feat: add snakemake provider

resource_secretary/providers/__init__.py

@@ -44,7 +44,14 @@ def find_provider_classes(root_path=None):
                         yield category, obj
 
 
-def discover_providers(probe=True, path=None) -> Dict[str, List[BaseProvider]]:
+def discover_catalogs(probe=True, path=None):
+    """
+    Discover catalogs, user specific and asked for groups of tools.
+    """
+    return discover_providers(probe=probe, path=path, is_catalog=True)
+
+
+def discover_providers(probe=True, path=None, is_catalog=False) -> Dict[str, List[BaseProvider]]:
     """
     Recursively discovers and probes providers in subdirectories.
     Returns a dictionary categorized by the subdirectory name.
@@ -61,6 +68,9 @@ def discover_providers(probe=True, path=None) -> Dict[str, List[BaseProvider]]:
         # that might have accidentally left is_provider=True
         try:
             instance = cls()
+            # Loading catalogs or not
+            if instance.is_catalog != is_catalog:
+                continue
             instance.category = category
             if not probe or instance.probe():
                 if category not in catalog:

resource_secretary/providers/provider.py

@@ -16,6 +16,7 @@ def wrapper(*args, **kwargs):
 
     # Attach categorical metadata
     wrapper.is_tool = True
+
     # Right now this can be secretary or dispatch
     wrapper.tool_category = category
 
@@ -52,7 +53,6 @@ def wrapper(*args, **kwargs):
 
 def secretary_tool(func: Callable):
     """
-    Labels a method as a tool for discovery and status retrieval.
     Used by the secretary agent primarily. We don't want the secretary to make
     system changes, it's like read only.
     """
@@ -61,12 +61,18 @@ def secretary_tool(func: Callable):
 
 def dispatch_tool(func: Callable):
     """
-    Labels a method as a tool for actions and state changes.
     Used by the dispatcher agent to actually interact with a system (submit, cancel, etc).
     """
     return _base_tool_decorator(func, "dispatch")
 
 
+def workflow_tool(func: Callable):
+    """
+    Used by the workflow agent to execute workflow steps.
+    """
+    return _base_tool_decorator(func, "workflow")
+
+
 class BaseProvider:
     """
     BaseProvider is that - a base provider class. Note that we set is_provider by default
@@ -78,6 +84,10 @@ class BaseProvider:
 
     is_provider = True
 
+    # A catalog needs to be requested on demand, usually because
+    # it requires additional work at probe (e.g., snakemake wrappers)
+    is_catalog = False
+
     def __init__(self, *args, **kwargs):
         self.tools: Dict[str, Callable] = {}
         self.category: str = "unknown"

resource_secretary/providers/workflow/__init__.py

@@ -0,0 +1 @@
+from .snakemake import SnakemakeProvider