spatial-graph 0.0.1__tar.gz → 0.0.2__tar.gz

{spatial_graph-0.0.1 → spatial_graph-0.0.2}/.github/workflows/ci.yaml

@@ -2,11 +2,9 @@ name: CI
 
 on:
   pull_request:
-    branches:
-      - main
+    branches: [main]
   push:
-    branches:
-      - main
+    branches: [main]
     tags: [v*]
   workflow_dispatch:
 
@@ -29,20 +27,20 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.11", "3.13"]
 
     steps:
       - uses: actions/checkout@v2
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+      - uses: astral-sh/setup-uv@v6
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Install dependencies
-        run: |
-          pip install ".[dev]"
-      - name: Test with pytest
-        run: |
-          pytest --color=yes -v tests
+          enable-cache: true
+          cache-dependency-glob: "**/pyproject.toml"
+      - name: Test with coverage
+        run: uv run pytest -v --cov=spatial_graph --cov-report=xml
+      - uses: codecov/codecov-action@v5
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
 
   deploy:
     name: Deploy
@@ -58,21 +56,19 @@ jobs:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-
-      - name: 🐍 Set up Python
-        uses: actions/setup-python@v5
+      - uses: astral-sh/setup-uv@v6
         with:
-          python-version: "3.x"
+          python-version: ${{ matrix.python-version }}
+          enable-cache: true
+          cache-dependency-glob: "**/pyproject.toml"
 
       - name: 👷 Build
-        run: |
-          python -m pip install build
-          python -m build
+        run: uv build
 
       - name: 🚢 Publish to PyPI
         uses: pypa/gh-action-pypi-publish@release/v1
         with:
-           password: ${{ secrets.PYPI_API_TOKEN }}
+          password: ${{ secrets.PYPI_API_TOKEN }}
 
       - uses: softprops/action-gh-release@v2
         with:

{spatial_graph-0.0.1 → spatial_graph-0.0.2}/.gitignore

@@ -11,3 +11,6 @@ build
 dist
 .vscode
 docs/_build/
+
+# remove me to enforce synchrony across development environments
+uv.lock

{spatial_graph-0.0.1 → spatial_graph-0.0.2}/.pre-commit-config.yaml

@@ -15,13 +15,13 @@ repos:
       - id: check-added-large-files
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.7.2
+    rev: v0.12.2
     hooks:
       - id: ruff
         args: [--fix, --unsafe-fixes]
       - id: ruff-format
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.13.0
+    rev: v1.16.1
     hooks:
       - id: mypy

spatial_graph-0.0.1/README.md → spatial_graph-0.0.2/PKG-INFO

@@ -1,15 +1,42 @@
-# spatial_graph
-
+Metadata-Version: 2.4
+Name: spatial-graph
+Version: 0.0.2
+Summary: A spatial graph datastructure for python.
+Project-URL: homepage, https://github.com/funkelab/spatial_graph
+Project-URL: repository, https://github.com/funkelab/spatial_graph
+Author-email: Jan Funke <funkej@janelia.hhmi.org>, Talley Lambert <talley.lambert@gmail.com>
+License: MIT
+License-File: LICENSE
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Typing :: Typed
+Requires-Python: >=3.9
+Requires-Dist: ct3>=3.3.3
+Requires-Dist: numpy
+Requires-Dist: setuptools>=75.8.0
+Requires-Dist: witty>=v0.2.1
+Description-Content-Type: text/markdown
+
+# spatial-graph
+
+[![License](https://img.shields.io/pypi/l/spatial-graph.svg?color=green)](https://github.com/funkelab/spatial_graph/raw/main/LICENSE)
+[![PyPI](https://img.shields.io/pypi/v/spatial-graph.svg?color=green)](https://pypi.org/project/spatial-graph)
+[![Python Version](https://img.shields.io/pypi/pyversions/spatial-graph.svg?color=green)](https://python.org)
 [![CI](https://github.com/funkelab/spatial_graph/actions/workflows/ci.yaml/badge.svg)](https://github.com/funkelab/spatial_graph/actions/workflows/ci.yaml)
+[![codecov](https://codecov.io/gh/funkelab/spatial_graph/branch/main/graph/badge.svg)](https://codecov.io/gh/funkelab/spatial_graph)
 
 `spatial_graph` provides a data structure for directed and undirected graphs,
 where each node has an nD position (in time or space).
 
