water-column-sonar-processing 0.0.7__tar.gz → 0.0.9__tar.gz

{water_column_sonar_processing-0.0.7/src/water_column_sonar_processing.egg-info → water_column_sonar_processing-0.0.9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: water_column_sonar_processing
-Version: 0.0.7
+Version: 0.0.9
 Summary: A processing tool for water column sonar data.
 Author-email: Rudy Klucik <rudy.klucik@noaa.gov>
 Project-URL: Homepage, https://github.com/CI-CMG/water-column-sonar-processing
@@ -11,26 +11,27 @@ Classifier: Operating System :: OS Independent
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: aiobotocore~=2.9.0
-Requires-Dist: aiohttp~=3.10.10
-Requires-Dist: boto3==1.33.13
-Requires-Dist: botocore~=1.33.13
+Requires-Dist: aiobotocore==2.15.2
+Requires-Dist: boto3==1.35.36
+Requires-Dist: botocore==1.35.36
 Requires-Dist: echopype==0.9.0
 Requires-Dist: fiona==1.10.1
 Requires-Dist: geopandas==1.0.1
-Requires-Dist: mock~=5.1.0
-Requires-Dist: moto~=5.0.18
+Requires-Dist: mock==5.1.0
+Requires-Dist: moto[all]==5.0.21
+Requires-Dist: moto[server]==5.0.21
 Requires-Dist: numcodecs==0.13.1
 Requires-Dist: numpy==1.26.4
 Requires-Dist: pandas==2.2.3
-Requires-Dist: pytest~=8.3.3
+Requires-Dist: pyarrow==18.1.0
 Requires-Dist: python-dotenv==1.0.0
 Requires-Dist: requests==2.32.3
-Requires-Dist: s3fs==2024.10.0
+Requires-Dist: s3fs==2023.12.1
 Requires-Dist: scipy==1.14.1
+Requires-Dist: setuptools==75.6.0
 Requires-Dist: shapely==2.0.3
 Requires-Dist: typing-extensions==4.10.0
-Requires-Dist: xarray==2022.12.0
+Requires-Dist: xarray==2024.10.0
 Requires-Dist: zarr==2.18.3
 
 # Water Column Sonar Processing
@@ -85,6 +86,8 @@ Processing tool for converting L0 data to L1 and L2 as well as generating geospa
 ```commandline
 pytest --disable-warnings
 ```
+or
+> pytest --cache-clear --cov=src tests/ --cov-report=xml
 
 # Instructions
 Following this tutorial:
@@ -122,3 +125,10 @@ https://plugins.jetbrains.com/plugin/20574-ruff
 
 # Colab Test
 https://colab.research.google.com/drive/1KiLMueXiz9WVB9o4RuzYeGjNZ6PsZU7a#scrollTo=AayVyvpBdfIZ
+
+# Test Coverage
+20241124
+8 failed, 32 passed, 3 skipped, 1 warning in 6.92s
+20241125
+5 failed, 35 passed, 3 skipped, 1 warning in 9.71s
+3 failed, 38 passed, 3 skipped, 1 warning in 7.24s

{water_column_sonar_processing-0.0.7 → water_column_sonar_processing-0.0.9}/README.md

@@ -50,6 +50,8 @@ Processing tool for converting L0 data to L1 and L2 as well as generating geospa
 ```commandline
 pytest --disable-warnings
 ```
+or
+> pytest --cache-clear --cov=src tests/ --cov-report=xml
 
 # Instructions
 Following this tutorial:
@@ -86,4 +88,11 @@ Ruff
 https://plugins.jetbrains.com/plugin/20574-ruff
 
 # Colab Test
-https://colab.research.google.com/drive/1KiLMueXiz9WVB9o4RuzYeGjNZ6PsZU7a#scrollTo=AayVyvpBdfIZ
+https://colab.research.google.com/drive/1KiLMueXiz9WVB9o4RuzYeGjNZ6PsZU7a#scrollTo=AayVyvpBdfIZ
+
+# Test Coverage
+20241124
+8 failed, 32 passed, 3 skipped, 1 warning in 6.92s
+20241125
+5 failed, 35 passed, 3 skipped, 1 warning in 9.71s
+3 failed, 38 passed, 3 skipped, 1 warning in 7.24s

{water_column_sonar_processing-0.0.7 → water_column_sonar_processing-0.0.9}/pyproject.toml

