Fix linting issues

.gitignore

@@ -64,6 +64,8 @@ docs/_build
 .build
 .ve
 .env
+.venv
+.vscode
 .cache
 .pytest
 .bootstrap

pyproject.toml

@@ -184,13 +184,14 @@ max-complexity = 10
 py_version=39
 force_single_line = true
 known_first_party = ["dtscalibration"]
-skip = [".gitignore", ".tox", "docs"]
+skip = [".gitignore", ".tox", "docs", ".venv"]
 src_paths = ["src", "tests"]
 line_length = 120
 
 [tool.black]
 line-length = 88
 target-version = ['py39', 'py310', 'py311']
+extend-exclude = ".venv"
 
 [tool.mypy]
 ignore_missing_imports = true  # Preferably false, but matplotlib, scipy and statsmodels are missing typing stubs

src/dtscalibration/calibration/section_utils.py

@@ -1,7 +1,10 @@
+from typing import Dict
+from typing import List
+
+import numpy as np
 import xarray as xr
-from typing import Dict, List
 import yaml
-import numpy as np
+
 from dtscalibration.datastore_utils import ufunc_per_section_helper
 
 
@@ -20,9 +23,7 @@ def validate_sections(ds: xr.Dataset, sections: Dict[str, List[slice]]):
 
     # be less restrictive for capitalized labels
     # find lower cases label
-    labels = np.reshape(
-        [[s.lower(), s] for s in ds.data_vars.keys()], (-1,)
-    ).tolist()
+    labels = np.reshape([[s.lower(), s] for s in ds.data_vars.keys()], (-1,)).tolist()
 
     sections_fix = dict()
     for k, v in sections.items():
@@ -44,8 +45,7 @@ def validate_sections(ds: xr.Dataset, sections: Dict[str, List[slice]]):
 
     for k, v in sections_fix.items():
         assert isinstance(v, (list, tuple)), (
-            "The values of the sections-dictionary "
-            "should be lists of slice objects."
+            "The values of the sections-dictionary " "should be lists of slice objects."
         )
 
         for vi in v:

src/dtscalibration/datastore.py

@@ -1,7 +1,5 @@
 import os
 import warnings
-from typing import Dict
-from typing import List
 
 import dask
 import dask.array as da
@@ -17,13 +15,14 @@
 from dtscalibration.calibrate_utils import calibration_single_ended_helper
 from dtscalibration.calibrate_utils import match_sections
 from dtscalibration.calibrate_utils import parse_st_var
+from dtscalibration.calibration.section_utils import set_sections
+from dtscalibration.calibration.section_utils import validate_sections
 from dtscalibration.datastore_utils import ParameterIndexDoubleEnded
 from dtscalibration.datastore_utils import ParameterIndexSingleEnded
 from dtscalibration.datastore_utils import check_deprecated_kwargs
 from dtscalibration.datastore_utils import check_timestep_allclose
 from dtscalibration.datastore_utils import ufunc_per_section_helper
 from dtscalibration.io_utils import _dim_attrs
-from dtscalibration.calibration.section_utils import set_sections, validate_sections
 
 dtsattr_namelist = ["double_ended_flag"]
 dim_attrs = {k: v for kl, v in _dim_attrs.items() for k in kl}

tests/test_datastore.py

@@ -17,10 +17,10 @@
 from dtscalibration import read_sensornet_files
 from dtscalibration import read_sensortran_files
 from dtscalibration import read_silixa_files
+from dtscalibration.calibration.section_utils import set_sections
 from dtscalibration.datastore_utils import merge_double_ended
 from dtscalibration.datastore_utils import shift_double_ended
 from dtscalibration.datastore_utils import suggest_cable_shift_double_ended
-from dtscalibration.calibration.section_utils import set_sections
 
 np.random.seed(0)
 
@@ -168,8 +168,11 @@ def test_sections_property():
     ds = set_sections(
         ds,
         {
-            "probe1Temperature": [slice(np.array(0.0), np.array(17.0)), slice(70.0, 80.0)]
-        }
+            "probe1Temperature": [
+                slice(np.array(0.0), np.array(17.0)),
+                slice(70.0, 80.0),
+            ]
+        },
     )
 
 

tests/test_dtscalibration.py

@@ -10,7 +10,6 @@
 from dtscalibration import read_silixa_files
 from dtscalibration.calibrate_utils import wls_sparse
 from dtscalibration.calibrate_utils import wls_stats
-from dtscalibration.calibration.section_utils import set_sections
 
 np.random.seed(0)