run_tests.yml

name: Run tests
on:
  push:
    branches:
      - main
  pull_request:

jobs:
  run-tests:
    name: Run tests on ${{ matrix.os }}
    runs-on: ${{ matrix.os }}
    defaults:
      run:
        shell: bash
    strategy:
      fail-fast: false
      matrix:
        include:
          - { os: ubuntu-latest , opt_req: true }
          - { os: windows-latest, opt_req: false }
          - { os: macos-latest  , opt_req: true }
    steps:
      - name: Cancel non-latest runs
        uses: styfle/cancel-workflow-action@0.11.0
        with:
          all_but_latest: true
          access_token: ${{ github.token }}

      - uses: actions/checkout@v3

      - name: Set up Python
        uses: actions/setup-python@v4
        with:
          python-version: '3.11'

      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip
          python -m pip install -r requirements-dev.txt -r requirements.txt

      - name: Install package
        run: |
          python -m pip install .  # must install in editable mode for coverage to find sources
          python -m pip list

      - name: Run tests
        run: |
          pytest

      - name: Run GTNet Predict on Bins
        run: |
          gtnet predict data/small.fna > data/small.raw.test.csv
          python -c 'import pandas as pd; pd.testing.assert_frame_equal(pd.read_csv("data/small.raw.csv"), pd.read_csv("data/small.raw.test.csv"), check_exact=False, atol=1e-4)'

      - name: Run GTNet Filter on Bins
        run: |
          gtnet filter --fpr 0.05 data/small.raw.csv > data/small.tax.test.csv
          python -c 'import pandas as pd; pd.testing.assert_frame_equal(pd.read_csv("data/small.tax.0.05.csv"), pd.read_csv("data/small.tax.test.csv"), check_exact=False, atol=1e-4)'

      - name: Run GTNet Classify on Bins
        run: |
          gtnet classify --fpr 0.05 data/small.fna > data/small.tax.test.csv
          python -c 'import pandas as pd; pd.testing.assert_frame_equal(pd.read_csv("data/small.tax.0.05.csv"), pd.read_csv("data/small.tax.test.csv"), check_exact=False, atol=1e-4)'

      - name: Run GTNet Predict on Contigs
        run: |
          gtnet predict --seqs data/small.fna > data/small.seqs.raw.test.csv
          python -c 'import pandas as pd; pd.testing.assert_frame_equal(pd.read_csv("data/small.seqs.raw.csv"), pd.read_csv("data/small.seqs.raw.test.csv"), check_exact=False, atol=1e-4)'

      - name: Run GTNet Filter on Contigs
        run: |
          gtnet filter --fpr 0.05 data/small.seqs.raw.csv > data/small.seqs.tax.test.csv
          python -c 'import pandas as pd; pd.testing.assert_frame_equal(pd.read_csv("data/small.seqs.tax.0.05.csv"), pd.read_csv("data/small.seqs.tax.test.csv"), check_exact=False, atol=1e-4)'

      - name: Run GTNet Classify on Bins
        run: |
          gtnet classify --seqs --fpr 0.05 data/small.fna > data/small.seqs.tax.test.csv
          python -c 'import pandas as pd; pd.testing.assert_frame_equal(pd.read_csv("data/small.seqs.tax.0.05.csv"), pd.read_csv("data/small.seqs.tax.test.csv"), check_exact=False, atol=1e-4)'