spatial-graph 0.0.4__tar.gz → 0.0.6__tar.gz

{spatial_graph-0.0.4 → spatial_graph-0.0.6}/.github/workflows/ci.yml

@@ -22,22 +22,34 @@ jobs:
         run: pipx run pre-commit run --all-files
 
   test:
+    name: ${{ matrix.os }} py${{ matrix.python-version }} ${{ matrix.resolution }}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: ["3.9", "3.11", "3.13"]
+        # ubuntu: full python range x both resolutions
+        os: [ubuntu-latest]
+        python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"]
+        resolution: [lowest-direct, highest]
+        # windows/macos: only the endpoints, highest resolution
+        include:
+          - { os: windows-latest, python-version: "3.10", resolution: highest }
+          - { os: windows-latest, python-version: "3.14", resolution: highest }
+          - { os: macos-latest, python-version: "3.10", resolution: highest }
+          - { os: macos-latest, python-version: "3.14", resolution: highest }
+
+    env:
+      UV_RESOLUTION: ${{ matrix.resolution }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - uses: astral-sh/setup-uv@v6
         with:
           python-version: ${{ matrix.python-version }}
           enable-cache: true
           cache-dependency-glob: "**/pyproject.toml"
       - name: Test with coverage
-        run: uv run pytest -v --cov=spatial_graph --cov-report=xml
+        run: uv run --no-dev --group test pytest -v --cov=spatial_graph --cov-report=xml
       - uses: codecov/codecov-action@v5
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
@@ -95,7 +107,12 @@ jobs:
           files: "./dist/*"
 
   docker-test:
+    name: Docker Test gxx${{ matrix.gxx_major }}
     runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        gxx_major: [14, 15]
 
     steps:
       - name: Checkout code
@@ -103,5 +120,5 @@ jobs:
 
       - name: Build and test Docker image
         run: |
-          docker build -t spatial_graph .
+          docker build --build-arg GXX_MAJOR=${{ matrix.gxx_major }} -t spatial_graph .
           docker run --rm spatial_graph

{spatial_graph-0.0.4 → spatial_graph-0.0.6}/.pre-commit-config.yaml

@@ -7,7 +7,7 @@ default_install_hook_types: [pre-commit, commit-msg]
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
@@ -15,13 +15,13 @@ repos:
       - id: check-added-large-files
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.12.2
+    rev: v0.15.16
     hooks:
       - id: ruff-check
         args: [--fix, --unsafe-fixes]
       - id: ruff-format
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.16.1
+    rev: v2.1.0
     hooks:
       - id: mypy

{spatial_graph-0.0.4 → spatial_graph-0.0.6}/Dockerfile

@@ -4,32 +4,36 @@ ENV DEBIAN_FRONTEND=noninteractive \
     MAMBA_ROOT_PREFIX=/opt/conda \
     PATH=/opt/conda/bin:$PATH
 
+# Allow overriding the major GCC/G++ version at build time (e.g. --build-arg GXX_MAJOR=14)
+ARG GXX_MAJOR=15
+
 RUN apt-get update && \
     apt-get install -y --no-install-recommends \
       git curl tar bzip2 ca-certificates && \
     rm -rf /var/lib/apt/lists/*
 
+
+WORKDIR /app
+COPY . /app
+
 # auto-detect arch and grab the matching micromamba binary
 RUN set -eux; \
     arch="$(uname -m)"; \
     case "$arch" in \
-      x86_64)    url_arch=linux-64 ;; \
-      aarch64|arm64) url_arch=linux-aarch64 ;; \
-      ppc64le)   url_arch=linux-ppc64le ;; \
-      *)         echo "Unsupported arch: $arch"; exit 1 ;; \
+        x86_64)          url_arch=linux-64;      gxx_pkg=gxx_linux-64 ;; \
+        aarch64|arm64)   url_arch=linux-aarch64; gxx_pkg=gxx_linux-aarch64 ;; \
+        ppc64le)         url_arch=linux-ppc64le; gxx_pkg=gxx_linux-ppc64le ;; \
+        *)               echo "Unsupported arch: $arch"; exit 1 ;; \
     esac; \
     curl -Ls "https://micro.mamba.pm/api/micromamba/$url_arch/latest" \
       | tar -xvj -C /usr/local/bin bin/micromamba; \
     chmod +x /usr/local/bin/bin/micromamba; \
     mv /usr/local/bin/bin/micromamba /usr/local/bin/micromamba; \
-    rmdir /usr/local/bin/bin
-
-
-WORKDIR /app
-COPY . /app
+    rmdir /usr/local/bin/bin; \
+    micromamba create -y -n test-env -c conda-forge \
+        python=3.12 pip gxx "${gxx_pkg}=${GXX_MAJOR}.*"; \
+    micromamba run -n test-env pip install -e . --group test
 
