one additional job #239
Workflow file for this run
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| 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/[email protected] | ||
| - 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 | ||
| ### Full test job | ||
| ### Full test job | ||
| full-test: | ||
| needs: build-and-dryrun | ||
| steps: | ||
| steps: | ||
| - name: Clone Example Data Repository | ||
| run: git clone https://github.com/metagenome-atlas/example_data.git | ||
| - name: Run Test | ||
| run: | | ||
| ls -l | ||
| ls -l example_data | ||
| 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 | ||
