python-package-conda.yml

name: Combined Workflow

on: [push]

jobs:
  build-and-dryrun:
    runs-on: ubuntu-latest
    strategy:
      max-parallel: 5
    defaults:
      run:
        shell: bash -el {0} # use default shell
    env:
      DATABASE_DIR: databases
      N_THREADS: 2
      MEM: 3

    steps:
      - name: Checkout
        uses: actions/checkout@v3.5.2

      - name: Get current month
        id: date
        run: echo "date=$(date +%Y-%m)" >> "${GITHUB_OUTPUT}"

      - uses: mamba-org/setup-micromamba@v1
        with:
          environment-file: atlasenv.yml
          environment-name: atlasenv
          # persist on the same month.
          cache-environment-key: environment-${{ steps.date.outputs.date }}
          cache-downloads-key: downloads-${{ steps.date.outputs.date }}

      - name: Install atlas
        run: |
           python -m pip install . --no-deps -vv

      - name: Test atlas
        run: |
          atlas --help
          atlas --version

      - name: test import modules atlas
        run: |
          python -c "from atlas import utils"

      - name: Dryrun
        run: |
          test/dryrun.sh

      - name: Test init many samples
        run: ./test/test_init_many_samples.sh

      - name: Clone Example Data Repository
        run: git clone https://github.com/metagenome-atlas/example_data.git



#### start test

      - name: Run Test
        run: |
          source activate ./atlasenv
          ls -l
          pwd
          chmod +x test/test_ci.sh
          test/test_ci.sh --resources mem=$MEM java_mem=$MEM --jobs=$N_THREADS --restart-times=2

      - name: Store Logs
        uses: actions/upload-artifact@v2
        with:
          name: logs
          path: test_ci/logs

      - name: Store Sample Logs
        uses: actions/upload-artifact@v2
        with:
          name: sample_logs
          path: test_ci/Streptococcus/logs