pepe-cli 1.0.0__py3-none-any.whl

pepe/__init__.py

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+import logging
+import sys
+
+# Package metadata - single source of truth
+__version__ = "1.0.0"
+__package_name__ = "pepe-cli"
+__module_name__ = "pepe"
+__author__ = "Jahn Zhong"
+__author_email__ = "jahn.zhong@medisin.uio.no"
+__description__ = "Pipeline for Easy Protein Embedding - Extract embeddings and attention matrices from protein sequences"
+__homepage__ = "https://github.com/csi-greifflab/pepe-cli"
+
+
+# Configure logging for the embedairr package
+def setup_logging(level=logging.INFO):
+    """Set up logging configuration for the PEPE package."""
+    # Create formatter
+    formatter = logging.Formatter(
+        "%(asctime)s - %(name)s - %(levelname)s - %(message)s",
+        datefmt="%Y-%m-%d %H:%M:%S",
+    )
+
+    # Create console handler
+    console_handler = logging.StreamHandler(sys.stdout)
+    console_handler.setFormatter(formatter)
+
+    # Get root logger for the package
+    logger = logging.getLogger("src")
+    logger.setLevel(level)
+
+    # Remove existing handlers to avoid duplication
+    logger.handlers.clear()
+
+    # Add handler
+    logger.addHandler(console_handler)
+
+    return logger
+
+
+# Set up default logging
+setup_logging()

pepe/__main__.py

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+import logging
+from pepe.model_selecter import select_model
+from pepe.parse_arguments import parse_arguments
+
+logger = logging.getLogger("src.__main__")
+
+
+def main():
+    args = parse_arguments()
+
+    selected_model = select_model(args.model_name)
+
+    embedder = selected_model(args)
+
+    logger.info("Embedder initialized")
+
+    embedder.run()
+
+    logger.info("All outputs saved.")
+
+
+if __name__ == "__main__":
+    main()