Update to work with new networkx dispatching (#68)

Author: eriknw

Diff for: .github/workflows/publish_pypi.yml

@@ -35,7 +35,7 @@ jobs:
       - name: Check with twine
         run: python -m twine check --strict dist/*
       - name: Publish to PyPI
-        uses: pypa/[email protected].6
+        uses: pypa/[email protected].10
         with:
           user: __token__
           password: ${{ secrets.PYPI_TOKEN }}

Diff for: .github/workflows/test.yml

@@ -30,7 +30,7 @@ jobs:
           activate-environment: testing
       - name: Install dependencies
         run: |
-          conda install -c conda-forge python-graphblas scipy pandas pytest-cov pytest-randomly
+          conda install -c conda-forge 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
@@ -39,7 +39,8 @@ jobs:
           python -c 'import sys, graphblas_algorithms; assert "networkx" not in sys.modules'
           coverage run --branch -m pytest --color=yes -v --check-structure
           coverage report
-          NETWORKX_GRAPH_CONVERT=graphblas pytest --color=yes --pyargs networkx --cov --cov-append
+          # NETWORKX_GRAPH_CONVERT=graphblas pytest --color=yes --pyargs networkx --cov --cov-append
+          ./run_nx_tests.sh --color=yes --cov --cov-append
           coverage report
           coverage xml
       - name: Coverage

Diff for: .pre-commit-config.yaml

@@ -7,7 +7,7 @@
 ci:
     # See: https://pre-commit.ci/#configuration
     autofix_prs: false
-    autoupdate_schedule: monthly
+    autoupdate_schedule: quarterly
     skip: [no-commit-to-branch]
 fail_fast: true
 default_language_version:
@@ -17,21 +17,27 @@ repos:
     rev: v4.4.0
     hooks:
       - id: check-added-large-files
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: check-symlinks
       - id: check-ast
       - id: check-toml
       - id: check-yaml
       - id: debug-statements
       - id: end-of-file-fixer
+        exclude_types: [svg]
       - id: mixed-line-ending
       - id: trailing-whitespace
+      - id: name-tests-test
+        args: ["--pytest-test-first"]
   - repo: https://github.com/abravalheri/validate-pyproject
-    rev: v0.13
+    rev: v0.14
     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: v2.1.1
+    rev: v2.2.0
     hooks:
       - id: autoflake
         args: [--in-place]
@@ -40,7 +46,7 @@ repos:
     hooks:
       - id: isort
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.4.0
+    rev: v3.10.1
     hooks:
       - id: pyupgrade
         args: [--py38-plus]
@@ -50,38 +56,38 @@ repos:
       - id: auto-walrus
         args: [--line-length, "100"]
   - repo: https://github.com/psf/black
-    rev: 23.3.0
+    rev: 23.7.0
     hooks:
       - id: black
       # - id: black-jupyter
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.0.270
+    rev: v0.0.285
     hooks:
       - id: ruff
         args: [--fix-only, --show-fixes]
   - repo: https://github.com/PyCQA/flake8
-    rev: 6.0.0
+    rev: 6.1.0
     hooks:
       - id: flake8
         additional_dependencies: &flake8_dependencies
         # These versions need updated manually
-        - flake8==6.0.0
-        - flake8-bugbear==23.5.9
+        - flake8==6.1.0
+        - flake8-bugbear==23.7.10
         - flake8-simplify==0.20.0
   - repo: https://github.com/asottile/yesqa
-    rev: v1.4.0
+    rev: v1.5.0
     hooks:
       - id: yesqa
         additional_dependencies: *flake8_dependencies
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.4
+    rev: v2.2.5
     hooks:
       - id: codespell
         types_or: [python, rst, markdown]
         additional_dependencies: [tomli]
         files: ^(graphblas_algorithms|docs)/
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.0.270
+    rev: v0.0.285
     hooks:
       - id: ruff
   # `pyroma` may help keep our package standards up to date if best practices change.

