water-column-sonar-processing 25.1.2__tar.gz → 25.1.4__tar.gz

water_column_sonar_processing-25.1.4/.github/workflows/test_action.yaml

@@ -0,0 +1,46 @@
+name: Testing
+
+on: [push]
+
+jobs:
+#  build:
+#    runs-on: ubuntu-latest
+#    steps:
+#      - name: Check out
+#        uses: actions/checkout@v4
+#      - name: Set up Python
+#        uses: actions/setup-python@v5
+#        with:
+#          # Semantic version range syntax or exact version of a Python version
+#          python-version: '3.10'
+#          # Optional - x64 or x86 architecture, defaults to x64
+##          architecture: 'x64'
+#          cache: 'pip'
+#      - name: Install dependencies
+#        run: |
+#          python -m pip install --upgrade pip
+#          pip install -r requirements_dev.txt
+#      - name: Run the tests
+#        run: python -m pytest
+
+  build:
+    name: python
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          version: "0.5.25"
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version-file: ".python-version"
+
+      - name: Install the project
+        run: uv sync --all-extras --dev
+
+      - name: Run tests
+        run: uv run pytest tests

water_column_sonar_processing-25.1.4/.python-version

@@ -0,0 +1 @@
+3.10.12

{water_column_sonar_processing-25.1.2 → water_column_sonar_processing-25.1.4}/PKG-INFO

@@ -1,14 +1,14 @@
 Metadata-Version: 2.2
 Name: water_column_sonar_processing
-Version: 25.1.2
-Summary: A processing tool for water column sonar data.
+Version: 25.1.4
+Summary: 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
 Project-URL: Issues, https://github.com/CI-CMG/water-column-sonar-processing/issues
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
-Requires-Python: >=3.8
+Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: aiobotocore==2.19.0
@@ -34,6 +34,19 @@ Requires-Dist: typing-extensions==4.10.0
 Requires-Dist: xarray==2024.10.0
 Requires-Dist: xbatcher==0.4.0
 Requires-Dist: zarr==2.18.3
+Provides-Extra: dev
+Requires-Dist: bandit[toml]==1.8.0; extra == "dev"
+Requires-Dist: build; extra == "dev"
+Requires-Dist: pre-commit; extra == "dev"
+Requires-Dist: pyinstaller; extra == "dev"
+Requires-Dist: twine; extra == "dev"
+Requires-Dist: flake8==7.1.1; extra == "dev"
+Requires-Dist: pooch==1.8.2; extra == "dev"
+Requires-Dist: pytest~=8.3.3; extra == "dev"
+Requires-Dist: tqdm; extra == "dev"
+Requires-Dist: bandit; extra == "dev"
+Provides-Extra: test
+Requires-Dist: pytest-cov; extra == "test"
 
 # Water Column Sonar Processing
 Processing tool for converting L0 data to L1 and L2 as well as generating geospatial information
@@ -80,14 +93,17 @@ Processing tool for converting L0 data to L1 and L2 as well as generating geospa
      3. Set interpreter 
 
 # Installing Dependencies
-
-  1. Add dependencies with versions to requirements.txt
-  2. ```pip install --upgrade pip && pip install -r requirements_dev.txt```
+```
+uv pip install --upgrade pip
+#uv pip install -r requirements_dev.txt
+uv pip install -r pyproject.toml --extra dev
+```
 
 
 # Pytest
 ```commandline
-pytest --disable-warnings
+uv run pytest tests
+#pytest --disable-warnings
 ```
 or
 > pytest --cache-clear --cov=src tests/ --cov-report=xml
@@ -120,7 +136,7 @@ https://colab.research.google.com/drive/1KiLMueXiz9WVB9o4RuzYeGjNZ6PsZU7a#scroll
 # Tag a Release
 Step 1 --> increment the semantic version in the zarr_manager.py "metadata" & the "pyproject.toml"
 ```commandline
-git tag -a v25.1.2 -m "Releasing version v25.1.2"
+git tag -a v25.1.4 -m "Releasing version v25.1.4"
 git push origin --tags
 ```
 

