Merge branch 'develop' into numbaRiddance

.gitlab-ci.yml

@@ -134,12 +134,39 @@ doctest:
 # Building stage
 # ===========================================================
 # check if we are able to build a wheel
-wheel:
+# and if the import works
+wheel38:
   stage: build
+  image: python:3.8
+  script:
+    - pip install wheel
+    - pip wheel .
+    - pip install .
+    - python -c 'import saqc; print(f"{saqc.__version__=}")'
+wheel39:
+  stage: build
+  image: python:3.9
+  script:
+    - pip install wheel
+    - pip wheel .
+    - pip install .
+    - python -c 'import saqc; print(f"{saqc.__version__=}")'
+wheel310:
+  stage: build
+  image: python:3.10
+  script:
+    - pip install wheel
+    - pip wheel .
+    - pip install .
+    - python -c 'import saqc; print(f"{saqc.__version__=}")'
+wheel311:
+  stage: build
+  image: python:3.11
   script:
     - pip install wheel
     - pip wheel .
     - pip install .
+    - python -c 'import saqc; print(f"{saqc.__version__=}")'
 
 docs:
   stage: build

CHANGELOG.md

@@ -11,7 +11,9 @@ SPDX-License-Identifier: GPL-3.0-or-later
 ### Added
 ### Changed
 ### Removed
+- removed deprecated `DictOfSeries.to_df` 
 ### Fixed
+### Deprecated
 
 ## [2.4.0](https://git.ufz.de/rdm-software/saqc/-/tags/v2.4.0) - 2023-04-25
 [List of commits](https://git.ufz.de/rdm-software/saqc/-/compare/v2.3.0...v2.4.0)
@@ -21,11 +23,8 @@ SPDX-License-Identifier: GPL-3.0-or-later
 - Expose the `History` via `SaQC._history`
 - Config function `cv` (coefficient of variation)
 ### Changed
-- Deprecate `interpolate`, `linear` and `shift` in favor of `align`
-- Deprecate `roll` in favor of `rolling`
 - Rename `interplateInvalid` to `interpolate`
 - Rename `interpolateIndex` to `align`
-- Deprecate `flagMVScore` parameters: `partition` in favor of `window`, `partition_min` in favor of `min_periods`, `min_periods` in favor of `min_periods_r`
 - Rewrite of `dios.DictOfSeries`
 ### Removed
 - Parameter `limit` from `align`
@@ -36,6 +35,11 @@ SPDX-License-Identifier: GPL-3.0-or-later
 - `reample` was not writing meta entries
 - `flagByStatLowPass` was overwriting existing flags
 - `flagUniLOF` and `flagLOF` were overwriting existing flags
+### Deprecated
+- Deprecate `flagMVScore` parameters: `partition` in favor of `window`, `partition_min` in favor of `min_periods`, `min_periods` in favor of `min_periods_r`
+- Deprecate `interpolate`, `linear` and `shift` in favor of `align`
+- Deprecate `roll` in favor of `rolling`
+- Deprecate `DictOfSeries.to_df` in favor of `DictOfSeries.to_pandas`
 
 ## [2.3.0](https://git.ufz.de/rdm-software/saqc/-/tags/v2.3.0) - 2023-01-17
 [List of commits](https://git.ufz.de/rdm-software/saqc/-/compare/v2.2.1...v2.3.0)

docs/cookbooks/ResidualOutlierDetection.rst

@@ -272,7 +272,7 @@ To see all the results obtained so far, plotted in one figure window, we make us
 
 .. doctest:: exampleOD
 
-   >>> data.to_df().plot()
+   >>> data.to_pandas().plot()
    <Axes...>
 
 .. plot::
@@ -281,7 +281,7 @@ To see all the results obtained so far, plotted in one figure window, we make us
    :width: 80 %
    :class: center
 
-   data.to_df().plot()
+   data.to_pandas().plot()
 
 
 Residuals and Scores

saqc/core/frame.py

@@ -4,10 +4,8 @@
 # -*- coding: utf-8 -*-
 from __future__ import annotations
 
-import warnings
 from typing import Any, Hashable, Mapping
 
-import numpy as np
 import pandas as pd
 from fancy_collections import DictOfPandas
 
@@ -37,19 +35,6 @@ class DictOfSeries(DictOfPandas):
     def attrs(self, value: Mapping[Hashable, Any]) -> None:
         self._attrs = dict(value)
 
-    def to_df(self, how="outer") -> pd.DataFrame:
-        """
-        Transform DictOfSeries to a pandas.DataFrame.
-
-        .. deprecated:: 2.4
-           use `DictOfSeries.to_pandas()` instead.
-        """
-        warnings.warn(
-            f"`to_df()` is deprecated use `to_pandas()` instead.",
-            category=DeprecationWarning,
-        )
-        return self.to_pandas(how)
-
     def flatten(self, promote_index: bool = False) -> DictOfSeries:
         """
         Return a copy.
@@ -57,16 +42,6 @@ class DictOfSeries(DictOfPandas):
         """
         return self.copy()
 
-    def to_pandas(self, how="outer"):
-        # This is a future feature from fancy_collections.DictOfPandas
-        # wich probably will come in the next version 0.1.4.
-        # We adopt this early, to prevent a second refactoring.
-        # The docstring will be different, so we keep the
-        # dynamic docstring allocation, down below.
-        # If the feature is present we just need to delete the
-        # entire method here.
-        return self.to_dataframe(how)
-
     def index_of(self, method="union") -> pd.Index:
         """Return an index with indices from all columns.
 
@@ -194,8 +169,3 @@ or is dropped if `how='inner'`
       a     b     c
 1  11.0  22.0  33.0
 """
-
-
-DictOfSeries.to_dataframe.__doc__ = DictOfSeries.to_pandas.__doc__.replace(
-    "to_pandas", "to_dataframe"
-)

saqc/funcs/tools.py

@@ -212,7 +212,7 @@ class ToolsMixin:
         """
         Plot data and flags or store plot to file.
 
-        There are two modes, 'interactive' and 'store', which are determind through the
+        There are two modes, 'interactive' and 'store', which are determined through the
         ``save_path`` keyword. In interactive mode (default) the plot is shown at runtime
         and the program execution stops until the plot window is closed manually. In
         store mode the generated plot is stored to disk and no manually interaction is

setup.py

@@ -39,7 +39,7 @@ setup(
         "numpy",
         "outlier-utils",
         "pyarrow",
-        "pandas",
+        "pandas>=2.0.0",
         "scikit-learn",
         "scipy",
         "typing_extensions",

tests/misc/__init__.py

+#!/usr/bin/env python
+# SPDX-FileCopyrightText: 2021 Helmholtz-Zentrum für Umweltforschung GmbH - UFZ
+# SPDX-License-Identifier: GPL-3.0-or-later

tests/misc/test_pickle.py

+#!/usr/bin/env python
+# SPDX-FileCopyrightText: 2021 Helmholtz-Zentrum für Umweltforschung GmbH - UFZ
+# SPDX-License-Identifier: GPL-3.0-or-later
+from __future__ import annotations
+
+import pickle
+
+import pytest
+
+from saqc import SaQC
+from tests.common import checkInvariants, initData
+
+
+@pytest.mark.parametrize("ncols", [4, 0])
+def test_pickling(ncols):
+    """Ensure that saqc and all its parts are pickleable"""
+    qc = SaQC(data=initData(ncols))
+    result = pickle.loads(pickle.dumps(qc))
+    assert isinstance(result, SaQC)
+    for k in qc.data.keys():
+        checkInvariants(qc._data, qc._flags, k)

tests/requirements.txt

@@ -3,7 +3,7 @@
 # SPDX-License-Identifier: GPL-3.0-or-later
 
 beautifulsoup4==4.12.2
-hypothesis==6.72.2
+hypothesis==6.75.1
 Markdown==3.4.3
 pytest==7.3.1
 pytest-lazy-fixture==0.6.3