Add type hints to modularitypruning

.github/workflows/python-package.yml

@@ -5,17 +5,16 @@ name: Python package
 
 on:
   push:
-    branches: [ master ]
+    branches: [master]
   pull_request:
-    branches: [ master ]
+    branches: [master]
 
 jobs:
   build:
-
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ "3.9", "3.10", "3.11", "3.12", "3.13", "3.14", "3.15" ]
+        python-version: ["3.10", "3.11", "3.12", "3.13", "3.14", "3.15"]
 
     steps:
       - uses: actions/checkout@v3
@@ -39,6 +38,13 @@ jobs:
           flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics --exclude env/
           # exit-zero treats all errors as warnings
           flake8 . --count --exit-zero --max-complexity=15 --max-line-length=120 --statistics --exclude env/
+      - name: Type checking with mypy
+        # numpy no longer supports <3.12, so typing is unreliable
+        if: ${{ !contains(fromJSON('["3.10", "3.11"]'), matrix.python-version) }}
+        run: |
+          source env/bin/activate
+          python -m pip install mypy
+          python -m mypy utilities/ --install-types --non-interactive
       - name: Test with pytest
         run: |
           source env/bin/activate

mypy.ini

@@ -0,0 +1,12 @@
+[mypy]
+strict = True
+disallow_any_explicit = True
+files = utilities/*.py, tests/*.py
+
+[mypy-sklearn.*,igraph.*,leidenalg.*]
+ignore_missing_imports = True
+
+# tests are untyped, but we want to check their usage is correct
+[mypy-tests.*]
+allow_untyped_defs = True
+allow_untyped_calls = True

pyproject.toml

@@ -7,7 +7,7 @@ name = "modularitypruning"
 version = "1.5.1"
 description = "Pruning tool to identify small subsets of network partitions that are significant from the perspective of stochastic block model inference."
 readme = "README.md"
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 license = "MIT"
 authors = [
     { name = "Ryan Gibson", email = "ryan.alex.gibson@gmail.com" }
@@ -17,14 +17,14 @@ classifiers = [
     "Development Status :: 5 - Production/Stable",
     "Topic :: Scientific/Engineering :: Information Analysis",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
     "Programming Language :: Python :: 3.13",
     "Programming Language :: Python :: 3.14",
     "Programming Language :: Python :: 3.15",
-    "Programming Language :: Python :: 3 :: Only"
+    "Programming Language :: Python :: 3 :: Only",
+    "Typing :: Typed"
 ]
 dependencies = [
     "leidenalg",
@@ -44,5 +44,8 @@ packages = ["modularitypruning"]
 [tool.setuptools.package-dir]
 modularitypruning = "utilities"
 
+[tool.setuptools.package-data]
+modularitypruning = ["py.typed"]
+
 [tool.autopep8]
 max_line_length = 120

tests/shared_testing_functions.py

@@ -86,7 +86,7 @@ def generate_multilayer_intralayer_SBM(copying_probability, p_in, p_out, first_l
                     if random() < p_out:
                         intralayer_edges.append((u, v))
 
-    G_intralayer = ig.Graph(intralayer_edges, directed=False)
+    G_intralayer = ig.Graph(n=len(combined_community_labels), edges=intralayer_edges, directed=False)
 
     return G_intralayer, layer_membership
 

tests/test_documentation_examples.py

@@ -256,7 +256,7 @@ def test_plot_multiplex_community(self):
         ax = plot_multiplex_community(np.array(membership), np.array(layer_vec))
         ax.set_xticks(np.linspace(0, num_layers, 2 * num_layers + 1))
         ax.set_xticklabels(["", "Advice", "", "Coworker", "", "Friend", ""], fontsize=14)
-        plt.title(f"Multiplex Communities", fontsize=14)
+        plt.title("Multiplex Communities", fontsize=14)
         plt.ylabel("Node ID", fontsize=14)
         plt.close()  # closing this these figures instead of showing
 

tests/test_parallel_leiden_performance.py

@@ -44,8 +44,8 @@ def determine_target_parallelization_speedup(num_calculations=32):
     cpu_utilization = psutil.cpu_percent(interval=5)
     if cpu_utilization > 20:
         PERFORMANCE_TARGET_RELATIVE_TO_PERFECT_SCALING = 0.5
-        warnings.warn(f"System CPU utilization is non-negligible during parallel performance test! "
-                      f"Dropping performance scaling target to 50%.")
+        warnings.warn("System CPU utilization is non-negligible during parallel performance test! "
+                      "Dropping performance scaling target to 50%.")
 
     start_time = time()
     _ = [mock_calculation(i) for i in range(num_calculations)]

tests/test_temporal_multilevel_parameter_estimation.py

@@ -77,6 +77,7 @@ def retry_test_across_graph_sizes(self, test_fn, sizes=[50, 100, 250, 500], retr
                     if not isinstance(e, AssertionError):
                         # test failed in unusual way (perhaps keyboard interrupt?), raising immediately
                         raise e
+        assert last_error is not None
         raise last_error
 
     def test_temporal_SBM_correct_convergence_varying_copying_probabilty(self):

utilities/__init__.py

@@ -1,2 +1,7 @@
 # this makes prune_to_stable_partitions and prune_to_multilayer_stable_partitions importable from the top-level package
-from .parameter_estimation_utilities import prune_to_stable_partitions, prune_to_multilayer_stable_partitions  # noqa
+from .parameter_estimation_utilities import (
+    prune_to_multilayer_stable_partitions as prune_to_multilayer_stable_partitions,
+    prune_to_stable_partitions as prune_to_stable_partitions,
+)
+
+__all__ = ["prune_to_stable_partitions", "prune_to_multilayer_stable_partitions"]