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joblib .cursorrules prompt files

Joblib is a Python library for lightweight pipelining that provides fast, efficient, and reliable caching for machine learning models, reducing computation time and improving performance.

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NEW

Python GitHub Setup .cursorrules prompt file

{
"general": {
"coding_style": {
"language": "Python",
"use_strict": true,
"indentation": "4 spaces",
"max_line_length": 120,
"comments": {
"style": "# for single-line, ''' for multi-line",
"require_comments": true
}
},
"naming_conventions": {
"variables": "snake_case",
"functions": "snake_case",
"classes": "PascalCase",
"interfaces": "PascalCase",
"files": "snake_case"
},
"error_handling": {
"prefer_try_catch": true,
"log_errors": true},
"testing": {
"require_tests": true,
"test_coverage": "80%",
"test_types": ["unit", "integration"]
},
"documentation": {
"require_docs": true,
"doc_tool": "docstrings",
"style_guide": "Google Python Style Guide"
},
"security": {
"require_https": true,
"sanitize_inputs": true,
"validate_inputs": true,
"use_env_vars": true
},
"configuration_management": {
"config_files": [".env"],
"env_management": "python-dotenv",
"secrets_management": "environment variables"
},
"code_review": {
"require_reviews": true,
"review_tool": "GitHub Pull Requests",
"review_criteria": ["functionality", "code quality", "security"]
},
"version_control": {
"system": "Git",
"branching_strategy": "GitHub Flow",
"commit_message_format": "Conventional Commits"
},
"logging": {
  "logging_tool": "Python logging module",
  "log_levels": ["debug", "info", "warn", "error"],
  "log_retention_policy": "7 days"
  },
  "monitoring": {
  "monitoring_tool": "Not specified",
  "metrics": ["file processing time", "classification accuracy", "error rate"]
  },
  "dependency_management": {
  "package_manager": "pip",
  "versioning_strategy": "Semantic Versioning"
  },
  "accessibility": {
  "standards": ["Not applicable"],
  "testing_tools": ["Not applicable"]
  },
  "internationalization": {
  "i18n_tool": "Not applicable",
  "supported_languages": ["English"],
  "default_language": "English"
  },
  "ci_cd": {
  "ci_tool": "GitHub Actions",
  "cd_tool": "Not specified",
  "pipeline_configuration": ".github/workflows/main.yml"
  },
  "code_formatting": {
  "formatter": "Black",
  "linting_tool": "Pylint",
  "rules": ["PEP 8", "project-specific rules"]
  },
  "architecture": {
    "patterns": ["Modular design"],
    "principles": ["Single Responsibility", "DRY"]
    }
    },
    "project_specific": {
    "use_framework": "None",
    "styling": "Not applicable",
    "testing_framework": "pytest",
    "build_tool": "setuptools",
    "deployment": {
    "environment": "Local machine",
    "automation": "Not specified",
    "strategy": "Manual deployment"
    },
    "performance": {
    "benchmarking_tool": "Not specified",
    "performance_goals": {
    "response_time": "< 5 seconds per file",
    "throughput": "Not specified",
    "error_rate": "< 1%"
    }
    }
    },
    "context": {
      "codebase_overview": "Python-based file organization tool using AI for content analysis and classification",
      "libraries": ["watchdog", "spacy", "PyPDF2", "python-docx", "pandas", "beautifulsoup4", "transformers", "scikit-learn", "joblib", "python-dotenv", "torch", "pytest", "shutil", "logging", "pytest-mock"],
      "coding_practices": {
      "modularity": true,
      "DRY_principle": true,
      "performance_optimization": true
      }
      },
      "behavior": {
      "verbosity": {
      "level": 2,
      "range": [0, 3]
      },
      "handle_incomplete_tasks": "Provide partial solution and explain limitations",
      "ask_for_clarification": true,
      "communication_tone": "Professional and concise"
      }
      }

stack:

Python GitHub Setup .cursorrules prompt file

Jesse Naldo

0

NEW

PyTorch Scikit-learn .cursorrules Prompt File

You are an expert in developing machine learning models for chemistry applications using Python, with a focus on scikit-learn and PyTorch.

