sampledisco 0.1.0__py3-none-any.whl

sampledisco/__init__.py

@@ -0,0 +1,27 @@
+"""SampleDisco — cross-omics, cross-condition sample embedding for single-cell data.
+
+Public API (imported lazily so ``import sampledisco`` stays light and does not
+pull scanpy / torch / scGLUE until you actually call into the pipeline):
+
+    import sampledisco
+    sampledisco.wrapper(...)                 # full pipeline (RNA / ATAC / multi-omics)
+    sampledisco.compute_sample_embedding(...)  # the core method only
+
+The CLI entry point is ``sampledisco --config <yaml>`` (see ``sampledisco.cli``).
+"""
+from __future__ import annotations
+
+__version__ = "0.1.0"
+
+__all__ = ["wrapper", "compute_sample_embedding"]
+
+
+def __getattr__(name: str):
+    # PEP 562 lazy attribute access — defer heavy imports to first use.
+    if name == "wrapper":
+        from sampledisco.wrapper.wrapper import wrapper
+        return wrapper
+    if name == "compute_sample_embedding":
+        from sampledisco.sample_embedding import compute_sample_embedding
+        return compute_sample_embedding
+    raise AttributeError(f"module {__name__!r} has no attribute {name!r}")

sampledisco/cli.py

@@ -0,0 +1,70 @@
+import argparse
+import sys
+import traceback
+import yaml
+import os
+import inspect
+from sampledisco.wrapper.wrapper import wrapper
+
+def parse_args():
+    parser = argparse.ArgumentParser(description="Run the data processing wrapper.")
+
+    parser.add_argument("-m", "--mode", type=str, required=True, choices=["simple", "complex"],
+                        help="Run mode. Choose 'simple' or 'complex'.")
+
+    # Simple mode args
+    parser.add_argument("-c", "--count_data", type=str, help="Path to count data file")
+    parser.add_argument("-s", "--sample_meta_data", type=str, help="(Optional) Path to sample metadata file")
+    parser.add_argument("-o", "--output_directory", type=str, help="Path to output directory")
+
+    # Complex mode args
+    parser.add_argument("--config", type=str, help="Path to YAML config file")
+
+    return parser.parse_args()
+
+def load_config(config_path):
+    if not os.path.exists(config_path):
+        print(f"Error: Config file '{config_path}' does not exist.", file=sys.stderr)
+        sys.exit(1)
+    with open(config_path, 'r') as f:
+        return yaml.safe_load(f)
+
+def validate_config(config, func):
+    valid_params = inspect.signature(func).parameters
+    for key in config:
+        if key not in valid_params:
+            raise ValueError(f"Unexpected parameter in config: '{key}'")
+    for key in valid_params:
+        if key not in config:
+            raise ValueError(f"Missing required parameter in config: '{key}'")
+
+def main():
+    args = parse_args()
+
+    if args.mode == "simple":
+        if not args.count_data or not args.output_directory:
+            print("Error: In 'simple' mode, -c and -o must be provided.", file=sys.stderr)
+            sys.exit(1)
+
+        if args.sample_meta_data:
+            wrapper(args.count_data, args.sample_meta_data, args.output_directory)
+        else:
+            wrapper(args.count_data, output_directory=args.output_directory)
+
+    elif args.mode == "complex":
+        if not args.config:
+            print("Error: In 'complex' mode, --config must be provided.", file=sys.stderr)
+            sys.exit(1)
+
+        config = load_config(args.config)
+
+        try:
+            validate_config(config, wrapper)
+            wrapper(**config)
+        except Exception as e:
+            print(f"Error: {e}", file=sys.stderr)
+            print(traceback.format_exc(), file=sys.stderr)
+            sys.exit(1)
+
+if __name__ == "__main__":
+    main()