Prepare release 0.103.0 #27
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| name: Test Pipeline from SpikeInterface | |
| on: | |
| pull_request: | |
| branches: [main] | |
| types: [synchronize, opened, reopened] | |
| env: | |
| NXF_SYNTAX_PARSER: v1 | |
| jobs: | |
| test: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.11" | |
| - name: Free up disk space | |
| run: | | |
| echo "Before cleanup:" | |
| df -h | |
| sudo rm -rf /usr/local/lib/android | |
| sudo rm -rf /opt/ghc | |
| sudo rm -rf /usr/share/dotnet | |
| sudo rm -rf /opt/hostedtoolcache | |
| echo "After cleanup:" | |
| df -h | |
| - name: Install packages | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install $(grep -E '^(spikeinterface|pynwb)==' environment/requirements.txt | tr '\n' ' ') | |
| - name: Generate test SpikeInterface files | |
| run: | | |
| python sample_dataset/create_test_spikeinterface.py | |
| - name: Set up Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| with: | |
| version: latest-stable | |
| - name: Run Nextflow pipeline | |
| run: | | |
| DATA_PATH="$(pwd)/sample_dataset/spikeinterface" RESULTS_PATH="$(pwd)/sample_dataset/spikeinterface_results" \ | |
| nextflow -C "$(pwd)/.github/workflows/nextflow_test.config" run pipeline/main_multi_backend.nf \ | |
| --params_file "$(pwd)/.github/workflows/params_test_si.json" | |
| - name: Check pipeline results | |
| run: | | |
| python "$(pwd)/tests/check_pipeline_results.py" --results-path "$(pwd)/sample_dataset/spikeinterface_results" \ | |
| --data-path "$(pwd)/sample_dataset/spikeinterface" --num-streams 3 --num-success 2 --num-nwb 3 |