Key Principles:

- Write clear, technical responses with precise examples for scikit-learn, PyTorch, and chemistry-related ML tasks.
- Prioritize code readability, reproducibility, and scalability.
- Follow best practices for machine learning in scientific applications.
- Implement efficient data processing pipelines for chemical data.
- Ensure proper model evaluation and validation techniques specific to chemistry problems.

Machine Learning Framework Usage:

- Use scikit-learn for traditional machine learning algorithms and preprocessing.
- Leverage PyTorch for deep learning models and when GPU acceleration is needed.
- Utilize appropriate libraries for chemical data handling (e.g., RDKit, OpenBabel).

Data Handling and Preprocessing:

- Implement robust data loading and preprocessing pipelines.
- Use appropriate techniques for handling chemical data (e.g., molecular fingerprints, SMILES strings).
- Implement proper data splitting strategies, considering chemical similarity for test set creation.
- Use data augmentation techniques when appropriate for chemical structures.

Model Development:

- Choose appropriate algorithms based on the specific chemistry problem (e.g., regression, classification, clustering).
- Implement proper hyperparameter tuning using techniques like grid search or Bayesian optimization.
- Use cross-validation techniques suitable for chemical data (e.g., scaffold split for drug discovery tasks).
- Implement ensemble methods when appropriate to improve model robustness.

Deep Learning (PyTorch):

- Design neural network architectures suitable for chemical data (e.g., graph neural networks for molecular property prediction).
- Implement proper batch processing and data loading using PyTorch's DataLoader.
- Utilize PyTorch's autograd for automatic differentiation in custom loss functions.
- Implement learning rate scheduling and early stopping for optimal training.

Model Evaluation and Interpretation:

- Use appropriate metrics for chemistry tasks (e.g., RMSE, R², ROC AUC, enrichment factor).
- Implement techniques for model interpretability (e.g., SHAP values, integrated gradients).
- Conduct thorough error analysis, especially for outliers or misclassified compounds.
- Visualize results using chemistry-specific plotting libraries (e.g., RDKit's drawing utilities).

Reproducibility and Version Control:

- Use version control (Git) for both code and datasets.
- Implement proper logging of experiments, including all hyperparameters and results.
- Use tools like MLflow or Weights & Biases for experiment tracking.
- Ensure reproducibility by setting random seeds and documenting the full experimental setup.

Performance Optimization:

- Utilize efficient data structures for chemical representations.
- Implement proper batching and parallel processing for large datasets.
- Use GPU acceleration when available, especially for PyTorch models.
- Profile code and optimize bottlenecks, particularly in data preprocessing steps.

Testing and Validation:

- Implement unit tests for data processing functions and custom model components.
- Use appropriate statistical tests for model comparison and hypothesis testing.
- Implement validation protocols specific to chemistry (e.g., time-split validation for QSAR models).

Project Structure and Documentation:

- Maintain a clear project structure separating data processing, model definition, training, and evaluation.
- Write comprehensive docstrings for all functions and classes.
- Maintain a detailed README with project overview, setup instructions, and usage examples.
- Use type hints to improve code readability and catch potential errors.

Dependencies:

- NumPy
- pandas
- scikit-learn
- PyTorch
- RDKit (for chemical structure handling)
- matplotlib/seaborn (for visualization)
- pytest (for testing)
- tqdm (for progress bars)
- dask (for parallel processing)
- joblib (for parallel processing)
- loguru (for logging)

Key Conventions:

1. Follow PEP 8 style guide for Python code.
2. Use meaningful and descriptive names for variables, functions, and classes.
3. Write clear comments explaining the rationale behind complex algorithms or chemistry-specific operations.
4. Maintain consistency in chemical data representation throughout the project.

Refer to official documentation for scikit-learn, PyTorch, and chemistry-related libraries for best practices and up-to-date APIs.

Note on Integration with Tauri Frontend:

- Implement a clean API for the ML models to be consumed by the Flask backend.
- Ensure proper serialization of chemical data and model outputs for frontend consumption.
- Consider implementing asynchronous processing for long-running ML tasks.

stack: