url typo #65
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# configuration derived from q2-katharoseq | |
name: Python Package using Conda | |
on: [push] | |
jobs: | |
build-linux: | |
runs-on: ${{ matrix.os }} | |
strategy: | |
max-parallel: 5 | |
matrix: | |
os: ["ubuntu-latest", "macos-latest"] | |
steps: | |
- uses: actions/checkout@v2 | |
- name: Set up Python 3.8 | |
uses: actions/setup-python@v2 | |
with: | |
python-version: 3.8 | |
- uses: conda-incubator/setup-miniconda@v2 | |
with: | |
auto-update-conda: true | |
python-version: ${{ matrix.python-version }} | |
- name: Add conda to system path | |
run: | | |
# $CONDA is an environment variable pointing to the root of the miniconda directory | |
echo $CONDA/bin >> $GITHUB_PATH | |
- name: Install QIIME 2 ${{ matrix.os }} | |
if: matrix.os == 'macos-latest' | |
shell: bash -l {0} | |
run: | | |
wget -q https://raw.githubusercontent.com/qiime2/environment-files/master/latest/staging/qiime2-latest-py38-osx-conda.yml | |
conda env create -q -n test-env --file qiime2-latest-py38-osx-conda.yml | |
- name: Install QIIME 2 ${{ matrix.os }} | |
if: matrix.os == 'ubuntu-latest' | |
shell: bash -l {0} | |
run: | | |
wget -q https://raw.githubusercontent.com/qiime2/environment-files/master/latest/staging/qiime2-latest-py38-linux-conda.yml | |
conda env create -q -n test-env --file qiime2-latest-py38-linux-conda.yml | |
- name: Install q2-greengenes2 | |
shell: bash -l {0} | |
run: | | |
source activate test-env | |
conda install flake8 pytest | |
pip install -e . | |
- name: Lint with flake8 | |
shell: bash -l {0} | |
run: | | |
source activate test-env | |
flake8 q2_gg2 | |
- name: Test with pytest | |
shell: bash -l {0} | |
run: | | |
source activate test-env | |
pytest | |
lint: | |
runs-on: ubuntu-latest | |
steps: | |
- name: flake8 | |
uses: actions/setup-python@v2 | |
with: | |
python-version: 3.8 | |
- name: install dependencies | |
shell: bash -l {0} | |
run: | | |
python -m pip install --upgrade pip | |
- name: Check out repository code | |
uses: actions/checkout@v2 | |
- name: lint | |
shell: bash -l {0} | |
run: | | |
pip install -q flake8 | |
flake8 q2_gg2 |