Expand CI pipeline to support Windows and macOS

.github/workflows/project-ci.yaml

@@ -9,12 +9,12 @@ on:
 
 jobs:
   tests:
-    runs-on: ubuntu-24.04
-    timeout-minutes: 30
+    name: Run tests
+    runs-on: ${{ matrix.os }}
     strategy:
       matrix:
+        os: [ubuntu-24.04, windows-2025, macos-15]
         python-version: ["3.11", "3.12", "3.13"]
-    name: Run tests
     steps:
       - name: Checkout repo
         uses: actions/checkout@v5.0.0
@@ -36,7 +36,7 @@ jobs:
           github-token: ${{ secrets.GITHUB_TOKEN }}
 
   docs:
-    runs-on: ubuntu-24.04
+    runs-on: ubuntu-latest
     timeout-minutes: 15
     steps:
       - uses: actions/checkout@v5.0.0

.gitignore

@@ -110,6 +110,7 @@ ENV/
 *.csv
 Example_output/
 Example/data/*.csv
+*.lock
 
 # profraw files from LLVM? Unclear exactly what triggers this
 # There are reports this comes from LLVM profiling, but also Xcode 9.

docs/developer_guide.rst

@@ -19,7 +19,7 @@ Clone the repository::
 
 Install development dependencies::
 
-    pip install -e .[testing,docs,pre-commit]
+    pip install -e ".[testing,docs,pre-commit]"
 
 Running Tests
 -------------

docs/getting_started.rst

@@ -57,9 +57,6 @@ The program assumes the following default unit
 
 Quick start guide
 --------------------
-.. Warning::
-
-    CodeEntropy has not been tested on Windows
 
 A quick and easy way to get started is to use the command-line tool which you can run in bash by simply typing ``CodeEntropy``
 

tests/test_CodeEntropy/test_arg_config_manager.py

@@ -1,27 +1,24 @@
 import argparse
 import logging
 import os
-import shutil
-import tempfile
 import unittest
 from unittest.mock import MagicMock, mock_open, patch
 
 import tests.data as data
 from CodeEntropy.config.arg_config_manager import ConfigManager
 from CodeEntropy.main import main
+from tests.test_CodeEntropy.test_base import BaseTestCase
 
 
-class test_arg_config_manager(unittest.TestCase):
+class TestArgConfigManager(BaseTestCase):
     """
     Unit tests for the ConfigManager.
     """
 
     def setUp(self):
-        """
-        Setup test data and output directories.
-        """
+        super().setUp()
+
         self.test_data_dir = os.path.dirname(data.__file__)
-        self.test_dir = tempfile.mkdtemp(prefix="CodeEntropy_")
         self.config_file = os.path.join(self.test_dir, "config.yaml")
 
         # Create a mock config file
@@ -30,18 +27,6 @@ def setUp(self):
             with open(self.config_file, "w") as f:
                 f.write(mock_file.return_value.read())
 
-        # Change to test directory
-        self._orig_dir = os.getcwd()
-        os.chdir(self.test_dir)
-
-    def tearDown(self):
-        """
-        Clean up after each test.
-        """
-        os.chdir(self._orig_dir)
-        if os.path.exists(self.test_dir):
-            shutil.rmtree(self.test_dir)
-
     def list_data_files(self):
         """
         List all files in the test data directory.

tests/test_CodeEntropy/test_base.py

@@ -0,0 +1,45 @@
+import os
+import shutil
+import tempfile
+import unittest
+
+
+class BaseTestCase(unittest.TestCase):
+    """
+    Base test case class for cross-platform unit tests.
+
+    Provides:
+    1. A unique temporary directory for each test to avoid filesystem conflicts.
+    2. Automatic restoration of the working directory after each test.
+    3. Prepares a logs folder path for tests that need logging configuration.
+    """
+
+    def setUp(self):
+        """
+        Prepare the test environment before each test method runs.
+
+        Actions performed:
+        1. Creates a unique temporary directory for the test.
+        2. Creates a 'logs' subdirectory within the temp directory.
+        3. Changes the current working directory to the temporary directory.
+        """
+        # Create a unique temporary test directory
+        self.test_dir = tempfile.mkdtemp(prefix="CodeEntropy_")
+        self.logs_path = os.path.join(self.test_dir, "logs")
+        os.makedirs(self.logs_path, exist_ok=True)
+
+        self._orig_dir = os.getcwd()
+        os.chdir(self.test_dir)
+
+    def tearDown(self):
+        """
+        Clean up the test environment after each test method runs.
+
+        Actions performed:
+        1. Restores the original working directory.
+        2. Deletes the temporary test directory along with all its contents.
+        """
+        os.chdir(self._orig_dir)
+
+        if os.path.exists(self.test_dir):
+            shutil.rmtree(self.test_dir, ignore_errors=True)

tests/test_CodeEntropy/test_data_logger.py

@@ -1,7 +1,4 @@
 import json
-import os
-import shutil
-import tempfile
 import unittest
 
 import numpy as np
@@ -10,38 +7,20 @@
 from CodeEntropy.config.data_logger import DataLogger
 from CodeEntropy.config.logging_config import LoggingConfig
 from CodeEntropy.main import main
+from tests.test_CodeEntropy.test_base import BaseTestCase
 
