Merge pull request #1253 from OSOceanAcoustics/pre-commit-ci-update-c…

…onfig

[pre-commit.ci] pre-commit autoupdate

.ci_helpers/docker/setup-services.py

@@ -3,6 +3,7 @@
 Script to help bring up docker services for testing.
 
 """
+
 import argparse
 import logging
 import shutil

.ci_helpers/run-test.py

@@ -3,6 +3,7 @@
 Script to run tests in Github and locally.
 
 """
+
 import argparse
 import glob
 import os

.pre-commit-config.yaml

@@ -24,12 +24,12 @@ repos:
         args: ["--profile", "black", "--filter-files"]
 
   - repo: https://github.com/psf/black
-    rev: 23.12.1
+    rev: 24.1.1
     hooks:
       - id: black
 
   - repo: https://github.com/PyCQA/flake8
-    rev: 6.1.0
+    rev: 7.0.0
     hooks:
       - id: flake8
 

echopype/calibrate/cal_params.py

@@ -500,9 +500,9 @@ def _get_fs():
                     elif p == "gain_correction":
                         # interpolate or pull from narrowband table
                         out_dict[p] = _get_interp_da(
-                            da_param=None
-                            if "gain" not in vend
-                            else vend["gain"],  # freq-dep values
+                            da_param=(
+                                None if "gain" not in vend else vend["gain"]
+                            ),  # freq-dep values
                             freq_center=freq_center,
                             alternative=get_vend_cal_params_power(beam=beam, vend=vend, param=p),
                         )

echopype/commongrid/api.py

@@ -1,6 +1,7 @@
 """
 Functions for enhancing the spatial and temporal coherence of data.
 """
+
 import logging
 from typing import Literal
 

echopype/consolidate/split_beam_angle.py

@@ -2,6 +2,7 @@
 Contains functions necessary to compute the split-beam (alongship/athwartship)
 angles and add them to a Dataset.
 """
+
 from typing import List, Tuple
 
 import numpy as np

echopype/convert/__init__.py

@@ -7,6 +7,7 @@
 - Simrad EK80 echosounder ``.raw`` data
 - ASL Environmental Sciences AZFP echosounder ``.01A`` data
 """
+
 # flake8: noqa
 from .parse_ad2cp import ParseAd2cp
 from .parse_azfp import ParseAZFP

echopype/convert/set_groups_ad2cp.py

@@ -203,12 +203,14 @@ def _make_dataset(self, var_names: Dict[str, str]) -> xr.Dataset:
             Union[Tuple[List[str], np.ndarray, Dict[str, str]], Tuple[Tuple[()], None]],
         ] = {
             var_name: (
-                [dim.dimension_name() for dim in dims[field_name]],
-                combined_fields[field_name],
-                attrs.get(field_name, {}),
+                (
+                    [dim.dimension_name() for dim in dims[field_name]],
+                    combined_fields[field_name],
+                    attrs.get(field_name, {}),
+                )
+                if field_exists[field_name]
+                else ((), None)
             )
-            if field_exists[field_name]
-            else ((), None)
             for field_name, var_name in var_names.items()
         }  # type: ignore
         coords: Dict[str, np.ndarray] = dict()

echopype/convert/set_groups_azfp.py

@@ -1,6 +1,7 @@
 """
 Class to save unpacked echosounder data to appropriate groups in netcdf or zarr.
 """
+
 from typing import List
 
 import numpy as np

echopype/convert/set_groups_ek80.py

@@ -170,9 +170,11 @@ def set_env(self) -> xr.Dataset:
                 ),
                 "sound_velocity_profile_depth": (
                     ["sound_velocity_profile_depth"],
-                    self.parser_obj.environment["sound_velocity_profile"][::2]
-                    if "sound_velocity_profile" in self.parser_obj.environment
-                    else [],
+                    (
+                        self.parser_obj.environment["sound_velocity_profile"][::2]
+                        if "sound_velocity_profile" in self.parser_obj.environment
+                        else []
+                    ),
                     {
                         "standard_name": "depth",
                         "units": "m",

echopype/echodata/__init__.py

@@ -2,6 +2,7 @@
 EchoData is an object that handles interfacing raw converted data.
 It is used for calibration and other processing.
 """
+
 from . import convention
 from .echodata import EchoData
 

echopype/echodata/combine.py

@@ -733,9 +733,11 @@ def _combine(
             {
                 "is_combined": is_combined,
                 "attrs_dict": _get_prov_attrs(ed["Provenance"], is_combined),
-                "echodata_filename": [str(s) for s in ed["Provenance"][ED_FILENAME].values]
-                if is_combined
-                else [echodata_filenames[idx]],
+                "echodata_filename": (
+                    [str(s) for s in ed["Provenance"][ED_FILENAME].values]
+                    if is_combined
+                    else [echodata_filenames[idx]]
+                ),
             }
         )
     # Get single boolean value to see if there's any combined files
@@ -755,9 +757,11 @@ def _combine(
 
