Docufixes

.gitlab-ci.yml

@@ -12,6 +12,7 @@ variables:
 stages:
   - compliance
   - test
+  - build
   - deploy
 
 default:
@@ -108,12 +109,31 @@ python310:
     reports:
       junit: report.xml
 
+doctest:
+  stage: test
+  script:
+    - cd docs
+    - pip install -r requirements.txt
+    - make testonly
+
+
+# ===========================================================
+# Building stage
+# ===========================================================
 # check if we are able to build a wheel
 wheel:
-  stage: test
+  stage: build
   script:
     - pip install wheel
     - pip wheel .
+    - pip install .
+
+docs:
+  stage: build
+  script:
+    - cd docs
+    - pip install -r requirements.txt
+    - make doconly
 
 # ===========================================================
 # Extra Pipeline (run with a successful run of all other jobs on develop)

docs/Makefile

@@ -36,11 +36,6 @@ doc:
 	# generate environment table from dictionary
 	@$(SPHINXBUILD) -M doctest "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 	@$(SPHINXBUILD) -M html "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
-	rm -f *.automodsumm
-	rm -f *.automodapi
-	rm -f modules/*.automodsumm
-	rm -f modules/*.automodapi
-	rm -f */*.automodsumm
 
 # make documentation
 doconly:
@@ -49,14 +44,8 @@ doconly:
 
 # make test, clean up
 testonly:
-    # generate parent fake module for the functions to be documented
+	# generate parent fake module for the functions to be documented
 	@$(SPHINXBUILD) -M doctest "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
-	rm -f *.automodsumm
-	rm -f *.automodapi
-	rm -f modules/*.automodsumm
-	rm -f modules/*.automodapi
-	rm -f */*.automodsumm
-	rm -f -r coredoc
 
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).

docs/gettingstarted/TutorialAPI.rst

@@ -16,7 +16,7 @@ The Python API of SaQC consists of three distinct components:
 
 1. the core class, :py:class:`saqc.SaQC`
 2. a number of flagging schemes
-3. a collection of :doc:`functions <../modules/saqcFuncTOC>`.
+3. a collection of :doc:`functions <../modules/SaQCFunctions>`.
 
 One and two are implemented as distinct classes, the core object is called ``SaQC`` and we currently
 provide three flagging schemes, namely:

docs/gettingstarted/TutorialCLI.rst

@@ -78,7 +78,7 @@ In this case, we trigger a :py:meth:`range <saqc.SaQC.flagRange>` test, that fla
 the range of the bounds of the interval *[10,60]*. Subsequently, a test to detect spikes, is applied,
 using the MAD-method. (:py:meth:`~saqc.SaQC.flagMAD`).
 You can find an overview of all available quality control tests
-:ref:`here <modules/saqcFuncTOC:SaQC Methods>`. Note that the tests are
+:ref:`here <modules/SaQCFunctions:Test Functions>`. Note that the tests are
 *executed in the order that you define in the configuration file*. The quality
 flags that are set during one test are always passed on to the subsequent one.
 

docs/index.rst

@@ -45,30 +45,31 @@ Getting Started
    documentation/ConfigurationFiles
    documentation/Customizations
 
-.. toctree::
-   :caption: Functions
-   :hidden:
-   :maxdepth: 1
-   :glob:
-   :titlesonly:
-
-   resampling <funcs/resampling>
-   generic <funcs/generic>
-   outliers <funcs/outliers>
-   breaks <funcs/breaks>
-   constants <funcs/constants>
-   changepoints <funcs/changepoints>
-   drift <funcs/drift>
-   curvefit <funcs/curvefit>
-   interpolation <funcs/interpolation>
-   residuals <funcs/residuals>
-   tools <funcs/tools>
-   flagtools <funcs/flagtools>
-   rolling <funcs/rolling>
-   scores <funcs/scores>
-   transformation <funcs/transformation>
-   noise <funcs/noise>
-   pattern <funcs/pattern>
+..
+   .. toctree::
+      :caption: Functions
+      :hidden:
+      :maxdepth: 1
+      :glob:
+      :titlesonly:
+
+      resampling <funcs/resampling>
+      generic <funcs/generic>
+      outliers <funcs/outliers>
+      breaks <funcs/breaks>
+      constants <funcs/constants>
+      changepoints <funcs/changepoints>
+      drift <funcs/drift>
+      curvefit <funcs/curvefit>
+      interpolation <funcs/interpolation>
+      residuals <funcs/residuals>
+      tools <funcs/tools>
+      flagtools <funcs/flagtools>
+      rolling <funcs/rolling>
+      scores <funcs/scores>
+      transformation <funcs/transformation>
+      noise <funcs/noise>
+      pattern <funcs/pattern>
 
