Rename types.{Array -> Vec} to avoid name clash with funlib.persisten…

…ce.Array

funlib/persistence/graphs/graph_database.py

@@ -1,6 +1,6 @@
 from networkx import Graph
 from funlib.geometry import Roi
-from ..types import Array
+from ..types import Vec
 
 import logging
 from abc import ABC, abstractmethod
@@ -10,7 +10,7 @@
 logger = logging.getLogger(__name__)
 
 
-AttributeType = type | str | Array
+AttributeType = type | str | Vec
 
 
 class GraphDataBase(ABC):

funlib/persistence/graphs/pgsql_graph_database.py

@@ -1,5 +1,5 @@
 from .sql_graph_database import SQLGraphDataBase
-from ..types import Array
+from ..types import Vec
 from funlib.geometry import Roi
 
 import logging
@@ -186,7 +186,7 @@ def __sql_value(self, value):
             return str(value)
 
     def __sql_type(self, type):
-        if isinstance(type, Array):
+        if isinstance(type, Vec):
             return self.__sql_type(type.dtype) + f"[{type.size}]"
         try:
             return {bool: "BOOLEAN", int: "INTEGER", str: "VARCHAR", float: "REAL"}[

funlib/persistence/graphs/sql_graph_database.py

@@ -1,5 +1,5 @@
 from .graph_database import GraphDataBase, AttributeType
-from ..types import Array, type_to_str
+from ..types import Vec, type_to_str
 
 from funlib.geometry import Coordinate
 from funlib.geometry import Roi
@@ -120,12 +120,12 @@ def get(value, default):
             )
 
             position_type = node_attrs[self.position_attribute]
-            if isinstance(position_type, Array):
+            if isinstance(position_type, Vec):
                 self.ndims = position_type.size
                 assert self.ndims > 1, (
-                    "Don't use Arrays of size 1 for the position, use the "
+                    "Don't use Vecs of size 1 for the position, use the "
                     "scalar type directly instead (i.e., 'float' instead of "
-                    "'Array(float, 1)'."
+                    "'Vec(float, 1)'."
                 )
                 # if ndims == 1, we know that we have a single scalar now
             else:

funlib/persistence/graphs/sqlite_graph_database.py

@@ -1,5 +1,5 @@
 from .sql_graph_database import SQLGraphDataBase, AttributeType
-from ..types import Array
+from ..types import Vec
 
 from funlib.geometry import Roi
 
@@ -50,14 +50,14 @@ def __init__(
                 f"{attr}_{d}" for d in range(attr_type.size)
             ]
             for attr, attr_type in self.node_attrs.items()
-            if isinstance(attr_type, Array)
+            if isinstance(attr_type, Vec)
         }
         self.edge_array_columns = {
             attr: [
                 f"{attr}_{d}" for d in range(attr_type.size)
             ]
             for attr, attr_type in self.edge_attrs.items()
-            if isinstance(attr_type, Array)
+            if isinstance(attr_type, Vec)
         }
 
     def _drop_tables(self) -> None:
@@ -175,7 +175,7 @@ def _node_attrs_to_columns(self, attrs):
         columns = []
         for attr in attrs:
             attr_type = self.node_attrs[attr]
-            if isinstance(attr_type, Array):
+            if isinstance(attr_type, Vec):
                 columns += [
                     f"{attr}_{d}" for d in range(attr_type.size)
                 ]
@@ -200,7 +200,7 @@ def _edge_attrs_to_columns(self, attrs):
         columns = []
         for attr in attrs:
             attr_type = self.edge_attrs[attr]
-            if isinstance(attr_type, Array):
+            if isinstance(attr_type, Vec):
                 columns += [
                     f"{attr}_{d}" for d in range(attr_type.size)
                 ]

funlib/persistence/types.py

@@ -2,13 +2,13 @@
 
 
 @dataclass
-class Array:
+class Vec:
     dtype: type | str
     size: int
 
 
 def type_to_str(type):
-    if isinstance(type, Array):
-        return f"Array({type_to_str(type.dtype)}, {type.size})"
+    if isinstance(type, Vec):
+        return f"Vec({type_to_str(type.dtype)}, {type.size})"
     else:
         return type.__name__

tests/test_graph.py

@@ -1,13 +1,13 @@
 from funlib.geometry import Roi, Coordinate
-from funlib.persistence.types import Array
+from funlib.persistence.types import Vec
 
 import networkx as nx
 import pytest
 
 
 def test_graph_filtering(provider_factory):
     graph_writer = provider_factory(
-        "w", node_attrs={"position": Array(float, 3), "selected": bool}, edge_attrs={"selected": bool}
+        "w", node_attrs={"position": Vec(float, 3), "selected": bool}, edge_attrs={"selected": bool}
     )
     roi = Roi((0, 0, 0), (10, 10, 10))
     graph = graph_writer[roi]
@@ -54,7 +54,7 @@ def test_graph_filtering(provider_factory):
 def test_graph_filtering_complex(provider_factory):
     graph_provider = provider_factory(
         "w",
-        node_attrs={"position": Array(float, 3), "selected": bool, "test": str},
+        node_attrs={"position": Vec(float, 3), "selected": bool, "test": str},
         edge_attrs={"selected": bool, "a": int, "b": int},
     )
     roi = Roi((0, 0, 0), (10, 10, 10))
@@ -104,7 +104,7 @@ def test_graph_filtering_complex(provider_factory):
 def test_graph_read_and_update_specific_attrs(provider_factory):
     graph_provider = provider_factory(
         "w",
-        node_attrs={"position": Array(float, 3), "selected": bool, "test": str},
+        node_attrs={"position": Vec(float, 3), "selected": bool, "test": str},
         edge_attrs={"selected": bool, "a": int, "b": int, "c": int},
     )
     roi = Roi((0, 0, 0), (10, 10, 10))
@@ -155,7 +155,7 @@ def test_graph_read_and_update_specific_attrs(provider_factory):
 def test_graph_read_unbounded_roi(provider_factory):
     graph_provider = provider_factory(
         "w",
-        node_attrs={"position": Array(float, 3), "selected": bool, "test": str},
+        node_attrs={"position": Vec(float, 3), "selected": bool, "test": str},
         edge_attrs={"selected": bool, "a": int, "b": int},
     )
     roi = Roi((0, 0, 0), (10, 10, 10))
@@ -197,14 +197,14 @@ def test_graph_read_unbounded_roi(provider_factory):
 
 def test_graph_read_meta_values(provider_factory):
     roi = Roi((0, 0, 0), (10, 10, 10))
-    provider_factory("w", True, roi, node_attrs={"position": Array(float, 3)})
+    provider_factory("w", True, roi, node_attrs={"position": Vec(float, 3)})
     graph_provider = provider_factory("r", None, None)
     assert True == graph_provider.directed
     assert roi == graph_provider.total_roi
 
 
 def test_graph_default_meta_values(provider_factory):
-    provider = provider_factory("w", False, None, node_attrs={"position": Array(float, 3)})
+    provider = provider_factory("w", False, None, node_attrs={"position": Vec(float, 3)})
     assert False == provider.directed
     assert provider.total_roi is None or provider.total_roi == Roi(
         (None, None, None), (None, None, None)
@@ -220,7 +220,7 @@ def test_graph_io(provider_factory):
     graph_provider = provider_factory(
         "w",
         node_attrs={
-            "position": Array(float, 3),
+            "position": Vec(float, 3),
             "swip": str,
             "zap": str,
         }
@@ -263,7 +263,7 @@ def test_graph_fail_if_exists(provider_factory):
     graph_provider = provider_factory(
         "w",
         node_attrs={
-            "position": Array(float, 3),
+            "position": Vec(float, 3),
             "swip": str,
             "zap": str,
         }
@@ -289,7 +289,7 @@ def test_graph_fail_if_not_exists(provider_factory):
     graph_provider = provider_factory(
         "w",
         node_attrs={
-            "position": Array(float, 3),
+            "position": Vec(float, 3),
             "swip": str,
             "zap": str,
         }
@@ -316,7 +316,7 @@ def test_graph_write_attributes(provider_factory):
     graph_provider = provider_factory(
         "w",
         node_attrs={
-            "position": Array(int, 3),
+            "position": Vec(int, 3),
             "swip": str,
             "zap": str,
         }
@@ -372,7 +372,7 @@ def test_graph_write_roi(provider_factory):
     graph_provider = provider_factory(
         "w",
         node_attrs={
-            "position": Array(float, 3),
+            "position": Vec(float, 3),
             "swip": str,
             "zap": str,
         }
@@ -411,7 +411,7 @@ def test_graph_connected_components(provider_factory):
     graph_provider = provider_factory(
         "w",
         node_attrs={
-            "position": Array(float, 3),
+            "position": Vec(float, 3),
             "swip": str,
             "zap": str,
         }
@@ -449,7 +449,7 @@ def test_graph_has_edge(provider_factory):
     graph_provider = provider_factory(
         "w",
         node_attrs={
-            "position": Array(float, 3),
+            "position": Vec(float, 3),
             "swip": str,
             "zap": str,
         }