{water_column_sonar_processing-25.1.2 → water_column_sonar_processing-25.1.4}/README.md

@@ -43,14 +43,17 @@ Processing tool for converting L0 data to L1 and L2 as well as generating geospa
      3. Set interpreter 
 
 # Installing Dependencies
-
-  1. Add dependencies with versions to requirements.txt
-  2. ```pip install --upgrade pip && pip install -r requirements_dev.txt```
+```
+uv pip install --upgrade pip
+#uv pip install -r requirements_dev.txt
+uv pip install -r pyproject.toml --extra dev
+```
 
 
 # Pytest
 ```commandline
-pytest --disable-warnings
+uv run pytest tests
+#pytest --disable-warnings
 ```
 or
 > pytest --cache-clear --cov=src tests/ --cov-report=xml
@@ -83,7 +86,7 @@ https://colab.research.google.com/drive/1KiLMueXiz9WVB9o4RuzYeGjNZ6PsZU7a#scroll
 # Tag a Release
 Step 1 --> increment the semantic version in the zarr_manager.py "metadata" & the "pyproject.toml"
 ```commandline
-git tag -a v25.1.2 -m "Releasing version v25.1.2"
+git tag -a v25.1.4 -m "Releasing version v25.1.4"
 git push origin --tags
 ```
 
@@ -105,4 +108,4 @@ Experimental Plotting in Xarray (hvPlot):
 https://colab.research.google.com/drive/18vrI9LAip4xRGEX6EvnuVFp35RAiVYwU#scrollTo=q9_j9p2yXsLV
 
 HB0707 Cruise zoomable:
-https://hb0707.s3.us-east-1.amazonaws.com/index.html
+https://hb0707.s3.us-east-1.amazonaws.com/index.html

water_column_sonar_processing-25.1.4/pyproject.toml

@@ -0,0 +1,73 @@
+[build-system]
+requires = [
+    "setuptools>=61.0",
+    "wheel >= 0.29.0",
+]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "water_column_sonar_processing"
+version = "25.1.4"
+authors = [
+  { name="Rudy Klucik", email="rudy.klucik@noaa.gov" },
+]
+description = "Processing tool for water column sonar data."
+readme = "README.md"
+requires-python = ">=3.10"
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+]
+
+dependencies = [
+    "aiobotocore==2.19.0",
+    "boto3==1.36.3",
+    "botocore==1.36.3",
+    "echopype==0.9.0",
+    "fiona==1.10.1",
+    "geopandas==1.0.1",
+    "mock==5.1.0",
+    "moto[all]==5.0.27",
+    "moto[server]==5.0.27",
+    "numcodecs==0.13.1",
+    "numpy==1.26.4",
+    "pandas==2.2.3",
+    "pyarrow==18.1.0",
+    "python-dotenv==1.0.1",
+    "requests==2.32.3",
+    "s3fs==2024.2.0",
+    "scipy==1.14.1",
+    "setuptools",
+    "shapely==2.0.3",
+    "typing-extensions==4.10.0",
+    "xarray==2024.10.0",
+    "xbatcher==0.4.0",
+    "zarr==2.18.3",
+]
+
+[project.optional-dependencies]
+dev = [
+    "bandit[toml]==1.8.0",
+    "build",
+    "pre-commit",
+    "pyinstaller",
+    "twine",
+    "flake8==7.1.1",
+    "pooch==1.8.2",
+    "pytest~=8.3.3",
+    "tqdm",
+    "bandit"
+]
+test = [
+    "pytest-cov",
+]
+
+[project.urls]
+Homepage = "https://github.com/CI-CMG/water-column-sonar-processing"
+Issues = "https://github.com/CI-CMG/water-column-sonar-processing/issues"
+
+[tool.bandit]
+exclude_dirs = ["tests"]
+[tool.pre-commit-hooks.bandit]
+exclude = ["*/tests/*"]

{water_column_sonar_processing-25.1.2 → water_column_sonar_processing-25.1.4}/water_column_sonar_processing/aws/dynamodb_manager.py

@@ -140,15 +140,7 @@ class DynamoDBManager:
         To be used to initialize a cruise, deletes all entries associated with that cruise
         in the database.
         """
-        expression_attribute_values = {
-            ":cr": {"S": cruise_name},
-            ":se": {"S": sensor_name},
-            ":sh": {"S": ship_name},
-        }
-        filter_expression = (
-            "CRUISE_NAME = :cr and SENSOR_NAME = :se and SHIP_NAME = :sh"
-        )
-        # filter_expression = "CRUISE_NAME = :cr"
+        filter_expression = "CRUISE_NAME = :cr"
         response = self.dynamodb_client.scan(
             TableName=table_name,
             # Limit=1000,
@@ -156,7 +148,7 @@ class DynamoDBManager:
             # ExclusiveStartKey=where to pick up
             #ReturnConsumedCapacity='INDEXES' | 'TOTAL' | 'NONE', ...not sure
             # ProjectionExpression='#SH, #CR, #FN', # what to specifically return — from expression_attribute_names
-            FilterExpression='CRUISE_NAME = :cr',#
+            FilterExpression=filter_expression,
             # ExpressionAttributeNames={
             #     '#SH': 'SHIP_NAME',
             #     '#CR': 'CRUISE_NAME',
@@ -170,7 +162,6 @@ class DynamoDBManager:
             ConsistentRead=True
             # ExclusiveStartKey=response["LastEvaluatedKey"],
         )
-        print(response)
         # Note: table.scan() has 1 MB limit on results so pagination is used
 
         if len(response["Items"]) == 0 and "LastEvaluatedKey" not in response:
@@ -183,7 +174,7 @@ class DynamoDBManager:
                 TableName=table_name,
                 ### Either 'Select' or 'ExpressionAttributeNames'/'ProjectionExpression'
                 Select='ALL_ATTRIBUTES', # or 'SPECIFIC_ATTRIBUTES',
-                FilterExpression='CRUISE_NAME = :cr',  #
+                FilterExpression=filter_expression,
                 #ProjectionExpression='#SH, #CR, #FN',  # what to specifically return — from expression_attribute_names
                 # ExpressionAttributeNames={ # would need to specify all cols in df
                 #     '#SH': 'SHIP_NAME',
@@ -205,6 +196,66 @@ class DynamoDBManager:
 
         return df.sort_values(by="START_TIME", ignore_index=True)
 
+    #####################################################################
+    # def get_cruise_list(
+    #     self,
+    #     table_name,
+    # ) -> list:
+    #     """
+    #     Experimental, gets all cruise names as list
+    #     """
+    #     filter_expression = "CRUISE_NAME = :cr"
+    #     response = self.dynamodb_client.scan(
+    #         TableName=table_name,
+    #         Select='SPECIFIC_ATTRIBUTES',
+    #         #ReturnConsumedCapacity='INDEXES' | 'TOTAL' | 'NONE', ...not sure
+    #         # ProjectionExpression='#SH, #CR, #FN', # what to specifically return — from expression_attribute_names
+    #         FilterExpression=filter_expression,
+    #         # ExpressionAttributeNames={
+    #         #     '#SH': 'SHIP_NAME',
+    #         #     '#CR': 'CRUISE_NAME',
+    #         #     '#FN': 'FILE_NAME',
+    #         # },
+    #         # ExpressionAttributeValues={ # criteria
+    #         #     ':cr': {
+    #         #         'S': cruise_name,
+    #         #     },
+    #         # },
+    #     )
+    #     # Note: table.scan() has 1 MB limit on results so pagination is used
+    #
+    #     if len(response["Items"]) == 0 and "LastEvaluatedKey" not in response:
+    #         return pd.DataFrame() # If no results, return empty dataframe
+    #
+    #     data = response["Items"]
+    #
+    #     while response.get('LastEvaluatedKey'): #"LastEvaluatedKey" in response:
+    #         response = self.dynamodb_client.scan(
+    #             TableName=table_name,
+    #             ### Either 'Select' or 'ExpressionAttributeNames'/'ProjectionExpression'
+    #             Select='ALL_ATTRIBUTES', # or 'SPECIFIC_ATTRIBUTES',
+    #             FilterExpression=filter_expression,
+    #             #ProjectionExpression='#SH, #CR, #FN',  # what to specifically return — from expression_attribute_names
+    #             # ExpressionAttributeNames={ # would need to specify all cols in df
+    #             #     '#SH': 'SHIP_NAME',
+    #             #     '#CR': 'CRUISE_NAME',
+    #             #     '#FN': 'FILE_NAME',
+    #             # },
+    #             ExpressionAttributeValues={  # criteria
+    #                 ':cr': {
+    #                     'S': cruise_name,
+    #                 },
+    #             },
+    #             ConsistentRead=True,
+    #             ExclusiveStartKey=response["LastEvaluatedKey"],
+    #         )
+    #         data.extend(response["Items"])
+    #
+    #     deserializer = self.type_deserializer
+    #     df = pd.DataFrame([deserializer.deserialize({"M": i}) for i in data])
+    #
+    #     return df.sort_values(by="START_TIME", ignore_index=True)
+
     #####################################################################
     # TODO: WIP
     def delete_item(