@@ -7,7 +7,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "water_column_sonar_processing"
-version = "0.0.7"
+version = "0.0.9"
 authors = [
   { name="Rudy Klucik", email="rudy.klucik@noaa.gov" },
 ]
@@ -25,19 +25,29 @@ dynamic = ["dependencies"]
 Homepage = "https://github.com/CI-CMG/water-column-sonar-processing"
 Issues = "https://github.com/CI-CMG/water-column-sonar-processing/issues"
 
-#[pytest]
+#[tool.pytest.ini_options]
+#filterwarnings = [
+#    "error",
+#    "ignore::UserWarning",
+#    # note the use of single quote below to denote "raw" strings in TOML
+#    'ignore:function ham\(\) is deprecated:DeprecationWarning',
+#]
 #pythonpath = "src"
 #testpaths = "tests"
+#[pytest]
+#addopts = [
+#    "-p no:warnings"
+#]
 
-[tool.pytest.ini_options]
-minversion = "6.0"
-#addopts = "-ra -q"
-testpaths = [
-    "tests",
-]
+#[tool.pytest.ini_options]
+#minversion = "6.0"
+##addopts = "-ra -q"
+#testpaths = [
+#    "tests",
+#]
 
 [tool.setuptools.dynamic]
 dependencies = {file = ["requirements.txt"]}
-optional-dependencies = {dev = { file = ["requirements-dev.txt"] }}
+optional-dependencies = {dev = { file = ["requirements_dev.txt"] }}
 
 # https://packaging.python.org/en/latest/guides/writing-pyproject-toml/

{water_column_sonar_processing-0.0.7 → water_column_sonar_processing-0.0.9}/requirements.txt

@@ -2,26 +2,27 @@
 # defined for Python 3.12
 # Note: be careful with conversions for pandas >=2.0.0, timestamps will have a lot of problems
 
-aiobotocore~=2.9.0
-aiohttp~=3.10.10
-boto3==1.33.13
-botocore~=1.33.13
+aiobotocore==2.15.2
+boto3==1.35.36
+botocore==1.35.36
 echopype==0.9.0
 fiona==1.10.1
+# Alternative to geopandas: pyogrio
 geopandas==1.0.1
-mock~=5.1.0
-moto~=5.0.18
+mock==5.1.0
+moto[all]==5.0.21
+moto[server]==5.0.21
 numcodecs==0.13.1
 numpy==1.26.4
 pandas==2.2.3
-pytest~=8.3.3
+pyarrow==18.1.0
 python-dotenv==1.0.0
 requests==2.32.3
-#s3fs==2023.12.2
-s3fs==2024.10.0
+#s3fs==2024.10.0 # this version creates problems
+s3fs==2023.12.1
 scipy==1.14.1
+setuptools==75.6.0
 shapely==2.0.3
 typing-extensions==4.10.0
-xarray==2022.12.0
-#zarr==2.16.1
+xarray==2024.10.0
 zarr==2.18.3

{water_column_sonar_processing-0.0.7 → water_column_sonar_processing-0.0.9}/tests/test_create_empty_zarr_store.py

@@ -4,9 +4,11 @@ from dotenv import find_dotenv, load_dotenv
 from moto import mock_aws
 
 from water_column_sonar_processing.aws import DynamoDBManager, S3Manager
-from water_column_sonar_processing.cruise.create_empty_zarr_store import (
-    CreateEmptyZarrStore,
-)
+from water_column_sonar_processing.cruise import CreateEmptyZarrStore
+
+
+# from water_column_sonar_processing import DynamoDBManager, S3Manager
+# from water_column_sonar_processing import CreateEmptyZarrStore
 
 
 # TEMPDIR = "/tmp"
@@ -25,7 +27,7 @@ def teardown_module():
 
 #######################################################
 @mock_aws
-def test_create_empty_zarr_store():
+def test_create_empty_zarr_store():  # PASSING, needs modification at end
     dynamo_db_manager = DynamoDBManager()
     s3_manager = S3Manager()
 
@@ -39,9 +41,11 @@ def test_create_empty_zarr_store():
     # [0] create bucket with test files
     input_bucket_name = os.environ.get("INPUT_BUCKET_NAME")
     output_bucket_name = os.environ.get("OUTPUT_BUCKET_NAME")
+
     s3_manager.create_bucket(bucket_name=input_bucket_name)
     s3_manager.create_bucket(bucket_name=output_bucket_name)
     print(s3_manager.list_buckets())
+
     # TODO: put at the path where it needs to be deleted
     s3_manager.put(bucket_name=input_bucket_name, key="the_key", body="the_body")
 
