Update to NetworkX 3.2 (#77)

* Update to NetworkX 3.2

* Use mamba instead for faster environment creation

* Drop Python 3.8

Author: eriknw

.github/workflows/test.yml

@@ -21,16 +21,34 @@ jobs:
         uses: actions/checkout@v3
         with:
           fetch-depth: 0
-      - name: Conda
+      - name: Setup mamba
         uses: conda-incubator/setup-miniconda@v2
+        id: setup_mamba
+        continue-on-error: true
+        with:
+          miniforge-variant: Mambaforge
+          miniforge-version: latest
+          use-mamba: true
+          python-version: ${{ matrix.python-version }}
+          channels: conda-forge,${{ contains(matrix.python-version, 'pypy') && 'defaults' || 'nodefaults' }}
+          channel-priority: ${{ contains(matrix.python-version, 'pypy') && 'flexible' || 'strict' }}
+          activate-environment: graphblas
+          auto-activate-base: false
+      - name: Setup conda
+        uses: conda-incubator/setup-miniconda@v2
+        id: setup_conda
+        if: steps.setup_mamba.outcome == 'failure'
+        continue-on-error: false
         with:
           auto-update-conda: true
           python-version: ${{ matrix.python-version }}
-          channels: conda-forge
-          activate-environment: testing
+          channels: conda-forge,${{ contains(matrix.python-version, 'pypy') && 'defaults' || 'nodefaults' }}
+          channel-priority: ${{ contains(matrix.python-version, 'pypy') && 'flexible' || 'strict' }}
+          activate-environment: graphblas
+          auto-activate-base: false
       - name: Install dependencies
         run: |
-          conda install -c conda-forge python-graphblas scipy pandas pytest-cov pytest-randomly pytest-mpl
+          $(command -v mamba || command -v conda) install python-graphblas scipy pandas pytest-cov pytest-randomly pytest-mpl
             # matplotlib lxml pygraphviz pydot sympy  # Extra networkx deps we don't need yet
           pip install git+https://github.com/networkx/networkx.git@main --no-deps
           pip install -e . --no-deps

.pre-commit-config.yaml

@@ -5,21 +5,23 @@
 # To update: `pre-commit autoupdate`
 #  - &flake8_dependencies below needs updated manually
 ci:
-    # See: https://pre-commit.ci/#configuration
-    autofix_prs: false
-    autoupdate_schedule: quarterly
-    skip: [no-commit-to-branch]
+  # See: https://pre-commit.ci/#configuration
+  autofix_prs: false
+  autoupdate_schedule: quarterly
+  autoupdate_commit_msg: "chore: update pre-commit hooks"
+  autofix_commit_msg: "style: pre-commit fixes"
+  skip: [no-commit-to-branch]
 fail_fast: true
 default_language_version:
     python: python3
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
       - id: check-added-large-files
       - id: check-case-conflict
       - id: check-merge-conflict
-      - id: check-symlinks
+      # - id: check-symlinks
       - id: check-ast
       - id: check-toml
       - id: check-yaml
@@ -37,7 +39,7 @@ repos:
         name: Validate pyproject.toml
   # I don't yet trust ruff to do what autoflake does
   - repo: https://github.com/PyCQA/autoflake
-    rev: v2.2.0
+    rev: v2.2.1
     hooks:
       - id: autoflake
         args: [--in-place]
@@ -46,22 +48,22 @@ repos:
     hooks:
       - id: isort
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.10.1
+    rev: v3.15.0
     hooks:
       - id: pyupgrade
-        args: [--py38-plus]
+        args: [--py39-plus]
   - repo: https://github.com/MarcoGorelli/auto-walrus
     rev: v0.2.2
     hooks:
       - id: auto-walrus
         args: [--line-length, "100"]
   - repo: https://github.com/psf/black
-    rev: 23.7.0
+    rev: 23.9.1
     hooks:
       - id: black
       # - id: black-jupyter
-  - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.0.285
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.0.292
     hooks:
       - id: ruff
         args: [--fix-only, --show-fixes]
@@ -72,22 +74,22 @@ repos:
         additional_dependencies: &flake8_dependencies
         # These versions need updated manually
         - flake8==6.1.0
-        - flake8-bugbear==23.7.10
-        - flake8-simplify==0.20.0
+        - flake8-bugbear==23.9.16
+        - flake8-simplify==0.21.0
   - repo: https://github.com/asottile/yesqa
     rev: v1.5.0
     hooks:
       - id: yesqa
         additional_dependencies: *flake8_dependencies
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.5
+    rev: v2.2.6
     hooks:
       - id: codespell
         types_or: [python, rst, markdown]
         additional_dependencies: [tomli]
         files: ^(graphblas_algorithms|docs)/
-  - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.0.285
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.0.292
     hooks:
       - id: ruff
   # `pyroma` may help keep our package standards up to date if best practices change.
@@ -98,6 +100,6 @@ repos:
       - id: pyroma
         args: [-n, "10", .]
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
       - id: no-commit-to-branch  # no commit directly to main

