Merge pull request #8 from tlambert03/ruff

use ruff, fix mypy

.github/workflows/tests.yaml

@@ -1,15 +1,22 @@
 name: Test
 
-on:
-  push:
+on: [push, pull_request]
 
 jobs:
+  lint:
+    name: Lint
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Run pre-commit
+        run: pipx run pre-commit run --all-files
+
   test:
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10"]
+        python-version: ["3.9", "3.10", "3.11"]
 
     steps:
     - uses: actions/checkout@v2

.pre-commit-config.yaml

@@ -7,19 +7,21 @@ default_install_hook_types: [pre-commit, commit-msg]
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v3.2.0
+    rev: v5.0.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
       - id: check-yaml
       - id: check-added-large-files
 
-  - repo: https://github.com/psf/black
-    rev: 23.1.0
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.7.2
     hooks:
-      - id: black
+      - id: ruff
+        args: [--fix, --unsafe-fixes]
+      - id: ruff-format
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.0.1
+    rev: v1.13.0
     hooks:
       - id: mypy

pyproject.toml

@@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta"
 name = "spatial_graph"
 description = "A spatial graph datastructure for python."
 readme = "README.md"
-requires-python = ">=3.7"
+requires-python = ">=3.9"
 classifiers = [
   "Programming Language :: Python :: 3",
 ]
@@ -18,13 +18,14 @@ authors = [
 dynamic = ["version"]
 dependencies = [
   "witty @ git+https://github.com/funkelab/[email protected]",
-  "cheetah3"
+  "cheetah3",
+  "numpy",
 ]
 
 [project.optional-dependencies]
 dev = [
   'pytest',
-  'black',
+  'ruff',
   'mypy',
   'pdoc',
   'pre-commit',
@@ -38,3 +39,7 @@ repository = "https://github.com/funkelab/spatial_graph"
 [tool.setuptools]
 packages = ["spatial_graph"]
 package-data = { "spatial_graph" = ["*.pyi"] }
+
+[tool.ruff]
+target-version = "py39"
+src = ["spatial_graph"]

spatial_graph/__init__.py

@@ -2,3 +2,6 @@
 from .rtree import LineRTree
 from .graph import Graph
 from .spatial_graph import SpatialGraph
+
+
+__all__ = ["PointRTree", "LineRTree", "Graph", "SpatialGraph"]

spatial_graph/graph/__init__.py

@@ -1 +1,3 @@
 from .graph import Graph
+
+__all__ = ["Graph"]

spatial_graph/graph/graph.py

@@ -84,7 +84,7 @@ def __init__(self, graph, nodes):
                 _ = len(nodes)
                 # if so, convert to ndarray
                 nodes = np.array(nodes, dtype=graph.node_dtype)
-            except Exception as e:
+            except Exception:
                 # must be a single node
                 for name in graph.node_attr_dtypes.keys():
                     super().__setattr__(
@@ -152,10 +152,10 @@ def __init__(self, graph, edges):
                 # edges should be an iteratable
                 try:
                     # does it have a length?
-                    num_edges = len(edges)
+                    len(edges)
                     # case 2 and 3
                     edges = np.array(edges, dtype=graph.node_dtype)
-                except Exception as e:
+                except Exception:
                     raise RuntimeError(f"Can not handle edges type {type(edges)}")
 
         if isinstance(edges, np.ndarray):

spatial_graph/rtree/__init__.py

@@ -1,2 +1,5 @@
 from .point_rtree import PointRTree
 from .line_rtree import LineRTree
+
+
+__all__ = ["PointRTree", "LineRTree"]

spatial_graph/rtree/line_rtree.py

@@ -3,19 +3,19 @@
 
 
 class LineRTree(RTree):
-    pyx_item_t_declaration = f"""
+    pyx_item_t_declaration = """
     cdef struct item_t:
         item_base_t u
         item_base_t v
         bool corner_mask[DIMS]
 """
 
-    c_item_t_declaration = f"""
-typedef struct item_t {{
+    c_item_t_declaration = """
+typedef struct item_t {
     item_base_t u;
     item_base_t v;
     bool corner_mask[DIMS];
-}} item_t;
+} item_t;
 """
 
     c_converter_functions = """

spatial_graph/rtree/rtree.py

@@ -1,3 +1,4 @@
+from typing import ClassVar
 import witty
 import numpy as np
 from Cheetah.Template import Template
@@ -50,17 +51,17 @@ class RTree:
     """
 
     # overwrite in subclasses for custom item_t structures
-    pyx_item_t_declaration = None
-    c_item_t_declaration = None
+    pyx_item_t_declaration: ClassVar[str] = ""
+    c_item_t_declaration: ClassVar[str] = ""
 
     # overwrite in subclasses for custom converters
-    c_converter_functions = None
+    c_converter_functions: ClassVar[str] = ""
 
     # overwrite in subclasses for custom item comparison code
-    c_equal_function = None
+    c_equal_function: ClassVar[str] = ""
 
