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-feature-classifier
@@ -19,20 +18,28 @@ requirements:
run:
- python {{ python }}
- - scikit-learn 0.23.1
+ - scikit-learn ==0.24.1
- joblib
- scikit-bio
- biom-format >=2.1.5,<2.2.0
- blast >=2.6.0
# There are issues with 2.8.2, and no OS X builds exist after 2.7.0
- vsearch <=2.7.0
- - qiime2 {{ release }}.*
- - q2-types {{ release }}.*
- - q2-quality-control {{ release }}.*
- - q2-taxa {{ release }}.*
- - q2-feature-table {{ release }}.*
+ - qiime2 {{ qiime2_epoch }}.*
+ - q2-types {{ qiime2_epoch }}.*
+ - q2-quality-control {{ qiime2_epoch }}.*
+ - q2-taxa {{ qiime2_epoch }}.*
+ - q2-feature-table {{ qiime2_epoch }}.*
test:
+ requires:
+ - qiime2 >={{ qiime2 }}
+ - q2-types >={{ q2_types }}
+ - q2-quality-control >={{ q2_quality_control }}
+ - q2-taxa >={{ q2_taxa }}
+ - q2-feature-table >={{ q2_feature_table }}
+ - pytest
+
imports:
- q2_feature_classifier
- qiime2.plugins.feature_classifier
=====================================
q2_feature_classifier/__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_feature_classifier/_blast.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_feature_classifier/_consensus_assignment.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_feature_classifier/_cutter.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_feature_classifier/_skl.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_feature_classifier/_taxonomic_classifier.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_feature_classifier/_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 = "977304e2f5b04d9b36edce8f978282e524957e64"
- git_date = "2020-12-05 20:44:56 +0000"
+ git_refnames = " (tag: 2021.8.0)"
+ git_full = "9eb351f285c83f247214317a0db456f983bd5b25"
+ git_date = "2021-09-09 18:35:30 +0000"
keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}
return keywords
=====================================
q2_feature_classifier/_vsearch.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.
#
@@ -77,7 +77,7 @@ def classify_hybrid_vsearch_sklearn(ctx,
min_consensus=0.51,
maxhits='all',
maxrejects='all',
- reads_per_batch=0,
+ reads_per_batch='auto',
confidence=0.7,
read_orientation='auto',
threads=1,
=====================================
q2_feature_classifier/classifier.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.
#
@@ -199,13 +199,13 @@ def _autotune_reads_per_batch(reads, n_jobs):
def classify_sklearn(reads: DNAFASTAFormat, classifier: Pipeline,
- reads_per_batch: int = 0, n_jobs: int = 1,
+ reads_per_batch: int = 'auto', n_jobs: int = 1,
pre_dispatch: str = '2*n_jobs', confidence: float = 0.7,
read_orientation: str = 'auto'
) -> pd.DataFrame:
try:
# autotune reads per batch
- if reads_per_batch == 0:
+ if reads_per_batch == 'auto':
reads_per_batch = _autotune_reads_per_batch(reads, n_jobs)
# transform reads to DNAIterator
@@ -233,7 +233,7 @@ def classify_sklearn(reads: DNAFASTAFormat, classifier: Pipeline,
_classify_parameters = {
- 'reads_per_batch': Int % Range(0, None),
+ 'reads_per_batch': Int % Range(1, None) | Str % Choices(['auto']),
'n_jobs': Int,
'pre_dispatch': Str,
'confidence': Float % Range(
=====================================
q2_feature_classifier/custom.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_feature_classifier/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_feature_classifier/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_feature_classifier/tests/test_classifier.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_feature_classifier/tests/test_consensus_assignment.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_feature_classifier/tests/test_custom.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_feature_classifier/tests/test_cutter.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_feature_classifier/tests/test_taxonomic_classifier.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-feature-classifier/-/commit/55ef240e9a46112de08db228e89fd595e55f420d
--
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