Compare revisions

Peter Lünenschloß · Peter Lünenschloß · Peter Lünenschloß · Peter Lünenschloß · Peter Lünenschloß · Peter Lünenschloß
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,11 +13,16 @@ This changelog starts with version 2.0.0. Basically all parts of the system, inc
 [List of commits](https://git.ufz.de/rdm-software/saqc/-/compare/v2.0.1...develop)

 ### Added
+- generic documentation module `docurator.py` added to `lib`
 ### Changed
+- documentation pipeline changed to base on methods decorators
 - `flagOffsets` parameters `thresh` and `thresh_relative` now both are optional
+- corrected false notion of *residual* concept (old notion: *residue* got replaced by *residual*)
 ### Removed
 ### Fixed
 - `flagOffset` bug with zero-valued threshold
+- `flagCrossStatistics` bug with unaligned input variables
+- `plot` fixed data loss when using *dfilter* kwarg

 ## [2.0.1](https://git.ufz.de/rdm-software/saqc/-/tags/v2.0.1) - 2021-12-20
 [List of commits](https://git.ufz.de/rdm-software/saqc/-/compare/v2.0.0...v2.0.1)

--- a/requirements.txt
+++ b/requirements.txt
@@ -6,8 +6,8 @@ Click==8.0.3
 dtw==1.4.0
 hypothesis==6.34.1
 matplotlib==3.5.1
-numba==0.54.1
-numpy==1.20.3
+numba>=0.55.0
+numpy>=1.21.5
 outlier-utils==0.0.3
 pyarrow==6.0.1
 pandas==1.3.5

--- a/saqc/core/modules/__init__.py
+++ b/saqc/core/modules/__init__.py
@@ -17,7 +17,7 @@ from saqc.core.modules.interpolation import Interpolation
 from saqc.core.modules.outliers import Outliers
 from saqc.core.modules.pattern import Pattern
 from saqc.core.modules.resampling import Resampling
-from saqc.core.modules.residues import Residues
+from saqc.core.modules.residuals import Residuals
 from saqc.core.modules.rolling import Rolling
 from saqc.core.modules.scores import Scores
 from saqc.core.modules.tools import Tools
@@ -38,7 +38,7 @@ class FunctionsMixin(
    Outliers,
    Pattern,
    Resampling,
-    Residues,
+    Residuals,
    Rolling,
    Scores,
    Tools,

--- a/saqc/core/modules/breaks.py
+++ b/saqc/core/modules/breaks.py
@@ -9,14 +9,18 @@ from __future__ import annotations

 from saqc.constants import BAD, FILTER_ALL
 import saqc
+from saqc.lib.docurator import doc
+import saqc.funcs


 class Breaks:
+    @doc(saqc.funcs.breaks.flagMissing.__doc__)
    def flagMissing(
        self, field: str, flag: float = BAD, dfilter: float = FILTER_ALL, **kwargs
    ) -> saqc.SaQC:
        return self._defer("flagMissing", locals())

+    @doc(saqc.funcs.breaks.flagIsolated.__doc__)
    def flagIsolated(
        self,
        field: str,
@@ -27,6 +31,7 @@ class Breaks:
    ) -> saqc.SaQC:
        return self._defer("flagIsolated", locals())

+    @doc(saqc.funcs.breaks.flagJumps.__doc__)
    def flagJumps(
        self,
        field: str,

--- a/saqc/core/modules/changepoints.py
+++ b/saqc/core/modules/changepoints.py
@@ -14,9 +14,12 @@ from typing_extensions import Literal

 from saqc.constants import BAD
 import saqc
+from saqc.lib.docurator import doc
+import saqc.funcs


 class ChangePoints:
+    @doc(saqc.funcs.changepoints.flagChangePoints.__doc__)
    def flagChangePoints(
        self,
        field: str,
@@ -32,6 +35,7 @@ class ChangePoints:
    ) -> saqc.SaQC:
        return self._defer("flagChangePoints", locals())

+    @doc(saqc.funcs.changepoints.assignChangePointCluster.__doc__)
    def assignChangePointCluster(
        self,
        field: str,

--- a/saqc/core/modules/constants.py
+++ b/saqc/core/modules/constants.py
@@ -9,9 +9,12 @@ from __future__ import annotations

 from saqc.constants import BAD
 import saqc
+from saqc.lib.docurator import doc
+import saqc.funcs


 class Constants:
+    @doc(saqc.funcs.constants.flagByVariance.__doc__)
    def flagByVariance(
        self,
        field: str,
@@ -24,6 +27,7 @@ class Constants:
    ) -> saqc.SaQC:
        return self._defer("flagByVariance", locals())

+    @doc(saqc.funcs.constants.flagConstants.__doc__)
    def flagConstants(
        self, field: str, thresh: float, window: str, flag: float = BAD, **kwargs
    ) -> saqc.SaQC:

