Final tweaks for refined CI structure:

- Pulled in changes from upstream branches
- Updaated naming conventions on the `MDAnalysis` tests

Author: harryswift01

.github/workflows/project-ci.yaml

@@ -77,7 +77,7 @@ jobs:
       matrix:
         python-version: ["3.11", "3.12", "3.13"]
         mdanalysis-version: ["2.7.0", "2.8.0", "2.9.0", "latest"]
-    name: MDAnalysis v${{ matrix.mdanalysis-version }} / Python ${{ matrix.python-version }}
+    name: MDAnalysis Compatibility Tests
     steps:
       - name: Checkout repo
         uses: actions/checkout@v4

tests/test_CodeEntropy/test_run.py

@@ -136,9 +136,12 @@ def test_run_entropy_workflow(self):
         run_manager._config_manager.merge_configs.return_value = mock_args
 
         mock_entropy_manager = MagicMock()
-        with unittest.mock.patch(
-            "CodeEntropy.run.EntropyManager", return_value=mock_entropy_manager
-        ), unittest.mock.patch("CodeEntropy.run.mda.Universe") as mock_universe:
+        with (
+            unittest.mock.patch(
+                "CodeEntropy.run.EntropyManager", return_value=mock_entropy_manager
+            ),
+            unittest.mock.patch("CodeEntropy.run.mda.Universe") as mock_universe,
+        ):
 
             run_manager.run_entropy_workflow()