-Design Principles
-=================
+## Design Principles
 
-Goals
------
+### Goals
 
 * support for arbitrary number of dimensions
 * typed node identifiers and attributes
@@ -27,8 +54,7 @@ Goals
     * numpy for array interfaces
 * PYX API for graph algorithms in C/C++
 
-Non-Goals
----------
+### Non-Goals
 
 * graph algorithms
 * I/O
@@ -37,8 +63,7 @@ Non-Goals
 * out-of-memory support
 * networkx compatibility
 
-Python API
-==========
+## Python API
 
 Graph creation:
 
@@ -104,9 +129,21 @@ Delete nodes/edges:
 graph.remove_nodes(nodes[:1000])
 ```
 
-Implementation Details
-======================
+## Implementation Details
 
 A `SpatialGraph` consists of three data structures:
+
 * The `Graph` itself, holding nodes, edges, and their attributes ([graphlite](https://github.com/haasdo95/graphlite)).
 * Two R-trees for spatial node and edge queries (based on [rtree.c](https://github.com/tidwall/rtree.c)).
+
+## For Developers
+
+To create a new release, tag the current commit with a
+version number and push it to the `upstream` remote:
+
+```bash
+git tag -a "vX.Y.Z" -m "vX.Y.Z"
+git push upstream --follow-tags
+```
+
+This will trigger the CI workflow, which will build the package and upload it to PyPI.

spatial_graph-0.0.1/PKG-INFO → spatial_graph-0.0.2/README.md

@@ -1,33 +1,17 @@
-Metadata-Version: 2.4
-Name: spatial-graph
-Version: 0.0.1
-Summary: A spatial graph datastructure for python.
-Project-URL: homepage, https://github.com/funkelab/spatial_graph
-Project-URL: repository, https://github.com/funkelab/spatial_graph
-Author-email: Jan Funke <funkej@janelia.hhmi.org>
-License: MIT
-License-File: LICENSE
-Requires-Python: >=3.9
-Requires-Dist: cheetah3
-Requires-Dist: numpy
-Requires-Dist: setuptools>=75.8.0
-Requires-Dist: witty>=v0.2.0
-Provides-Extra: dev
-Requires-Dist: pytest>=8.3.4; extra == 'dev'
-Description-Content-Type: text/markdown
-
-# spatial_graph
+# spatial-graph
 
+[![License](https://img.shields.io/pypi/l/spatial-graph.svg?color=green)](https://github.com/funkelab/spatial_graph/raw/main/LICENSE)
+[![PyPI](https://img.shields.io/pypi/v/spatial-graph.svg?color=green)](https://pypi.org/project/spatial-graph)
+[![Python Version](https://img.shields.io/pypi/pyversions/spatial-graph.svg?color=green)](https://python.org)
 [![CI](https://github.com/funkelab/spatial_graph/actions/workflows/ci.yaml/badge.svg)](https://github.com/funkelab/spatial_graph/actions/workflows/ci.yaml)
+[![codecov](https://codecov.io/gh/funkelab/spatial_graph/branch/main/graph/badge.svg)](https://codecov.io/gh/funkelab/spatial_graph)
 
 `spatial_graph` provides a data structure for directed and undirected graphs,
 where each node has an nD position (in time or space).
 
-Design Principles
-=================
+## Design Principles
 
-Goals
------
+### Goals
 
 * support for arbitrary number of dimensions
 * typed node identifiers and attributes
@@ -45,8 +29,7 @@ Goals
     * numpy for array interfaces
 * PYX API for graph algorithms in C/C++
 
-Non-Goals
----------
+### Non-Goals
 
 * graph algorithms
 * I/O
@@ -55,8 +38,7 @@ Non-Goals
 * out-of-memory support
 * networkx compatibility
 
-Python API
-==========
+## Python API
 
 Graph creation:
 
@@ -122,9 +104,21 @@ Delete nodes/edges:
 graph.remove_nodes(nodes[:1000])
 ```
 