--- a/saqc/core/modules/curvefit.py
+++ b/saqc/core/modules/curvefit.py
@@ -13,9 +13,12 @@ from typing_extensions import Literal

 from saqc.constants import BAD
 import saqc
+from saqc.lib.docurator import doc
+import saqc.funcs


 class Curvefit:
+    @doc(saqc.funcs.curvefit.fitPolynomial.__doc__)
    def fitPolynomial(
        self,
        field: str,

--- a/saqc/core/modules/drift.py
+++ b/saqc/core/modules/drift.py
@@ -17,9 +17,12 @@ from saqc.constants import BAD
 import saqc
 from saqc.funcs import LinkageString
 from saqc.lib.types import CurveFitter
+from saqc.lib.docurator import doc
+import saqc.funcs


 class Drift:
+    @doc(saqc.funcs.drift.flagDriftFromNorm.__doc__)
    def flagDriftFromNorm(
        self,
        field: Sequence[str],
@@ -36,6 +39,7 @@ class Drift:
    ) -> saqc.SaQC:
        return self._defer("flagDriftFromNorm", locals())

+    @doc(saqc.funcs.drift.flagDriftFromReference.__doc__)
    def flagDriftFromReference(
        self,
        field: Sequence[str],
@@ -51,6 +55,7 @@ class Drift:
    ) -> saqc.SaQC:
        return self._defer("flagDriftFromReference", locals())

+    @doc(saqc.funcs.drift.correctDrift.__doc__)
    def correctDrift(
        self,
        field: str,
@@ -61,6 +66,7 @@ class Drift:
    ) -> saqc.SaQC:
        return self._defer("correctDrift", locals())

+    @doc(saqc.funcs.drift.correctRegimeAnomaly.__doc__)
    def correctRegimeAnomaly(
        self,
        field: str,
@@ -72,6 +78,7 @@ class Drift:
    ) -> saqc.SaQC:
        return self._defer("correctRegimeAnomaly", locals())

+    @doc(saqc.funcs.drift.correctOffset.__doc__)
    def correctOffset(
        self,
        field: str,

--- a/saqc/core/modules/flagtools.py
+++ b/saqc/core/modules/flagtools.py
@@ -16,21 +16,28 @@ from typing_extensions import Literal

 from saqc.constants import BAD
 import saqc
+from saqc.lib.docurator import doc
+import saqc.funcs


 class FlagTools:
+    @doc(saqc.funcs.flagtools.clearFlags.__doc__)
    def clearFlags(self, field: str, **kwargs) -> saqc.SaQC:
        return self._defer("clearFlags", locals())

+    @doc(saqc.funcs.flagtools.forceFlags.__doc__)
    def forceFlags(self, field: str, flag: float = BAD, **kwargs) -> saqc.SaQC:
        return self._defer("forceFlags", locals())

+    @doc(saqc.funcs.flagtools.forceFlags.__doc__)
    def flagDummy(self, field: str, **kwargs) -> saqc.SaQC:
        return self._defer("flagDummy", locals())

+    @doc(saqc.funcs.flagtools.flagUnflagged.__doc__)
    def flagUnflagged(self, field: str, flag: float = BAD, **kwargs) -> saqc.SaQC:
        return self._defer("flagUnflagged", locals())

+    @doc(saqc.funcs.flagtools.flagManual.__doc__)
    def flagManual(
        self,
        field: str,
@@ -45,6 +52,7 @@ class FlagTools:
    ) -> saqc.SaQC:
        return self._defer("flagManual", locals())

+    @doc(saqc.funcs.flagtools.transferFlags.__doc__)
    def transferFlags(
        self,
        field: str | Sequence[str],

--- a/saqc/core/modules/generic.py
+++ b/saqc/core/modules/generic.py
@@ -12,9 +12,12 @@ from typing import Sequence, Union
 import saqc
 from saqc.constants import UNFLAGGED, BAD, FILTER_ALL
 from saqc.lib.types import GenericFunction
+from saqc.lib.docurator import doc
+import saqc.funcs


 class Generic:
+    @doc(saqc.funcs.generic.processGeneric.__doc__)
    def processGeneric(
        self,
        field: str | Sequence[str],
@@ -26,6 +29,7 @@ class Generic:
    ) -> saqc.SaQC:
        return self._defer("processGeneric", locals())

+    @doc(saqc.funcs.generic.flagGeneric.__doc__)
    def flagGeneric(
        self,
        field: Union[str, Sequence[str]],

