Update to support NetworkX 3.3 (dev), and other maintenance

Author: eriknw

.github/workflows/lint.yml

@@ -17,7 +17,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: "3.10"
-      - uses: pre-commit/[email protected].0
+      - uses: pre-commit/[email protected].1

.github/workflows/publish_pypi.yml

@@ -18,7 +18,7 @@ jobs:
         with:
           fetch-depth: 0
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: "3.10"
       - name: Install build dependencies
@@ -27,15 +27,15 @@ jobs:
           python -m pip install build twine
       - name: Build wheel and sdist
         run: python -m build --sdist --wheel
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: releases
           path: dist
           if-no-files-found: error
       - name: Check with twine
         run: python -m twine check --strict dist/*
       - name: Publish to PyPI
-        uses: pypa/[email protected].10
+        uses: pypa/[email protected].11
         with:
           user: __token__
           password: ${{ secrets.PYPI_TOKEN }}

.github/workflows/test.yml

@@ -22,7 +22,7 @@ jobs:
         with:
           fetch-depth: 0
       - name: Setup mamba
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         id: setup_mamba
         continue-on-error: true
         with:
@@ -35,7 +35,7 @@ jobs:
           activate-environment: graphblas
           auto-activate-base: false
       - name: Setup conda
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         id: setup_conda
         if: steps.setup_mamba.outcome == 'failure'
         continue-on-error: false

.pre-commit-config.yaml

@@ -33,22 +33,22 @@ repos:
       - id: name-tests-test
         args: ["--pytest-test-first"]
   - repo: https://github.com/abravalheri/validate-pyproject
-    rev: v0.15
+    rev: v0.16
     hooks:
       - id: validate-pyproject
         name: Validate pyproject.toml
   # I don't yet trust ruff to do what autoflake does
   - repo: https://github.com/PyCQA/autoflake
-    rev: v2.2.1
+    rev: v2.3.0
     hooks:
       - id: autoflake
         args: [--in-place]
   - repo: https://github.com/pycqa/isort
-    rev: 5.13.1
+    rev: 5.13.2
     hooks:
       - id: isort
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.15.0
+    rev: v3.15.1
     hooks:
       - id: pyupgrade
         args: [--py310-plus]
@@ -58,23 +58,23 @@ repos:
       - id: auto-walrus
         args: [--line-length, "100"]
   - repo: https://github.com/psf/black
-    rev: 23.12.0
+    rev: 24.2.0
     hooks:
       - id: black
       # - id: black-jupyter
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.7
+    rev: v0.2.2
     hooks:
       - id: ruff
         args: [--fix-only, --show-fixes]
   - repo: https://github.com/PyCQA/flake8
-    rev: 6.1.0
+    rev: 7.0.0
     hooks:
       - id: flake8
         additional_dependencies: &flake8_dependencies
         # These versions need updated manually
-        - flake8==6.1.0
-        - flake8-bugbear==23.12.2
+        - flake8==7.0.0
+        - flake8-bugbear==24.2.6
         - flake8-simplify==0.21.0
   - repo: https://github.com/asottile/yesqa
     rev: v1.5.0
@@ -89,7 +89,7 @@ repos:
         additional_dependencies: [tomli]
         files: ^(graphblas_algorithms|docs)/
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.7
+    rev: v0.2.2
     hooks:
       - id: ruff
   # `pyroma` may help keep our package standards up to date if best practices change.

README.md

@@ -5,7 +5,7 @@
 [![PyPI - Python Version](https://img.shields.io/pypi/pyversions/graphblas-algorithms)](https://pypi.python.org/pypi/graphblas-algorithms/)
 [![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://github.com/python-graphblas/graphblas-algorithms/blob/main/LICENSE)
 <br>
-[![Tests](https://github.com/python-graphblas/graphblas-algorithms/workflows/Tests/badge.svg?branch=main)](https://github.com/python-graphblas/graphblas-algorithms/actions)
+[![Tests](https://github.com/python-graphblas/graphblas-algorithms/actions/workflows/test.yml/badge.svg?branch=main)](https://github.com/python-graphblas/graphblas-algorithms/actions)
 [![Coverage](https://codecov.io/gh/python-graphblas/graphblas-algorithms/branch/main/graph/badge.svg)](https://codecov.io/gh/python-graphblas/graphblas-algorithms)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7329185.svg)](https://doi.org/10.5281/zenodo.7329185)
 [![Discord](https://img.shields.io/badge/Chat-Discord-blue)](https://discord.com/invite/vur45CbwMz)

graphblas_algorithms/algorithms/_bfs.py

@@ -1,4 +1,4 @@
-"""BFS routines used by other algorithms"""
+"""BFS routines used by other algorithms."""
 
 import numpy as np
 from graphblas import Matrix, Vector, binary, indexunary, replace, semiring, unary

graphblas_algorithms/algorithms/_helpers.py

@@ -19,7 +19,7 @@ def normalize(x, how):
 
 
 def is_converged(xprev, x, tol):
-    """Check convergence, L1 norm: err = sum(abs(xprev - x)); err < N * tol
+    """Check convergence, L1 norm: ``err = sum(abs(xprev - x)); err < N * tol``.
 
