replace distDeviation by candidateScoreFactor #186
Workflow file for this run
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
| # This workflow will install Python dependencies, run tests and lint with a variety of Python versions | |
| # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
| name: build | |
| on: | |
| push: | |
| branches: | |
| - master | |
| - 0.1.0 | |
| tags: | |
| - '*' | |
| pull_request: | |
| branches: [ master ] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: [3.8] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install flake8 pytest wheel | |
| if [ -f requirements.txt ]; then pip install -r requirements.txt; fi | |
| - name: Lint with flake8 | |
| run: | | |
| # stop the build if there are Python syntax errors or undefined names | |
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
| flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | |
| - name: Test | |
| run: | | |
| pwd | |
| pip install . | |
| path=$(fdog.setup -d ./ --getSourcepath); for i in $(less $path/data/dependencies.txt); do sudo apt-get install -y -qq $i; done | |
| echo "TEST fdog.setup" | |
| fdog.setup -d /home/runner/work/fDOG/fDOG/dt --woFAS | |
| echo "TEST fdog.checkData" | |
| fdog.checkData -s /home/runner/work/fDOG/fDOG/dt/searchTaxa_dir -c /home/runner/work/fDOG/fDOG/dt/coreTaxa_dir -a /home/runner/work/fDOG/fDOG/dt/annotation_dir --reblast | |
| echo "TEST fdog.showTaxa" | |
| fdog.showTaxa | |
| echo "TEST fdog.run" | |
| fdog.run --seqFile infile.fa --jobName test --refspec HUMAN@9606@3 --fasOff --group mammalia | |
| mkdir seeds | |
| path=$(fdog.setup -d ./ --getSourcepath); a="1 2 3"; for i in ${a[@]}; do cp $path/data/infile.fa seeds/$i.fa; done | |
| echo "TEST fdogs.run" | |
| fdogs.run --seqFolder seeds --jobName test_multi --refspec HUMAN@9606@3 --fasOff --searchTaxa PARTE@5888@3,THAPS@35128@3 --hmmScoreType sequence | |
| echo "TEST fdog.addTaxon" | |
| head /home/runner/work/fDOG/fDOG/dt/searchTaxa_dir/HUMAN@9606@3/HUMAN@[email protected] > hm.fa | |
| fdog.addTaxon -f hm.fa -i 9606 -o ./ -c -a | |
| ls | |
| - name: Deploy | |
| if: startsWith(github.event.ref, 'refs/tags') | |
| uses: casperdcl/deploy-pypi@v2 | |
| with: | |
| password: ${{ secrets.pypi }} | |
| build: true | |
| upload: ${{ github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags') }} |