 
-class TestDataLogger(unittest.TestCase):
+class TestDataLogger(BaseTestCase):
     """
-    Unit tests for the DataLogger class. These tests verify the
-    correct behavior of data logging, JSON export, and table
-    logging functionalities.
+    Unit tests for the DataLogger class.
     """
 
     def setUp(self):
-        """
-        Set up a temporary test environment before each test.
-        Creates a temporary directory and initializes a DataLogger instance.
-        """
-        self.test_dir = tempfile.mkdtemp(prefix="CodeEntropy_")
+        super().setUp()
         self.code_entropy = main
-
-        self._orig_dir = os.getcwd()
-        os.chdir(self.test_dir)
-
         self.logger = DataLogger()
         self.output_file = "test_output.json"
 
-    def tearDown(self):
-        """
-        Clean up the test environment after each test.
-        Removes the temporary directory and restores the original working directory.
-        """
-        os.chdir(self._orig_dir)
-        if os.path.exists(self.test_dir):
-            shutil.rmtree(self.test_dir)
-
     def test_init(self):
         """
         Test that the DataLogger initializes with empty molecule and residue data lists.

tests/test_CodeEntropy/test_entropy.py

@@ -1,3 +1,4 @@
+import logging
 import math
 import os
 import shutil
@@ -20,32 +21,21 @@
 from CodeEntropy.levels import LevelManager
 from CodeEntropy.main import main
 from CodeEntropy.run import ConfigManager, RunManager
+from tests.test_CodeEntropy.test_base import BaseTestCase
 
 
-class TestEntropyManager(unittest.TestCase):
+class TestEntropyManager(BaseTestCase):
     """
-    Unit tests for the functionality of EntropyManager.
+    Unit tests for EntropyManager.
     """
 
     def setUp(self):
-        """
-        Set up test environment.
-        """
-        self.test_dir = tempfile.mkdtemp(prefix="CodeEntropy_")
+        super().setUp()
         self.test_data_dir = os.path.dirname(data.__file__)
-        self.code_entropy = main
-
-        # Change to test directory
-        self._orig_dir = os.getcwd()
-        os.chdir(self.test_dir)
 
-    def tearDown(self):
-        """
-        Clean up after each test.
-        """
-        os.chdir(self._orig_dir)
-        if os.path.exists(self.test_dir):
-            shutil.rmtree(self.test_dir)
+        # Disable MDAnalysis and commands file logging entirely
+        logging.getLogger("MDAnalysis").handlers = [logging.NullHandler()]
+        logging.getLogger("commands").handlers = [logging.NullHandler()]
 
     def test_execute_full_workflow(self):
         # Setup universe and args
@@ -56,7 +46,7 @@ def test_execute_full_workflow(self):
         args = MagicMock(
             bin_width=0.1, temperature=300, selection_string="all", water_entropy=False
         )
-        run_manager = RunManager("temp_folder")
+        run_manager = RunManager("mock_folder/job001")
         level_manager = LevelManager()
         data_logger = DataLogger()
         group_molecules = MagicMock()
@@ -153,7 +143,7 @@ def test_execute_triggers_handle_water_entropy_minimal(self):
         args = MagicMock(
             bin_width=0.1, temperature=300, selection_string="all", water_entropy=True
         )
-        run_manager = RunManager("temp_folder")
+        run_manager = RunManager("mock_folder/job001")
         level_manager = LevelManager()
         data_logger = DataLogger()
         group_molecules = MagicMock()
@@ -279,7 +269,7 @@ def test_initialize_molecules(self):
         args = MagicMock(
             bin_width=0.1, temperature=300, selection_string="all", water_entropy=False
         )
-        run_manager = RunManager("temp_folder")
+        run_manager = RunManager("mock_folder/job001")
         level_manager = LevelManager()
         data_logger = DataLogger()
         group_molecules = MagicMock()
@@ -486,7 +476,7 @@ def test_get_reduced_universe_reduced(self, mock_args):
         u = mda.Universe(tprfile, trrfile)
 
         config_manager = ConfigManager()
-        run_manager = RunManager("temp_folder")
+        run_manager = RunManager("mock_folder/job001")
 
         parser = config_manager.setup_argparse()
         args = parser.parse_args()
@@ -524,7 +514,7 @@ def test_get_molecule_container(self, mock_args):
 
