filled in and tested actions #6
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Continuous integration unit testing and lint | |
| on: [push] | |
| jobs: | |
| build: | |
| strategy: | |
| matrix: | |
| python-version: ['3.8'] | |
| os: [ubuntu-latest] | |
| runs-on: ${{ matrix.os }} | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - name: Get latest QIIME 2 Environment | |
| shell: bash | |
| run: | | |
| wget https://raw.githubusercontent.com/qiime2/environment-files/master/latest/staging/qiime2-latest-py38-linux-conda.yml | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| activate-environment: qiime2 | |
| environment-file: qiime2-latest-py38-linux-conda.yml | |
| auto-activate-base: false | |
| - name: Install pysyndna into qiime2 environment | |
| run: | | |
| wget https://raw.githubusercontent.com/AmandaBirmingham/pysyndna/main/environment.yml -O pysyndna.yml | |
| conda env update --name qiime2 --file pysyndna.yml | |
| pip install git+https://github.com/AmandaBirmingham/pysyndna.git | |
| - name: Install q2-pysyndna and run unit tests | |
| run: | | |
| conda install pytest | |
| which python | |
| pip install -e . --no-deps | |
| pytest | |
| - name: Lint with flake8 | |
| run: | | |
| conda activate qiime2 | |
| conda install flake8 | |
| # stop the build if there are Python syntax errors or undefined names | |
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
| flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics |