From 9f17f6758fd898dc211518a9a5ab3a7d106bab37 Mon Sep 17 00:00:00 2001
From: David Schaefer <david.schaefer@ufz.de>
Date: Mon, 6 May 2024 10:00:02 +0200
Subject: [PATCH] fix linting issues from ruff
---
saqc/__init__.py | 21 +++++++++++++++++---
saqc/__main__.py | 8 ++++----
saqc/core/__init__.py | 13 +++++++++++-
saqc/core/core.py | 4 ++--
saqc/core/flags.py | 3 +--
saqc/core/translation/__init__.py | 10 ++++++++++
saqc/core/translation/dmpscheme.py | 2 --
saqc/funcs/changepoints.py | 4 +---
saqc/funcs/flagtools.py | 3 +--
saqc/funcs/generic.py | 2 +-
saqc/funcs/interpolation.py | 3 ---
saqc/funcs/noise.py | 8 +-------
saqc/funcs/outliers.py | 3 +--
saqc/funcs/resampling.py | 10 ++++------
saqc/funcs/residuals.py | 2 +-
saqc/funcs/rolling.py | 7 +------
saqc/funcs/scores.py | 5 ++---
saqc/funcs/tools.py | 1 -
saqc/funcs/transformation.py | 2 +-
saqc/lib/plotting.py | 1 -
saqc/lib/tools.py | 2 +-
saqc/lib/ts_operators.py | 3 ---
saqc/lib/types.py | 10 +---------
saqc/parsing/environ.py | 2 --
tests/core/test_core.py | 3 ++-
tests/funcs/test_constants_detection.py | 4 ++--
tests/funcs/test_functions.py | 5 ++---
tests/funcs/test_generic_config_functions.py | 5 +++--
tests/funcs/test_outlier_detection.py | 4 ++--
tests/funcs/test_pattern_rec.py | 4 ++--
tests/funcs/test_proc_functions.py | 4 ++--
tests/funcs/test_resampling.py | 2 +-
tests/fuzzy/lib.py | 4 ++--
33 files changed, 81 insertions(+), 83 deletions(-)
diff --git a/saqc/__init__.py b/saqc/__init__.py
index a801471cf..254c45622 100644
--- a/saqc/__init__.py
+++ b/saqc/__init__.py
@@ -7,8 +7,25 @@
"""The System for automated Quality Control package."""
+__all__ = [
+ "BAD",
+ "DOUBTFUL",
+ "GOOD",
+ "UNFLAGGED",
+ "FILTER_ALL",
+ "FILTER_NONE",
+ "Flags",
+ "DictOfSeries",
+ "SaQC",
+ "DmpScheme",
+ "FloatScheme",
+ "PositionalScheme",
+ "SimpleScheme",
+ "AnnotatedFloatScheme",
+ "fromConfig",
+]
+
from saqc.constants import BAD, DOUBTFUL, FILTER_ALL, FILTER_NONE, GOOD, UNFLAGGED
-from saqc.exceptions import ParsingError
from saqc.core import Flags, DictOfSeries, SaQC
from saqc.core.translation import (
DmpScheme,
@@ -18,8 +35,6 @@ from saqc.core.translation import (
AnnotatedFloatScheme,
)
from saqc.parsing.reader import fromConfig
-from saqc.version import __version__
-
from . import _version
__version__ = _version.get_versions()["version"]
diff --git a/saqc/__main__.py b/saqc/__main__.py
index d5da00363..be2263500 100644
--- a/saqc/__main__.py
+++ b/saqc/__main__.py
@@ -136,10 +136,10 @@ def main(
config = str(config)
cr = _ConfigReader(data=data, scheme=scheme)
if config.endswith("json"):
- f = None
- if json_field is not None:
- f = lambda j: j[str(json_field)]
- cr = cr.readJson(config, unpack=f)
+ cr = cr.readJson(
+ config,
+ unpack=lambda j: j[str(json_field)] if json_field is not None else None,
+ )
else:
cr = cr.readCsv(config)
diff --git a/saqc/core/__init__.py b/saqc/core/__init__.py
index 1fbe7e27c..bd5ac9dc6 100644
--- a/saqc/core/__init__.py
+++ b/saqc/core/__init__.py
@@ -4,8 +4,19 @@
# -*- coding: utf-8 -*-
# isort: skip_file
+
+__all__ = [
+ "DictOfSeries",
+ "History",
+ "Flags",
+ "SaQC",
+ "flagging",
+ "processing",
+ "register",
+]
+
from saqc.core.frame import DictOfSeries
from saqc.core.history import History
-from saqc.core.flags import Flags, initFlagsLike
+from saqc.core.flags import Flags
from saqc.core.register import flagging, processing, register
from saqc.core.core import SaQC
diff --git a/saqc/core/core.py b/saqc/core/core.py
index c669da567..952b2ed8c 100644
--- a/saqc/core/core.py
+++ b/saqc/core/core.py
