action.yml

name: CI

# specify trigger events for ci workflow
on:
  push:
    branches: [main]
  pull_request:
    types: [opened, edited, reopened, synchronize, review_requested]

jobs:
  # apply formating and linting
  Format:
    runs-on: ubuntu-20.04
    steps:
      - uses: actions/checkout@v3
      - name: Apply snakefmt
        uses: github/super-linter@v4
        env:
          VALIDATE_ALL_CODEBASE: false
          DEFAULT_BRANCH: main
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

          LINTER_RULES_PATH: snekmer/rules/
          VALIDATE_SNAKEMAKE_SNAKEFMT: true

  # run all tests
  Test:
    runs-on: ubuntu-20.04
    needs:
      - Format

    permissions:
     contents: 'read'
     id-token: 'write'

    steps:
      - uses: actions/checkout@v3

      - name: Build test environment
        uses: conda-incubator/setup-miniconda@v2
        with:
          mamba-version: "*"
          channels: anaconda,conda-forge,bioconda,numba
          auto-activate-base: false
          activate-environment: snekmer
          environment-file: .test/test-env.yml
      - shell: bash -l {0}
        run: |
          conda info
          conda list
          conda config --show
      - shell: bash -l {0}
        run: mamba install -y -c conda-forge snakemake==7.0 tabulate==0.8.10
      - shell: bash -l {0}
        run: pip install -e git+https://github.com/PNNL-CompBio/Snekmer@kmer-association#egg=snekmer

      #test clustering step
      - name: Snekmer Cluster
        run: |
          export PATH="/usr/share/miniconda/bin:$PATH"
          conda info --envs
          source activate snekmer
          conda config --get channel_priority --json
          snekmer cluster --configfile .test/config.yaml -d .test
          rm -rf .test/output

      #  --use-conda --conda-cleanup-pkgs cache --show-failed-logs --conda-frontend mamba

      # run modeling step and move output files for search
      - name: Snekmer Model
        run: |
          export PATH="/usr/share/miniconda/bin:$PATH"
          source activate snekmer
          snekmer model --configfile .test/config.yaml -d .test --cores 1
          mkdir .test/output/example-model
          mv .test/output/model/*.model .test/output/example-model/
          mv .test/output/kmerize/*.kmers .test/output/example-model/
          mv .test/output/scoring/*.scorer .test/output/example-model/

      # search against previously generated model files
      - name: Snekmer Search
        run: |
          export PATH="/usr/share/miniconda/bin:$PATH"
          source activate snekmer
          ls .test
          pwd
          snekmer search --configfile .test/config.yaml -d .test --cores 1
          rm -rf .test/output
          
      # run Snekmer Learn kmer counts and confidence creation
      - name: Snekmer Learn
        run: |
          export PATH="/usr/share/miniconda/bin:$PATH"
          source activate snekmer
          snekmer learn --configfile .test/config_learnapp.yaml -d .test --cores 1
          mkdir .test/counts .test/confidence
          mv .test/output/learn/kmer-counts-total.csv .test/counts/kmer-counts-total.csv
          mv .test/output/eval_conf/global-confidence-scores.csv .test/confidence/global-confidence-scores.csv
          rm -rf .test/output
        
      # run Snekmer Learn against previously generated counts files
      - name: Snekmer Apply
        run: |
          export PATH="/usr/share/miniconda/bin:$PATH"
          source activate snekmer
          snekmer apply --configfile .test/config_learnapp.yaml -d .test --cores 1
          rm -rf .test/output