{water_column_sonar_processing-25.1.2 → water_column_sonar_processing-25.1.4}/water_column_sonar_processing/aws/s3fs_manager.py

@@ -16,7 +16,7 @@ class S3FSManager:
         # self.output_bucket_name = os.environ.get("OUTPUT_BUCKET_NAME")
         self.s3_region = os.environ.get("AWS_REGION", default="us-east-1")
         self.s3fs = s3fs.S3FileSystem(
-            asynchronous=False,
+            # asynchronous=False,
             endpoint_url=endpoint_url,
             key=os.environ.get("OUTPUT_BUCKET_ACCESS_KEY"),
             secret=os.environ.get("OUTPUT_BUCKET_SECRET_ACCESS_KEY"),

{water_column_sonar_processing-25.1.2 → water_column_sonar_processing-25.1.4}/water_column_sonar_processing/cruise/resample_regrid.py

@@ -1,5 +1,4 @@
 import gc
-import os
 from pathlib import Path
 
 import numcodecs
@@ -198,9 +197,9 @@ class ResampleRegrid:
                 #  df[df['PIPELINE_STATUS'] < PipelineStatus.LEVEL_1_PROCESSING] = np.nan
 
                 # Get index from all cruise files. Note: should be based on which are included in cruise.
-                index = cruise_df.index[
+                index = int(cruise_df.index[
                     cruise_df["FILE_NAME"] == f"{file_name_stem}.raw"
-                ][0]
+                ][0])
 
                 # get input store
                 input_xr_zarr_store = zarr_manager.open_s3_zarr_store_with_xarray(
@@ -227,18 +226,20 @@ class ResampleRegrid:
                 min_echo_range = np.nanmin(np.float32(cruise_df["MIN_ECHO_RANGE"]))
                 max_echo_range = np.nanmax(np.float32(cruise_df["MAX_ECHO_RANGE"]))
 
-                print(
-                    "Creating empty ndarray for Sv data."
-                )  # Note: cruise_zarr dimensions are (depth, time, frequency)
+                print("Creating empty ndarray for Sv data.")  # Note: cruise dims (depth, time, frequency)
+                output_zarr_store_shape = output_zarr_store.Sv.shape
+                end_ping_time_index - start_ping_time_index
+                output_zarr_store_height = output_zarr_store_shape[0]
+                output_zarr_store_width = end_ping_time_index - start_ping_time_index
+                output_zarr_store_depth = output_zarr_store_shape[2]
                 cruise_sv_subset = np.empty(
-                    shape=output_zarr_store.Sv[
-                        :, start_ping_time_index:end_ping_time_index, :
-                    ].shape
+                    shape=(output_zarr_store_height, output_zarr_store_width, output_zarr_store_depth)
                 )
                 cruise_sv_subset[:, :, :] = np.nan
 
                 all_cruise_depth_values = zarr_manager.get_depth_values(
-                    min_echo_range=min_echo_range, max_echo_range=max_echo_range
+                    min_echo_range=min_echo_range,
+                    max_echo_range=max_echo_range
                 ) # (5262,) and
 
                 print(" ".join(list(input_xr_zarr_store.Sv.dims)))
@@ -282,16 +283,6 @@ class ResampleRegrid:
                 #########################################################################
                 # write Sv values to cruise-level-model-store
                 output_zarr_store.Sv[:, start_ping_time_index:end_ping_time_index, :] = regrid_resample.values
-
-                #########################################################################
-                # [5] write subset of latitude/longitude
-                output_zarr_store.latitude[
-                    start_ping_time_index:end_ping_time_index
-                ] = geospatial.dropna()["latitude"].values # TODO: get from ds_sv directly, dont need geojson anymore
-                output_zarr_store.longitude[
-                    start_ping_time_index:end_ping_time_index
-                ] = geospatial.dropna()["longitude"].values
-
                 #########################################################################
                 # TODO: add the "detected_seafloor_depth/" to the
                 #  L2 cruise dataarrays
@@ -311,6 +302,15 @@ class ResampleRegrid:
                     output_zarr_store.bottom[
                         start_ping_time_index:end_ping_time_index
                     ] = detected_seafloor_depths
+                #
+                #########################################################################
+                # [5] write subset of latitude/longitude
+                output_zarr_store.latitude[
+                    start_ping_time_index:end_ping_time_index
+                ] = geospatial.dropna()["latitude"].values # TODO: get from ds_sv directly, dont need geojson anymore
+                output_zarr_store.longitude[
+                    start_ping_time_index:end_ping_time_index
+                ] = geospatial.dropna()["longitude"].values
                 #########################################################################
                 #########################################################################
         except Exception as err:

{water_column_sonar_processing-25.1.2 → water_column_sonar_processing-25.1.4}/water_column_sonar_processing/model/zarr_manager.py

@@ -2,6 +2,7 @@ import numcodecs
 import numpy as np
 import xarray as xr
 import zarr
+import importlib.metadata
 from numcodecs import Blosc
 
 from water_column_sonar_processing.aws import S3FSManager
@@ -249,9 +250,9 @@ class ZarrManager:
         root.attrs["sensor_name"] = sensor_name
         #
         root.attrs["processing_software_name"] = Coordinates.PROJECT_NAME.value
-        root.attrs["processing_software_version"] = (
-            "25.1.2"  # TODO: get programmatically, echopype>utils>prov.py
-        )
+
+        current_project_version = importlib.metadata.version('water_column_sonar_processing')
+        root.attrs["processing_software_version"] = current_project_version
         root.attrs["processing_software_time"] = Timestamp.get_timestamp()
         #
         root.attrs["calibration_status"] = calibration_status
@@ -290,7 +291,7 @@ class ZarrManager:
         # zarr_synchronizer: Union[str, None] = None, # TODO:
         output_bucket_name: str,
         endpoint_url=None,
-    ):
+    ) -> zarr.hierarchy.Group:
         # Mounts a Zarr store using pythons Zarr implementation. The mounted store
         #  will have read/write privileges so that store can be updated.
         print("Opening L2 Zarr store with Zarr for writing.")
@@ -316,18 +317,21 @@ class ZarrManager:
         input_bucket_name: str,
         endpoint_url=None,
     ) -> xr.Dataset:
-        print("Opening L1 Zarr store in S3 with Xarray.")
+        print("Opening L1 Zarr store in S3 with Xarray.") # TODO: Is this only used for reading from?
         try:
             zarr_path = f"s3://{input_bucket_name}/level_1/{ship_name}/{cruise_name}/{sensor_name}/{file_name_stem}.zarr"
             s3fs_manager = S3FSManager(endpoint_url=endpoint_url)
             store_s3_map = s3fs_manager.s3_map(s3_zarr_store_path=zarr_path)
-            ds = xr.open_zarr(
-                store=store_s3_map, consolidated=None
-            )  # synchronizer=SYNCHRONIZER
+            ds = xr.open_dataset(
+                filename_or_obj=store_s3_map,
+                engine="zarr",
+                chunks={}
+            )
         except Exception as err:
             print("Problem opening Zarr store in S3 as Xarray.")
             raise err
-        print("Done opening Zarr store in S3 as Xarray.")
+        finally:
+            print("Exiting opening Zarr store in S3 as Xarray.")
         return ds
 
