main.yml

name: GitHub Actions CI

on:
  push:
    branches: [ master ]
    paths-ignore:
      - '**.md'
  pull_request:
    branches: [ master ]      
  workflow_dispatch:

jobs:

  
  linux-remote:
    name: Linux test (remote)
    runs-on: ubuntu-latest
    env: 
      EXE: ./bin/kmc
      EXE_DUMP: ./bin/kmc_dump
      KMC_SINGLE_READ: ./tests/kmc_CLI/data/single_read.fq
      DATA_DIR: ./tests/kmc_CLI/data/
    steps:
    - uses: actions/checkout@v3
      with:
        submodules: recursive
    - name: make
      run: |
        g++ -v
        make -j12 kmc kmc_tools kmc_dump

    - name: KMC single read, k=28, ci=1
      run: |
        $EXE -k28 -ci1 -jstats.json $KMC_SINGLE_READ 28mers .        
        cmp <(cat stats.json | grep '#Total no. of k-mers' | cut -f 2 -d ':' | cut -f 2 -d ' ' | cut -f 1 -d ',') <(echo "70")
    
    - name: small k, no counters
      run: |
        $EXE -k4 -cs1 -v $KMC_SINGLE_READ 4mers .
        
    - name: count k-mers from KMC1 database when small-k-opt may be applied
      run: |
        $EXE -k10 -v  $KMC_SINGLE_READ 10mers .
        $EXE -k9 -v -fkmc 10mers 9mers .
    - name: issue 180
      run: |
        $EXE -v -k5 -fa -ci1 -t1 $DATA_DIR/issue-180/input.fa bug-report.kmc .
        $EXE_DUMP bug-report.kmc issue-180.kmers
        cmp issue-180.kmers $DATA_DIR/issue-180/pattern.dump
        
  macos-remote:
    name: macOS build (remote)
    runs-on: macOS-latest

    steps:
    - uses: actions/checkout@v3
      with:
        submodules: recursive
    - uses: maxim-lobanov/setup-xcode@v1
      with:
        xcode-version: '14.1'
    - name: make
      run: make -j12 kmc