Merge pull request #92 from neuro-ml/dev

closes #28 #91

.github/workflows/docs.yml

@@ -11,6 +11,6 @@ jobs:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
         with:
-          python-version: 3.9
+          python-version: '3.10'
       - run: pip install -r docs/requirements.txt
       - run: mkdocs gh-deploy --force

.github/workflows/release.yml

@@ -14,10 +14,10 @@ jobs:
 
     steps:
       - uses: actions/checkout@v3
-      - name: Set up Python 3.9
+      - name: Set up Python
         uses: actions/setup-python@v4
         with:
-          python-version: 3.9
+          python-version: '3.10'
 
       - id: get_version
         name: Get the release version

.github/workflows/tests.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-20.04
     strategy:
       matrix:
-        python-version: [ '3.6', '3.7', '3.8', '3.9', '3.10', '3.11' ]
+        python-version: [ '3.7', '3.8', '3.9', '3.10', '3.11' ]
 
     services:
       redis:

connectome/__version__.py

@@ -1 +1 @@
-__version__ = '0.6.1'
+__version__ = '0.7.0'

connectome/cache/memory.py

@@ -11,6 +11,7 @@ class MemoryCache(Cache):
     def __init__(self, size: Union[int, None]):
         super().__init__()
         self._lock = Lock()
+        self.size = size
         if size is not None:
             self._cache = lrucache(size)
         else:
@@ -31,3 +32,6 @@ def set(self, key: NodeHash, value: Any, context):
     def clear(self):
         with self._lock:
             self._cache = {}
+
+    def __reduce__(self):
+        return self.__class__, (self.size,)

connectome/engine/base.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 from abc import ABC, abstractmethod
 from enum import Enum
 from typing import Any, Collection, Dict, Generator, Iterable, NamedTuple, Optional, Sequence, Set, Tuple, Type, Union
@@ -8,6 +10,7 @@
 __all__ = (
     'Command', 'HashOutput', 'Request', 'Response', 'HashError',
     'Edge', 'Node', 'Nodes', 'NodeSet', 'BoundEdge', 'BoundEdges', 'TreeNode', 'TreeNodes', 'Details',
+    'EvalGen', 'HashGen',
 )
 
 
@@ -19,44 +22,47 @@ class Command(Enum):
 HashOutput = Tuple[NodeHash, Any]
 Request = Tuple  # [RequestType, Any, ...]
 Response = Union[NodeHash, Any, Tuple[NodeHash, Any]]
+HashGen = Generator[Request, Response, HashOutput]
+EvalGen = Generator[Request, Response, Any]
 
 
 class Edge(ABC):
     def __init__(self, arity: int):
         self.arity = arity
 
     @abstractmethod
-    def compute_hash(self) -> Generator[Request, Response, HashOutput]:
+    def compute_hash(self) -> HashGen:
         """ Computes the hash of the output given the input hashes. """
 
     @abstractmethod
-    def evaluate(self) -> Generator[Request, Response, Any]:
+    def evaluate(self) -> EvalGen:
         """ Computes the output value. """
 
     def hash_graph(self, inputs: NodeHashes) -> NodeHash:
         """ Propagates the graph's hash without any control flow. """
+        # TODO: remove this check
         assert len(inputs) == self.arity
         return self._hash_graph(inputs)
 
     @abstractmethod
     def _hash_graph(self, inputs: NodeHashes) -> NodeHash:
         """ Propagates the graph's hash without any control flow. """
 
-    def bind(self, inputs: Union['Node', 'Nodes'], output: 'Node') -> 'BoundEdge':
+    def bind(self, inputs: Union[Node, Nodes], output: Node) -> BoundEdge:
         if isinstance(inputs, Node):
             inputs = [inputs]
         assert len(inputs) == self.arity, (len(inputs), self.arity)
         return BoundEdge(self, inputs, output)
 
 
 class Details:
-    def __init__(self, layer: Union[str, Type], parent: Optional['Details'] = None):
+    def __init__(self, layer: Union[str, Type], parent: Optional[Details] = None):
         if isinstance(layer, type):
             layer = layer.__name__
         self.layer = layer
         self.parent = parent
 
-    def update(self, mapping: Dict['Details', 'Details'], parent: Union['Details', None]):
+    def update(self, mapping: Dict[Details, Details], parent: Union[Details, None]):
         """ Update the whole tree based on a mapping """
         assert isinstance(parent, Details) or parent is None, parent
         if self.parent is not None:
@@ -77,7 +83,7 @@ def __str__(self):
 class TreeNode:
     __slots__ = 'name', '_edge', 'details'
 
-    def __init__(self, name: str, edge: Optional[Tuple[Edge, Sequence['TreeNode']]],
+    def __init__(self, name: str, edge: Optional[Tuple[Edge, Sequence[TreeNode]]],
                  details: Union[Details, None] = None):
         self.name, self._edge, self.details = name, edge, details
 
@@ -94,7 +100,7 @@ def parents(self):
         return self._edge[1]
 
     @classmethod
-    def from_edges(cls, edges: Iterable['BoundEdge']) -> Dict['Node', 'TreeNode']:
+    def from_edges(cls, edges: Iterable[BoundEdge]) -> Dict[Node, TreeNode]:
         def update(node: Node):
             if node in mapping:
                 return mapping[node]
@@ -122,13 +128,13 @@ def update(node: Node):
         return mapping
 
     @staticmethod
-    def to_edges(nodes: Iterable['TreeNode']) -> Sequence['BoundEdge']:
+    def to_edges(nodes: Iterable[TreeNode]) -> Sequence[BoundEdge]:
         def reverse(node) -> Node:
             if node not in _reversed:
                 _reversed[node] = Node(node.name, node.details)
             return _reversed[node]
 
-        def visit(node: 'TreeNode'):
+        def visit(node: TreeNode):
             if node in visited or node.is_leaf:
                 return
             visited.add(node)
@@ -166,7 +172,7 @@ def __repr__(self):
 
 class BoundEdge(NamedTuple):
     edge: Edge
-    inputs: 'Nodes'
+    inputs: Nodes
     output: Node