-Implementation Details
-======================
+## Implementation Details
 
 A `SpatialGraph` consists of three data structures:
+
 * The `Graph` itself, holding nodes, edges, and their attributes ([graphlite](https://github.com/haasdo95/graphlite)).
 * Two R-trees for spatial node and edge queries (based on [rtree.c](https://github.com/tidwall/rtree.c)).
+
+## For Developers
+
+To create a new release, tag the current commit with a
+version number and push it to the `upstream` remote:
+
+```bash
+git tag -a "vX.Y.Z" -m "vX.Y.Z"
+git push upstream --follow-tags
+```
+
+This will trigger the CI workflow, which will build the package and upload it to PyPI.

spatial_graph-0.0.2/examples/basic_usage.py

@@ -0,0 +1,142 @@
+# /// script
+# requires-python = ">=3.13"
+# dependencies = [
+#     "spatial-graph",
+# ]
+# [tool.uv.sources]
+# spatial-graph = { path = ".." }
+# ///
+
+import numpy as np
+
+import spatial_graph as sg
+
+
+def main():
+    print("=== Spatial Graph Basic Usage Example ===\n")
+
+    # 1. Graph creation
+    print("1. Creating a 3D spatial graph...")
+    graph = sg.SpatialGraph(
+        ndims=3,
+        node_dtype="uint64",
+        node_attr_dtypes={"position": "double[3]"},
+        edge_attr_dtypes={"score": "float32"},
+        position_attr="position",
+        directed=False,
+    )
+    print(f"   Created graph with {graph.ndims} dimensions")
+    print(f"   Node dtype: {graph.node_dtype}")
+    print(f"   Directed: {graph.directed}")
+    print()
+
+    # 2. Adding nodes
+    print("2. Adding nodes with positions...")
+    nodes = np.array([1, 2, 3, 4, 5], dtype="uint64")
+    positions = np.array(
+        [
+            [0.1, 0.1, 0.1],
+            [0.2, 0.2, 0.2],
+            [0.3, 0.3, 0.3],
+            [0.4, 0.4, 0.4],
+            [0.5, 0.5, 0.5],
+        ],
+        dtype="double",
+    )
+
+    graph.add_nodes(nodes, position=positions)
+    print(f"   Added {len(nodes)} nodes")
+    print(f"   Node IDs: {nodes}")
+    print(f"   Positions shape: {positions.shape}")
+    print()
+
+    # 3. Adding edges
+    print("3. Adding edges with scores...")
+    edges = np.array([[1, 2], [3, 4], [5, 1]], dtype="uint64")
+    scores = np.array([0.2, 0.3, 0.4], dtype="float32")
+
+    graph.add_edges(edges, score=scores)
+    print(f"   Added {len(edges)} edges")
+    print(f"   Edges: {edges}")
+    print(f"   Scores: {scores}")
+    print()
+
+    # 4. Query nodes in ROI
+    print("4. Querying nodes in ROI...")
+    roi = np.array([[0.0, 0.0, 0.0], [0.25, 0.25, 0.25]])
+    nodes_in_roi = graph.query_nodes_in_roi(roi)
+    print(f"   ROI: {roi}")
+    print(f"   Nodes in ROI: {nodes_in_roi}")
+    print()
+
+    # 5. Query edges in ROI
+    print("5. Querying edges in ROI...")
+    edges_in_roi = graph.query_edges_in_roi(roi)
+    print(f"   Edges in ROI: {edges_in_roi}")
+    print()
+
+    # 6. Query nearest nodes
+    print("6. Querying nearest nodes...")
+    query_point = np.array([0.3, 0.3, 0.3])
+    nearest_nodes = graph.query_nearest_nodes(query_point, k=3)
+    print(f"   Query point: {query_point}")
+    print(f"   3 nearest nodes: {nearest_nodes}")
+    print()
+
+    # 7. Query nearest edges
+    print("7. Querying nearest edges...")
+    nearest_edges = graph.query_nearest_edges(query_point, k=2)
+    print(f"   2 nearest edges: {nearest_edges}")
+    print()
+
+    # 8. Access node attributes
+    print("8. Accessing node attributes...")
+    if len(nodes_in_roi) > 0:
+        node_positions = graph.node_attrs[nodes_in_roi].position
+        print("   Positions of nodes in ROI:")
+        for i, (node_id, pos) in enumerate(zip(nodes_in_roi, node_positions)):
+            print(f"     Node {node_id}: {pos}")
+    print()
+
+    # 9. Access edge attributes
+    print("9. Accessing edge attributes...")
+    if len(edges_in_roi) > 0:
+        edge_scores = graph.edge_attrs[edges_in_roi].score
+        print("   Scores of edges in ROI:")
+        for i, (edge_idx, score) in enumerate(zip(edges_in_roi, edge_scores)):
+            print(f"     Edge index {edge_idx}: score = {score}")
+    print()
+
+    # 10. Graph statistics before removal
+    print("10. Graph statistics before node removal...")
+    print(f"    Total nodes: {len(graph.nodes)}")
+    print(f"    Total edges: {len(graph.edges)}")
+    print()
+
+    # 11. Remove some nodes
+    print("11. Removing nodes...")
+    nodes_to_remove = nodes[:2]  # Remove first 2 nodes
+    print(f"    Removing nodes: {nodes_to_remove}")
+    graph.remove_nodes(nodes_to_remove)
+    print(f"    Nodes after removal: {len(graph.nodes)}")
+    print(f"    Edges after removal: {len(graph.edges)}")
+    print()
+
+    # 12. Final query to show updated graph
+    print("12. Final query on updated graph...")
+    remaining_nodes = graph.query_nodes_in_roi(
+        np.array([[0.0, 0.0, 0.0], [1.0, 1.0, 1.0]])
+    )
+    print(f"    Remaining nodes: {remaining_nodes}")
+
+    if len(remaining_nodes) > 0:
+        remaining_positions = graph.node_attrs[remaining_nodes].position
+        print("    Remaining node positions:")
+        for node_id, pos in zip(remaining_nodes, remaining_positions):
+            print(f"      Node {node_id}: {pos}")
+
+    print("\n=== Example completed successfully! ===")
+
+
+if __name__ == "__main__":
+    main()