@@ -80,7 +84,7 @@ def test_create_empty_zarr_store():
         249.792,
         249.792,
         249.792,
-        999.744,
+        999.744, # note: different depth
         249.792,
         249.792,
         249.792,
@@ -211,7 +215,7 @@ def test_create_empty_zarr_store():
         tempdir="/tmp",
     )
 
-    assert os.path.exists(f"/tmp/{cruise_name}.zarr")
+    assert os.path.exists(f"/tmp/{cruise_name}.zarr") # TODO: create better tmp directory for testing
     # TODO: should actually assert in the bucket
     # mount and verify:
     # shape

water_column_sonar_processing-0.0.9/tests/test_dynamodb_manager.py

@@ -0,0 +1,376 @@
+import numpy as np
+from dotenv import find_dotenv, load_dotenv
+from moto import mock_aws
+
+from water_column_sonar_processing.aws import DynamoDBManager
+from water_column_sonar_processing.utility import PipelineStatus
+
+
+#######################################################
+def setup_module():
+    print("setup")
+    env_file = find_dotenv(".env-test")
+    load_dotenv(dotenv_path=env_file, override=True)
+
+
+def teardown_module():
+    print("teardown")
+
+
+#######################################################
+def test_serializer_deserializer():
+    # ---Initialize--- #
+    low_level_data = {
+        "ACTIVE": {"BOOL": True},
+        "CRC": {"N": "-1600155180"},
+        "ID": {"S": "bewfv43843b"},
+        "params": {"M": {"customer": {"S": "TEST"}, "index": {"N": "1"}}},
+        "THIS_STATUS": {"N": "10"},
+        "TYPE": {"N": "22"},
+    }
+
+    # Lazy-eval the dynamodb attribute (boto3 is dynamic!)
+    dynamo_db_manager = DynamoDBManager()
+
+    # To go from low-level format to python
+    deserializer = dynamo_db_manager.type_deserializer
+    python_data = {k: deserializer.deserialize(v) for k, v in low_level_data.items()}
+
+    assert python_data["ACTIVE"]
+    assert python_data["CRC"] == -1600155180
+    assert python_data["ID"]
+    assert python_data["params"] == {"customer": "TEST", "index": 1}
+    assert python_data["THIS_STATUS"] == 10
+    assert python_data["TYPE"] == 22
+
+    # To go from python to low-level format
+    serializer = dynamo_db_manager.type_serializer
+    low_level_copy = {k: serializer.serialize(v) for k, v in python_data.items()}
+
+    assert low_level_data == low_level_copy
+
+
+#######################################################
+@mock_aws
+def test_dynamodb_manager(): # PASSING
+    # ---Initialize--- #
+    table_name = "test_table"
+    dynamo_db_manager = DynamoDBManager()
+
+    # ---Create Table--- #
+    dynamo_db_manager.create_water_column_sonar_table(table_name=table_name)
+
+    # ---Add Items to Table--- #
+    test_channels = [
+        "GPT  38 kHz 009072055a7f 2 ES38B",
+        "GPT  70 kHz 00907203400a 3 ES70-7C",
+        "GPT 120 kHz 009072034d52 1 ES120-7",
+        "GPT 200 kHz 0090720564e4 4 ES200-7C",
+    ]
+    test_frequencies = [38_000, 70_000, 120_000, 200_000]
+    ship_name = "David_Starr_Jordan"
+    cruise_name = "DS0604"
+    sensor_name = "EK60"
+    file_name = "DSJ0604-D20060419-T184612.raw"
+
+    dynamo_db_manager.update_item(
+        table_name=table_name,
+        key={
+            "FILE_NAME": {"S": file_name},  # Partition Key
+            "CRUISE_NAME": {"S": cruise_name},  # Sort Key
+        },
+        expression_attribute_names={
+            "#CH": "CHANNELS",
+            "#ET": "END_TIME",
+            "#ED": "ERROR_DETAIL",
+            "#FR": "FREQUENCIES",
+            "#MA": "MAX_ECHO_RANGE",
+            "#MI": "MIN_ECHO_RANGE",
+            "#ND": "NUM_PING_TIME_DROPNA",
+            "#PS": "PIPELINE_STATUS",  # testing this updated
+            "#PT": "PIPELINE_TIME",  # testing this updated
+            "#SE": "SENSOR_NAME",
+            "#SH": "SHIP_NAME",
+            "#ST": "START_TIME",
+            "#ZB": "ZARR_BUCKET",
+            "#ZP": "ZARR_PATH",
+        },
+        expression_attribute_values={
+            ":ch": {"L": [{"S": i} for i in test_channels]},
+            ":et": {"S": "2006-04-19T20:07:33.623Z"},
+            ":ed": {"S": ""},
+            ":fr": {"L": [{"N": str(i)} for i in test_frequencies]},
+            ":ma": {"N": str(np.round(500.785201, 4))},
+            ":mi": {"N": str(np.round(0.25001, 4))},
+            ":nd": {"N": str(2428)},
+            ":ps": {"S": "PROCESSING_RESAMPLE_AND_WRITE_TO_ZARR_STORE"},