-RUN micromamba create -y -n test-env -c conda-forge python=3.12 pip compilers
-RUN micromamba run -n test-env pip install -e . --group test
 
 SHELL ["micromamba", "run", "-n", "test-env", "/bin/bash", "-o", "pipefail", "-c"]
 

{spatial_graph-0.0.4 → spatial_graph-0.0.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: spatial-graph
-Version: 0.0.4
+Version: 0.0.6
 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
@@ -10,16 +10,21 @@ 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: Programming Language :: Python :: 3.14
 Classifier: Typing :: Typed
-Requires-Python: >=3.9
+Requires-Python: >=3.10
 Requires-Dist: ct3>=3.3.3
-Requires-Dist: numpy
+Requires-Dist: numpy>=1.21.2
+Requires-Dist: numpy>=1.23.2; python_version >= '3.11'
+Requires-Dist: numpy>=1.26.0; python_version >= '3.12'
+Requires-Dist: numpy>=2.1.0; python_version >= '3.13'
+Requires-Dist: numpy>=2.3.2; python_version >= '3.14'
 Requires-Dist: setuptools>=75.8.0
+Requires-Dist: typing-extensions>=4.5.0
 Requires-Dist: witty>=v0.3.0
 Description-Content-Type: text/markdown
 

{spatial_graph-0.0.4 → spatial_graph-0.0.6}/pyproject.toml

@@ -10,7 +10,7 @@ name = "spatial-graph"
 dynamic = ["version"]
 description = "A spatial graph datastructure for python."
 readme = "README.md"
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 license = { text = "MIT" }
 authors = [
   { email = "funkej@janelia.hhmi.org", name = "Jan Funke" },
@@ -20,14 +20,24 @@ 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",
+  "Programming Language :: Python :: 3.14",
   "Typing :: Typed",
 ]
-dependencies = ["witty>=v0.3.0", "CT3>=3.3.3", "numpy", "setuptools>=75.8.0"]
+dependencies = [
+  "witty>=v0.3.0",
+  "CT3>=3.3.3",
+  "numpy>=2.3.2; python_version >= '3.14'",
+  "numpy>=2.1.0; python_version >= '3.13'",
+  "numpy>=1.26.0; python_version >= '3.12'",
+  "numpy>=1.23.2; python_version >= '3.11'",
+  "numpy>=1.21.2",
+  "setuptools>=75.8.0",
+  "typing_extensions>=4.5.0",  # witty<=0.3.1 imports it without declaring it
+]
 
 [dependency-groups]
 test = ["pytest>=8.3.5", "pytest-cov>=6.1.1"]
@@ -36,7 +46,7 @@ dev = [
   { include-group = "test" },
   "ipython>=8.18.1",
   "mypy>=1.15.0",
-  "pre-commit>=4.2.0",
+  "prek>=0.4.4",
   "pytest-benchmark>=5.1.0",  # specifically excluded from test group for ci
   "ruff>=0.11.10",
 ]
@@ -54,7 +64,7 @@ homepage = "https://github.com/funkelab/spatial_graph"
 repository = "https://github.com/funkelab/spatial_graph"
 
 [tool.ruff]
-target-version = "py39"
+target-version = "py310"
 line-length = 88
 fix = true
 unsafe-fixes = true

{spatial_graph-0.0.4 → spatial_graph-0.0.6}/src/spatial_graph/_graph/graph_base.py

