Merge branch 'release2.3' into 'develop'

Release2.3

See merge request !606

.github/workflows/main.yml

@@ -61,11 +61,11 @@ jobs:
           pytest tests dios/test -Werror 
           python -m saqc --config docs/resources/data/config.csv --data docs/resources/data/data.csv --outfile /tmp/test.csv
       
-      - name: run doc tests    
-        run: |
-          cd docs
-          pip install -r requirements.txt
-          make doc
-          make test
+      # - name: run doc tests    
+      #   run: |
+      #     cd docs
+      #     pip install -r requirements.txt
+      #     make doc
+      #     make test
           
           

docs/Makefile

@@ -18,9 +18,6 @@ help:
 
 .PHONY: help Makefile clean
 
-test:
-	for k in $(MDLIST); do echo docs/"$$k"; done
-
 # clean sphinx generated stuff
 clean:
 	rm -rf _build _static _api

docs/cookbooks/MultivariateFlagging.rst

@@ -347,7 +347,7 @@ correlated with relatively high *kNNscores*, we could try to calculate a thresho
 `STRAY <https://arxiv.org/pdf/1908.04000.pdf>`_ algorithm, which is available as the method:
 :py:meth:`~saqc.SaQC.flagByStray`. This method will mark some samples of the `kNNscore` variable as anomaly.
 Subsequently we project this marks (or *flags*) on to the *sac* variable with a call to
-:py:meth:`~saqc.SaQC.transferFlags`. For the sake of demonstration, we also project the flags
+:py:meth:`~saqc.SaQC.concatFlags`. For the sake of demonstration, we also project the flags
 on the normalized *sac* and plot the flagged values in the *sac254_norm* - *level_norm* feature space.
 
 
@@ -355,8 +355,8 @@ on the normalized *sac* and plot the flagged values in the *sac254_norm* - *leve
 .. doctest:: exampleMV
 
    >>> qc = qc.flagByStray(field='kNNscores', freq='30D', alpha=.3)
-   >>> qc = qc.transferFlags(field='kNNscores', target='sac254_corrected', label='STRAY')
-   >>> qc = qc.transferFlags(field='kNNscores', target='sac254_norm', label='STRAY')
+   >>> qc = qc.concatFlags(field='kNNscores', target='sac254_corrected', label='STRAY')
+   >>> qc = qc.concatFlags(field='kNNscores', target='sac254_norm', label='STRAY')
    >>> qc.plot('sac254_corrected', xscope='2016-11') # doctest:+SKIP
    >>> qc.plot('sac254_norm', phaseplot='level_norm', xscope='2016-11') # doctest:+SKIP
 
@@ -365,8 +365,8 @@ on the normalized *sac* and plot the flagged values in the *sac254_norm* - *leve
    :include-source: False
 
    qc = qc.flagByStray(field='kNNscores', freq='30D', alpha=.3)
-   qc = qc.transferFlags(field='kNNscores', target='sac254_corrected', label='STRAY')
-   qc = qc.transferFlags(field='kNNscores', target='sac254_norm', label='STRAY')
+   qc = qc.concatFlags(field='kNNscores', target='sac254_corrected', label='STRAY')
+   qc = qc.concatFlags(field='kNNscores', target='sac254_norm', label='STRAY')
 
 .. plot::
    :context: close-figs

docs/requirements.txt

@@ -3,11 +3,10 @@
 # SPDX-License-Identifier: GPL-3.0-or-later
 
 recommonmark==0.7.1
-sphinx<6
+sphinx<7
 sphinx-automodapi==0.14.1
 sphinxcontrib-fulltoc==1.2.0
 sphinx-markdown-tables==0.0.17
-m2r==0.2.1
 jupyter-sphinx==0.3.2
 sphinx_autodoc_typehints==1.18.2
 sphinx-tabs==3.4.1

docs/resources/data/hydro_config.csv

@@ -16,6 +16,6 @@ water_z                 ; transform(field=['water_temp_raw'], func=zScore(x), fr
 sac_z                   ; transform(field=['sac254_raw'], func=zScore(x), freq='20D')
 kNN_scores              ; assignKNNScore(field=['level_z', 'water_z', 'sac_z'], freq='20D')
 kNN_scores              ; flagByStray(freq='20D')
-level_raw               ; transferFlags(field=['kNN_scores'], label='STRAY')
-sac254_corr             ; transferFlags(field=['kNN_scores'], label='STRAY')
-water_temp_raw          ; transferFlags(field=['kNN_scores'], label='STRAY')
\ No newline at end of file
+level_raw               ; concatFlags(field=['kNN_scores'], label='STRAY')
+sac254_corr             ; concatFlags(field=['kNN_scores'], label='STRAY')
+water_temp_raw          ; concatFlags(field=['kNN_scores'], label='STRAY')