 
 .. toctree::
@@ -76,10 +77,11 @@ Getting Started
    :hidden:
    :maxdepth: 2
 
-   Package <modules/saqc>
-   Core <modules/saqcCore>
-   Methods <modules/saqcFuncTOC>
-   Constants <modules/saqcConstants>
+   Package <modules/SaQC>
+   Core <modules/SaQCCore>
+   Test Functions <modules/SaQCFunctions>
+   Translations <modules/SaQCTranslation>
+   Constants <modules/SaQCConstants>
 
 .. toctree::
    :caption: Developer Resources

docs/modules/saqcCore.rst → docs/modules/SaQCCore.rst

@@ -2,7 +2,7 @@
 ..
 .. SPDX-License-Identifier: GPL-3.0-or-later
 
-saqc
+SaQC
 ====
 
 .. automodapi:: saqc.core

docs/modules/saqcFuncTOC.rst → docs/modules/SaQCFunctions.rst

@@ -2,8 +2,11 @@
 ..
 .. SPDX-License-Identifier: GPL-3.0-or-later
 
-SaQC Methods
-------------
+SaQC
+====
+
+Test Functions
+--------------
 
 .. toctree::
    :glob:

docs/funcs/allFunctions.rst → docs/modules/SaQCTranslation.rst

-.. SPDX-FileCopyrightText: 2021 Helmholtz-Zentrum für Umweltforschung GmbH - UFZ
-..
-.. SPDX-License-Identifier: GPL-3.0-or-later
-
-SaQC Object Methods
-===================
-
-
-
-.. currentmodule:: saqc
-
-.. autosummary::
-
-   SaQC
+.. SPDX-FileCopyrightText: 2021 Helmholtz-Zentrum für Umweltforschung GmbH - UFZ
+..
+.. SPDX-License-Identifier: GPL-3.0-or-later
+
+SaQC
+====
+
+.. automodapi:: saqc.core.translation
+   :include-all-objects:

saqc/__init__.py

@@ -5,7 +5,8 @@
 # SPDX-License-Identifier: GPL-3.0-or-later
 
 # -*- coding: utf-8 -*-
-"""The system for automated quality controll package."""
+
+"""The System for automated Quality Control package."""
 
 from saqc.constants import BAD, DOUBTFUL, FILTER_ALL, FILTER_NONE, GOOD, UNFLAGGED
 

saqc/core/history.py

@@ -8,7 +8,7 @@ from __future__ import annotations
 
 from copy import copy as shallowcopy
 from copy import deepcopy
-from typing import Any, Dict, List, Tuple, Union
+from typing import Any, Callable, Dict, List, Tuple, Union
 
 import numpy as np
 import pandas as pd
@@ -25,9 +25,8 @@ class History:
     names are increasing integers starting with 0. After initialisation
     the FH is empty and has no columns at all.
 
-    To get the worst flags (highest value) that are currently stored in
-    the FH, we provide a ``max()`` method. It returns a pd.Series indicating
-    the worst flag per row.
+    To get the latest flags, that are currently stored in the FH, we provide
+    a ``squeeze()`` method.
 
     For more details and a detailed discussion, why this is needed, how this
     works and possible other implementations, see #GL143 [1].
@@ -44,7 +43,7 @@ class History:
     createHistoryFromData: function to create History from existing data
     """
 
-    def __init__(self, index: pd.Index):
+    def __init__(self, index: pd.Index | None):
 
         self.hist = pd.DataFrame(index=index)
         self.meta = []
@@ -125,7 +124,9 @@ class History:
 
         return self
 
-    def append(self, value: Union[pd.Series, History], meta: dict = None) -> History:
+    def append(
+        self, value: Union[pd.Series, History], meta: dict | None = None
+    ) -> History:
         """
         Create a new FH column and insert given pd.Series to it.
 
@@ -211,11 +212,11 @@ class History:
 
     def squeeze(self, raw=False) -> pd.Series:
         """
-        Get the maximum value per row of the FH.
+        Get the last flag value per row of the FH.
 
         Returns
         -------
-        pd.Series: maximum values
+        pd.Series
         """
         result = self.hist.astype(float)
         if result.empty:
@@ -266,7 +267,7 @@ class History:
     def apply(
         self,
         index: pd.Index,
-        func: callable,
+        func: Callable,
         func_kws: dict,
         func_handle_df: bool = False,
         copy: bool = True,

saqc/core/translation/basescheme.py

@@ -37,6 +37,7 @@ class TranslationScheme:
     the inverse of the 'forward' translation.
 
     The translation mechanism imposes a few restrictions:
+
     - The scheme must be well definied, i.e. we need a backward translation for
       every forward translation (each value in `self._forward` needs a key in
       `self._backward`).

tests/docs/test_markdown.py

@@ -29,7 +29,6 @@ def test_codeSnippets(fname):
 FILEURL = "https://git.ufz.de/rdm-software/saqc/-/blob/develop/"
 
 
-@pytest.mark.skip
 @pytest.mark.parametrize("fname", ["README.md"])
 def test_links(fname):
     with open(fname, "r") as f: