main.yml

name: PhylUp build and tests

on:
  push:
    branches:
      - main
      - dev

jobs:
  run_python:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v2
      - uses: actions/setup-python@v2
        with:
          python-version: '3.7'
          architecture: 'x64'
#      - uses: conda-incubator/setup-miniconda@v2
#        with:
#          installer-url: https://github.com/conda-forge/miniforge/releases/download/4.8.3-2/Miniforge-pypy3-4.8.3-2-Linux-x86_64.sh
#          allow-softlinks: true
#          show-channel-urls: true
#          use-only-tar-bz2: true
          #conda install -c bioconda blast

      #- uses: mkandziora/PhylUp@dev
      - name: Install dependencies
        run: |
              python -m pip install --upgrade pip
              pip install pytest pytest-cov pytest-xdist codecov
              pip install -r requirements.txt
              python setup.py install

              wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.9.0/ncbi-blast-2.9.0+-x64-linux.tar.gz
              tar -xvf ncbi-blast-2.9.0+-x64-linux.tar.gz
              cd ncbi-blast-2.9.0+/bin/
              echo PATH="$PATH:$(pwd)" >> $GITHUB_PATH
              cd ..
              cd ..

              mkdir PaPaRa
              cd PaPaRa
              wget https://cme.h-its.org/exelixis/resource/download/software/papara_nt-2.5-static_x86_64.tar.gz
              gunzip  -cd papara_nt-2.5-static_x86_64.tar.gz | (tar xvf - )
              chmod +x papara_static_x86_64
              echo PATH="$PATH:$(pwd)" >> $GITHUB_PATH
              cd ..
      - name: download data
        run: |
            wget 'https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz'
            gunzip  -cd taxdump.tar.gz | (tar xvf - names.dmp nodes.dmp)
            mv *.dmp ./data/
            mkdir tests/output
            mkdir tests/output/test_runs
      - name: Test with pytest
        run: |
            pytest --cov=PhylUp tests/test_*

#      - name: upload coverage
#        run: |
#            codecov
#            curl -s https://codecov.io/bash | bash

      - name: Upload coverage to Codecov
        uses: codecov/codecov-action@v1