v2.4.0 #153
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| name: Phigaro Tests | |
| # on: push | |
| on: | |
| push: | |
| paths-ignore: | |
| - '.github/**' | |
| - 'README.md' | |
| - 'docs/*' | |
| - 'version_tracker.md' | |
| jobs: | |
| test_at_python: | |
| # if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags') | |
| runs-on: ubuntu-latest | |
| container: tikhonovapolly/phigaro_test_for_git | |
| strategy: | |
| max-parallel: 2 | |
| matrix: | |
| python-version: [3] | |
| steps: | |
| - name: Download data | |
| run: | | |
| mkdir /home/data | |
| cd /home/data | |
| wget https://raw.githubusercontent.com/bobeobibo/phigaro/master/test_data_gitaction/latest_version.txt | |
| wget https://raw.githubusercontent.com/bobeobibo/phigaro/master/test_data_gitaction/test_short_seq.fasta | |
| cp -r /root/.phigaro ~/.phigaro | |
| cd ~/.phigaro | |
| rm config.yml | |
| wget https://raw.githubusercontent.com/bobeobibo/phigaro/master/config.yml | |
| - name: Test Phigaro at python${{ matrix.python-version }} | |
| shell: bash | |
| run: | | |
| /root/miniconda3/envs/python${{ matrix.python-version }}/bin/pip install -r /home/data/latest_version.txt | |
| echo Run Phigaro | |
| /root/miniconda3/envs/python${{ matrix.python-version }}/bin/python /root/miniconda3/envs/python${{ matrix.python-version }}/bin/phigaro -f /home/data/test_short_seq.fasta -o /home/outpy${{ matrix.python-version }}/output -e html tsv gff bed --mode basic --not-open -d --save-fasta | |
| echo Deleting Phigaro | |
| /root/miniconda3/envs/python${{ matrix.python-version }}/bin/pip uninstall phigaro -y | |
| echo Phigaro works fine at python${{ matrix.python-version }} | |
| - name: Check outputs | |
| shell: bash | |
| run: | | |
| echo "ls /home/outpy${{ matrix.python-version }}" | |
| ls /home/outpy${{ matrix.python-version }} | |
| upload_to_pypi: | |
| if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags') | |
| needs: test_at_python | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v1 | |
| - name: Pypi upload | |
| uses: pypa/gh-action-pypi-publish@master | |
| with: | |
| user: __token__ | |
| password: ${{ secrets.phigaro_pypi_token }} | |
| check_pypi_upload: | |
| needs: upload_to_pypi | |
| runs-on: ubuntu-latest | |
| container: tikhonovapolly/phigaro_test_for_git | |
| steps: | |
| - name: Check outputs | |
| shell: bash | |
| run: | | |
| mkdir /home/data | |
| cd /home/data | |
| wget https://raw.githubusercontent.com/bobeobibo/phigaro/master/test_data_gitaction/test_short_seq.fasta | |
| cp -r /root/.phigaro ~/.phigaro | |
| cd ~/.phigaro | |
| rm config.yml | |
| wget https://raw.githubusercontent.com/bobeobibo/phigaro/master/config.yml | |
| /root/miniconda3/envs/python3/bin/pip install phigaro --no-cache | |
| echo Phigaro version: | |
| /root/miniconda3/envs/python3/bin/pip freeze | grep phigaro | |
| echo Run Phigaro | |
| /root/miniconda3/envs/python3/bin/python /root/miniconda3/envs/python3/bin/phigaro -f /home/data/test_short_seq.fasta -o /home/outpy3/output -e html tsv gff bed --mode basic --not-open -d --save-fasta | |
| update_containers: | |
| needs: check_pypi_upload | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@master | |
| - name: Publish to Docker | |
| uses: HurricanKai/Publish-Docker-Github-Action@master | |
| with: | |
| name: tikhonovapolly/phigaro | |
| username: ${{ secrets.DOCKER_USERNAME }} | |
| password: ${{ secrets.DOCKER_PASSWORD }} | |
| tagging: true | |