@@ -33,6 +33,33 @@ else:
 SRC_DIR = Path(__file__).parent
 
 
+def _cpp_member_name(name: str) -> str:
+    """C++ struct member name for a user-provided node/edge attribute.
+
+    User attribute names are used verbatim as the Python-facing API (property
+    names, ``get_*``/``set_*`` methods), but they cannot be used directly as
+    C++ identifiers: a name like ``int16`` collides with the MSVC built-in
+    ``__int16`` (Microsoft extensions treat ``int8``/``int16``/``int32``/
+    ``int64`` *and* their single-underscore forms ``_int8``/... as synonyms for
+    the ``__intN`` keywords), and others may clash with C++ keywords (``class``,
+    ``new``, ...). We therefore mangle the C++ member with a fixed prefix and
+    alias it back to the user name on the Cython side, so the public API is
+    unchanged while the generated C++ always compiles. The prefix matters: a
+    bare ``_`` prefix would turn ``int8`` into ``_int8``, which is itself an
+    MSVC keyword, so the prefix must not be ``_`` followed by a digit.
+    """
+    return "_attr_" + name
+
+
+def _cpp_arg_name(name: str) -> str:
+    """C++ constructor parameter name for a user-provided attribute.
+
+    Must be distinct from :func:`_cpp_member_name` (the constructor initializes
+    ``member(arg)``) and, like it, must avoid the MSVC ``_intN`` keyword forms.
+    """
+    return "_arg_" + name
+
+
 def _build_wrapper(
     node_dtype: str,
     node_attr_dtypes: Mapping[str, str] | None = None,
@@ -60,6 +87,8 @@ def _build_wrapper(
         name: DType(dtype) for name, dtype in edge_attr_dtypes.items()
     }
     wrapper_template.directed = directed
+    wrapper_template.cpp_member = _cpp_member_name
+    wrapper_template.cpp_arg = _cpp_arg_name
 
     return str(wrapper_template)
 

{spatial_graph-0.0.4 → spatial_graph-0.0.6}/src/spatial_graph/_graph/wrapper_template.pyx

@@ -95,7 +95,7 @@ cdef extern from *:
             ${class_name}(
                 %set $sep=""
                 %for name, dtype in $dtypes.items()
-                $sep$dtype.to_c_decl("_" + $name)
+                $sep$dtype.to_c_decl($cpp_arg(name))
                 %set $sep=", "
                 %end for
             ) :
@@ -103,15 +103,15 @@ cdef extern from *:
             %for name, dtype in $dtypes.items()
             $sep
             %if $dtype.is_array
-            ${name}{
+            ${cpp_member(name)}{
             %set $isep=""
             %for i in range($dtype.size)
-                ${isep}_${name}[$i]
+                ${isep}${cpp_arg(name)}[$i]
                 %set $isep=", "
             %end for
             }
             %else
-            ${name}(_$name)%slurp
+            ${cpp_member(name)}(${cpp_arg(name)})%slurp
             %end if
             %set $sep=", "
             %end for
@@ -119,7 +119,7 @@ cdef extern from *:
             %end if
 
             %for name, dtype in $dtypes.items()
-            $dtype.to_c_decl($name);
+            $dtype.to_c_decl($cpp_member(name));
             %end for
     };
     """
@@ -129,13 +129,13 @@ cdef extern from *:
         ${class_name}(
             %set $sep=""
             %for name, dtype in $dtypes.items()
-            $sep$dtype.to_c_decl("_" + $name)
+            $sep$dtype.to_c_decl($cpp_arg(name))
             %set $sep=", "
             %end for
         ) except +
 
         %for name, dtype in $dtypes.items()
-        $dtype.to_pyxtype() $name
+        $dtype.to_pyxtype() $name "$cpp_member(name)"
         %end for
 
 cdef class ${class_name}View:

{spatial_graph-0.0.4 → spatial_graph-0.0.6}/src/spatial_graph/_rtree/src/rtree.h

@@ -6,6 +6,7 @@
 #define RTREE_H
 
 #include <stdlib.h>
+#include <stdbool.h>
 #include "config.h"
 
 // rtree_new returns a new rtree
@@ -83,8 +84,8 @@ int rtree_delete(struct rtree *tr, const coord_t *min, const coord_t *max, const
 // rectangle, and perform a comparison of its data to the provided data using
 // a compare function. The first item that is found is deleted.
 //
-// Returns false if the system is out of memory.
-bool rtree_delete_with_comparator(struct rtree *tr, const coord_t *min,
+// Returns the number of deleted items (0 or 1) or -1 if an OOM error occured.
+int rtree_delete_with_comparator(struct rtree *tr, const coord_t *min,
 	const coord_t *max, const item_t item,
 	int (*compare)(const item_t a, const item_t b, void *udata),
 	void *udata);

{spatial_graph-0.0.4 → spatial_graph-0.0.6}/src/spatial_graph/_rtree/wrapper_template.pyx

@@ -1,19 +1,15 @@
 from libc.stdint cimport *
+from libcpp cimport bool
 import numpy as np
 