spatial_graph-0.0.2/examples/query_nearest_vispy.py

@@ -0,0 +1,123 @@
+# /// script
+# requires-python = ">=3.13"
+# dependencies = [
+#     "pyopengl",
+#     "pyqt6",
+#     "vispy",
+#     "spatial-graph",
+# ]
+# [tool.uv.sources]
+# spatial-graph = { path = ".." }
+# ///
+from time import time
+
+import numpy as np
+from vispy import app, scene
+
+from spatial_graph import SpatialGraph
+
+canvas = scene.SceneCanvas(keys="interactive", size=(800, 600), show=True)
+canvas.measure_fps()
+
+view = canvas.central_widget.add_view()
+
+camera = scene.cameras.FlyCamera(parent=view.scene, fov=60.0, name="Fly")
+view.camera = camera
+
+graph = SpatialGraph(
+    ndims=3,
+    node_dtype="uint64",
+    node_attr_dtypes={"position": "double[3]"},
+    edge_attr_dtypes={"score": "float32"},
+    position_attr="position",
+    directed=False,
+)
+nodes = np.arange(100_000, dtype="uint64")
+graph.add_nodes(nodes, position=np.random.random((100_000, 3)))
+
+highlight_markers = scene.visuals.Markers(size=20.0, scaling="scene", spherical=True)
+highlight_markers.parent = view.scene
+node_markers = scene.visuals.Markers(
+    pos=graph.node_attrs[nodes].position, size=10.0, scaling="scene", spherical=True
+)
+node_markers.parent = view.scene
+axis_markers = scene.visuals.Markers(
+    pos=np.array(
+        [
+            [0, 0, 0],
+            [1, 0, 0],
+            [0, 1, 0],
+            [0, 0, 1],
+        ]
+    ),
+    face_color=np.array(
+        [
+            [0.5, 0.5, 0.5],
+            [1, 0, 0],
+            [0, 1, 0],
+            [0, 0, 1],
+        ]
+    ),
+    size=11,
+    scaling="scene",
+    spherical=True,
+)
+axis_markers.parent = view.scene
+
+get_data_time = 0.0
+set_data_time = 0.0
+set_data_count = 0
+
+
+@canvas.events.mouse_move.connect
+def on_mouse_move(event):
+    global get_data_time
+    global set_data_time
+    global set_data_count
+    start = time()
+    positions = graph.node_attrs[nodes].position
+    get_data_time += time() - start
+    start = time()
+    node_markers.set_data(pos=positions, size=10)
+    set_data_time += time() - start
+    set_data_count += 1
+    if set_data_count > 100:
+        print(f"get_data(): {get_data_time / 100:.3f}s")
+        print(f"set_data(): {set_data_time / 100:.3f}s")
+        set_data_count = 0
+        get_data_time = 0.0
+        set_data_time = 0.0
+
+    x_pos = event.pos[0]
+    y_pos = event.pos[1]
+
+    transform = node_markers.transforms.get_transform(map_from="scene", map_to="canvas")
+    direction = transform.imap([x_pos, y_pos, 1.0])
+    direction = -((direction / direction[3])[:3])
+    direction /= np.linalg.norm(direction)
+    camera_center = np.array(camera.center)
+    z0_plane_intersection = (
+        camera_center - (camera_center[2] / direction[2]) * direction
+    )
+
+    # get closest nodes to mouse position
+    closest, distances = graph.query_nearest_nodes(
+        z0_plane_intersection, k=10_000, return_distances=True
+    )
+    positions = graph.node_attrs[closest].position
+    query = np.array([z0_plane_intersection])
+    max_distance = distances.max()
+    blend_coeffs = distances[:, np.newaxis] / max_distance
+    colors = (
+        np.tile([1.0, 0.5, 0.0], (len(positions), 1)) * (1.0 - blend_coeffs)
+        + np.ones((len(positions), 3)) * blend_coeffs
+    )
+    highlight_markers.set_data(
+        pos=np.concatenate((query, positions)),
+        size=np.concatenate(([14], 10.0 + (1.0 - distances / max_distance) * 2)),
+        face_color=np.concatenate(([[1.0, 0.5, 1.0]], colors)),
+    )
+
+
+if __name__ == "__main__":
+    app.run()

