drop cioos-siooc-data-transform from odf parser

ocean_data_parser/parsers/dfo/odf.py

@@ -7,11 +7,8 @@
 """
 
 import logging
-from typing import Union
 
 import xarray
-from odf_transform.process import odf_to_xarray
-from odf_transform.process import read_config as cioos_odf_config
 
 from ocean_data_parser.parsers.dfo.odf_source.process import parse_odf
 
@@ -60,37 +57,6 @@
 }
 
 
-def bio_odf_cioos(path: str, config: Union[dict, str]) -> xarray.Dataset:
-    """Read BIO ODF with the CIOOS Data Transform package
-
-    Args:
-        path (str): file path to read.
-        config (Union[dict, str]): cioos-ioos-data-transform configurations
-
-    Returns:
-        xarray.Dataset: CIOOS Compliant Xarray object
-    """
-
-    config = cioos_odf_config(config)
-    config["organisationVocabulary"] = ["BIO", "GF3"]
-    return odf_to_xarray(path, config)
-
-
-def mli_odf_cioos(path: str, config: Union[dict, str]) -> xarray.Dataset:
-    """Read MLI ODF with the CIOOS Data Transform package
-
-    Args:
-        path (str): file path to read.
-        config (Union[dict, str]): cioos-ioos-data-transform configurations
-
-    Returns:
-        xarray.Dataset: CIOOS Compliant Xarray object
-    """
-    config = cioos_odf_config(config)
-    config["organisationVocabulary"] = ["MLI", "GF3"]
-    return odf_to_xarray(path, config)
-
-
 def bio_odf(path: str, global_attributes: dict = None) -> xarray.Dataset:
     """Bedford Institute of Ocean ODF format parser
 

ocean_data_parser/parsers/dfo/odf_source/attributes.py

@@ -166,7 +166,7 @@ def _define_cdm_data_type_from_odf(odf_header: dict) -> dict:
         attributes["cdm_data_type"] = "Point"
     else:
         logger.error(
-            "ODF_transform is not yet incompatible with ODF DATA_TYPE: %s",
+            "ODF parser is not yet incompatible with ODF DATA_TYPE: %s",
             odf_data_type,
         )
     return attributes

ocean_data_parser/parsers/dfo/odf_source/process.py

@@ -3,6 +3,8 @@
 import re
 from pathlib import Path
 
+import xarray as xr
+
 import ocean_data_parser.parsers.seabird as seabird
 from ocean_data_parser._version import __version__
 from ocean_data_parser.parsers.dfo.odf_source import attributes, flags
@@ -38,26 +40,35 @@
 
 
 def parse_odf(
-    odf_path,
-    global_attributes=None,
-    vocabularies=None,
-    add_attributes_existing_variables=True,
-    generate_new_vocabulary_variables=True,
-):
+    odf_path: str,
+    global_attributes: dict = None,
+    vocabularies: list = None,
+    add_attributes_existing_variables: bool = True,
+    generate_new_vocabulary_variables: bool = True,
+) -> xr.Dataset:
     """Convert an ODF file to an xarray object.
+
     Args:
-        odf_path (str): path to ODF file to convert
-        config (dictionary, optional): Conversion configuration to apply.
-            Defaults to odf_transform/config.json.
+        odf_path (str): ODF file path
+        global_attributes (dict, optional): Global attribtes to append to dataaset.
+            Defaults to None.
+        vocabularies (list, optional): Vocabularies to use ['GF3','BIO','IML'].
+            Defaults to None.
+        add_attributes_existing_variables (bool, optional): Append vocabulary attributes.
+            Defaults to True.
+        generate_new_vocabulary_variables (bool, optional): Generate vocabulary variables.
+            Defaults to True.
+
+    Returns:
+        xr.Dataset: Parsed dataset
     """
-
     # Parse the ODF file with the CIOOS python parsing tool
     metadata, dataset = odf_parser.read(odf_path)
 
-    # Review ODF data type compatible with odf_transform
+    # Review ODF data type compatible with ODF parser
     if metadata["EVENT_HEADER"]["DATA_TYPE"] not in ODF_COMPATIBLE_DATA_TYPES:
         logger.warning(
-            "ODF_transform is not yet fully compatible with the ODF Data Type: %s",
+            "ODF parser is not yet fully compatible with the ODF Data Type: %s",
             metadata["EVENT_HEADER"]["DATA_TYPE"],
         )
 
@@ -76,7 +87,7 @@ def parse_odf(
     dataset = attributes.global_attributes_from_header(dataset, metadata)
     dataset.attrs[
         "history"
-    ] += f"# Convert ODF to NetCDF with cioos_data_trasform.odf_transform V {__version__}\n"
+    ] += f"# Convert ODF to NetCDF with ocean_data_parser V {__version__}\n"
 
     # Handle ODF flag variables
     dataset = flags.rename_qqqq_flags(dataset)

tests/test_reference_netcdf.py

@@ -102,7 +102,7 @@ def ignore_from_attr(attr, expression, placeholder):
     ignore_from_attr(
         "history",
         r"cioos_data_trasform.odf_transform V \d+\.\d+.\d+",
-        "cioos_data_trasform.odf_transform V VERSION",
+        "package_name_version",
     )
     ignore_from_attr(
         "history", r"\d\d\d\d-\d\d-\d\dT\d\d:\d\d:\d\d\.*\d*Z", "TIMESTAMP"