2 workflows re install #241
Workflow file for this run
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| 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: 2 | |
| 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: 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 | |
| # - name: Cache atlas instalation | |
| # uses: actions/cache@v2 | |
| # env: | |
| # cache-name: cache-atlas | |
| # with: | |
| # # npm cache files are stored in `~/.npm` on Linux/macOS | |
| # path: ~/.npm | |
| # key: ${{ runner.os }}-build-${{ env.cache-name }}-${{ hashFiles('**/package-lock.json') }} | |
| # restore-keys: | | |
| # ${{ runner.os }}-build-${{ env.cache-name }}- | |
| # ${{ runner.os }}-build- | |
| # ${{ runner.os }}- | |
| full-test: | |
| runs-on: ubuntu-latest | |
| needs: build-and-dryrun | |
| strategy: | |
| max-parallel: 1 | |
| env: | |
| N_THREADS: 2 | |
| MEM: 3 | |
| steps: | |
| - name: Checkout | |
| uses: actions/[email protected] | |
| - uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: atlasenv.yml | |
| environment-name: atlasenv | |
| # persist on the same month. | |
| cache-environment-key: atlasenv- | |
| - name: Install atlas | |
| run: | | |
| python -m pip install . --no-deps -vv | |
| atlas --help | |
| - name: Clone Example Data Repository | |
| run: git clone https://github.com/metagenome-atlas/example_data.git | |
| - name: Run Test | |
| run: | | |
| ls -l | |
| ls -l example_data | |
| chmod +x test/test_ci.sh | |
| test/test_ci.sh --resources mem=$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 |