     This modifies `xprev`.
     """

graphblas_algorithms/algorithms/shortest_paths/weighted.py

@@ -116,13 +116,14 @@ def bellman_ford_path_length(G, source, target):
 
 
 def bellman_ford_path_lengths(G, nodes=None, *, expand_output=False):
-    """Extra parameter: expand_output
+    """Extra parameter: expand_output.
 
     Parameters
     ----------
     expand_output : bool, default False
         When False, the returned Matrix has one row per node in nodes.
         When True, the returned Matrix has the same shape as the input Matrix.
+
     """
     # Same algorithms as in `single_source_bellman_ford_path_length`, but with
     # `Cur` as a Matrix with each row corresponding to a source node.

graphblas_algorithms/classes/_utils.py

@@ -177,7 +177,7 @@ def matrix_to_vectornodemap(self, A):
 
 
 def matrix_to_dicts(self, A, *, use_row_index=False, use_column_index=False, values_are_keys=False):
-    """Convert a Matrix to a dict of dicts of the form ``{row: {col: val}}``
+    """Convert a Matrix to a dict of dicts of the form ``{row: {col: val}}``.
 
     Use ``use_row_index=True`` to return the row index as keys in the dict,
     and likewise for `use_column_index=True``.
@@ -256,7 +256,7 @@ def _cacheit(self, key, func, *args, **kwargs):
 
 
 def renumber_key_to_id(self, indices):
-    """Create `key_to_id` for e.g. a subgraph with node ids from `indices`"""
+    """Create `key_to_id` for e.g. a subgraph with node ids from `indices`."""
     id_to_key = self.id_to_key
     return {id_to_key[index]: i for i, index in enumerate(indices)}
     # Alternative (about the same performance)

graphblas_algorithms/classes/digraph.py

@@ -22,7 +22,7 @@
 
 
 def get_AT(G, mask=None):
-    """A.T"""
+    """``A.T``."""
     A = G._A
     cache = G._cache
     if "AT" not in cache:
@@ -31,7 +31,7 @@ def get_AT(G, mask=None):
 
 
 def get_Up(G, mask=None):
-    """select.triu(A)"""
+    """``select.triu(A)``."""
     A = G._A
     cache = G._cache
     if "U+" not in cache:
@@ -50,7 +50,7 @@ def get_Up(G, mask=None):
 
 
 def get_Lp(G, mask=None):
-    """select.tril(A)"""
+    """``select.tril(A)``."""
     A = G._A
     cache = G._cache
     if "L+" not in cache:
@@ -69,7 +69,7 @@ def get_Lp(G, mask=None):
 
 
 def get_Um(G, mask=None):
-    """select.triu(A, 1)"""
+    """``select.triu(A, 1)``."""
     A = G._A
     cache = G._cache
     if "U-" not in cache:
@@ -93,7 +93,7 @@ def get_Um(G, mask=None):
 
 
 def get_Lm(G, mask=None):
-    """select.tril(A, -1)"""
+    """``select.tril(A, -1)``."""
     A = G._A
     cache = G._cache
     if "L-" not in cache:
@@ -117,7 +117,7 @@ def get_Lm(G, mask=None):
 
 
 def get_recip_degreesp(G, mask=None):
-    """pair(A & A.T).reduce_rowwise()"""
+    """``pair(A & A.T).reduce_rowwise()``."""
     A = G._A
     cache = G._cache
     AT = cache.get("AT", A.T)
@@ -159,7 +159,7 @@ def get_recip_degreesp(G, mask=None):
 
 
 def get_recip_degreesm(G, mask=None):
-    """C = select.offdiag(A) ; pair(C & C.T).reduce_rowwise()"""
+    """``C = select.offdiag(A) ; pair(C & C.T).reduce_rowwise()``."""
     A = G._A
     cache = G._cache
     if "AT" in cache:
@@ -236,7 +236,7 @@ def get_recip_degreesm(G, mask=None):
 
 
 def get_total_degreesp(G, mask=None):
-    """A.reduce_rowwise(agg.count) + A.reduce_columnwise(agg.count)"""
+    """``A.reduce_rowwise(agg.count) + A.reduce_columnwise(agg.count)``."""
     cache = G._cache
     if mask is not None:
         if "total_degrees+" in cache:
@@ -266,7 +266,7 @@ def get_total_degreesp(G, mask=None):
 