Diff for: graphblas_algorithms/interface.py

@@ -171,20 +171,71 @@ class Dispatcher:
     # End auto-generated code: dispatch
 
     @staticmethod
-    def convert_from_nx(graph, weight=None, *, name=None):
+    def convert_from_nx(
+        graph,
+        edge_attrs=None,
+        node_attrs=None,
+        preserve_edge_attrs=False,
+        preserve_node_attrs=False,
+        preserve_graph_attrs=False,
+        name=None,
+        graph_name=None,
+        *,
+        weight=None,  # For nx.__version__ <= 3.1
+    ):
         import networkx as nx
 
         from .classes import DiGraph, Graph, MultiDiGraph, MultiGraph
 
+        if preserve_edge_attrs:
+            if graph.is_multigraph():
+                attrs = set().union(
+                    *(
+                        datadict
+                        for nbrs in graph._adj.values()
+                        for keydict in nbrs.values()
+                        for datadict in keydict.values()
+                    )
+                )
+            else:
+                attrs = set().union(
+                    *(datadict for nbrs in graph._adj.values() for datadict in nbrs.values())
+                )
+            if len(attrs) == 1:
+                [attr] = attrs
+                edge_attrs = {attr: None}
+            elif attrs:
+                raise NotImplementedError("`preserve_edge_attrs=True` is not fully implemented")
+        if node_attrs:
+            raise NotImplementedError("non-None `node_attrs` is not yet implemented")
+        if preserve_node_attrs:
+            attrs = set().union(*(datadict for node, datadict in graph.nodes(data=True)))
+            if attrs:
+                raise NotImplementedError("`preserve_node_attrs=True` is not implemented")
+        if edge_attrs:
+            if len(edge_attrs) > 1:
+                raise NotImplementedError(
+                    "Multiple edge attributes is not implemented (bad value for edge_attrs)"
+                )
+            if weight is not None:
+                raise TypeError("edge_attrs and weight both given")
+            [[weight, default]] = edge_attrs.items()
+            if default is not None and default != 1:
+                raise NotImplementedError(f"edge default != 1 is not implemented; got {default}")
+
         if isinstance(graph, nx.MultiDiGraph):
-            return MultiDiGraph.from_networkx(graph, weight=weight)
-        if isinstance(graph, nx.MultiGraph):
-            return MultiGraph.from_networkx(graph, weight=weight)
-        if isinstance(graph, nx.DiGraph):
-            return DiGraph.from_networkx(graph, weight=weight)
-        if isinstance(graph, nx.Graph):
-            return Graph.from_networkx(graph, weight=weight)
-        raise TypeError(f"Unsupported type of graph: {type(graph)}")
+            G = MultiDiGraph.from_networkx(graph, weight=weight)
+        elif isinstance(graph, nx.MultiGraph):
+            G = MultiGraph.from_networkx(graph, weight=weight)
+        elif isinstance(graph, nx.DiGraph):
+            G = DiGraph.from_networkx(graph, weight=weight)
+        elif isinstance(graph, nx.Graph):
+            G = Graph.from_networkx(graph, weight=weight)
+        else:
+            raise TypeError(f"Unsupported type of graph: {type(graph)}")
+        if preserve_graph_attrs:
+            G.graph.update(graph.graph)
+        return G
 
     @staticmethod
     def convert_to_nx(obj, *, name=None):

Diff for: graphblas_algorithms/tests/test_match_nx.py

@@ -22,13 +22,29 @@
         "Matching networkx namespace requires networkx to be installed", allow_module_level=True
     )
 else:
-    from networkx.classes import backends  # noqa: F401
+    try:
+        from networkx.utils import backends
+
+        IS_NX_30_OR_31 = False
+    except ImportError:  # pragma: no cover (import)
+        # This is the location in nx 3.1
+        from networkx.classes import backends  # noqa: F401
+
+        IS_NX_30_OR_31 = True
 
 
 def isdispatched(func):
     """Can this NetworkX function dispatch to other backends?"""
+    if IS_NX_30_OR_31:
+        return (
+            callable(func)
+            and hasattr(func, "dispatchname")
+            and func.__module__.startswith("networkx")
+        )
     return (
-        callable(func) and hasattr(func, "dispatchname") and func.__module__.startswith("networkx")
+        callable(func)
+        and hasattr(func, "preserve_edge_attrs")
+        and func.__module__.startswith("networkx")
     )
 
