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To hook up to the new CI/CD system, the following changes were made: - Added/updated conda recipe - Every commit is now a version thanks to versioneer - Removed `install_requires` from `setup.py` (dependencies now handled by conda recipe) - Standardized travis configuration to use latest development builds of QIIME 2 Pair programmed with: @jairideout, @ebolyen, and @thermokarst
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q2_feature_classifier/_version.py export-subst |
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dist: trusty | ||
sudo: false | ||
language: python | ||
env: | ||
- PYTHON_VERSION=3.5 | ||
before_install: | ||
- wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh | ||
- chmod +x miniconda.sh | ||
- ./miniconda.sh -b | ||
- export PATH=/home/travis/miniconda3/bin:$PATH | ||
- export MPLBACKEND='Agg' | ||
- wget -q https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh | ||
- export MINICONDA_PREFIX="$HOME/miniconda" | ||
- bash miniconda.sh -b -p $MINICONDA_PREFIX | ||
- export PATH="$MINICONDA_PREFIX/bin:$PATH" | ||
- conda config --set always_yes yes | ||
- conda update -q conda | ||
- conda info -a | ||
- git clone https://github.com/qiime2/q2lint ../q2lint | ||
install: | ||
# TODO some of the dependencies here aren't directly required by this | ||
# package. For now, install them this way for faster build times. Ultimately | ||
# we can let conda do dependency resolution when there are conda packages for | ||
# the various QIIME 2 projects. Until then, avoid installing heavyweight | ||
# dependencies via pip. | ||
- conda create --yes -n test-env -c biocore python=$PYTHON_VERSION scikit-bio jupyter click pytest pytest-cov scikit-learn | ||
- conda create -q -n test-env --file https://raw.githubusercontent.com/qiime2/environment-files/master/latest/staging/qiime2-latest-conda-linux-64.txt | ||
- source activate test-env | ||
- conda install --yes -c bioconda blast=2.6.0 | ||
- conda install --yes -c bioconda vsearch=2.3.2 | ||
- pip install https://github.com/qiime2/qiime2/archive/master.zip | ||
- pip install https://github.com/qiime2/q2-types/archive/master.zip | ||
- pip install flake8 coveralls | ||
- pip install . | ||
- 'echo "backend: Agg" > matplotlibrc' | ||
- git clone https://github.com/qiime2/q2lint | ||
- conda install -q pytest-cov | ||
- pip install -q flake8 coveralls | ||
- python setup.py install | ||
script: | ||
- py.test --cov=q2_feature_classifier | ||
- flake8 | ||
- python q2lint/q2lint.py | ||
- python ../q2lint/q2lint.py | ||
- py.test --cov=q2_feature_classifier | ||
after_success: | ||
- coveralls |
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include versioneer.py | ||
include q2_feature_classifier/_version.py |
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{% set data = load_setup_py_data() %} | ||
{% set version = data.get('version') or 'placehold' %} | ||
{% set release = '.'.join(version.split('.')[:2]) %} | ||
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package: | ||
name: q2-feature-classifier | ||
version: {{ version }} | ||
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source: | ||
path: ../.. | ||
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build: | ||
script: python setup.py install | ||
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requirements: | ||
build: | ||
- python 3.5* | ||
- setuptools | ||
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run: | ||
- python 3.5* | ||
- setuptools | ||
- scikit-learn | ||
- scikit-bio | ||
- biom-format >=2.1.5,<2.2.0 | ||
- blast 2.6.0 | ||
- vsearch | ||
- qiime2 {{ release }}.* | ||
- q2-types {{ release }}.* | ||
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test: | ||
imports: | ||
- q2_feature_classifier | ||
- qiime2.plugins.feature_classifier | ||
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about: | ||
home: https://qiime2.org | ||
license: BSD-3-Clause | ||
license_family: BSD |
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