@@ -12,7 +12,7 @@ import warnings
from copy import copy as shallowcopy
from copy import deepcopy
from functools import partial
-from typing import Any, Hashable, Iterable, MutableMapping
+from typing import Any, Hashable, Iterable
import numpy as np
import pandas as pd
@@ -332,7 +332,7 @@ class SaQC(FunctionsMixin):
def _castData(self, data) -> DictOfSeries:
if isinstance(data, pd.Series):
if not isinstance(data.name, str):
- raise ValueError(f"Cannot init from unnamed pd.Series")
+ raise ValueError("Cannot init from unnamed pd.Series")
data = data.to_frame()
if isinstance(data, pd.DataFrame):
for idx in [data.index, data.columns]:
diff --git a/saqc/core/flags.py b/saqc/core/flags.py
index e597e0ee1..fc1684193 100644
--- a/saqc/core/flags.py
+++ b/saqc/core/flags.py
@@ -7,7 +7,6 @@
from __future__ import annotations
import typing
-import warnings
from typing import DefaultDict, Dict, Iterable, Mapping, Tuple, Type, Union, overload
import numpy as np
@@ -243,7 +242,7 @@ class Flags:
if history.empty:
return history
- errm = f"History "
+ errm = "History "
if colname:
errm += f"of column {colname} "
diff --git a/saqc/core/translation/__init__.py b/saqc/core/translation/__init__.py
index 7549e43c5..1aaca2982 100644
--- a/saqc/core/translation/__init__.py
+++ b/saqc/core/translation/__init__.py
@@ -5,6 +5,16 @@
# SPDX-License-Identifier: GPL-3.0-or-later
# -*- coding: utf-8 -*-
+__all__ = [
+ "MappingScheme",
+ "TranslationScheme",
+ "DmpScheme",
+ "AnnotatedFloatScheme",
+ "FloatScheme",
+ "PositionalScheme",
+ "SimpleScheme",
+]
+
from saqc.core.translation.basescheme import MappingScheme, TranslationScheme
from saqc.core.translation.dmpscheme import DmpScheme
from saqc.core.translation.floatscheme import AnnotatedFloatScheme, FloatScheme
diff --git a/saqc/core/translation/dmpscheme.py b/saqc/core/translation/dmpscheme.py
index fb68713d5..f80267c93 100644
--- a/saqc/core/translation/dmpscheme.py
+++ b/saqc/core/translation/dmpscheme.py
@@ -9,7 +9,6 @@
from __future__ import annotations
import json
-from functools import reduce
import numpy as np
import pandas as pd
@@ -18,7 +17,6 @@ from saqc import BAD, DOUBTFUL, GOOD, UNFLAGGED
from saqc.core import Flags, History
from saqc.core.frame import DictOfSeries
from saqc.core.translation.basescheme import BackwardMap, ForwardMap, MappingScheme
-from saqc.lib.tools import getUnionIndex
_QUALITY_CAUSES = [
"",
diff --git a/saqc/funcs/changepoints.py b/saqc/funcs/changepoints.py
index ff706f691..b0ce725b3 100644
--- a/saqc/funcs/changepoints.py
+++ b/saqc/funcs/changepoints.py
@@ -13,13 +13,11 @@ import numpy as np
import pandas as pd
from saqc import BAD, UNFLAGGED
-from saqc.core import DictOfSeries, Flags, flagging, register
+from saqc.core import flagging, register
from saqc.lib.checking import (
- isInBounds,
validateCallable,
validateChoice,
validateMinPeriods,
- validateValueBounds,
validateWindow,
)
diff --git a/saqc/funcs/flagtools.py b/saqc/funcs/flagtools.py
index d7ea5015a..f57822e35 100644
--- a/saqc/funcs/flagtools.py
+++ b/saqc/funcs/flagtools.py
@@ -17,7 +17,6 @@ from typing_extensions import Literal
from saqc import BAD, FILTER_ALL, UNFLAGGED
from saqc.core import DictOfSeries, flagging, register
-from saqc.core.flags import Flags
from saqc.core.history import History
from saqc.lib.checking import validateChoice, validateWindow
from saqc.lib.tools import (
@@ -446,7 +445,7 @@ class FlagtoolsMixin:
fields, targets, broadcasting = multivariateParameters(field, target)
meta = {
- "func": f"transferFlags",
+ "func": "transferFlags",
"args": (),