_nx_graphblas/__init__.py

@@ -0,0 +1,107 @@
+def get_info():
+    return {
+        "backend_name": "graphblas",
+        "project": "graphblas-algorithms",
+        "package": "graphblas_algorithms",
+        "url": "https://github.com/python-graphblas/graphblas-algorithms",
+        "short_summary": "Fast, OpenMP-enabled backend using GraphBLAS",
+        # "description": "TODO",
+        "functions": {
+            "adjacency_matrix": {},
+            "all_pairs_bellman_ford_path_length": {
+                "extra_parameters": {
+                    "chunksize": "Split the computation into chunks; "
+                    'may specify size as string or number of rows. Default "10 MiB"',
+                },
+            },
+            "all_pairs_shortest_path_length": {
+                "extra_parameters": {
+                    "chunksize": "Split the computation into chunks; "
+                    'may specify size as string or number of rows. Default "10 MiB"',
+                },
+            },
+            "ancestors": {},
+            "average_clustering": {},
+            "bellman_ford_path": {},
+            "bellman_ford_path_length": {},
+            "bethe_hessian_matrix": {},
+            "bfs_layers": {},
+            "boundary_expansion": {},
+            "clustering": {},
+            "complement": {},
+            "compose": {},
+            "conductance": {},
+            "cut_size": {},
+            "degree_centrality": {},
+            "descendants": {},
+            "descendants_at_distance": {},
+            "difference": {},
+            "directed_modularity_matrix": {},
+            "disjoint_union": {},
+            "edge_boundary": {},
+            "edge_expansion": {},
+            "efficiency": {},
+            "ego_graph": {},
+            "eigenvector_centrality": {},
+            "fast_could_be_isomorphic": {},
+            "faster_could_be_isomorphic": {},
+            "floyd_warshall": {},
+            "floyd_warshall_numpy": {},
+            "floyd_warshall_predecessor_and_distance": {},
+            "full_join": {},
+            "generalized_degree": {},
+            "google_matrix": {},
+            "has_path": {},
+            "hits": {},
+            "in_degree_centrality": {},
+            "inter_community_edges": {},
+            "intersection": {},
+            "intra_community_edges": {},
+            "is_connected": {},
+            "is_dominating_set": {},
+            "is_isolate": {},
+            "is_k_regular": {},
+            "isolates": {},
+            "is_regular": {},
+            "is_simple_path": {},
+            "is_tournament": {},
+            "is_triad": {},
+            "is_weakly_connected": {},
+            "katz_centrality": {},
+            "k_truss": {},
+            "laplacian_matrix": {},
+            "lowest_common_ancestor": {},
+            "mixing_expansion": {},
+            "modularity_matrix": {},
+            "mutual_weight": {},
+            "negative_edge_cycle": {},
+            "node_boundary": {},
+            "node_connected_component": {},
+            "node_expansion": {},
+            "normalized_cut_size": {},
+            "normalized_laplacian_matrix": {},
+            "number_of_isolates": {},
+            "out_degree_centrality": {},
+            "overall_reciprocity": {},
+            "pagerank": {},
+            "reciprocity": {},
+            "reverse": {},
+            "score_sequence": {},
+            "single_source_bellman_ford_path_length": {},
+            "single_source_shortest_path_length": {},
+            "single_target_shortest_path_length": {},
+            "s_metric": {},
+            "square_clustering": {
+                "extra_parameters": {
+                    "chunksize": "Split the computation into chunks; "
+                    'may specify size as string or number of rows. Default "256 MiB"',
+                },
+            },
+            "symmetric_difference": {},
+            "tournament_matrix": {},
+            "transitivity": {},
+            "triangles": {},
+            "union": {},
+            "volume": {},
+        },
+    }

graphblas_algorithms/classes/digraph.py

@@ -442,6 +442,7 @@ def __missing__(self, key):
 
 
 class DiGraph(Graph):
+    __networkx_backend__ = "graphblas"
     __networkx_plugin__ = "graphblas"
 