--- a/saqc/core/modules/interpolation.py
+++ b/saqc/core/modules/interpolation.py
@@ -15,9 +15,12 @@ import pandas as pd
 from saqc.constants import UNFLAGGED
 import saqc
 from saqc.funcs.interpolation import _SUPPORTED_METHODS
+from saqc.lib.docurator import doc
+import saqc.funcs


 class Interpolation:
+    @doc(saqc.funcs.interpolation.interpolateByRolling.__doc__)
    def interpolateByRolling(
        self,
        field: str,
@@ -30,6 +33,7 @@ class Interpolation:
    ) -> saqc.SaQC:
        return self._defer("interpolateByRolling", locals())

+    @doc(saqc.funcs.interpolation.interpolateInvalid.__doc__)
    def interpolateInvalid(
        self,
        field: str,
@@ -42,6 +46,7 @@ class Interpolation:
    ) -> saqc.SaQC:
        return self._defer("interpolateInvalid", locals())

+    @doc(saqc.funcs.interpolation.interpolateIndex.__doc__)
    def interpolateIndex(
        self,
        field: str,

--- a/saqc/core/modules/noise.py
+++ b/saqc/core/modules/noise.py
@@ -13,9 +13,12 @@ from typing import Callable

 from saqc.constants import BAD
 import saqc
+from saqc.lib.docurator import doc
+import saqc.funcs


 class Noise:
+    @doc(saqc.funcs.noise.flagByStatLowPass.__doc__)
    def flagByStatLowPass(
        self,
        field: str,

--- a/saqc/core/modules/outliers.py
+++ b/saqc/core/modules/outliers.py
@@ -15,9 +15,12 @@ from typing_extensions import Literal

 from saqc.constants import BAD
 import saqc
+from saqc.lib.docurator import doc
+import saqc.funcs


 class Outliers:
+    @doc(saqc.funcs.outliers.flagByStray.__doc__)
    def flagByStray(
        self,
        field: str,
@@ -30,6 +33,7 @@ class Outliers:
    ) -> saqc.SaQC:
        return self._defer("flagByStray", locals())

+    @doc(saqc.funcs.outliers.flagMVScores.__doc__)
    def flagMVScores(
        self,
        field: Sequence[str],
@@ -49,6 +53,7 @@ class Outliers:
    ) -> saqc.SaQC:
        return self._defer("flagMVScores", locals())

+    @doc(saqc.funcs.outliers.flagRaise.__doc__)
    def flagRaise(
        self,
        field: str,
@@ -64,6 +69,7 @@ class Outliers:
    ) -> saqc.SaQC:
        return self._defer("flagRaise", locals())

+    @doc(saqc.funcs.outliers.flagMAD.__doc__)
    def flagMAD(
        self,
        field: str,
@@ -74,6 +80,7 @@ class Outliers:
    ) -> saqc.SaQC:
        return self._defer("flagMAD", locals())

+    @doc(saqc.funcs.outliers.flagOffset.__doc__)
    def flagOffset(
        self,
        field: str,
@@ -86,6 +93,7 @@ class Outliers:
    ) -> saqc.SaQC:
        return self._defer("flagOffset", locals())

+    @doc(saqc.funcs.outliers.flagByGrubbs.__doc__)
    def flagByGrubbs(
        self,
        field: str,
@@ -98,6 +106,7 @@ class Outliers:
    ) -> saqc.SaQC:
        return self._defer("flagByGrubbs", locals())

+    @doc(saqc.funcs.outliers.flagRange.__doc__)
    def flagRange(
        self,
        field: str,
@@ -108,6 +117,7 @@ class Outliers:
    ) -> saqc.SaQC:
        return self._defer("flagRange", locals())

+    @doc(saqc.funcs.outliers.flagCrossStatistics.__doc__)
    def flagCrossStatistics(
        self,
        field: Sequence[str],
@@ -116,4 +126,4 @@ class Outliers:
        flag: float = BAD,
        **kwargs,
    ) -> saqc.SaQC:
-        return self._defer("flagCrossStatistic", locals())
+        return self._defer("flagCrossStatistics", locals())
--- a/saqc/core/modules/pattern.py
+++ b/saqc/core/modules/pattern.py
@@ -9,9 +9,12 @@ from __future__ import annotations

 from saqc.constants import BAD
 import saqc
+from saqc.lib.docurator import doc
+import saqc.funcs


 class Pattern:
+    @doc(saqc.funcs.pattern.flagPatternByDTW.__doc__)
    def flagPatternByDTW(
        self,
        field,

--- a/saqc/core/modules/resampling.py
+++ b/saqc/core/modules/resampling.py
@@ -16,9 +16,12 @@ from typing_extensions import Literal
 from saqc.constants import BAD
 import saqc
 from saqc.funcs.interpolation import _SUPPORTED_METHODS
+from saqc.lib.docurator import doc
+import saqc.funcs


 class Resampling:
+    @doc(saqc.funcs.resampling.linear.__doc__)
    def linear(
        self,
        field: str,
@@ -27,6 +30,7 @@ class Resampling:
    ) -> saqc.SaQC:
        return self._defer("linear", locals())