 
 def get_total_degreesm(G, mask=None):
-    """C = select.offdiag(A) ; C.reduce_rowwise(agg.count) + C.reduce_columnwise(agg.count)"""
+    """``C = select.offdiag(A) ; C.reduce_rowwise(agg.count) + C.reduce_columnwise(agg.count)``."""
     cache = G._cache
     if mask is not None:
         if "total_degrees-" in cache:
@@ -296,7 +296,7 @@ def get_total_degreesm(G, mask=None):
 
 
 def get_total_recipp(G, mask=None):
-    """pair(A & A.T).reduce_scalar()"""
+    """``pair(A & A.T).reduce_scalar()``."""
     A = G._A
     cache = G._cache
     if "total_recip+" not in cache:
@@ -315,7 +315,7 @@ def get_total_recipp(G, mask=None):
 
 
 def get_total_recipm(G, mask=None):
-    """C = select.offdiag(A) ; pair(C & C.T).reduce_scalar()"""
+    """``C = select.offdiag(A) ; pair(C & C.T).reduce_scalar()``."""
     cache = G._cache
     if "total_recip-" not in cache:
         if "total_recip+" in cache and cache.get("has_self_edges") is False:
@@ -330,7 +330,7 @@ def get_total_recipm(G, mask=None):
 
 
 def has_self_edges(G, mask=None):
-    """A.diag().nvals > 0"""
+    """``A.diag().nvals > 0``."""
     A = G._A
     cache = G._cache
     if "has_self_edges" not in cache:

graphblas_algorithms/classes/graph.py

@@ -10,19 +10,19 @@
 
 
 def get_A(G, mask=None):
-    """A"""
+    """``A``."""
     return G._A
 
 
 def get_AT(G, mask=None):
-    """A.T"""
+    """``A.T``."""
     A = G._A
     G._cache["AT"] = A
     return A
 
 
 def get_offdiag(G, mask=None):
-    """select.offdiag(A)"""
+    """``select.offdiag(A)``."""
     A = G._A
     cache = G._cache
     if "offdiag" not in cache:
@@ -38,7 +38,7 @@ def get_offdiag(G, mask=None):
 
 
 def get_Up(G, mask=None):
-    """select.triu(A)"""
+    """``select.triu(A)``."""
     A = G._A
     cache = G._cache
     if "U+" not in cache:
@@ -54,7 +54,7 @@ def get_Up(G, mask=None):
 
 
 def get_Lp(G, mask=None):
-    """select.tril(A)"""
+    """``select.tril(A)``."""
     A = G._A
     cache = G._cache
     if "L+" not in cache:
@@ -70,7 +70,7 @@ def get_Lp(G, mask=None):
 
 
 def get_Um(G, mask=None):
-    """select.triu(A, 1)"""
+    """``select.triu(A, 1)``."""
     A = G._A
     cache = G._cache
     if "U-" not in cache:
@@ -91,7 +91,7 @@ def get_Um(G, mask=None):
 
 
 def get_Lm(G, mask=None):
-    """select.tril(A, -1)"""
+    """``select.tril(A, -1)``."""
     A = G._A
     cache = G._cache
     if "L-" not in cache:
@@ -112,7 +112,7 @@ def get_Lm(G, mask=None):
 
 
 def get_diag(G, mask=None):
-    """A.diag()"""
+    """``A.diag()``."""
     A = G._A
     cache = G._cache
     if "diag" not in cache:
@@ -193,7 +193,7 @@ def has_negative_edgesm(G, mask=None):
 
 
 def has_self_edges(G, mask=None):
-    """A.diag().nvals > 0"""
+    """``A.diag().nvals > 0``."""
     A = G._A
     cache = G._cache
     if "has_self_edges" not in cache:

graphblas_algorithms/conftest.py

@@ -3,7 +3,7 @@
 
 @pytest.fixture(scope="session", autouse=True)
 def ic():
-    """Make `ic` available everywhere during testing for easier debugging"""
+    """Make `ic` available everywhere during testing for easier debugging."""
     try:
         import icecream
     except ImportError:

graphblas_algorithms/nxapi/_utils.py

@@ -88,7 +88,7 @@ def normalize_chunksize(chunksize, itemsize=1, N=None):
 
 
 def partition(chunksize, L, *, evenly=True):
-    """Partition a list into chunks"""
+    """Partition a list into chunks."""
     N = len(L)
     if N == 0:
         return
@@ -109,7 +109,7 @@ def partition(chunksize, L, *, evenly=True):
 
 
 def split_evenly(k, L):
-    """Split a list into approximately-equal parts"""
+    """Split a list into approximately-equal parts."""
     N = len(L)
     if N == 0:
         return