Dev

aide_predict/bespoke_models/base.py

@@ -158,7 +158,7 @@ def __init_subclass__(cls, **kwargs):
         Initialize the subclass and register mixin hooks.
 
         This method is called when a subclass is created. It collects and registers
-        all hooks from mixins in the inheritance chain.
+        all hooks from mixins in the inheritance chain, avoiding duplicates.
         """
         super().__init_subclass__(**kwargs)
 
@@ -169,23 +169,47 @@ def __init_subclass__(cls, **kwargs):
         cls._pre_transform_hooks = []
         cls._post_transform_hooks = []
 
+        # Keep track of function objects we've already added to avoid duplicates
+        seen_init_handlers = set()
+        seen_pre_fit_hooks = set()
+        seen_post_fit_hooks = set()
+        seen_pre_transform_hooks = set()
+        seen_post_transform_hooks = set()
+
         # Collect hooks from all mixin bases
         for base in cls.__mro__[1:]:  # Skip self, look at all parents
             # Init handlers
             if hasattr(base, '_init_handler') and callable(base._init_handler):
-                cls._mixin_init_handlers.append(base._init_handler)
+                handler = base._init_handler
+                if handler not in seen_init_handlers:
+                    cls._mixin_init_handlers.append(handler)
+                    seen_init_handlers.add(handler)
 
             # Fit hooks
             if hasattr(base, '_pre_fit_hook') and callable(base._pre_fit_hook):
-                cls._pre_fit_hooks.append(base._pre_fit_hook)
+                hook = base._pre_fit_hook
+                if hook not in seen_pre_fit_hooks:
+                    cls._pre_fit_hooks.append(hook)
+                    seen_pre_fit_hooks.add(hook)
+
             if hasattr(base, '_post_fit_hook') and callable(base._post_fit_hook):
-                cls._post_fit_hooks.append(base._post_fit_hook)
+                hook = base._post_fit_hook
+                if hook not in seen_post_fit_hooks:
+                    cls._post_fit_hooks.append(hook)
+                    seen_post_fit_hooks.add(hook)
 
             # Transform hooks
             if hasattr(base, '_pre_transform_hook') and callable(base._pre_transform_hook):
-                cls._pre_transform_hooks.append(base._pre_transform_hook)
+                hook = base._pre_transform_hook
+                if hook not in seen_pre_transform_hooks:
+                    cls._pre_transform_hooks.append(hook)
+                    seen_pre_transform_hooks.add(hook)
+
             if hasattr(base, '_post_transform_hook') and callable(base._post_transform_hook):
-                cls._post_transform_hooks.append(base._post_transform_hook)
+                hook = base._post_transform_hook
+                if hook not in seen_post_transform_hooks:
+                    cls._post_transform_hooks.append(hook)
+                    seen_post_transform_hooks.add(hook)
 
             # Stop at ProteinModelWrapper (don't include its parents)
             if base is ProteinModelWrapper:

environment.yaml

@@ -4,7 +4,7 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - python<=3.10
+  - python<=3.11
   - hmmer=3.3.2
   - mmseqs2
   - plmc