+    @doc(saqc.funcs.resampling.interpolate.__doc__)
    def interpolate(
        self,
        field: str,
@@ -37,6 +41,7 @@ class Resampling:
    ) -> saqc.SaQC:
        return self._defer("interpolate", locals())

+    @doc(saqc.funcs.resampling.shift.__doc__)
    def shift(
        self,
        field: str,
@@ -47,6 +52,7 @@ class Resampling:
    ) -> saqc.SaQC:
        return self._defer("shift", locals())

+    @doc(saqc.funcs.resampling.resample.__doc__)
    def resample(
        self,
        field: str,
@@ -63,6 +69,7 @@ class Resampling:
    ) -> saqc.SaQC:
        return self._defer("resample", locals())

+    @doc(saqc.funcs.resampling.concatFlags.__doc__)
    def concatFlags(
        self,
        field: str,

--- a/saqc/core/modules/residues.py
+++ b/saqc/core/modules/residues.py
@@ -15,10 +15,13 @@ from typing_extensions import Literal

 from saqc.constants import BAD
 import saqc
+from saqc.lib.docurator import doc
+import saqc.funcs


-class Residues:
-    def calculatePolynomialResidues(
+class Residuals:
+    @doc(saqc.funcs.residuals.calculatePolynomialResiduals.__doc__)
+    def calculatePolynomialResiduals(
        self,
        field: str,
        window: Union[str, int],
@@ -26,9 +29,10 @@ class Residues:
        min_periods: Optional[int] = 0,
        **kwargs,
    ) -> saqc.SaQC:
-        return self._defer("calculatePolynomialResidues", locals())
+        return self._defer("calculatePolynomialResiduals", locals())

-    def calculateRollingResidues(
+    @doc(saqc.funcs.residuals.calculateRollingResiduals.__doc__)
+    def calculateRollingResiduals(
        self,
        field: str,
        window: Union[str, int],
@@ -37,4 +41,4 @@ class Residues:
        center: bool = True,
        **kwargs,
    ) -> saqc.SaQC:
-        return self._defer("calculateRollingResidues", locals())
+        return self._defer("calculateRollingResiduals", locals())
--- a/saqc/core/modules/rolling.py
+++ b/saqc/core/modules/rolling.py
@@ -12,9 +12,12 @@ import numpy as np
 import pandas as pd

 from saqc.constants import BAD
+from saqc.lib.docurator import doc
+import saqc.funcs


 class Rolling:
+    @doc(saqc.funcs.rolling.roll.__doc__)
    def roll(
        self,
        field: str,

--- a/saqc/core/modules/scores.py
+++ b/saqc/core/modules/scores.py
@@ -14,9 +14,12 @@ import pandas as pd
 from typing_extensions import Literal

 import saqc
+from saqc.lib.docurator import doc
+import saqc.funcs


 class Scores:
+    @doc(saqc.funcs.scores.assignKNNScore.__doc__)
    def assignKNNScore(
        self,
        field: Sequence[str],

--- a/saqc/core/modules/tools.py
+++ b/saqc/core/modules/tools.py
@@ -14,20 +14,26 @@ import saqc
 import numpy as np

 from saqc.constants import FILTER_NONE
+from saqc.lib.docurator import doc
+import saqc.funcs


 class Tools:
+    @doc(saqc.funcs.tools.copyField.__doc__)
    def copyField(
        self, field: str, target: str, overwrite: bool = False, **kwargs
    ) -> saqc.SaQC:
        return self._defer("copyField", locals())

+    @doc(saqc.funcs.tools.dropField.__doc__)
    def dropField(self, field: str, **kwargs) -> saqc.SaQC:
        return self._defer("dropField", locals())

+    @doc(saqc.funcs.tools.renameField.__doc__)
    def renameField(self, field: str, new_name: str, **kwargs) -> saqc.SaQC:
        return self._defer("renameField", locals())

+    @doc(saqc.funcs.tools.maskTime.__doc__)
    def maskTime(
        self,
        field: str,
@@ -40,6 +46,7 @@ class Tools:
    ) -> saqc.SaQC:
        return self._defer("maskTime", locals())

+    @doc(saqc.funcs.tools.plot.__doc__)
    def plot(
        self,
        field: str,

--- a/saqc/core/modules/transformation.py
+++ b/saqc/core/modules/transformation.py
@@ -12,9 +12,12 @@ from typing import Callable, Optional, Union
 import pandas as pd

 import saqc
+from saqc.lib.docurator import doc
+import saqc.funcs


 class Transformation:
+    @doc(saqc.funcs.transformation.transform.__doc__)
    def transform(
        self,
        field: str,
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