isort . black .

ocean_data_parser/geo.py

@@ -1,15 +1,14 @@
 import json
 import os
-from geographiclib.geodesic import Geodesic
 
-from shapely.geometry import shape, Point, Polygon
+from geographiclib.geodesic import Geodesic
+from shapely.geometry import Point, Polygon, shape
 
 
 def read_geojson(
     path: str,
     encoding: str = "UTF-8",
 ) -> dict:
-
     """Parse geojson files and return it as a dictionary.
 
     If features are available, generate a shapely feature object.

ocean_data_parser/metadata/pdc.py

@@ -7,6 +7,7 @@
 
 logger = logging.getLogger(__name__)
 
+
 # def fgdc_to_acdd(xml)
 def fgdc_to_acdd(url=None, xml=None):
     """Convert PDC FGDC XML format to an ACDD 1.3 standard dictionary format."""

ocean_data_parser/read/__init__.py

@@ -1 +1 @@
-from ocean_data_parser.read.auto import file, detect_file_format
+from ocean_data_parser.read.auto import detect_file_format, file

ocean_data_parser/read/amundsen.py

@@ -1,14 +1,15 @@
 """Module use to handle int file format generated historically ArcticNet and the Amundsen inc."""
 __version__ = "0.1.0"
 
-import re
+import json
 import logging
 import os
-import json
+import re
 
 import pandas as pd
 from gsw import z_from_p
-from .utils import standardize_dataset, get_history_handler
+
+from .utils import get_history_handler, standardize_dataset
 
 logger = logging.getLogger(__name__)
 string_attributes = ["Cruise_Number", "Cruise_Name", "Station"]

ocean_data_parser/read/auto.py

@@ -1,7 +1,7 @@
-from importlib import import_module
-import re
-import os
 import logging
+import os
+import re
+from importlib import import_module
 
 logger = logging.getLogger(__name__)
 
@@ -84,7 +84,6 @@ def detect_file_format(file: str, encoding: str = "UTF-8") -> str:
 
 
 def file(path, parser=None, **kwargs):
-
     # Review the file format if no parser is specified
     if parser is None:
         parser = detect_file_format(path)

ocean_data_parser/read/dfo/odf.py

@@ -4,6 +4,7 @@
 the different data formats developped by the different Canadian DFO offices.
 """
 from typing import Union
+
 from ocean_data_parser.read.dfo.odf_source.process import (
     parse_odf,
     read_config,

ocean_data_parser/read/dfo/odf_source/attributes.py

@@ -10,6 +10,7 @@
 from difflib import get_close_matches
 
 import pandas as pd
+
 from ocean_data_parser.read.seabird import (
     get_seabird_instrument_from_header,
     get_seabird_processing_history,

ocean_data_parser/read/dfo/odf_source/process.py

@@ -19,9 +19,9 @@
 # )
 import ocean_data_parser.read.dfo.odf_source.attributes as attributes
 import ocean_data_parser.read.dfo.odf_source.parser as odf_parser
+from ocean_data_parser.geo import get_geo_code, get_nearest_station, read_geojson
 from ocean_data_parser.read import seabird
 from ocean_data_parser.read.utils import standardize_dataset
-from ocean_data_parser.geo import get_nearest_station, read_geojson, get_geo_code
 
 tqdm.pandas()
 

ocean_data_parser/read/electricblue.py

@@ -1,10 +1,11 @@
 import logging
+import re
 
 import pandas as pd
-import re
+
 from ocean_data_parser.read.utils import (
-    standardize_dataset,
     rename_variables_to_valid_netcdf,
+    standardize_dataset,
 )
 
 logger = logging.getLogger(__name__)
@@ -114,7 +115,6 @@ def csv(
 
 
 def log_csv(path, encoding="UTF-8", rename_variables=True):
-
     df = pd.read_csv(path, encoding=encoding, parse_dates=True, index_col=["time"])
     ds = df.to_xarray()
     # add default attributes

ocean_data_parser/read/nmea.py

@@ -214,7 +214,6 @@ def rename_variable(name):
     nmea = []
     long_names = {}
     with open(path, encoding=encoding) as f:
-
         for row, line in enumerate(f):
             if not line:
                 continue

ocean_data_parser/read/onset.py

@@ -88,7 +88,6 @@ def _parse_onset_time(time, timezone="UTC"):
 
 
 def _parse_onset_csv_header(header_lines):
-
     full_header = "\n".join(header_lines)
     header = {
         "instrument_manufacturer": "Onset",
@@ -157,7 +156,6 @@ def csv(
     read_csv_kwargs: dict = None,
     standardize_variable_names: bool = True,
 ):
-
     """tidbit_csv parses the Onset Tidbit CSV format into a pandas dataframe
 
     Returns:

ocean_data_parser/read/rbr.py

@@ -5,6 +5,7 @@
 import re
 
 import pandas as pd
+
 from ocean_data_parser.read.utils import test_parsed_dataset
 
 

ocean_data_parser/read/seabird.py

@@ -237,7 +237,6 @@ def read_number_line(line):
     header["history"] = []
     read_next_line = True
     while "*END*" not in line and line.startswith(("*", "#")):
-
         if read_next_line:
             line = f.readline()
         else:
@@ -490,7 +489,6 @@ def generate_binned_attributes(ds, seabird_header):
         ds.attrs["time_coverage_resolution"] = pd.Timedelta(bin_str).isoformat()
     for var in ds:
         if (len(ds.dims) == 1 and len(ds[var].dims) == 1) or binvar in ds[var].dims:
-
             ds[var].attrs["cell_method"] = f"{binvar}: mean (interval: {bin_str})"
     return ds
 

ocean_data_parser/read/star_oddi.py

@@ -1,7 +1,7 @@
-import pandas as pd
+import logging
 import re
 
-import logging
+import pandas as pd
 
 logger = logging.getLogger(__name__)
 

ocean_data_parser/read/van_essen_instruments.py

@@ -5,7 +5,7 @@
 
 import pandas as pd
 
-from .utils import test_parsed_dataset, standardize_dataset
+from .utils import standardize_dataset, test_parsed_dataset
 
 logger = logging.getLogger(__name__)
 

ocean_data_parser/tools/postgresql.py

@@ -1,6 +1,6 @@
-from io import StringIO
 import csv
 import logging
+from io import StringIO
 
 logger = logging.getLogger(__name__)
 

scripts/pdc_amundsen_conversion.py

@@ -4,13 +4,14 @@
 Those NetCDFs are then served by the PDC Hyrax and CIOOS ERDAP servers
 """
 
-from glob import glob
 import logging
+from glob import glob
 
-from ocean_data_parser.read import amundsen
-from ocean_data_parser.metadata import pdc
 from tqdm import tqdm
 
+from ocean_data_parser.metadata import pdc
+from ocean_data_parser.read import amundsen
+
 FORMAT = "%(asctime)s [%(levelname)s] %(message)s"
 logging.basicConfig(
     filename="pdc-amundsen-conversion.log", level=logging.WARNING, format=FORMAT

setup.py

@@ -1,5 +1,4 @@
-from setuptools import setup, find_packages
-
+from setuptools import find_packages, setup
 
 setup(
     name="ocean_data_parser",

tests/parser_detection_test.py

@@ -1,10 +1,10 @@
 import logging
+import os
+import re
 import unittest
 from glob import glob
-import re
-import os
 
-from ocean_data_parser.read import file, detect_file_format
+from ocean_data_parser.read import detect_file_format, file
 
 logging.basicConfig(level=logging.DEBUG)
 logger = logging.getLogger()

tests/parsers_test.py

@@ -1,26 +1,27 @@
 import logging
+import os
 import re
 import unittest
 from glob import glob
-import os
 
-import xarray as xr
-import pandas as pd
 import numpy as np
+import pandas as pd
+import xarray as xr
+
 from ocean_data_parser.read import (
-    seabird,
-    van_essen_instruments,
-    onset,
     amundsen,
-    electricblue,
-    star_oddi,
-    rbr,
-    sunburst,
     dfo,
+    electricblue,
+    file,
     nmea,
+    onset,
     pme,
+    rbr,
+    seabird,
+    star_oddi,
+    sunburst,
+    van_essen_instruments,
 )
-from ocean_data_parser.read import file
 
 logging.basicConfig(level=logging.DEBUG)
 logger = logging.getLogger()
@@ -80,7 +81,6 @@ def ignore_from_attr(attr, expression, placeholder):
         test = standardize_dataset(test)
 
         if not ref.identical(test):
-
             # Global attributes
             for key in ref.attrs.keys():
                 if not_identical(ref.attrs[key], test.attrs.get(key)):