"kwargs": {
"field": field,
diff --git a/saqc/funcs/generic.py b/saqc/funcs/generic.py
index ad8b20067..4973883db 100644
--- a/saqc/funcs/generic.py
+++ b/saqc/funcs/generic.py
@@ -267,7 +267,7 @@ class GenericMixin:
)
if not result.empty and not isAllBoolean(result):
- raise TypeError(f"generic expression does not return a boolean array")
+ raise TypeError("generic expression does not return a boolean array")
# update flags & data
for i, col in enumerate(targets):
diff --git a/saqc/funcs/interpolation.py b/saqc/funcs/interpolation.py
index 481c87d72..65501df34 100644
--- a/saqc/funcs/interpolation.py
+++ b/saqc/funcs/interpolation.py
@@ -7,7 +7,6 @@
# -*- coding: utf-8 -*-
from __future__ import annotations
-import warnings
from typing import TYPE_CHECKING, Callable, Tuple, Union
import numpy as np
@@ -18,8 +17,6 @@ from saqc import UNFLAGGED
from saqc.core import register
from saqc.core.history import History
from saqc.lib.checking import (
- isValidChoice,
- validateCallable,
validateChoice,
validateFuncSelection,
validateMinPeriods,
diff --git a/saqc/funcs/noise.py b/saqc/funcs/noise.py
index 7e18add8f..db60bf214 100644
--- a/saqc/funcs/noise.py
+++ b/saqc/funcs/noise.py
@@ -13,16 +13,10 @@ from typing import TYPE_CHECKING, Callable, Literal
import numpy as np
import pandas as pd
-from scipy.stats import median_abs_deviation
from saqc.constants import BAD
from saqc.core.register import flagging
-from saqc.lib.checking import (
- isCallable,
- validateFuncSelection,
- validateMinPeriods,
- validateWindow,
-)
+from saqc.lib.checking import validateFuncSelection, validateMinPeriods, validateWindow
from saqc.lib.tools import isunflagged, statPass
from saqc.parsing.environ import ENV_OPERATORS
diff --git a/saqc/funcs/outliers.py b/saqc/funcs/outliers.py
index 5ea2e2dda..ab8782402 100644
--- a/saqc/funcs/outliers.py
+++ b/saqc/funcs/outliers.py
@@ -10,7 +10,7 @@ from __future__ import annotations
import uuid
import warnings
-from typing import TYPE_CHECKING, Callable, List, Optional, Sequence, Tuple
+from typing import TYPE_CHECKING, Callable, Sequence, Tuple
import numpy as np
import numpy.polynomial.polynomial as poly
@@ -27,7 +27,6 @@ from saqc.lib.checking import (
validateChoice,
validateFraction,
validateFrequency,
- validateFuncSelection,
validateMinPeriods,
validateValueBounds,
validateWindow,
diff --git a/saqc/funcs/resampling.py b/saqc/funcs/resampling.py
index 168d16fc0..fb803e26c 100644
--- a/saqc/funcs/resampling.py
+++ b/saqc/funcs/resampling.py
@@ -7,11 +7,10 @@
# -*- coding: utf-8 -*-
from __future__ import annotations
-import re
import typing
import uuid
import warnings
-from typing import TYPE_CHECKING, Callable, Union
+from typing import TYPE_CHECKING, Callable
import numpy as np
import pandas as pd
@@ -21,10 +20,9 @@ import saqc.constants
from saqc.constants import UNFLAGGED
from saqc.core import register
from saqc.core.history import History
-from saqc.funcs.interpolation import DATA_REINDEXER
from saqc.lib.checking import validateChoice, validateFuncSelection
from saqc.lib.docs import DOC_TEMPLATES
-from saqc.lib.tools import filterKwargs, getFreqDelta
+from saqc.lib.tools import getFreqDelta
from saqc.lib.ts_operators import isValid
if TYPE_CHECKING:
@@ -288,10 +286,10 @@ class ResamplingMixin:
done = True
if len(stack) == 0:
- raise ValueError(f"Could not find no last reindexing to invert")
+ raise ValueError("Could not find no last reindexing to invert")
reindex_method = METHODINVERTS.get(stack[-1], False)
- if reindex_method == False:
+ if reindex_method is False:
raise ValueError(f"cant invert {stack[-1]}")
return reindex_method
diff --git a/saqc/funcs/residuals.py b/saqc/funcs/residuals.py
index 5ef4a6a40..0ba870798 100644
--- a/saqc/funcs/residuals.py
+++ b/saqc/funcs/residuals.py
@@ -7,7 +7,7 @@
# -*- coding: utf-8 -*-
from __future__ import annotations
-from typing import TYPE_CHECKING, Callable, Optional, Union
+from typing import TYPE_CHECKING, Callable
import numpy as np
import pandas as pd
diff --git a/saqc/funcs/rolling.py b/saqc/funcs/rolling.py
index dfcdfd23c..77a9d9985 100644
--- a/saqc/funcs/rolling.py
+++ b/saqc/funcs/rolling.py
@@ -14,12 +14,7 @@ import pandas as pd
import saqc
from saqc.core import DictOfSeries, Flags, register
-from saqc.lib.checking import (
- validateCallable,
- validateFuncSelection,
- validateMinPeriods,
- validateWindow,
-)
+from saqc.lib.checking import validateFuncSelection, validateMinPeriods, validateWindow
from saqc.lib.tools import getFreqDelta
if TYPE_CHECKING:
diff --git a/saqc/funcs/scores.py b/saqc/funcs/scores.py
index f72e2362f..aacc76eb3 100644
--- a/saqc/funcs/scores.py
+++ b/saqc/funcs/scores.py
@@ -7,14 +7,13 @@
# -*- coding: utf-8 -*-
from __future__ import annotations
-from typing import TYPE_CHECKING, Callable, Optional, Sequence, Tuple, Union
+from typing import TYPE_CHECKING, Callable, Optional, Sequence, Tuple
import numpy as np
import pandas as pd
from sklearn.neighbors import LocalOutlierFactor
from typing_extensions import Literal
-from saqc import UNFLAGGED
from saqc.core import register
from saqc.lib.checking import (
validateChoice,
@@ -25,7 +24,7 @@ from saqc.lib.checking import (
from saqc.lib.docs import DOC_TEMPLATES
from saqc.lib.tools import getApply, toSequence
from saqc.lib.ts_operators import kNN
-from saqc.parsing.environ import ENV_OPERATORS, ENV_TRAFOS
+from saqc.parsing.environ import ENV_OPERATORS
if TYPE_CHECKING:
from saqc import SaQC
diff --git a/saqc/funcs/tools.py b/saqc/funcs/tools.py
index 453d28d88..5038df629 100644
--- a/saqc/funcs/tools.py
+++ b/saqc/funcs/tools.py
@@ -9,7 +9,6 @@ from __future__ import annotations
import pickle
import tkinter as tk
-import warnings
from typing import TYPE_CHECKING
import matplotlib as mpl
diff --git a/saqc/funcs/transformation.py b/saqc/funcs/transformation.py
index 2b2d6db44..cfc4d226a 100644
--- a/saqc/funcs/transformation.py
+++ b/saqc/funcs/transformation.py
@@ -7,7 +7,7 @@
# -*- coding: utf-8 -*-
from __future__ import annotations
-from typing import TYPE_CHECKING, Callable, Optional, Union
+from typing import TYPE_CHECKING, Callable
import numpy as np
import pandas as pd
diff --git a/saqc/lib/plotting.py b/saqc/lib/plotting.py
index 5dd0e944b..41a5b5a53 100644
--- a/saqc/lib/plotting.py
+++ b/saqc/lib/plotting.py
@@ -9,7 +9,6 @@
from __future__ import annotations
import itertools
-from collections import OrderedDict
import matplotlib as mpl
import matplotlib.pyplot as plt
diff --git a/saqc/lib/tools.py b/saqc/lib/tools.py
index 72c201c8f..7fd671036 100644
--- a/saqc/lib/tools.py
+++ b/saqc/lib/tools.py
@@ -442,7 +442,7 @@ def getApply(in_obj, apply_obj, attr_access="__name__", attr_or="apply") -> pd.S
try:
# let's try to run it somewhat optimized
out = getattr(in_obj, attr_or)(apply_obj, raw=True)
- except:
+ except Exception:
# did't work out, fallback
out = getattr(in_obj, attr_or)(apply_obj)
diff --git a/saqc/lib/ts_operators.py b/saqc/lib/ts_operators.py
index c983a314f..4b0c4ad44 100644
--- a/saqc/lib/ts_operators.py
+++ b/saqc/lib/ts_operators.py
@@ -9,10 +9,7 @@
"""
The module gathers all kinds of timeseries tranformations.