+            ":pt": {"S": "2023-10-02T08:08:08Z"},
+            ":se": {"S": sensor_name},
+            ":sh": {"S": ship_name},
+            ":st": {"S": "2006-04-19T18:46:12.564Z"},
+            ":zb": {"S": "r2d2-dev-echofish2-118234403147-echofish-dev-output"},
+            ":zp": {
+                "S": f"level_1/{ship_name}/{cruise_name}/{sensor_name}/DSJ0604-D20060419-T184612.zarr"
+            },
+        },
+        update_expression=(
+            "SET "
+            "#CH = :ch, "
+            "#ET = :et, "
+            "#ED = :ed, "
+            "#FR = :fr, "
+            "#MA = :ma, "
+            "#MI = :mi, "
+            "#ND = :nd, "
+            "#PS = :ps, "
+            "#PT = :pt, "
+            "#SE = :se, "
+            "#SH = :sh, "
+            "#ST = :st, "
+            "#ZB = :zb, "
+            "#ZP = :zp"
+        ),
+    )
+
+    # ---Read From Table--- #
+    response = dynamo_db_manager.get_table_item(
+        table_name=table_name,
+        key={"FILE_NAME": "DSJ0604-D20060419-T184612.raw", "CRUISE_NAME": "DS0604"},
+    )
+    assert (
+        response["Item"]["PIPELINE_STATUS"]
+        == "PROCESSING_RESAMPLE_AND_WRITE_TO_ZARR_STORE"
+    )
+
+    # ---Change Items in Table (using src)--- #
+    dynamo_db_manager.update_item(
+        table_name=table_name,
+        key={
+            "FILE_NAME": {
+                "S": "DSJ0604-D20060419-T184612.raw",
+            },
+            "CRUISE_NAME": {
+                "S": "DS0604",
+            },
+        },
+        expression_attribute_names={
+            "#PS": "PIPELINE_STATUS",
+            "#PT": "PIPELINE_TIME",
+        },
+        expression_attribute_values={
+            ":ps": {"S": PipelineStatus.SUCCESS_CRUISE_PROCESSOR.name},
+            ":pt": {"S": "2023-10-02T09:09:09Z"},
+        },
+        update_expression=("SET " "#PS = :ps, " "#PT = :pt"),
+    )
+
+    # ---Read From Table Again--- #
+    response = dynamo_db_manager.get_table_item(
+        table_name=table_name,
+        key={"FILE_NAME": "DSJ0604-D20060419-T184612.raw", "CRUISE_NAME": "DS0604"},
+    )
+
+    assert response["Item"]["PIPELINE_STATUS"] == "SUCCESS_CRUISE_PROCESSOR"
+
+    # TODO: get the table as a dataframe
+    df = dynamo_db_manager.get_table_as_df(
+        table_name=table_name,
+        ship_name="David_Starr_Jordan",
+        cruise_name="DS0604",
+        sensor_name="EK60",
+    )
+
+    assert df.shape[1] == 16
+    # TODO: check fields
+
+
+#######################################################
+def update_dynamodb_item(
+        dynamo_db_manager,
+        table_name,
+        ship_name,
+        sensor_name,
+        cruise_name,
+        file_name,
+        test_channels,
+        test_frequencies,
+):
+    dynamo_db_manager.update_item(
+        table_name=table_name,
+        key={
+            "FILE_NAME": {"S": file_name},  # Partition Key
+            "CRUISE_NAME": {"S": cruise_name},  # Sort Key
+            # TODO: should be FILE_NAME & SENSOR_NAME? so they are truly unique for when two sensors are processed within one cruise
+        },
+        expression_attribute_names={
+            "#CH": "CHANNELS",
+            "#ET": "END_TIME",
+            "#ED": "ERROR_DETAIL",
+            "#FR": "FREQUENCIES",
+            "#MA": "MAX_ECHO_RANGE",
+            "#MI": "MIN_ECHO_RANGE",
+            "#ND": "NUM_PING_TIME_DROPNA",
+            "#PS": "PIPELINE_STATUS",  # testing this updated
+            "#PT": "PIPELINE_TIME",  # testing this updated
+            "#SE": "SENSOR_NAME",
+            "#SH": "SHIP_NAME",
+            "#ST": "START_TIME",
+            "#ZB": "ZARR_BUCKET",
+            "#ZP": "ZARR_PATH",
+        },
+        expression_attribute_values={
+            ":ch": {"L": [{"S": i} for i in test_channels]},
+            ":et": {"S": "2006-04-19T20:07:33.623Z"},
+            ":ed": {"S": ""},
+            ":fr": {"L": [{"N": str(i)} for i in test_frequencies]},
+            ":ma": {"N": str(np.round(500.785201, 4))},
+            ":mi": {"N": str(np.round(0.25001, 4))},
+            ":nd": {"N": str(2428)},
+            ":ps": {"S": "PROCESSING_RESAMPLE_AND_WRITE_TO_ZARR_STORE"},
+            ":pt": {"S": "2023-10-02T08:08:080Z"}, # datetime.now().isoformat(timespec="seconds") + "Z"
+            ":se": {"S": sensor_name},
+            ":sh": {"S": ship_name},
+            ":st": {"S": "2006-04-19T18:46:12.564Z"},
