diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index bc244d486167c9d7a6dc69c3b963f695260b5652..036ec6241efd8d50151c1744dea1362980d0cbe0 100644 --- a/.github/workflows/main.yml +++ b/.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 diff --git a/docs/Makefile b/docs/Makefile index 411507f8e898ef163b1eb0ea89cf4692bb8c3a77..304194f644e35bf811546526ecb2077f2f4034e8 100644 --- a/docs/Makefile +++ b/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 diff --git a/docs/cookbooks/MultivariateFlagging.rst b/docs/cookbooks/MultivariateFlagging.rst index c7297ade17f4497c58b3ae5766beb2433c8ad702..8d0c4d915b6d6dea8059aae7a9e20474c49066f4 100644 --- a/docs/cookbooks/MultivariateFlagging.rst +++ b/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 diff --git a/docs/requirements.txt b/docs/requirements.txt index 2ff705310e0b6b7a232101d5af5023f2c3c5fc1b..412a452a20ca0b408634ec6172a52d36cd492bde 100644 --- a/docs/requirements.txt +++ b/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 diff --git a/docs/resources/data/hydro_config.csv b/docs/resources/data/hydro_config.csv index c97df2be1da86607ce0a1e0ddff58ab945d63180..d9858e02317f94f6956978cd35c38ab4c0145176 100644 --- a/docs/resources/data/hydro_config.csv +++ b/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') diff --git a/docs/resources/temp/SM1processingResults.png b/docs/resources/temp/SM1processingResults.png index 86021e3e77d34d037666fc827d525e28702e59fe..09f3b4885ebb5885a5dcd8ef314205d334485ad1 100644 Binary files a/docs/resources/temp/SM1processingResults.png and b/docs/resources/temp/SM1processingResults.png differ diff --git a/docs/resources/temp/SM2processingResults.png b/docs/resources/temp/SM2processingResults.png index d1d9563e167425063663ff1b7b9e9b99b7c8aab4..82f7f65d49217007c8f7ff950a41755dde28d57c 100644 Binary files a/docs/resources/temp/SM2processingResults.png and b/docs/resources/temp/SM2processingResults.png differ