Rearranged MachineConfiguration keys according to purpose and grouped them under comment blocks

Author: tieneupin

src/murfey/util/config.py

@@ -12,37 +12,53 @@
 
 
 class MachineConfig(BaseModel, extra=Extra.allow):  # type: ignore
-    acquisition_software: List[str]
-    calibrations: Dict[str, Dict[str, Union[dict, float]]]
-    data_directories: List[Path]
-    rsync_basepath: Path
-    default_model: Path
+    """
+    Keys that describe the type of workflow conducted on the client side, and how
+    Murfey will handle its data transfer and processing
+    """
+
+    # General info --------------------------------------------------------------------
     display_name: str = ""
     instrument_name: str = ""
     image_path: Optional[Path] = None
+    machine_override: str = ""
+
+    # Hardware and software -----------------------------------------------------------
+    camera: str = "FALCON"
+    superres: bool = False
+    calibrations: Dict[str, Dict[str, Union[dict, float]]]
+    acquisition_software: List[str]
     software_versions: Dict[str, str] = {}
-    external_executables: Dict[str, str] = {}
-    external_executables_eer: Dict[str, str] = {}
-    external_environment: Dict[str, str] = {}
-    rsync_module: str = ""
+    software_settings_output_directories: Dict[str, List[str]] = {}
+    data_required_substrings: Dict[str, Dict[str, List[str]]] = {}
+
+    # Client side directory setup -----------------------------------------------------
+    data_directories: List[Path]
     create_directories: list[str] = ["atlas"]
     analyse_created_directories: List[str] = []
     gain_reference_directory: Optional[Path] = None
     eer_fractionation_file_template: str = ""
-    processed_directory_name: str = "processed"
-    gain_directory_name: str = "processing"
-    node_creator_queue: str = "node_creator"
-    superres: bool = False
-    camera: str = "FALCON"
-    data_required_substrings: Dict[str, Dict[str, List[str]]] = {}
-    allow_removal: bool = False
+
+    # Data transfer setup -------------------------------------------------------------
+    # Rsync setup
     data_transfer_enabled: bool = True
+    rsync_url: str = ""
+    rsync_module: str = ""
+    rsync_basepath: Path
+    allow_removal: bool = False
+
+    # Upstream data download setup
+    upstream_data_directories: List[Path] = []  # Previous sessions
+    upstream_data_download_directory: Optional[Path] = None  # Set by microscope config
+    upstream_data_tiff_locations: List[str] = ["processed"]  # Location of CLEM TIFFs
+
+    # Data processing setup -----------------------------------------------------------
+    # General processing setup
     processing_enabled: bool = True
-    machine_override: str = ""
-    processed_extra_directory: str = ""
-    plugin_packages: Dict[str, Path] = {}
-    software_settings_output_directories: Dict[str, List[str]] = {}
     process_by_default: bool = True
+    gain_directory_name: str = "processing"
+    processed_directory_name: str = "processed"
+    processed_extra_directory: str = ""
     recipes: Dict[str, str] = {
         "em-spa-bfactor": "em-spa-bfactor",
         "em-spa-class2d": "em-spa-class2d",
@@ -53,22 +69,27 @@ class MachineConfig(BaseModel, extra=Extra.allow):  # type: ignore
         "em-tomo-align": "em-tomo-align",
     }
 
-    # Find and download upstream directories
-    upstream_data_directories: List[Path] = []  # Previous sessions
-    upstream_data_download_directory: Optional[Path] = None  # Set by microscope config
-    upstream_data_tiff_locations: List[str] = ["processed"]  # Location of CLEM TIFFs
-
+    # Particle picking setup
+    default_model: Path
     model_search_directory: str = "processing"
     initial_model_search_directory: str = "processing/initial_model"
 
-    failure_queue: str = ""
-    instrument_server_url: str = "http://localhost:8001"
-    frontend_url: str = "http://localhost:3000"
-    murfey_url: str = "http://localhost:8000"
-    rsync_url: str = ""
+    # Data analysis plugins
+    external_executables: Dict[str, str] = {}
+    external_executables_eer: Dict[str, str] = {}
+    external_environment: Dict[str, str] = {}
+    plugin_packages: Dict[str, Path] = {}
 
+    # Server and network setup --------------------------------------------------------
+    # Configurations and URLs
     security_configuration_path: Optional[Path] = None
+    murfey_url: str = "http://localhost:8000"
+    frontend_url: str = "http://localhost:3000"
+    instrument_server_url: str = "http://localhost:8001"
 
+    # Messaging queues
+    failure_queue: str = ""
+    node_creator_queue: str = "node_creator"
     notifications_queue: str = "pato_notification"