Migrate to uv (#153)

* chore: switch poetry to uv

* chore: update CI

* lint: fix ruff complaints

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

CHANGELOG.md

@@ -1,5 +1,11 @@
 # Changelog
 
+-   **0.16.0** (January 08, 2026)
+    -   Housekeeping:
+        -   Migrated from Poetry to uv for package management
+        -   Updated GitHub Actions workflows to use uv and added testing for Python 3.12 through 3.14
+        -   Upgraded from `lark-parser` to `lark` for parsing
+        -   Updated copyright years
 -   **0.15.0** (August 21 2024)
     -   Backwards-incompatible changes:
         -   Removed the Docker container provisioning functionality from the `Neo4jExecutor` class. To continue using this functionality, please use the `tamarind` package directly, or install `dotmotif==0.14.0`

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():
@@ -235,3 +248,6 @@ def load(fname: Union[str, IO[bytes]]) -> "Motif":
         result = pickle.load(f)
         f.close()
         return result
+
+
+__all__ = ["Motif", "MotifError", "NetworkXExecutor", "GrandIsoExecutor"]

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.

dotmotif/executors/test_neo4jexecutor.py

@@ -1,7 +1,6 @@
 import dotmotif
 from dotmotif.executors.Neo4jExecutor import Neo4jExecutor, _quoted_if_necessary
 import unittest
-import networkx as nx
 
 
 class TestNeo4jExecutor_Automorphisms(unittest.TestCase):

dotmotif/ingest/__init__.py

@@ -19,8 +19,7 @@ class NetworkXConverter(abc.ABC):
 
     pass
 
-    def to_graph(self) -> nx.Graph:
-        ...
+    def to_graph(self) -> nx.Graph: ...
 
 
 class EdgelistConverter(NetworkXConverter):
@@ -53,12 +52,12 @@ def __init__(
             raise KeyError(f"Dataframe does not contain column {v_id_column}.")
         self._graph = nx.DiGraph() if directed else nx.Graph()
         for i, row in data.iterrows():
-            if u_id_column_dtype != str:
+            if u_id_column_dtype is not str:
                 u = np.format_float_positional(row[u_id_column])
             else:
                 u = row[u_id_column]
 
-            if v_id_column_dtype != str:
+            if v_id_column_dtype is not str:
                 v = np.format_float_positional(row[v_id_column])
             else:
                 v = row[v_id_column]

dotmotif/ingest/test_ingest.py

@@ -24,7 +24,7 @@ def test_ingest(self):
 
     def test_read_csv(self):
         converter = EdgelistConverter(
-            io.StringIO("source,target\n" "A,B\n" "A,C\n"),
+            io.StringIO("source,target\nA,B\nA,C\n"),
             "source",
             "target",
         )

dotmotif/parsers/v2/test_v2_parser.py

@@ -51,7 +51,7 @@ def test_can_create_variables_with_underscores(self):
 
     def test_cannot_create_variables_with_dashes(self):
         with self.assertRaises(Exception):
-            dm = dotmotif.Motif("""A -> B-""")
+            dotmotif.Motif("""A -> B-""")
 
     def test_can_create_variables_with_numbers(self):
         dm = dotmotif.Motif("""A_2 -> B1""")
@@ -503,7 +503,7 @@ def test_failed_node_lookup(self):
         C.radius < B.radius
         """
         with self.assertRaises(KeyError):
-            dm = dotmotif.Motif(exp)
+            dotmotif.Motif(exp)
 
 
 class TestEdgeAliasConstraints(unittest.TestCase):
@@ -546,7 +546,7 @@ def test_failed_edge_lookup(self):
         acb.radius = 3
         """
         with self.assertRaises(KeyError):
-            dm = dotmotif.Motif(exp)
+            dotmotif.Motif(exp)
 
     def test_quoted_attribute_edge_constraint(self):
         exp = """\

dotmotif/tests/test_dm_flags.py

@@ -70,18 +70,6 @@ def test_dm_parser_limit(self):
         dm.from_motif(_DEMO_G_MIN)
         self.assertFalse("LIMIT" in Neo4jExecutor.motif_to_cypher(dm).strip())
 
-    def test_from_nx_import(self):
-        G = nx.Graph()
-        G.add_edge("A", "B")
-        G.add_edge("B", "C")
-
-        g = nx.Graph()
-        g.add_edge("A", "B")
-        dm = dotmotif.Motif().from_nx(g)
-
-        E = GrandIsoExecutor(graph=G)
-        self.assertEqual(len(E.find(dm)), 4)
-
     def test_from_nx_import(self):
         G = nx.Graph()
         G.add_edge("A", "B")

dotmotif/utils.py

@@ -5,6 +5,7 @@
 
 Requires nx>=2.0
 """
+
 import hashlib
 import json
 import networkx as nx
@@ -13,12 +14,12 @@
 def untype_string(string):
     try:
         return eval(string)
-    except:
+    except:  # noqa
         try:
             if int(string) == float(string):
                 return int(string)
             return float(string)
-        except:
+        except:  # noqa
             return str(string)