chore: update CI

Author: j6k4m8

.github/workflows/python-package.yml

@@ -1,7 +1,4 @@
-# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
-# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
-
-name: Python package
+name: Test and lint
 
 on:
   push:
@@ -11,34 +8,45 @@ on:
 
 jobs:
   build:
-
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.8, 3.9, '3.10', '3.11']
+        python-version: ['3.9', '3.10', '3.11', '3.12', '3.13', '3.14']
 
     steps:
-
-    - uses: actions/checkout@v2
-
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install flake8 pytest
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-
-    - name: Lint with flake8
-      run: |
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-
-    - name: Test with pytest
-      run: |
-        pytest
+      - uses: actions/checkout@v3
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v3
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install uv
+        run: |
+          curl -LsSf https://astral.sh/uv/install.sh | sh
+          echo "$HOME/.cargo/bin" >> $GITHUB_PATH
+
+      - name: Cache virtual environment
+        uses: actions/cache@v3
+        with:
+          path: .venv
+          key: venv-${{ matrix.python-version }}-${{ hashFiles('**/pyproject.toml') }}
+          restore-keys: |
+            venv-${{ matrix.python-version }}-
+
+      - name: Set up uv venv and install dependencies
+        run: |
+          uv venv
+          source .venv/bin/activate
+          uv pip install ruff pytest pytest-cov pytest-codspeed
+          uv pip install -e .
+
+      - name: Lint with ruff
+        run: |
+          source .venv/bin/activate
+          ruff check dotmotif
+
+      - name: Test with pytest
+        run: |
+          source .venv/bin/activate
+          pytest

dotmotif/__init__.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 """
-Copyright 2022 The Johns Hopkins University Applied Physics Laboratory.
+Copyright 2022-2026 The Johns Hopkins Applied Physics Laboratory.
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
@@ -170,7 +170,20 @@ def list_automorphisms(self):
             return self._automorphisms
 
         g = self.to_nx()
-        res = isomorphism.GraphMatcher(g, g).subgraph_isomorphisms_iter()
+        # Choose the appropriate VF2 matcher depending on directedness
+        # and whether the graph is a multigraph.
+        if g.is_directed():
+            if g.is_multigraph():
+                matcher_cls = isomorphism.MultiDiGraphMatcher
+            else:
+                matcher_cls = isomorphism.DiGraphMatcher
+        else:
+            if g.is_multigraph():
+                matcher_cls = isomorphism.MultiGraphMatcher
+            else:
+                matcher_cls = isomorphism.GraphMatcher
+
+        res = matcher_cls(g, g).subgraph_isomorphisms_iter()
         autos = set()
         for auto in res:
             for k, v in auto.items():

dotmotif/executors/NetworkXExecutor.py

@@ -1,5 +1,5 @@
 """
-Copyright 2022 The Johns Hopkins University Applied Physics Laboratory.
+Copyright 2022-2026 The Johns Hopkins Applied Physics Laboratory.
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.