"""
-import re
import sys
-import warnings
-from typing import Literal, Union
import numpy as np
import numpy.polynomial.polynomial as poly
diff --git a/saqc/lib/types.py b/saqc/lib/types.py
index 8b5b6e5fa..c5e784527 100644
--- a/saqc/lib/types.py
+++ b/saqc/lib/types.py
@@ -8,20 +8,12 @@
from __future__ import annotations
import abc
-from typing import Any, Dict, TypeVar, Union
+from typing import TypeVar, Union
import numpy as np
import pandas as pd
from typing_extensions import Protocol
-__all__ = [
- "T",
- "ArrayLike",
- "CurveFitter",
- "ExternalFlag",
- "OptionalNone",
-]
-
T = TypeVar("T")
ArrayLike = TypeVar("ArrayLike", np.ndarray, pd.Series, pd.DataFrame)
diff --git a/saqc/parsing/environ.py b/saqc/parsing/environ.py
index a3095b363..d494ed666 100644
--- a/saqc/parsing/environ.py
+++ b/saqc/parsing/environ.py
@@ -7,8 +7,6 @@
# -*- coding: utf-8 -*-
import numpy as np
-import pandas as pd
-import scipy.stats as st
import saqc.lib.ts_operators as ts_ops
from saqc import BAD, DOUBTFUL, FILTER_ALL, FILTER_NONE, GOOD, UNFLAGGED
diff --git a/tests/core/test_core.py b/tests/core/test_core.py
index 4109eb6e4..b5062f33f 100644
--- a/tests/core/test_core.py
+++ b/tests/core/test_core.py
@@ -13,7 +13,8 @@ import pandas as pd
import pytest
from saqc import BAD, FILTER_ALL, FILTER_NONE, UNFLAGGED, SaQC
-from saqc.core import DictOfSeries, Flags, flagging, initFlagsLike, processing, register
+from saqc.core import DictOfSeries, Flags, flagging, processing, register
+from saqc.core.flags import initFlagsLike
from saqc.lib.types import OptionalNone
from tests.common import initData
diff --git a/tests/funcs/test_constants_detection.py b/tests/funcs/test_constants_detection.py
index 8cbf3290d..a6ec79792 100644
--- a/tests/funcs/test_constants_detection.py
+++ b/tests/funcs/test_constants_detection.py
@@ -9,8 +9,8 @@
import numpy as np
import pytest
-from saqc import BAD, UNFLAGGED
-from saqc.core import SaQC, initFlagsLike
+from saqc import BAD, UNFLAGGED, SaQC
+from saqc.core.flags import initFlagsLike
from tests.common import initData
diff --git a/tests/funcs/test_functions.py b/tests/funcs/test_functions.py
index d956e39b1..8a3e14a53 100644
--- a/tests/funcs/test_functions.py
+++ b/tests/funcs/test_functions.py
@@ -10,9 +10,8 @@ import numpy as np
import pandas as pd
import pytest
-import saqc
-from saqc import BAD, DOUBTFUL, UNFLAGGED, SaQC
-from saqc.core import DictOfSeries, initFlagsLike
+from saqc import BAD, DOUBTFUL, UNFLAGGED, DictOfSeries, SaQC
+from saqc.core.flags import initFlagsLike
from tests.common import initData
from tests.fixtures import char_dict, course_1 # noqa, todo: fix fixtures
diff --git a/tests/funcs/test_generic_config_functions.py b/tests/funcs/test_generic_config_functions.py
index f19342a39..d9af808da 100644
--- a/tests/funcs/test_generic_config_functions.py
+++ b/tests/funcs/test_generic_config_functions.py
@@ -12,8 +12,9 @@ import numpy as np
import pandas as pd
import pytest
