refactor(convert): Initial full refactor of the swap feature

This is an initial full refactoring for swap feature.
Changes include the removal of Parsed2Zarr objects and its
downstream implementation in favor of direct zarr file writing
during the data parsing within the Parser object.

echopype/convert/api.py

@@ -7,7 +7,6 @@
 # fmt: off
 # black and isort have conflicting ideas about how this should be formatted
 from ..core import SONAR_MODELS
-from .parsed_to_zarr import Parsed2Zarr
 
 if TYPE_CHECKING:
     from ..core import EngineHint, PathHint, SonarModelsHint
@@ -17,7 +16,9 @@
 from ..utils.coding import COMPRESSION_SETTINGS
 from ..utils.log import _init_logger
 from ..utils.prov import add_processing_level
-from .utils.ek import should_use_swap
+
+# TODO: Fix and revive auto swap
+# from .utils.ek import should_use_swap
 
 BEAM_SUBGROUP_DEFAULT = "Beam_group1"
 
@@ -318,7 +319,7 @@ def open_raw(
     use_swap: bool = False,
     destination_path: Optional[str] = None,
     destination_storage_options: Optional[Dict[str, str]] = None,
-    max_mb: int = 100,
+    max_chunk_size: str = "100MB",
 ) -> Optional[EchoData]:
     """Create an EchoData object containing parsed data from a single raw data file.
 
@@ -435,30 +436,28 @@ def open_raw(
     else:
         params = "ALL"  # reserved to control if only wants to parse a certain type of datagram
 
-    # obtain dict associated with directly writing to zarr
-    dgram_zarr_vars = SONAR_MODELS[sonar_model]["dgram_zarr_vars"]
-
     # Parse raw file and organize data into groups
     parser = SONAR_MODELS[sonar_model]["parser"](
         file_chk,
         params=params,
         storage_options=storage_options,
-        dgram_zarr_vars=dgram_zarr_vars,
         sonar_model=sonar_model,
     )
 
     parser.parse_raw()
 
     # Direct offload to zarr and rectangularization only available for some sonar models
     if sonar_model in ["EK60", "ES70", "EK80", "ES80", "EA640"]:
+        # Determine whether to use swap
         swap_map = {
             "swap": True,
             "no_swap": False,
         }
         if destination_path == "auto":
             # Overwrite use_swap if it's True below
             # Use local swap directory
-            use_swap = should_use_swap(parser.zarr_datagrams, dgram_zarr_vars, mem_mult=0.4)
+            # use_swap = should_use_swap(parser.zarr_datagrams, dgram_zarr_vars, mem_mult=0.4)
+            raise NotImplementedError("Automatic swap is not yet implemented.")
         elif destination_path in swap_map:
             use_swap = swap_map[destination_path]
         else:
@@ -473,21 +472,13 @@ def open_raw(
                     )
                 )
 
-        if use_swap:
-            # Create sonar_model-specific p2z object
-            p2z = SONAR_MODELS[sonar_model]["parsed2zarr"](parser)
-            p2z.datagram_to_zarr(
-                dest_path=destination_path,
-                dest_storage_options=destination_storage_options,
-                max_mb=max_mb,
-            )
-        else:
-            p2z = Parsed2Zarr(parser)  # Create general p2z object
-            parser.rectangularize_data()
-
-    else:
         # No rectangularization for other sonar models
-        p2z = Parsed2Zarr(parser)  # Create general p2z object
+        parser.rectangularize_data(
+            use_swap,
+            dest_path=destination_path,
+            dest_storage_options=destination_storage_options,
+            max_chunk_size=max_chunk_size,
+        )
 
     setgrouper = SONAR_MODELS[sonar_model]["set_groups"](
         parser,
@@ -496,7 +487,6 @@ def open_raw(
         output_path=None,
         sonar_model=sonar_model,
         params=_set_convert_params(convert_params),
-        parsed2zarr_obj=p2z,
     )
 
     # Setup tree dictionary
@@ -547,9 +537,7 @@ def open_raw(
     # Create tree and echodata
     # TODO: make the creation of tree dynamically generated from yaml
     tree = DataTree.from_dict(tree_dict, name="root")
-    echodata = EchoData(
-        source_file=file_chk, xml_path=xml_chk, sonar_model=sonar_model, parsed2zarr_obj=p2z
-    )
+    echodata = EchoData(source_file=file_chk, xml_path=xml_chk, sonar_model=sonar_model)
     echodata._set_tree(tree)
     echodata._load_tree()