     # overwrite in subclasses for custom distance computation
-    c_distance_function = None
+    c_distance_function: ClassVar[str] = ""
 
     def __new__(
         cls,
@@ -69,8 +70,6 @@ def __new__(
         dims,
     ):
         item_dtype = DType(item_dtype)
-        item_is_array = item_dtype.is_array
-        item_size = item_dtype.size
         coord_dtype = DType(coord_dtype)
 
         ############################################

spatial_graph/spatial_graph.py

@@ -69,8 +69,7 @@ def remove_nodes(self, nodes):
             edges = self.edges_by_nodes(nodes)
         else:
             edges = np.concatenate(
-                self.in_edges_by_nodes(nodes),
-                self.out_edges_by_nodes(nodes)
+                self.in_edges_by_nodes(nodes), self.out_edges_by_nodes(nodes)
             )
         positions_u = getattr(self.node_attrs[edges[:, 0]], self.position_attr)
         positions_v = getattr(self.node_attrs[edges[:, 1]], self.position_attr)

tests/test_graph.py

@@ -21,7 +21,7 @@
 @pytest.mark.parametrize("edge_attr_dtypes", edge_attr_dtypes)
 @pytest.mark.parametrize("directed", [True, False])
 def test_construction(node_dtype, node_attr_dtypes, edge_attr_dtypes, directed):
-    graph = sg.Graph(node_dtype, node_attr_dtypes, edge_attr_dtypes, directed)
+    sg.Graph(node_dtype, node_attr_dtypes, edge_attr_dtypes, directed)
 
 
 @pytest.mark.parametrize("directed", [True, False])
@@ -119,12 +119,16 @@ def test_attribute_modification():
         np.array([1, 2, 3, 4, 5], dtype="uint64"),
         attr1=np.array([0.1, 0.2, 0.3, 0.4, 0.5], dtype="double"),
         attr2=np.array([1, 2, 3, 4, 5], dtype="int"),
-        attr3=np.array([
-            [0.1, 0.2, 0.3],
-            [0.1, 0.2, 0.3],
-            [0.1, 0.2, 0.3],
-            [0.1, 0.2, 0.3],
-            [0.1, 0.2, 0.3]], dtype="float32")
+        attr3=np.array(
+            [
+                [0.1, 0.2, 0.3],
+                [0.1, 0.2, 0.3],
+                [0.1, 0.2, 0.3],
+                [0.1, 0.2, 0.3],
+                [0.1, 0.2, 0.3],
+            ],
+            dtype="float32",
+        ),
     )
 
     graph.add_edges(
@@ -165,10 +169,14 @@ def test_attribute_modification():
     assert graph.node_attrs[3].attr2 == 60
     assert graph.node_attrs[4].attr2 == 80
 
-    graph.node_attrs[[2, 3, 4]].attr3 += np.array([
-        [1, 1, 1],
-        [2, 2, 2],
-        [3, 3, 3]], dtype="float32")
+    graph.node_attrs[[2, 3, 4]].attr3 += np.array(
+        [
+            [1, 1, 1],
+            [2, 2, 2],
+            [3, 3, 3],
+        ],
+        dtype="float32",
+    )
     np.testing.assert_array_almost_equal(graph.node_attrs[2].attr3, [1.3, 1.6, 1.9])
     np.testing.assert_array_almost_equal(graph.node_attrs[3].attr3, [2.3, 2.6, 2.9])
     np.testing.assert_array_almost_equal(graph.node_attrs[4].attr3, [3.3, 3.6, 3.9])
@@ -178,25 +186,26 @@ def test_attribute_modification():
         graph.edge_attrs[[[1, 2], [5, 1]]].attr1,
         [
             [1, 2, 3, 4],
-            [3, 4, 5, 6]
-        ]
+            [3, 4, 5, 6],
+        ],
     )
     graph.edge_attrs[[[1, 2], [5, 1]]].attr1 = np.array(
         [
             [11, 22, 33, 44],
-            [30, 40, 50, 60]
+            [30, 40, 50, 60],
         ],
-        dtype="int"
+        dtype="int",
     )
     np.testing.assert_array_equal(
         graph.edge_attrs[[[1, 2], [3, 4], [5, 1]]].attr1,
         [
             [11, 22, 33, 44],
             [2, 3, 4, 5],
-            [30, 40, 50, 60]
-        ]
+            [30, 40, 50, 60],
+        ],
     )
 
+
 def test_missing_nodes_edges():
     graph = sg.Graph(
         "uint64", {"node_attr": "float32"}, {"edge_attr": "float32"}, directed=False

tests/test_rtree.py

@@ -208,8 +208,8 @@ def test_line_rtree_nearest():
     )
     np.testing.assert_almost_equal(distances[0], 0.5)
 
-def test_line_rtree_delete():
 
+def test_line_rtree_delete():
     line_rtree = LineRTree("uint64[2]", "double", 2)
 
     line_rtree.insert_lines(