Benchmarking - handle all NaN signal for WFDB write_waveform format
#37
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| name: Benchmark new formats | |
| on: | |
| pull_request: | |
| paths: | |
| - 'waveform_benchmark/formats/**' | |
| jobs: | |
| benchmark-new-formats: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ["3.10"] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Setup Java | |
| uses: actions/setup-java@v3 | |
| with: | |
| java-version: '11' | |
| distribution: 'adopt' | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install flake8 pytest | |
| pip install -r requirements.txt | |
| - name: Discover JVM Path | |
| run: | | |
| JAVA_HOME=$(dirname $(dirname $(readlink -f $(which java)))) | |
| echo "JAVA_HOME: $JAVA_HOME" | |
| if [ -d "$JAVA_HOME/lib/server" ]; then | |
| echo "JPY_JVM_DLL=$JAVA_HOME/lib/server/libjvm.so" | |
| elif [ -d "$JAVA_HOME/jre/lib/server" ]; then | |
| echo "JPY_JVM_DLL=$JAVA_HOME/jre/lib/server/libjvm.so" | |
| elif [ -d "$JAVA_HOME/lib/client" ]; then | |
| echo "JPY_JVM_DLL=$JAVA_HOME/lib/client/libjvm.so" | |
| else | |
| echo "libjvm.so not found in usual locations" | |
| fi | |
| - name: Copy .env.example to .env | |
| run: cp .env.example .env | |
| - name: Update .env with JVM DLL Path | |
| run: | | |
| echo "export JPY_JVM_DLL='/opt/hostedtoolcache/Java_Adopt_jdk/11.0.23-9/x64/lib/server/libjvm.so'" >> .env | |
| cat .env # Optionally display the .env file to verify changes | |
| - name: Find new or modified benchmark files | |
| id: find-formats | |
| run: | | |
| git fetch origin main | |
| FILES=$(git diff --diff-filter=AM --name-only origin/main...HEAD 'waveform_benchmark/formats/*.py') | |
| echo "$FILES" > format_files.txt | |
| cat format_files.txt | |
| - name: Run benchmark tests on new or modified format files | |
| run: | | |
| FORMAT_FILES=$(cat format_files.txt) | |
| if [ -z "$FORMAT_FILES" ]; then | |
| echo "No format files found to process." | |
| exit 0 | |
| fi | |
| IFS=' ' read -ra FILES <<< "$FORMAT_FILES" | |
| RECORD_NAME="./data/waveforms/mimic_iv/waves/p100/p10079700/85594648/85594648" | |
| for file in "${FILES[@]}" | |
| do | |
| # Skip base.py file | |
| if [[ "$file" == *"base.py" ]]; then | |
| echo "Skipping benchmark for $file" | |
| continue | |
| fi | |
| # Extract the module path from the file path | |
| MODULE_PATH=$(echo "$file" | sed 's/\//./g' | sed 's/\.py$//') | |
| # Find and list all classes in the module | |
| echo "Running benchmarks for classes in $MODULE_PATH" | |
| CLASSES=$(python3 -c "import sys; import inspect; from importlib import import_module; mod = import_module('$MODULE_PATH'); print(' '.join(cls for cls, obj in inspect.getmembers(mod, inspect.isclass) if obj.__module__ == mod.__name__ and not cls.startswith('Base')))") | |
| IFS=' ' read -ra CLS <<< "$CLASSES" | |
| for cls in "${CLS[@]}" | |
| do | |
| CLASS_PATH="$MODULE_PATH.$cls" | |
| FILENAME="benchmark_results_${cls}.txt" | |
| echo "Benchmarking $CLASS_PATH" | |
| ./waveform_benchmark.py -r "$RECORD_NAME" -f "$CLASS_PATH" > "$FILENAME" | |
| done | |
| done | |
| - name: Concatenate results | |
| run: | | |
| cat benchmark_results_*.txt > final_results.txt | |
| echo "Benchmark results:" | |
| cat final_results.txt | |
| - name: Post results to pull request | |
| uses: actions/github-script@v7 | |
| with: | |
| script: | | |
| if [ ! -s final_results.txt ]; then | |
| echo "No results to post." | |
| exit 0 | |
| fi | |
| const fs = require('fs'); | |
| const resultContent = fs.readFileSync('final_results.txt', 'utf8'); | |
| await github.rest.issues.createComment({ | |
| owner: context.repo.owner, | |
| repo: context.repo.repo, | |
| issue_number: context.issue.number, | |
| body: `Benchmark results:\n\`\`\`${resultContent}\`\`\`` | |
| }); |