     def open_l2_zarr_store_with_xarray(

{water_column_sonar_processing-25.1.2 → water_column_sonar_processing-25.1.4}/water_column_sonar_processing/utility/constants.py

@@ -3,7 +3,7 @@ from enum import Enum, Flag, unique
 
 @unique
 class Constants(Flag):
-    TILE_SIZE = 256 # TODO: add tile size to metadata?
+    TILE_SIZE = 1024
 
     # Average https://noaa-wcsd-zarr-pds.s3.us-east-1.amazonaws.com/level_2/Henry_B._Bigelow/HB0902/EK60/HB0902.zarr/time/927
     # chunk size is ~1.3 kB, HB0902 cruise takes ~30 seconds to load all time/lat/lon data

{water_column_sonar_processing-25.1.2 → water_column_sonar_processing-25.1.4}/water_column_sonar_processing.egg-info/PKG-INFO

@@ -1,14 +1,14 @@
 Metadata-Version: 2.2
 Name: water_column_sonar_processing
-Version: 25.1.2
-Summary: A processing tool for water column sonar data.
+Version: 25.1.4
+Summary: 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
 Project-URL: Issues, https://github.com/CI-CMG/water-column-sonar-processing/issues
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
-Requires-Python: >=3.8
+Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: aiobotocore==2.19.0
@@ -34,6 +34,19 @@ Requires-Dist: typing-extensions==4.10.0
 Requires-Dist: xarray==2024.10.0
 Requires-Dist: xbatcher==0.4.0
 Requires-Dist: zarr==2.18.3
+Provides-Extra: dev
+Requires-Dist: bandit[toml]==1.8.0; extra == "dev"
+Requires-Dist: build; extra == "dev"
+Requires-Dist: pre-commit; extra == "dev"
+Requires-Dist: pyinstaller; extra == "dev"
+Requires-Dist: twine; extra == "dev"
+Requires-Dist: flake8==7.1.1; extra == "dev"
+Requires-Dist: pooch==1.8.2; extra == "dev"
+Requires-Dist: pytest~=8.3.3; extra == "dev"
+Requires-Dist: tqdm; extra == "dev"
+Requires-Dist: bandit; extra == "dev"
+Provides-Extra: test
+Requires-Dist: pytest-cov; extra == "test"
 
 # Water Column Sonar Processing
 Processing tool for converting L0 data to L1 and L2 as well as generating geospatial information
@@ -80,14 +93,17 @@ Processing tool for converting L0 data to L1 and L2 as well as generating geospa
      3. Set interpreter 
 
 # Installing Dependencies
-
-  1. Add dependencies with versions to requirements.txt
-  2. ```pip install --upgrade pip && pip install -r requirements_dev.txt```
+```
+uv pip install --upgrade pip
+#uv pip install -r requirements_dev.txt
+uv pip install -r pyproject.toml --extra dev
+```
 
 
 # Pytest
 ```commandline
-pytest --disable-warnings
+uv run pytest tests
+#pytest --disable-warnings
 ```
 or
 > pytest --cache-clear --cov=src tests/ --cov-report=xml
@@ -120,7 +136,7 @@ https://colab.research.google.com/drive/1KiLMueXiz9WVB9o4RuzYeGjNZ6PsZU7a#scroll
 # Tag a Release
 Step 1 --> increment the semantic version in the zarr_manager.py "metadata" & the "pyproject.toml"
 ```commandline
-git tag -a v25.1.2 -m "Releasing version v25.1.2"
+git tag -a v25.1.4 -m "Releasing version v25.1.4"
 git push origin --tags
 ```
 