+            ":zb": {"S": "r2d2-dev-echofish2-118234403147-echofish-dev-output"},
+            ":zp": {
+                "S": f"level_1/{ship_name}/{cruise_name}/{sensor_name}/DSJ0604-D20060419-T184612.zarr"
+            },
+        },
+        update_expression=(
+            "SET "
+            "#CH = :ch, "
+            "#ET = :et, "
+            "#ED = :ed, "
+            "#FR = :fr, "
+            "#MA = :ma, "
+            "#MI = :mi, "
+            "#ND = :nd, "
+            "#PS = :ps, "
+            "#PT = :pt, "
+            "#SE = :se, "
+            "#SH = :sh, "
+            "#ST = :st, "
+            "#ZB = :zb, "
+            "#ZP = :zp"
+        ),
+    )
+
+@mock_aws
+def test_delete_item(): # PASSING
+    # ---Initialize--- #
+    table_name = "test_table"
+    dynamo_db_manager = DynamoDBManager()
+
+    # ---Create Table--- #
+    dynamo_db_manager.create_water_column_sonar_table(table_name=table_name)
+
+    # ---Add Items to Table--- #
+    test_channels = [
+        "GPT  38 kHz 009072055a7f 2 ES38B",
+        "GPT  70 kHz 00907203400a 3 ES70-7C",
+        "GPT 120 kHz 009072034d52 1 ES120-7",
+        "GPT 200 kHz 0090720564e4 4 ES200-7C",
+    ]
+    test_frequencies = [38_000, 70_000, 120_000, 200_000]
+
+    sensor_name = "EK60"
+
+    # First Cruise
+    ship_name1 = "David_Starr_Jordan"
+    cruise_name1 = "DS0604"
+    file_name1a = "DSJ0604-D20060406-T035914.raw"
+    file_name1b = "DSJ0604-D20060406-T050022.raw"
+
+    # Second Cruise
+    ship_name2 = "David_Starr_Jordan"
+    cruise_name2 = "DS0704"
+    file_name2a = "DSJ270307-D20070327-T225442.raw"
+    file_name2b = "DSJ270307-D20070328-T001728.raw"
+
+    update_dynamodb_item(
+        dynamo_db_manager=dynamo_db_manager,
+        table_name=table_name,
+        ship_name=ship_name1,
+        sensor_name=sensor_name,
+        cruise_name=cruise_name1,
+        file_name=file_name1a,
+        test_channels=test_channels,
+        test_frequencies=test_frequencies,
+    )
+    update_dynamodb_item(
+        dynamo_db_manager=dynamo_db_manager,
+        table_name=table_name,
+        ship_name=ship_name1,
+        sensor_name=sensor_name,
+        cruise_name=cruise_name1,
+        file_name=file_name1b,
+        test_channels=test_channels,
+        test_frequencies=test_frequencies,
+    )
+    update_dynamodb_item(
+        dynamo_db_manager=dynamo_db_manager,
+        table_name=table_name,
+        ship_name=ship_name2,
+        sensor_name=sensor_name,
+        cruise_name=cruise_name2,
+        file_name=file_name2a,
+        test_channels=test_channels,
+        test_frequencies=test_frequencies,
+    )
+    update_dynamodb_item(
+        dynamo_db_manager=dynamo_db_manager,
+        table_name=table_name,
+        ship_name=ship_name2,
+        sensor_name=sensor_name,
+        cruise_name=cruise_name2,
+        file_name=file_name2b,
+        test_channels=test_channels,
+        test_frequencies=test_frequencies,
+    )
+
+    # ---Read From Table, verify four items--- #
+    response = dynamo_db_manager.describe_table(table_name=table_name)
+    assert response['Table']['ItemCount'] == 4
+    df1 = dynamo_db_manager.get_table_as_df(
+        ship_name=ship_name1,
+        cruise_name=cruise_name1,
+        sensor_name="EK60",
+        table_name=table_name,
+    )
+    df2 = dynamo_db_manager.get_table_as_df(
+        ship_name=ship_name2,
+        cruise_name=cruise_name2,
+        sensor_name="EK60",
+        table_name=table_name,
+    )
+    assert df1.shape[0] == 2 # TODO: check actual filenames
+    assert df2.shape[0] == 2
+
+    # ---Delete cruise From Table Again--- #
+    dynamo_db_manager.delete_item(
+        table_name=table_name,
+        cruise_name=cruise_name2,
+        file_name=file_name2a,
+    )
+    dynamo_db_manager.delete_item(
+        table_name=table_name,
+        cruise_name=cruise_name2,
+        file_name=file_name2b,
+    )
+
+    # ---Get count of items again---#
+    response = dynamo_db_manager.describe_table(table_name=table_name)
+    assert response['Table']['ItemCount'] == 2
+
+    df4 = dynamo_db_manager.get_table_as_df(
+        table_name=table_name,
+        ship_name=ship_name2,
+        cruise_name=cruise_name2,
+        sensor_name="EK60",
+    )
+    assert df4.shape == (0, 0)
+
+    # assert df.shape[1] == 16
+    # TODO: check fields
+
+#######################################################