 
@@ -37,7 +53,9 @@ def dispatchname(func):
     # Haha, there should be a better way to get this
     if not isdispatched(func):
         raise ValueError(f"Function is not dispatched in NetworkX: {func.__name__}")
-    return func.dispatchname
+    if IS_NX_30_OR_31:
+        return func.dispatchname
+    return func.name
 
 
 def fullname(func):

Diff for: pyproject.toml

@@ -214,12 +214,14 @@ ignore = [
     "RET502",  # Do not implicitly `return None` in function able to return non-`None` value
     "RET503",  # Missing explicit `return` at the end of function able to return non-`None` value
     "RET504",  # Unnecessary variable assignment before `return` statement
+    "RUF012",  # Mutable class attributes should be annotated with `typing.ClassVar` (Note: no annotations yet)
     "S110",  # `try`-`except`-`pass` detected, consider logging the exception (Note: good advice, but we don't log)
     "S112",  # `try`-`except`-`continue` detected, consider logging the exception (Note: good advice, but we don't log)
     "SIM102",  # Use a single `if` statement instead of nested `if` statements (Note: often necessary)
     "SIM105",  # Use contextlib.suppress(...) instead of try-except-pass (Note: try-except-pass is much faster)
     "SIM108",  # Use ternary operator ... instead of if-else-block (Note: if-else better for coverage and sometimes clearer)
     "TRY003",  # Avoid specifying long messages outside the exception class (Note: why?)
+    "FIX001", "FIX002", "FIX003", "FIX004",  # flake8-fixme (like flake8-todos)
 
     # Ignored categories
     "C90",  # mccabe (Too strict, but maybe we should make things less complex)

Diff for: run_nx_tests.sh

@@ -1,3 +1,6 @@
 #!/bin/bash
-NETWORKX_GRAPH_CONVERT=graphblas pytest --pyargs networkx "$@"
-# NETWORKX_GRAPH_CONVERT=graphblas pytest --pyargs networkx --cov --cov-report term-missing "$@"
+NETWORKX_GRAPH_CONVERT=graphblas \
+NETWORKX_TEST_BACKEND=graphblas \
+NETWORKX_FALLBACK_TO_NX=True \
+    pytest --pyargs networkx "$@"
+#    pytest --pyargs networkx --cov --cov-report term-missing "$@"

Diff for: scripts/bench.py

@@ -19,7 +19,7 @@
 
 datapaths = [
     Path(__file__).parent / ".." / "data",
-    Path("."),
+    Path(),
 ]
 
 
@@ -37,7 +37,7 @@ def find_data(dataname):
             if dataname not in download_data.data_urls:
                 raise FileNotFoundError(f"Unable to find data file for {dataname}")
             curpath = Path(download_data.main([dataname])[0])
-    return curpath.resolve().relative_to(Path(".").resolve())
+    return curpath.resolve().relative_to(Path().resolve())
 
 
 def get_symmetry(file_or_mminfo):

Diff for: scripts/download_data.py

@@ -47,7 +47,7 @@ def main(datanames, overwrite=False):
     for name in datanames:
         target = datapath / f"{name}.mtx"
         filenames.append(target)
-        relpath = target.resolve().relative_to(Path(".").resolve())
+        relpath = target.resolve().relative_to(Path().resolve())
         if not overwrite and target.exists():
             print(f"{relpath} already exists; skipping", file=sys.stderr)
             continue