{water_column_sonar_processing-25.1.2 → water_column_sonar_processing-25.1.4}/water_column_sonar_processing.egg-info/SOURCES.txt

@@ -5,15 +5,11 @@
 LICENSE
 README.md
 pyproject.toml
-pytest.ini
-requirements.txt
-requirements_dev.txt
 .github/workflows/test_action.yaml
 open-science-data-federation/ml/autoencoder_example.py
 open-science-data-federation/osdf_examples/foo.ipynb
 open-science-data-federation/osdf_examples/sonar_ai.ipynb
 tests/conftest.py
-tests/test_process.py
 tests/test_resources/index/calibrated_cruises.csv
 tests/test_resources/raw_to_zarr/D20070724-T042400.bot
 tests/test_resources/raw_to_zarr/D20070724-T042400.idx

{water_column_sonar_processing-25.1.2 → water_column_sonar_processing-25.1.4}/water_column_sonar_processing.egg-info/requires.txt

@@ -21,3 +21,18 @@ typing-extensions==4.10.0
 xarray==2024.10.0
 xbatcher==0.4.0
 zarr==2.18.3
+
+[dev]
+bandit[toml]==1.8.0
+build
+pre-commit
+pyinstaller
+twine
+flake8==7.1.1
+pooch==1.8.2
+pytest~=8.3.3
+tqdm
+bandit
+
+[test]
+pytest-cov

water_column_sonar_processing-25.1.2/.github/workflows/test_action.yaml

@@ -1,24 +0,0 @@
-name: Python package
-
-on: [push]
-
-jobs:
-  build:
-    runs-on: ubuntu-latest
-    steps:
-      - name: Check out
-        uses: actions/checkout@v4
-      - name: Set up Python
-        uses: actions/setup-python@v5
-        with:
-          # Semantic version range syntax or exact version of a Python version
-          python-version: '3.10'
-          # Optional - x64 or x86 architecture, defaults to x64
-#          architecture: 'x64'
-          cache: 'pip'
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install -r requirements_dev.txt
-      - name: Run the tests
-        run: python -m pytest

water_column_sonar_processing-25.1.2/.python-version

@@ -1,2 +0,0 @@
-3.10.12
-water-column-sonar-processing

water_column_sonar_processing-25.1.2/pyproject.toml

@@ -1,43 +0,0 @@
-[build-system]
-requires = [
-    "setuptools>=61.0",
-    #"setuptools_scm[toml] >= 4, <6",
-    "wheel >= 0.29.0",
-]
-build-backend = "setuptools.build_meta"
-
-[project]
-name = "water_column_sonar_processing"
-version = "25.1.2"
-authors = [
-  { name="Rudy Klucik", email="rudy.klucik@noaa.gov" },
-]
-description = "A processing tool for water column sonar data."
-readme = "README.md"
-#requires-python = ">=3.10"
-requires-python = ">=3.8"
-classifiers = [
-    "Programming Language :: Python :: 3",
-    "License :: OSI Approved :: MIT License",
-    "Operating System :: OS Independent",
-]
-dynamic = ["dependencies"]
-
-[project.urls]
-Homepage = "https://github.com/CI-CMG/water-column-sonar-processing"
-Issues = "https://github.com/CI-CMG/water-column-sonar-processing/issues"
-
-[tool.setuptools.dynamic]
-dependencies = {file = ["requirements.txt"]}
-optional-dependencies = {dev = { file = ["requirements_dev.txt"] }}
-
-#[tool.setuptools_scm]
-#fallback_version = "unknown"
-#local_scheme = "node-and-date"
-#write_to = "_water_column_sonar_processing_version.py"
-#write_to_template = 'version = "{version}"'
-
-[tool.bandit]
-exclude_dirs = ["tests"]
-[tool.pre-commit-hooks.bandit]
-exclude = ["*/tests/*"]