         # Setup managers
         config_manager = ConfigManager()
-        run_manager = RunManager("temp_folder")
+        run_manager = RunManager("mock_folder/job001")
 
         parser = config_manager.setup_argparse()
         args = parser.parse_args()
@@ -639,7 +629,7 @@ def test_process_vibrational_only_levels(self):
 
         # Setup managers and arguments
         args = MagicMock(bin_width=0.1, temperature=300, selection_string="all")
-        run_manager = RunManager("temp_folder")
+        run_manager = RunManager("mock_folder/job001")
         level_manager = LevelManager()
         data_logger = DataLogger()
         group_molecules = MagicMock()
@@ -751,7 +741,7 @@ def test_process_conformational_residue_level(self):
 
         # Setup managers and arguments
         args = MagicMock(bin_width=0.1, temperature=300, selection_string="all")
-        run_manager = RunManager("temp_folder")
+        run_manager = RunManager("mock_folder/job001")
         level_manager = LevelManager()
         data_logger = DataLogger()
         group_molecules = MagicMock()
@@ -1086,7 +1076,7 @@ def test_vibrational_entropy_init(self):
         args.temperature = 300
         args.selection_string = "all"
 
-        run_manager = RunManager("temp_folder")
+        run_manager = RunManager("mock_folder/job001")
         level_manager = LevelManager()
         data_logger = DataLogger()
         group_molecules = MagicMock()
@@ -1111,7 +1101,7 @@ def test_frequency_calculation_0(self):
         lambdas = [0]
         temp = 298
 
-        run_manager = RunManager("mock_folder")
+        run_manager = RunManager("mock_folder/job001")
 
         ve = VibrationalEntropy(
             run_manager, MagicMock(), MagicMock(), MagicMock(), MagicMock(), MagicMock()
@@ -1131,7 +1121,7 @@ def test_frequency_calculation_positive(self):
         temp = 298
 
         # Create a mock RunManager and set return value for get_KT2J
-        run_manager = RunManager("mock_folder")
+        run_manager = RunManager("mock_folder/job001")
 
         # Instantiate VibrationalEntropy with mocks
         ve = VibrationalEntropy(
@@ -1273,7 +1263,7 @@ def test_vibrational_entropy_polymer_force(self):
         temp = 298
         highest_level = "yes"
 
-        run_manager = RunManager("mock_folder")
+        run_manager = RunManager("mock_folder/job001")
         ve = VibrationalEntropy(
             run_manager, MagicMock(), MagicMock(), MagicMock(), MagicMock(), MagicMock()
         )
@@ -1303,7 +1293,7 @@ def test_vibrational_entropy_polymer_torque(self):
         temp = 298
         highest_level = "yes"
 
-        run_manager = RunManager("mock_folder")
+        run_manager = RunManager("mock_folder/job001")
         ve = VibrationalEntropy(
             run_manager, MagicMock(), MagicMock(), MagicMock(), MagicMock(), MagicMock()
         )
@@ -1561,7 +1551,7 @@ def test_confirmational_entropy_init(self):
         args.temperature = 300
         args.selection_string = "all"
 
-        run_manager = RunManager("temp_folder")
+        run_manager = RunManager("mock_folder/job001")
         level_manager = LevelManager()
         data_logger = DataLogger()
         group_molecules = MagicMock()
@@ -1603,7 +1593,7 @@ def test_assign_conformation(self):
 
         # Setup managers and arguments
         args = MagicMock(bin_width=0.1, temperature=300, selection_string="all")
-        run_manager = RunManager("temp_folder")
+        run_manager = RunManager("mock_folder/job001")
         level_manager = LevelManager()
         data_logger = DataLogger()
         group_molecules = MagicMock()
@@ -1635,7 +1625,7 @@ def test_conformational_entropy_calculation(self):
 
         # Setup managers and arguments
         args = MagicMock(bin_width=0.1, temperature=300, selection_string="all")
-        run_manager = RunManager("temp_folder")
+        run_manager = RunManager("mock_folder/job001")
         level_manager = LevelManager()
         data_logger = DataLogger()
         group_molecules = MagicMock()
@@ -1697,7 +1687,7 @@ def test_orientational_entropy_init(self):
         args.temperature = 300
         args.selection_string = "all"
 
-        run_manager = RunManager("temp_folder")
+        run_manager = RunManager("mock_folder/job001")
         level_manager = LevelManager()
         data_logger = DataLogger()
         group_molecules = MagicMock()