spatial_graph-0.0.2/pyproject.toml

@@ -0,0 +1,77 @@
+[build-system]
+requires = ["hatchling", "hatch-vcs"]
+build-backend = "hatchling.build"
+
+[tool.hatch.version]
+source = "vcs"
+
+
+[project]
+name = "spatial-graph"
+dynamic = ["version"]
+description = "A spatial graph datastructure for python."
+readme = "README.md"
+requires-python = ">=3.9"
+license = { text = "MIT" }
+authors = [
+  { email = "funkej@janelia.hhmi.org", name = "Jan Funke" },
+  { email = "talley.lambert@gmail.com", name = "Talley Lambert" },
+]
+classifiers = [
+  "Development Status :: 3 - Alpha",
+  "Intended Audience :: Developers",
+  "License :: OSI Approved :: MIT License",
+  "Programming Language :: Python :: 3.9",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: 3.13",
+  "Typing :: Typed",
+]
+dependencies = ["witty>=v0.2.1", "CT3>=3.3.3", "numpy", "setuptools>=75.8.0"]
+
+[dependency-groups]
+dev = [
+  "ipython>=8.18.1",
+  "mypy>=1.15.0",
+  "pre-commit>=4.2.0",
+  "pytest>=8.3.5",
+  "pytest-cov>=6.1.1",
+  "ruff>=0.11.10",
+]
+
+
+[project.urls]
+homepage = "https://github.com/funkelab/spatial_graph"
+repository = "https://github.com/funkelab/spatial_graph"
+
+[tool.ruff]
+target-version = "py39"
+line-length = 88
+
+[tool.ruff.lint]
+select = [
+  "E",   # style errors
+  "F",   # flakes
+  "W",   # warnings
+  "I",   # isort
+  "UP",  # pyupgrade
+  "TC",  # typing
+  "TID", # tidy imports
+  "RUF", # ruff
+]
+
+[tool.ruff.format]
+docstring-code-format = true
+
+[tool.mypy]
+files = "*.py"
+strict = false
+disallow_any_generics = false
+disallow_subclassing_any = false
+show_error_codes = true
+pretty = true
+
+[tool.pytest.ini_options]
+addopts = "-v --color=yes"
+filterwarnings = ["error", "ignore:'cgi' is deprecated"]

spatial_graph-0.0.2/src/spatial_graph/__init__.py

@@ -0,0 +1,13 @@
+from importlib.metadata import PackageNotFoundError, version
+
+try:
+    __version__ = version("spatial_graph")
+except PackageNotFoundError:
+    __version__ = "unknown"
+
+
+from .graph import Graph
+from .rtree import LineRTree, PointRTree
+from .spatial_graph import SpatialGraph
+
+__all__ = ["Graph", "LineRTree", "PointRTree", "SpatialGraph"]