     # "-" properties ignore self-edges, "+" properties include self-edges
@@ -611,7 +612,7 @@ def to_undirected(self, reciprocal=False, as_view=False, *, name=None):
         return Graph(B, key_to_id=self._key_to_id)
 
     def reverse(self, copy=True):
-        # We could even re-use many of the cached values
+        # We could even reuse many of the cached values
         A = self._A.T  # This probably mostly works, but does not yet support assignment
         if copy:
             A = A.new()

graphblas_algorithms/classes/graph.py

@@ -301,6 +301,7 @@ def __missing__(self, key):
 
 
 class Graph:
+    __networkx_backend__ = "graphblas"
     __networkx_plugin__ = "graphblas"
 
     # "-" properties ignore self-edges, "+" properties include self-edges

graphblas_algorithms/nxapi/smetric.py

@@ -1,13 +1,22 @@
+import warnings
+
 from graphblas_algorithms import algorithms
 from graphblas_algorithms.classes.digraph import to_graph
 
-from .exception import NetworkXError
-
 __all__ = ["s_metric"]
 
 
-def s_metric(G, normalized=True):
-    if normalized:
-        raise NetworkXError("Normalization not implemented")
+def s_metric(G, **kwargs):
+    if kwargs:
+        if "normalized" in kwargs:
+            warnings.warn(
+                "\n\nThe `normalized` keyword is deprecated and will be removed\n"
+                "in the future. To silence this warning, remove `normalized`\n"
+                "when calling `s_metric`.\n\nThe value of `normalized` is ignored.",
+                DeprecationWarning,
+                stacklevel=2,
+            )
+        else:
+            raise TypeError(f"s_metric got an unexpected keyword argument '{kwargs.popitem()[0]}'")
     G = to_graph(G)
     return algorithms.s_metric(G)

graphblas_algorithms/tests/test_core.py

@@ -27,6 +27,7 @@ def test_packages():
     path = pathlib.Path(ga.__file__).parent
     pkgs = [f"graphblas_algorithms.{x}" for x in setuptools.find_packages(path)]
     pkgs.append("graphblas_algorithms")
+    pkgs.append("_nx_graphblas")
     pkgs.sort()
     pyproject = path.parent / "pyproject.toml"
     if not pyproject.exists():

pyproject.toml

@@ -10,7 +10,7 @@ name = "graphblas-algorithms"
 dynamic = ["version"]
 description = "Graph algorithms written in GraphBLAS and backend for NetworkX"
 readme = "README.md"
-requires-python = ">=3.8"
+requires-python = ">=3.9"
 license = {file = "LICENSE"}
 authors = [
     {name = "Erik Welch", email = "[email protected]"},
@@ -43,7 +43,6 @@ classifiers = [
     "Operating System :: Microsoft :: Windows",
     "Programming Language :: Python",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
@@ -65,6 +64,12 @@ dependencies = [
 [project.entry-points."networkx.plugins"]
 graphblas = "graphblas_algorithms.interface:Dispatcher"
 
+[project.entry-points."networkx.backends"]
+graphblas = "graphblas_algorithms.interface:Dispatcher"
+
+[project.entry-points."networkx.backend_info"]
+graphblas = "_nx_graphblas:get_info"
+
 [project.urls]
 homepage = "https://github.com/python-graphblas/graphblas-algorithms"
 # documentation = "https://graphblas-algorithms.readthedocs.io"
@@ -90,6 +95,7 @@ all = [
 # $ find graphblas_algorithms/ -name __init__.py -print | sort | sed -e 's/\/__init__.py//g' -e 's/\//./g'
 # $ python -c 'import tomli ; [print(x) for x in sorted(tomli.load(open("pyproject.toml", "rb"))["tool"]["setuptools"]["packages"])]'
 packages = [
+    "_nx_graphblas",
     "graphblas_algorithms",
     "graphblas_algorithms.algorithms",
     "graphblas_algorithms.algorithms.centrality",
@@ -127,7 +133,7 @@ dirty_template = "{tag}+{ccount}.g{sha}.dirty"
 
 [tool.black]
 line-length = 100
-target-version = ["py38", "py39", "py310", "py311"]
+target-version = ["py39", "py310", "py311"]
 
 [tool.isort]
 sections = ["FUTURE", "STDLIB", "THIRDPARTY", "FIRSTPARTY", "LOCALFOLDER"]
@@ -143,6 +149,7 @@ skip = [
 ]
 
 [tool.pytest.ini_options]
+minversion = "6.0"
 testpaths = "graphblas_algorithms"
 xfail_strict = false
 markers = [
@@ -169,7 +176,10 @@ exclude_lines = [
 [tool.ruff]
 # https://github.com/charliermarsh/ruff/
 line-length = 100
-target-version = "py38"
+target-version = "py39"
+unfixable = [
+    "F841"  # unused-variable (Note: can leave useless expression)
+]
 select = [
     "ALL",
 ]