Merge pull request #170 from CCPBioSim/169-add-python-314

Add `Python v3.14` Support for `CodeEntropy`

Author: harryswift01

.github/workflows/project-ci.yaml

@@ -14,7 +14,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-24.04, windows-2025, macos-15]
-        python-version: ["3.11", "3.12", "3.13"]
+        python-version: ["3.11", "3.12", "3.13", "3.14"]
     steps:
       - name: Checkout repo
         uses: actions/checkout@v5.0.0
@@ -40,10 +40,10 @@ jobs:
     timeout-minutes: 15
     steps:
       - uses: actions/checkout@v5.0.0
-      - name: Set up Python 3.13
+      - name: Set up Python 3.14
         uses: actions/setup-python@v6.0.0
         with:
-          python-version: 3.13
+          python-version: 3.14
       - name: Install python dependencies
         run: |
           pip install --upgrade pip
@@ -56,10 +56,10 @@ jobs:
     timeout-minutes: 15
     steps:
       - uses: actions/checkout@v5.0.0
-      - name: Set up Python 3.13
+      - name: Set up Python 3.14
         uses: actions/setup-python@v6.0.0
         with:
-          python-version: 3.13
+          python-version: 3.14
       - name: Install python dependencies
         run: |
           pip install --upgrade pip
@@ -75,7 +75,7 @@ jobs:
     timeout-minutes: 15
     strategy:
       matrix:
-        python-version: ["3.11", "3.12", "3.13"]
+        python-version: ["3.11", "3.12", "3.13", "3.14"]
         mdanalysis-version: ["2.9.0", "latest"]
     name: MDAnalysis Compatibility Tests
     steps:

.github/workflows/release.yaml

@@ -23,7 +23,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v6.0.0
       with:
-        python-version: 3.13
+        python-version: 3.14
 
     - name: Get latest release from pip
       id: latestreleased
@@ -133,7 +133,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v6.0.0
       with:
-        python-version: 3.13
+        python-version: 3.14
 
     - name: Install flit
       run: |

CodeEntropy/main.py

@@ -25,4 +25,4 @@ def main():
 
 if __name__ == "__main__":
 
-    main()
+    main()  # pragma: no cover

pyproject.toml

@@ -29,6 +29,7 @@ classifiers = [
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
     "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
     "Intended Audience :: Science/Research",
     "License :: OSI Approved :: MIT License",
     "Natural Language :: English",
@@ -37,15 +38,15 @@ classifiers = [
 keywords = ["entropy", "macromolecular systems", "MD simulation"]
 requires-python = ">=3.11"
 dependencies = [
-    "numpy==2.2.3",
-    "mdanalysis>=2.9.0",
-    "pandas==2.2.3",
-    "psutil==5.9.5",
-    "PyYAML==6.0.2",
-    "python-json-logger==3.3.0",
-    "rich==14.0.0",
+    "numpy==2.3.4",
+    "mdanalysis>=2.10.0",
+    "pandas==2.3.3",
+    "psutil==7.1.3",
+    "PyYAML==6.0.3",
+    "python-json-logger==4.0.0",
+    "rich==14.2.0",
     "art==6.5",
-    "waterEntropy==1.2.0",
+    "waterEntropy==1.2.2",
     "requests>=2.32.5",
 ]
 
@@ -56,14 +57,14 @@ Documentation = "https://codeentropy.readthedocs.io"
 
 [project.optional-dependencies]
 testing = [
-    "pytest==8.2.2",
-    "pytest-cov==5.0.0",
-    "pytest-sugar==1.0.0"
+    "pytest>=8.4.2",
+    "pytest-cov>=7.0.0",
+    "pytest-sugar>=1.1.1"
 ]
 
 pre-commit = [
-    "pre-commit==3.7.1",
-    "pylint==3.2.5"
+    "pre-commit>=4.3.0",
+    "pylint>=4.0.0"
 ]
 docs = [
     "sphinx",

tests/test_CodeEntropy/test_data_logger.py

@@ -115,7 +115,6 @@ def test_save_dataframes_as_json(self):
 
     def test_log_tables_rich_output(self):
         console = LoggingConfig.get_console()
-        console.clear_live()
 
         self.logger.add_results_data(
             0, "united_atom", "Transvibrational", 653.4041220313459

tests/test_CodeEntropy/test_entropy.py

@@ -1657,6 +1657,51 @@ def test_assign_conformation(self):
         assert np.all(result >= 0)
         assert np.issubdtype(result.dtype, np.floating)
 
+    def test_assign_conformation_last_bin_peak(self):
+        """
+        Test that the last bin in the histogram is correctly evaluated as a peak
+        when its population is greater than or equal to its neighbors.
+        """
+
+        dihedral = MagicMock()
+        dihedral.value = MagicMock(side_effect=[5, 10, 250, 260, 350, 355])
+
+        # Mock trajectory frames
+        mock_timesteps = [MagicMock(frame=i) for i in range(6)]
+        data_container = MagicMock()
+        data_container.trajectory.__getitem__.return_value = mock_timesteps
+
+        # Create dummy universe and managers
+        tprfile = os.path.join(self.test_data_dir, "md_A4_dna.tpr")
+        trrfile = os.path.join(self.test_data_dir, "md_A4_dna_xf.trr")
+        u = mda.Universe(tprfile, trrfile)
+
+        args = MagicMock(bin_width=60, temperature=300, selection_string="all")
+        run_manager = RunManager("mock_folder/job001")
+        level_manager = LevelManager()
+        data_logger = DataLogger()
+        group_molecules = MagicMock()
+
+        ce = ConformationalEntropy(
+            run_manager, args, u, data_logger, level_manager, group_molecules
+        )
+
+        result = ce.assign_conformation(
+            data_container=data_container,
+            dihedral=dihedral,
+            number_frames=6,
+            bin_width=60,
+            start=0,
+            end=6,
+            step=1,
+        )
+
+        # Basic checks
+        assert isinstance(result, np.ndarray)
+        assert len(result) == 6
+        assert np.all(result >= 0)
+        assert np.issubdtype(result.dtype, np.floating)
+
     def test_conformational_entropy_calculation(self):
         """
         Test `conformational_entropy_calculation` method to verify

tests/test_CodeEntropy/test_levels.py

@@ -1065,6 +1065,73 @@ def test_update_force_torque_matrices_united_atom(self):
             np.testing.assert_array_equal(torque_avg["ua"][key], t_mat_mock)
             self.assertEqual(frame_counts["ua"][key], 1)
 
+    def test_update_force_torque_matrices_united_atom_increment(self):
+        """
+        Test that `update_force_torque_matrices` correctly updates force and torque
+        matrices for the 'united_atom' level when the key already exists.
+        """
+        level_manager = LevelManager()
+        entropy_manager = MagicMock()
+        mol = MagicMock()
+
+        # Simulate one residue with two atoms
+        residue = MagicMock()
+        residue.atoms.indices = [0, 1]
+        mol.residues = [residue]
+        mol.trajectory.__getitem__.return_value = None
+
+        selected_atoms = MagicMock()
+        entropy_manager._run_manager.new_U_select_atom.return_value = selected_atoms
+        selected_atoms.trajectory.__getitem__.return_value = None
+
+        f_mat_1 = np.array([[1.0]], dtype=np.float64)
+        t_mat_1 = np.array([[2.0]], dtype=np.float64)
+        f_mat_2 = np.array([[3.0]], dtype=np.float64)
+        t_mat_2 = np.array([[4.0]], dtype=np.float64)
+
+        level_manager.get_matrices = MagicMock(return_value=(f_mat_1, t_mat_1))
+
+        force_avg = {"ua": {}, "res": [None], "poly": [None]}
+        torque_avg = {"ua": {}, "res": [None], "poly": [None]}
+        frame_counts = {"ua": {}, "res": [None], "poly": [None]}
+
+        # First call: initialize
+        level_manager.update_force_torque_matrices(
+            entropy_manager=entropy_manager,
+            mol=mol,
+            group_id=0,
+            level="united_atom",
+            level_list=["residue", "united_atom"],
+            time_index=0,
+            num_frames=10,
+            force_avg=force_avg,
+            torque_avg=torque_avg,
+            frame_counts=frame_counts,
+        )
+
+        # Second call: update
+        level_manager.get_matrices = MagicMock(return_value=(f_mat_2, t_mat_2))
+
+        level_manager.update_force_torque_matrices(
+            entropy_manager=entropy_manager,
+            mol=mol,
+            group_id=0,
+            level="united_atom",
+            level_list=["residue", "united_atom"],
+            time_index=1,
+            num_frames=10,
+            force_avg=force_avg,
+            torque_avg=torque_avg,
+            frame_counts=frame_counts,
+        )
+
+        expected_force = f_mat_1 + (f_mat_2 - f_mat_1) / 2
+        expected_torque = t_mat_1 + (t_mat_2 - t_mat_1) / 2
+
+        np.testing.assert_array_almost_equal(force_avg["ua"][(0, 0)], expected_force)
+        np.testing.assert_array_almost_equal(torque_avg["ua"][(0, 0)], expected_torque)
+        self.assertEqual(frame_counts["ua"][(0, 0)], 2)
+
     def test_update_force_torque_matrices_residue(self):
         """
         Test that `update_force_torque_matrices` correctly updates force and torque