python-package-conda.yml

name: Combined Workflow

on: [push]

defaults:
  run:
    shell: bash -el {0} # use default shell
jobs:
  build-and-dryrun:
    runs-on: ubuntu-latest
    strategy:
      max-parallel: 1


    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: atlasenv-  #${{ 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

  run-qc-and-assembly:
    runs-on: ubuntu-latest
    needs: build-and-dryrun
    env:
      N_THREADS: 2
      MEM: 0.8
      DATABASE_DIR: databases

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


      - uses: mamba-org/setup-micromamba@v1
        with:
          environment-file: atlasenv.yml
          environment-name: atlasenv
          cache-environment-key: atlasenv-


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

      - name: cache example data
        id: get-data
        uses: actions/cache/restore@v3
        with:
          path: test_reads.tar.gz
          key: example-data

      - name: Download test data
        if: steps.get-data.outputs.cache-hit != 'true'
        run: wget --quiet https://zenodo.org/record/3992790/files/test_reads.tar.gz
          
      - name: cache example data
        if: steps.get-data.outputs.cache-hit != 'true'
        uses: actions/cache/save@v3
        with:
          path: test_reads.tar.gz
          key: ${{ steps.get-data.outputs.cache-primary-key }}
        
      - name: extract data
        run: |
          tar -xzf test_reads.tar.gz 
          ls -l test_reads

      - name: get conda envs
        id: get-envs
        uses: actions/cache/restore@v3
        with:
          path: $DATABASE_DIR/conda_envs
          key: assembly-conda-envs
  
        # - name: upack conda envs
        #   if: steps.get-envs.outputs.cache-hit != 'true'
        #   run: tar -xzf assembly_conda_envs.tar.gz


      - name: Init
        run: |
          atlas init "test_reads" --db-dir "$DATABASE_DIR" --threads "$N_THREADS" --working-dir wd


      - name: Install dependencies for qc and assembly
        if: steps.get-envs.outputs.cache-hit != 'true'
        run: atlas run assembly --conda-create-envs-only -w wd

      # - name: compress conda envs
      #   run: |
      #     tar -czf assembly_conda_envs.tar.gz $DATABASE_DIR/conda_envs
      - name: list databases
        run: | 
          echo $DATABASE_DIR
          ls -l $DATABASE_DIR
          ls -l $DATABASE_DIR/conda_envs

      - name: Store conda envs
        if: steps.get-envs.outputs.cache-hit != 'true'
        uses: actions/cache/save@v3
        with:
          path: $DATABASE_DIR/conda_envs
          key: ${{ steps.get-envs.outputs.cache-primary-key }}


      - name: Run QC
        run: |
          atlas run qc --max-mem $MEM --jobs=$N_THREADS --restart-times=2 --working-dir wd

      - name: Test Assembly
        run: |
          atlas run assembly --max-mem $MEM --jobs=$N_THREADS --restart-times=2 --working-dir wd

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

      - name: Store Sample Logs
        uses: actions/upload-artifact@v2
        with:
          name: sample_logs
          path: wd/sample1/logs

      - name: Store reports
        uses: actions/upload-artifact@v2
        with:
          name: reports
          path: wd/reports


      - name: Cache working dir
        uses: actions/cache/save@v3
        with:
          path: wd
          key: assembly-working-dir
      
  

  run-genecatalog:
    runs-on: ubuntu-latest
    needs: run-qc-and-assembly
    env:
      N_THREADS: 2
      MEM: 3

      DATABASE_DIR: databases

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


      - uses: mamba-org/setup-micromamba@v1
        with:
          environment-file: atlasenv.yml
          environment-name: atlasenv
          cache-environment-key: atlasenv-


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


      - name: get conda envs
        id: get-genecatalog-envs
        uses: actions/cache/restore@v3
        with:
          path: $DATABASE_DIR/conda_envs
          key: binning-conda-envs
          restore-keys: |
            assembly-conda-envs

      - name: Restore working dir
        uses: actions/cache/restore@v3
        with:
          path: wd
          key: assembly-working-dir

      - name: dryrun assembly shold need nothing to be done
        run: |
          ls -l wd
          atlas run assembly -n

  
      - name: Test Genecatalog
        run: |
          atlas run genecatalog --resources mem=$MEM java_mem=$MEM --jobs=$N_THREADS --restart-times=2 --working-dir wd

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

      - name: Store Sample Logs
        uses: actions/upload-artifact@v2
        with:
          name: sample_logs
          path: wd/Sample1/logs

  


  # full-test:
  #   runs-on: ubuntu-latest
  #   needs: build-and-dryrun
  #   strategy:
  #     max-parallel: 1
  #   env:
  #     N_THREADS: 2
  #     MEM: 3

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

  #     - uses: mamba-org/setup-micromamba@v1
  #       with:
  #         environment-file: atlasenv.yml
  #         environment-name: atlasenv
  #         cache-environment-key: atlasenv-


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

  #     # - name: Clone Example Data Repository
  #     #   run: git clone https://github.com/metagenome-atlas/example_data.git
      
  #     - name: Run Test
  #       run: |
  #         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/Sample1/logs