Merge pull request #135 from CCPBioSim/124-remove-config-yaml

Remove static `config.yaml` and implement dynamic config loading

Author: harryswift01

CodeEntropy/config/arg_config_manager.py

@@ -1,4 +1,5 @@
 import argparse
+import glob
 import logging
 import os
 
@@ -77,16 +78,26 @@ def __init__(self):
         self.arg_map = arg_map
 
     def load_config(self, file_path):
-        """Load YAML configuration file."""
-        if not os.path.exists(file_path):
-            raise FileNotFoundError(f"Configuration file '{file_path}' not found.")
+        """Load YAML configuration file from the given directory."""
+        yaml_files = glob.glob(os.path.join(file_path, "*.yaml"))
 
-        with open(file_path, "r") as file:
-            config = yaml.safe_load(file)
-
-            # If YAML content is empty, return an empty dictionary
-            if config is None:
-                config = {}
+        if not yaml_files:
+            logger.warning(
+                f"No YAML configuration files found in directory: {file_path}. "
+                "Expected a file with extension '.yaml'. "
+                "Proceeding with default configuration: {'run1': {}}."
+            )
+            return {"run1": {}}
+
+        try:
+            with open(yaml_files[0], "r") as file:
+                config = yaml.safe_load(file)
+                logger.info(f"Loaded configuration from: {yaml_files[0]}")
+                if config is None:
+                    config = {"run1": {}}
+        except Exception as e:
+            logger.error(f"Failed to load config file: {e}")
+            config = {"run1": {}}
 
         return config
 

CodeEntropy/run.py

@@ -95,12 +95,9 @@ def run_entropy_workflow(self):
         try:
             logger = self._logging_config.setup_logging()
 
-            config = self._config_manager.load_config("config.yaml")
-            if config is None:
-                raise ValueError(
-                    "No configuration file found, and no CLI arguments were provided."
-                )
+            current_directory = os.getcwd()
 
+            config = self._config_manager.load_config(current_directory)
             parser = self._config_manager.setup_argparse()
             args, _ = parser.parse_known_args()
             args.output_file = os.path.join(self.folder, args.output_file)

config.yaml

@@ -68,28 +68,50 @@ def setup_file(self, mock_file):
             "water_entropy: False"
         ).return_value
 
-    @patch("builtins.open", new_callable=mock_open)
-    @patch("os.path.exists", return_value=True)
-    def test_load_config(self, mock_exists, mock_file):
+    @patch("builtins.open")
+    @patch("glob.glob", return_value=["config.yaml"])
+    def test_load_config(self, mock_glob, mock_file):
         """
         Test loading a valid configuration file.
         """
-        arg_config = ConfigManager()
+        # Setup the mock file content
         self.setup_file(mock_file)
-        config = arg_config.load_config(self.config_file)
+
+        arg_config = ConfigManager()
+        config = arg_config.load_config("/some/path")
+
         self.assertIn("run1", config)
         self.assertEqual(
             config["run1"]["top_traj_file"], ["/path/to/tpr", "/path/to/trr"]
         )
+        self.assertEqual(config["run1"]["selection_string"], "all")
+        self.assertEqual(config["run1"]["start"], 0)
+        self.assertEqual(config["run1"]["end"], -1)
+        self.assertEqual(config["run1"]["step"], 1)
+        self.assertEqual(config["run1"]["bin_width"], 30)
+        self.assertEqual(config["run1"]["tempra"], 298.0)
+        self.assertFalse(config["run1"]["verbose"])
+        self.assertEqual(config["run1"]["thread"], 1)
+        self.assertEqual(config["run1"]["output_file"], "output_file.json")
+        self.assertEqual(config["run1"]["force_partitioning"], 0.5)
+        self.assertFalse(config["run1"]["water_entropy"])
+
+    @patch("glob.glob", return_value=[])
+    def test_load_config_no_yaml_files(self, mock_glob):
+        arg_config = ConfigManager()
+        config = arg_config.load_config("/some/path")
+        self.assertEqual(config, {"run1": {}})
 
     @patch("builtins.open", side_effect=FileNotFoundError)
-    def test_load_config_file_not_found(self, mock_file):
+    @patch("glob.glob", return_value=["config.yaml"])
+    def test_load_config_file_not_found(self, mock_glob, mock_open):
         """
-        Test loading a configuration file that does not exist.
+        Test loading a configuration file that exists but cannot be opened.
+        Should return default config instead of raising an error.
         """
         arg_config = ConfigManager()
-        with self.assertRaises(FileNotFoundError):
-            arg_config.load_config(self.config_file)
+        config = arg_config.load_config("/some/path")
+        self.assertEqual(config, {"run1": {}})
 
     @patch.object(ConfigManager, "load_config", return_value=None)
     def test_no_cli_no_yaml(self, mock_load_config):
@@ -480,19 +502,17 @@ def test_edge_case_argument_values(self, mock_args):
         self.assertEqual(args.end, -10)
 
     @patch("builtins.open", new_callable=mock_open, read_data="--- \n")
-    @patch("os.path.exists", return_value=True)
-    def test_empty_yaml_config(self, mock_exists, mock_file):
+    @patch("glob.glob", return_value=["config.yaml"])
+    def test_empty_yaml_config(self, mock_glob, mock_file):
         """
         Test behavior when an empty YAML file is provided.
-        Should use defaults or raise an appropriate error.
+        Should return default config {'run1': {}}.
         """
-
         arg_config = ConfigManager()
-
-        config = arg_config.load_config(self.config_file)
+        config = arg_config.load_config("/some/path")
 
         self.assertIsInstance(config, dict)
-        self.assertEqual(config, {})
+        self.assertEqual(config, {"run1": {}})
 
     def test_input_parameters_validation_all_valid(self):
         """Test that input_parameters_validation passes with all valid inputs."""