         # select only the appropriate channels from each Dataset
         ds_list = [
-            ds.sel(channel=ed_group_chan_sel[ed_group])
-            if ed_group_chan_sel[ed_group] is not None
-            else ds
+            (
+                ds.sel(channel=ed_group_chan_sel[ed_group])
+                if ed_group_chan_sel[ed_group] is not None
+                else ds
+            )
             for ds in all_chan_ds_list
         ]
 

echopype/echodata/sensor_ep_version_mapping/v05x_to_v06x.py

@@ -262,21 +262,21 @@ def _change_beam_var_names(ed_obj, sensor):
 
     if sensor in ["EK60", "EK80"]:
         for beam_group in ed_obj._tree["Sonar"].children.values():
-            beam_group.ds.angle_sensitivity_alongship.attrs[
-                "long_name"
-            ] = "alongship angle sensitivity of the transducer"
+            beam_group.ds.angle_sensitivity_alongship.attrs["long_name"] = (
+                "alongship angle sensitivity of the transducer"
+            )
 
-            beam_group.ds.angle_sensitivity_athwartship.attrs[
-                "long_name"
-            ] = "athwartship angle sensitivity of the transducer"
+            beam_group.ds.angle_sensitivity_athwartship.attrs["long_name"] = (
+                "athwartship angle sensitivity of the transducer"
+            )
 
-            beam_group.ds.angle_offset_alongship.attrs[
-                "long_name"
-            ] = "electrical alongship angle offset of the transducer"
+            beam_group.ds.angle_offset_alongship.attrs["long_name"] = (
+                "electrical alongship angle offset of the transducer"
+            )
 
-            beam_group.ds.angle_offset_athwartship.attrs[
-                "long_name"
-            ] = "electrical athwartship angle offset of the transducer"
+            beam_group.ds.angle_offset_athwartship.attrs["long_name"] = (
+                "electrical athwartship angle offset of the transducer"
+            )
 
 
 def _add_comment_to_beam_vars(ed_obj, sensor):
@@ -333,23 +333,23 @@ def _add_comment_to_beam_vars(ed_obj, sensor):
                 "angle corresponds to the major angle in SONAR-netCDF4 vers 2. "
             )
 
-            beam_group.ds.angle_sensitivity_alongship.attrs[
-                "comment"
-            ] = beam_group.ds.angle_offset_alongship.attrs["comment"]
+            beam_group.ds.angle_sensitivity_alongship.attrs["comment"] = (
+                beam_group.ds.angle_offset_alongship.attrs["comment"]
+            )
 
-            beam_group.ds.angle_sensitivity_athwartship.attrs[
-                "comment"
-            ] = beam_group.ds.angle_offset_athwartship.attrs["comment"]
+            beam_group.ds.angle_sensitivity_athwartship.attrs["comment"] = (
+                beam_group.ds.angle_offset_athwartship.attrs["comment"]
+            )
 
             if "angle_alongship" in beam_group.ds:
-                beam_group.ds.angle_alongship.attrs[
-                    "comment"
-                ] = beam_group.ds.angle_offset_alongship.attrs["comment"]
+                beam_group.ds.angle_alongship.attrs["comment"] = (
+                    beam_group.ds.angle_offset_alongship.attrs["comment"]
+                )
 
             if "angle_athwartship" in beam_group.ds:
-                beam_group.ds.angle_athwartship.attrs[
-                    "comment"
-                ] = beam_group.ds.angle_offset_athwartship.attrs["comment"]
+                beam_group.ds.angle_athwartship.attrs["comment"] = (
+                    beam_group.ds.angle_offset_athwartship.attrs["comment"]
+                )
 
 
 def _beam_groups_to_convention(ed_obj, set_grp_cls):

echopype/echodata/simrad.py

@@ -1,6 +1,7 @@
 """
 Contains functions that are specific to Simrad echo sounders
 """
+
 from typing import Optional, Tuple
 
 import numpy as np

echopype/metrics/__init__.py

@@ -1,6 +1,7 @@
 """
 Functions to compute summary statistics from echo data.
 """
+
 from .summary_statistics import abundance, aggregation, center_of_mass, dispersion, evenness
 
 __all__ = [

echopype/utils/compute.py

@@ -3,6 +3,7 @@
 Module containing various helper functions
 for performing computations within echopype.
 """
+
 from typing import Union
 
 import dask.array

echopype/utils/io.py

@@ -1,6 +1,7 @@
 """
 echopype utilities for file handling
 """
+
 import os
 import pathlib
 import platform

echopype/utils/uwa.py

@@ -1,6 +1,7 @@
 """
 Utilities for calculating seawater acoustic properties.
 """
+
 import numpy as np
 
 
@@ -36,12 +37,7 @@ def calc_sound_speed(temperature=27, salinity=35, pressure=10, formula_source="M
     temperature −2 to 30 °C, salinity 30 to 40 ppt, and depth 0 to 8000 m.
     """
     if formula_source == "Mackenzie":
-        ss = (
-            1448.96
-            + 4.591 * temperature
-            - 5.304e-2 * temperature**2
-            + 2.374e-4 * temperature**3
-        )
+        ss = 1448.96 + 4.591 * temperature - 5.304e-2 * temperature**2 + 2.374e-4 * temperature**3
         ss += 1.340 * (salinity - 35) + 1.630e-2 * pressure + 1.675e-7 * pressure**2
         ss += -1.025e-2 * temperature * (salinity - 35) - 7.139e-13 * temperature * pressure**3
     elif formula_source == "AZFP":