-from saqc import BAD, UNFLAGGED, SaQC
-from saqc.core import DictOfSeries, Flags, initFlagsLike, register
+from saqc import BAD, UNFLAGGED, DictOfSeries, Flags, SaQC
+from saqc.core import register
+from saqc.core.flags import initFlagsLike
from saqc.funcs.generic import _execGeneric
from saqc.parsing.reader import _ConfigReader
from saqc.parsing.visitor import ConfigFunctionParser
diff --git a/tests/funcs/test_outlier_detection.py b/tests/funcs/test_outlier_detection.py
index 81bd0ec28..61953bcd0 100644
--- a/tests/funcs/test_outlier_detection.py
+++ b/tests/funcs/test_outlier_detection.py
@@ -13,8 +13,8 @@ import pandas as pd
import pytest
import saqc
-from saqc import BAD, UNFLAGGED
-from saqc.core import DictOfSeries, SaQC, initFlagsLike
+from saqc import BAD, UNFLAGGED, DictOfSeries, SaQC
+from saqc.core.flags import initFlagsLike
from tests.fixtures import char_dict, course_1, course_2, course_3, course_4
diff --git a/tests/funcs/test_pattern_rec.py b/tests/funcs/test_pattern_rec.py
index 6b96ee0ca..b2be3a634 100644
--- a/tests/funcs/test_pattern_rec.py
+++ b/tests/funcs/test_pattern_rec.py
@@ -9,8 +9,8 @@
import pandas as pd
import pytest
-from saqc import BAD, UNFLAGGED, SaQC
-from saqc.core import DictOfSeries, initFlagsLike
+from saqc import BAD, UNFLAGGED, DictOfSeries, SaQC
+from saqc.core.flags import initFlagsLike
from tests.common import initData
diff --git a/tests/funcs/test_proc_functions.py b/tests/funcs/test_proc_functions.py
index df960969b..b2f097060 100644
--- a/tests/funcs/test_proc_functions.py
+++ b/tests/funcs/test_proc_functions.py
@@ -14,8 +14,8 @@ import pandas as pd
import pytest
import saqc
-from saqc import UNFLAGGED, SaQC
-from saqc.core import DictOfSeries, initFlagsLike
+from saqc import UNFLAGGED, DictOfSeries, SaQC
+from saqc.core.flags import initFlagsLike
from saqc.lib.ts_operators import linearInterpolation, polynomialInterpolation
from tests.fixtures import char_dict, course_3, course_5 # noqa, todo: fix fixtures
diff --git a/tests/funcs/test_resampling.py b/tests/funcs/test_resampling.py
index b765c074f..f077c283b 100644
--- a/tests/funcs/test_resampling.py
+++ b/tests/funcs/test_resampling.py
@@ -14,7 +14,7 @@ import pandas as pd
import pytest
from saqc import SaQC
-from saqc.core import initFlagsLike
+from saqc.core.flags import initFlagsLike
from saqc.funcs.resampling import (
_aggregationGrouper,
_constructAggregationReindexer,
diff --git a/tests/fuzzy/lib.py b/tests/fuzzy/lib.py
index a70a159f3..e0b30cac9 100644
--- a/tests/fuzzy/lib.py
+++ b/tests/fuzzy/lib.py
@@ -23,8 +23,8 @@ from hypothesis.strategies import (
)
from hypothesis.strategies._internal.types import _global_type_lookup
-from saqc import BAD
-from saqc.core import DictOfSeries, initFlagsLike
+from saqc import BAD, DictOfSeries
+from saqc.core.flags import initFlagsLike
from saqc.core.register import FUNC_MAP
MAX_EXAMPLES = 50
--
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