Refactor into modular molecular workloads

scimesh/core/__init__.py

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+"""Core workload abstractions."""

scimesh/core/registry.py

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+"""Registry for locally available workloads."""
+
+from __future__ import annotations
+
+import argparse
+
+from scimesh.core.workload import Workload
+
+
+class WorkloadRegistry:
+    """Collect workloads and expose each one as a CLI subcommand."""
+
+    def __init__(self) -> None:
+        self._workloads: dict[str, Workload] = {}
+
+    def register(self, workload: Workload) -> None:
+        """Register a workload by its unique command name."""
+        if workload.name in self._workloads:
+            raise ValueError(f"Workload already registered: {workload.name}")
+        self._workloads[workload.name] = workload
+
+    def add_subparsers(self, subparsers: argparse._SubParsersAction) -> None:
+        """Add a parser for every registered workload."""
+        for workload in self._workloads.values():
+            parser = subparsers.add_parser(workload.name, help=workload.help)
+            workload.configure_parser(parser)
+            parser.set_defaults(handler=workload.run)

scimesh/core/workload.py

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+"""Minimal interface implemented by every SciMesh workload."""
+
+from __future__ import annotations
+
+import argparse
+from typing import Protocol
+
+
+class Workload(Protocol):
+    """A workload that can add its CLI and execute from parsed arguments."""
+
+    name: str
+    help: str
+
+    def configure_parser(self, parser: argparse.ArgumentParser) -> None:
+        """Add workload-specific command-line arguments."""
+
+    def run(self, args: argparse.Namespace) -> int:
+        """Execute the workload."""