{water_column_sonar_processing-0.0.7 → water_column_sonar_processing-0.0.9}/tests/test_geometry_manager.py

@@ -2,7 +2,7 @@ import echopype as ep
 import numpy as np
 from dotenv import find_dotenv, load_dotenv
 
-from water_column_sonar_processing.geometry.geometry_manager import GeometryManager
+from water_column_sonar_processing.geometry import GeometryManager
 
 
 #######################################################
@@ -18,10 +18,13 @@ def teardown_module():
 
 #######################################################
 
-
 # @mock_s3
 def test_geometry_manager(tmp_path):
-    bucket_name = "noaa-wcsd-pds"
+    """
+    # TODO: need to find a small file to test with, put into test bucket, read from there into
+    """
+    input_bucket_name = "noaa-wcsd-pds"
+    output_bucket_name = "noaa-wcsd-zarr-pds"
     # file_name = 'D20070719-T232718.raw'  # too big
     # file_name = 'D20070720-T224031.raw'  # has >4 points in dataset
     file_name = "D20070724-T042400.raw"
@@ -30,7 +33,7 @@ def test_geometry_manager(tmp_path):
     cruise_name = "HB0706"
     sensor_name = "EK60"
 
-    s3_path = f"s3://{bucket_name}/data/raw/{ship_name}/{cruise_name}/{sensor_name}/{file_name}"
+    s3_path = f"s3://{input_bucket_name}/data/raw/{ship_name}/{cruise_name}/{sensor_name}/{file_name}"
     # s3_path = f"r2d2-testing-level-2-data/level_2/Henry_B._Bigelow/HB0707/EK60/HB0707.model"
 
     print(s3_path)
@@ -44,13 +47,14 @@ def test_geometry_manager(tmp_path):
 
     geometry_manager = GeometryManager()
 
-    time, lat, lon = geometry_manager.read_echodata_gps_data(
+    time, lat, lon = geometry_manager.read_echodata_gps_data( # gps_df.index.values, gps_df.latitude.values, gps_df.longitude.values
         echodata=echodata,
+        output_bucket_name=output_bucket_name,
         ship_name=ship_name,
         cruise_name=cruise_name,
         sensor_name=sensor_name,
         file_name=file_name,
-        write_geojson=False,
+        write_geojson=False
     )
     # NOTE CHECK FOR NULL ISLAND ON RETURN
     null_island_indices = list(