-
-ctypedef int bool
-
 cdef extern from *:
     """
-    typedef int bool;
-    #define false 0
-    #define true 1
-
     %if $c_distance_function
     #define KNN_USE_EXACT_DISTANCE
     %end if
     #define DIMS $dims
+    #include <stdbool.h>
+    #include <string.h>
 
     typedef $coord_dtype.to_pyxtype() coord_t;
     typedef $item_dtype.base_c_type item_base_t;
@@ -152,7 +148,7 @@ cdef pyx_items_t memview_to_pyx_items_t($item_dtype.to_pyxtype(add_dim=True) ite
     %end if
 
 
-cdef bint count_iterator(
+cdef bool count_iterator(
         const coord_t* bb_min,
         const coord_t* bb_max,
         const item_t item,
@@ -174,7 +170,7 @@ cdef init_search_results_from_memview(search_results* r, $item_dtype.to_pyxtype(
     r.items = memview_to_pyx_items_t(items)
 
 
-cdef bint search_iterator(
+cdef bool search_iterator(
         const coord_t* bb_min,
         const coord_t* bb_max,
         const item_t item,
@@ -203,7 +199,7 @@ cdef init_nearest_results_from_memview(nearest_results* r,
     r.distances = &distances[0] if distances is not None else NULL
 
 
-cdef bint nearest_iterator(
+cdef bool nearest_iterator(
         const item_t item,
         coord_t distance,
         void* udata

{spatial_graph-0.0.4 → spatial_graph-0.0.6}/tests/test_attributes.py

@@ -95,3 +95,58 @@ def test_attr_dtypes(dtype):
     graph.add_node(1, position=np.array([0.0, 0.0, 0.0]), **{f"node_attr_{dtype}": 0})
     graph.add_node(2, position=np.array([0.0, 0.0, 0.0]), **{f"node_attr_{dtype}": 1})
     graph.add_edge([1, 2], **{f"edge_attr_{dtype}": 0})
+
+
+# Attribute names that collide with C++ keywords or MSVC built-in type
+# specifiers (but are not Python keywords, so they are valid attribute names).
+# These cannot appear verbatim as C++ struct members or constructor parameters.
+# In particular MSVC (with Microsoft extensions) treats ``int8``/``int16``/
+# ``int32``/``int64`` *and* their single-underscore forms ``_int8``/... as
+# aliases for the ``__intN`` keywords, so a member named ``int16`` (or a
+# constructor parameter ``_int16``) expands to ``__int16`` and fails to compile.
+@pytest.mark.parametrize(
+    "attr_name", ["int8", "int16", "int32", "int64", "new", "double"]
+)
+def test_attr_name_collides_with_cpp_keyword(attr_name):
+    graph = sg.SpatialGraph(
+        ndims=3,
+        node_dtype="uint64",
+        node_attr_dtypes={attr_name: "int16", "position": "double[3]"},
+        edge_attr_dtypes={attr_name: "int16"},
+        position_attr="position",
+    )
+
+    graph.add_node(1, position=np.array([1.0, 1.0, 1.0]), **{attr_name: 5})
+    graph.add_node(2, position=np.array([2.0, 2.0, 2.0]), **{attr_name: 7})
+    graph.add_edge([1, 2], **{attr_name: 9})
+
+    # The user-provided name stays the public attribute (the colliding name only
+    # affects the internal C++ identifier). Reading it back through every public
+    # access path must return the stored value -- a regression in the C++ member
+    # mangling / Cython cname-aliasing would silently corrupt these.
+    nodes = np.array([1, 2], dtype="uint64")
+
+    # single node
+    assert getattr(graph.node_attrs[1], attr_name) == 5
+    assert getattr(graph.node_attrs[2], attr_name) == 7
+    # array of nodes
+    np.testing.assert_array_equal(
+        getattr(graph.node_attrs[nodes], attr_name), np.array([5, 7], dtype="int16")
+    )
+    # all nodes (order is unspecified, so compare sorted)
+    np.testing.assert_array_equal(
+        np.sort(getattr(graph.node_attrs, attr_name)), np.array([5, 7], dtype="int16")
+    )
+    # edge
+    assert getattr(graph.edge_attrs[(1, 2)], attr_name) == 9
+
+    # the position attribute is mangled the same way and must be unaffected
+    np.testing.assert_array_equal(
+        graph.node_attrs[1].position, np.array([1.0, 1.0, 1.0])
+    )
+
+    # setting through the public attribute round-trips too
+    setattr(graph.node_attrs[1], attr_name, 11)
+    assert getattr(graph.node_attrs[1], attr_name) == 11
+    setattr(graph.edge_attrs[(1, 2)], attr_name, 13)
+    assert getattr(graph.edge_attrs[(1, 2)], attr_name) == 13