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pyOpenMS readthedocs documentation, additional utilities, addons, scripts, and examples.
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Lots of warnings and errors in sphinx autodoc #307

Closed jpfeuffer closed 1 year ago

jpfeuffer commented 2 years ago

https://readthedocs.org/projects/pyopenms/builds/18413435/

jpfeuffer commented 2 years ago 
reading sources... [ 33%] _autosummary/pyopenms.IonSource
:7: (SEVERE/4) Incomplete section title.

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For more complex instruments, the order should be defined.
docstring of pyopenms.pyopenms_1.BasicProteinInferenceAlgorithm:5: WARNING: Block quote ends without a blank line; unexpected unindent.
docstring of pyopenms.pyopenms_1.BasicProteinInferenceAlgorithm:6: WARNING: Title underline too short.

Algorithm class that implements simple protein inference by aggregation of peptide scores.
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docstring of pyopenms.pyopenms_1.BasicProteinInferenceAlgorithm:6: CRITICAL: Unexpected section title.

Algorithm class that implements simple protein inference by aggregation of peptide scores.
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docstring of pyopenms.pyopenms_1.BasicProteinInferenceAlgorithm:24: ERROR: Unexpected indentation.
docstring of pyopenms.pyopenms_1.BasicProteinInferenceAlgorithm:42: WARNING: Block quote ends without a blank line; unexpected unindent.
docstring of pyopenms.pyopenms_1.BasicProteinInferenceAlgorithm:42: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.BasicProteinInferenceAlgorithm.run:4: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.BasicProteinInferenceAlgorithm.run:12: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.BasicProteinInferenceAlgorithm.run:23: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.pyopenms_2.BayesianProteinInferenceAlgorithm:5: WARNING: Block quote ends without a blank line; unexpected unindent.
docstring of pyopenms.pyopenms_2.BayesianProteinInferenceAlgorithm:6: WARNING: Title underline too short.

Performs a Bayesian protein inference on Protein/Peptide identifications or ConsensusMap.
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docstring of pyopenms.pyopenms_2.BayesianProteinInferenceAlgorithm:6: CRITICAL: Unexpected section title.

Performs a Bayesian protein inference on Protein/Peptide identifications or ConsensusMap.
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docstring of pyopenms.pyopenms_2.BayesianProteinInferenceAlgorithm:22: WARNING: Bullet list ends without a blank line; unexpected unindent.
docstring of pyopenms.pyopenms_2.BayesianProteinInferenceAlgorithm:22: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.pyopenms_2.BayesianProteinInferenceAlgorithm:41: WARNING: Definition list ends without a blank line; unexpected unindent.
docstring of pyopenms.pyopenms_2.BayesianProteinInferenceAlgorithm:41: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.BayesianProteinInferenceAlgorithm.inferPosteriorProbabilities:5: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.BayesianProteinInferenceAlgorithm.inferPosteriorProbabilities:16: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.BayesianProteinInferenceAlgorithm.inferPosteriorProbabilities:27: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.BayesianProteinInferenceAlgorithm.inferPosteriorProbabilities:37: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.ChromatogramExtractorAlgorithm.extractChromatograms:3: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.pyopenms_1.ChromatogramSettings:5: WARNING: Block quote ends without a blank line; unexpected unindent.
docstring of pyopenms.CoarseIsotopePatternGenerator.approximateFromPeptideWeight:1:<autosummary>:1: ERROR: Unknown target name: "round_masses".
docstring of pyopenms.CoarseIsotopePatternGenerator.setRoundMasses:1: ERROR: Unknown target name: "round_masses".
docstring of pyopenms.pyopenms_4.ConsensusFeature:5: WARNING: Block quote ends without a blank line; unexpected unindent.
docstring of pyopenms.pyopenms_4.ConsensusFeature:6: WARNING: Title underline too short.

A consensus feature spanning multiple LC-MS/MS experiments.
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docstring of pyopenms.pyopenms_4.ConsensusFeature:6: CRITICAL: Unexpected section title.

A consensus feature spanning multiple LC-MS/MS experiments.
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docstring of pyopenms.ContinuousWaveletTransform.getLeftPaddingIndex:1:<autosummary>:1: ERROR: Unknown target name: "begin_right_padding".
docstring of pyopenms.ContinuousWaveletTransform.getRightPaddingIndex:1: ERROR: Unknown target name: "begin_right_padding".
docstring of pyopenms.ContinuousWaveletTransformNumIntegration.getLeftPaddingIndex:1:<autosummary>:1: ERROR: Unknown target name: "begin_right_padding".
docstring of pyopenms.ContinuousWaveletTransformNumIntegration.getRightPaddingIndex:1: ERROR: Unknown target name: "begin_right_padding".
docstring of pyopenms.pyopenms_6.DigestionEnzymeProtein:5: WARNING: Block quote ends without a blank line; unexpected unindent.
docstring of pyopenms.pyopenms_3.DigestionEnzymeRNA:5: WARNING: Block quote ends without a blank line; unexpected unindent.
docstring of pyopenms.pyopenms_3.DigestionEnzymeRNA:6: WARNING: Title underline too short.

Representation of a digestion enzyme for RNA (RNase)
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docstring of pyopenms.pyopenms_3.DigestionEnzymeRNA:6: CRITICAL: Unexpected section title.

Representation of a digestion enzyme for RNA (RNase)
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docstring of pyopenms.pyopenms_7.EnzymaticDigestion:5: WARNING: Title underline too short.

Class for the enzymatic digestion of proteins
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docstring of pyopenms.pyopenms_7.EnzymaticDigestion:5: CRITICAL: Unexpected section title.

Class for the enzymatic digestion of proteins
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docstring of pyopenms.EnzymaticDigestion.digestUnmodified:5: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.EnzymaticDigestion.isValidProduct:5: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.EnzymaticDigestionLogModel.peptideCount:3: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.pyopenms_3.ExperimentalSettings:5: WARNING: Block quote ends without a blank line; unexpected unindent.
docstring of pyopenms.FASTAFile.readNext:2: WARNING: Title underline too short.

Reads the next FASTA entry from file
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docstring of pyopenms.FASTAFile.readNext:2: CRITICAL: Unexpected section title.

Reads the next FASTA entry from file
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docstring of pyopenms.FASTAFile.readNext:4: WARNING: Title underline too short.

If you want to read all entries in one go, use load()
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docstring of pyopenms.FASTAFile.readNext:4: CRITICAL: Unexpected section title.

If you want to read all entries in one go, use load()
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docstring of pyopenms.FASTAFile.readStart:2: WARNING: Title underline too short.

Prepares a FASTA file given by 'filename' for streamed reading using readNext()
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docstring of pyopenms.FASTAFile.readStart:2: CRITICAL: Unexpected section title.

Prepares a FASTA file given by 'filename' for streamed reading using readNext()
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docstring of pyopenms.FASTAFile.readStart:7: WARNING: Field list ends without a blank line; unexpected unindent.
docstring of pyopenms.FASTAFile.readStart:8: WARNING: Title underline too short.

Reads the next FASTA entry from file
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docstring of pyopenms.FASTAFile.readStart:8: CRITICAL: Unexpected section title.

Reads the next FASTA entry from file
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docstring of pyopenms.FASTAFile.readStart:10: WARNING: Title underline too short.

If you want to read all entries in one go, use load()
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docstring of pyopenms.FASTAFile.readStart:10: CRITICAL: Unexpected section title.

If you want to read all entries in one go, use load()
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docstring of pyopenms.FASTAFile.writeNext:2: WARNING: Title underline too short.

Stores the data given by `protein`. Call writeStart() once before calling writeNext()
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docstring of pyopenms.FASTAFile.writeNext:2: CRITICAL: Unexpected section title.

Stores the data given by `protein`. Call writeStart() once before calling writeNext()
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docstring of pyopenms.FASTAFile.writeNext:4: WARNING: Title underline too short.

Call writeEnd() when done to close the file!
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docstring of pyopenms.FASTAFile.writeNext:4: CRITICAL: Unexpected section title.

Call writeEnd() when done to close the file!
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docstring of pyopenms.FASTAFile.writeStart:2: WARNING: Title underline too short.

Prepares a FASTA file given by 'filename' for streamed writing using writeNext()
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docstring of pyopenms.FASTAFile.writeStart:2: CRITICAL: Unexpected section title.

Prepares a FASTA file given by 'filename' for streamed writing using writeNext()
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docstring of pyopenms.FASTAFile.writeStart:5: WARNING: Field list ends without a blank line; unexpected unindent.
docstring of pyopenms.FASTAFile.writeStart:6: WARNING: Title underline too short.

Stores the data given by `protein`. Call writeStart() once before calling writeNext()
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docstring of pyopenms.FASTAFile.writeStart:6: CRITICAL: Unexpected section title.

Stores the data given by `protein`. Call writeStart() once before calling writeNext()
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docstring of pyopenms.FASTAFile.writeStart:8: WARNING: Title underline too short.

Call writeEnd() when done to close the file!
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docstring of pyopenms.FASTAFile.writeStart:8: CRITICAL: Unexpected section title.

Call writeEnd() when done to close the file!
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docstring of pyopenms.FIAMSDataProcessor.convertToFeatureMap:6: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.FIAMSDataProcessor.extractPeaks:3: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.FIAMSDataProcessor.run:15: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.FIAMSDataProcessor.trackNoise:6: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.pyopenms_5.Feature:5: WARNING: Block quote ends without a blank line; unexpected unindent.
docstring of pyopenms.pyopenms_5.Feature:6: WARNING: Title underline too short.

An LC-MS feature
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docstring of pyopenms.pyopenms_5.Feature:6: CRITICAL: Unexpected section title.

An LC-MS feature
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docstring of pyopenms.Feature.encloses:3: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.FeatureFinder.run:8: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.pyopenms_4.FeatureFinderIdentificationAlgorithm:5: WARNING: Block quote ends without a blank line; unexpected unindent.
docstring of pyopenms.pyopenms_4.FeatureFinderIdentificationAlgorithm:6: WARNING: Title underline too short.

Algorithm class for FeatureFinderIdentification
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docstring of pyopenms.pyopenms_4.FeatureFinderIdentificationAlgorithm:6: CRITICAL: Unexpected section title.

Algorithm class for FeatureFinderIdentification
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docstring of pyopenms.pyopenms_4.FeatureFinderIdentificationAlgorithm:16: ERROR: Unexpected indentation.
docstring of pyopenms.pyopenms_4.FeatureFinderIdentificationAlgorithm:49: WARNING: Block quote ends without a blank line; unexpected unindent.
docstring of pyopenms.pyopenms_4.FeatureFinderIdentificationAlgorithm:49: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.FeatureFinderIdentificationAlgorithm.run:4: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.FeatureFinderIdentificationAlgorithm.run:14: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.FeatureFinderIdentificationAlgorithm.run:25: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.pyopenms_4.__static_File_absolutePath:1:<autosummary>:1: ERROR: Unknown target name: "from".
docstring of pyopenms.pyopenms_4.__static_File_rename:1: ERROR: Unknown target name: "from".
docstring of pyopenms.FileHandler.loadExperiment:3: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.FileHandler.loadFeatures:3: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.FileHandler.storeExperiment:6: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.pyopenms_5.__static_FileHandler_computeFileHash:1:<autosummary>:1: ERROR: Unknown target name: "type".
docstring of pyopenms.pyopenms_5.__static_FileHandler_computeFileHash:1:<autosummary>:1: ERROR: Unknown target name: "type".
docstring of pyopenms.pyopenms_5.__static_FileHandler_hasValidExtension:1: ERROR: Unknown target name: "type".
docstring of pyopenms.pyopenms_5.__static_FileHandler_isSupported:1: ERROR: Unknown target name: "type".
docstring of pyopenms.FileTypes.nameToType:3: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.pyopenms_2.FloatDataArray:5: WARNING: Block quote ends without a blank line; unexpected unindent.
docstring of pyopenms.GNPSMetaValueFile.store:6: CRITICAL: Unexpected section title.

Parameters
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docstring of pyopenms.GNPSQuantificationFile.store:8: CRITICAL: Unexpected section title.

Parameters
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docstring of pyopenms.HyperScore.compute:7: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.IBSpectraFile.store:3: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.IDConflictResolverAlgorithm.resolve:8: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.IDConflictResolverAlgorithm.resolve:18: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.IDDecoyProbability.apply:4: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.IDFilter.extractPeptideSequences:3: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.IDFilter.filterHitsByRank:10: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.IDFilter.filterHitsByRank:22: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.IDFilter.filterPeptidesByRTPredictPValue:6: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.IDFilter.getBestHit:7: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.IDFilter.getBestHit:15: WARNING: Title underline too short.

Finds the best-scoring hit in a vector of peptide or protein identifications
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docstring of pyopenms.IDFilter.getBestHit:15: CRITICAL: Unexpected section title.

Finds the best-scoring hit in a vector of peptide or protein identifications
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docstring of pyopenms.IDFilter.getBestHit:18: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.IDFilter.keepBestPeptideHits:3: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.IDFilter.updateProteinGroups:3: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.IDMapper.annotate:9: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.IDMapper.annotate:28: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.IDMapper.annotate:46: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.IDMapper.annotate:68: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.IDMapper.mapPrecursorsToIdentifications:8: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.IDMapper.annotate:1:<autosummary>:1: ERROR: Unknown target name: "map".
docstring of pyopenms.IDMapper.annotate:16: ERROR: Unknown target name: "map".
docstring of pyopenms.IDMapper.annotate:32: ERROR: Unknown target name: "map".
docstring of pyopenms.IDMapper.annotate:54: ERROR: Unknown target name: "map".
docstring of pyopenms.IDMapper.annotate:75: ERROR: Unknown target name: "map".
docstring of pyopenms.pyopenms_2.IMSAlphabet:20: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.pyopenms_3.IMSIsotopeDistribution:5: WARNING: Title underline too short.

Represents a distribution of isotopes restricted to the first K elements
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docstring of pyopenms.pyopenms_3.IMSIsotopeDistribution:5: CRITICAL: Unexpected section title.

Represents a distribution of isotopes restricted to the first K elements
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docstring of pyopenms.pyopenms_3.IMSIsotopeDistribution:13: ERROR: Unexpected indentation.
docstring of pyopenms.pyopenms_3.IMSIsotopeDistribution:16: WARNING: Block quote ends without a blank line; unexpected unindent.
docstring of pyopenms.pyopenms_3.IMSIsotopeDistribution:16: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.pyopenms_3.IMSIsotopeDistribution:24: WARNING: Bullet list ends without a blank line; unexpected unindent.
docstring of pyopenms.pyopenms_3.IMSIsotopeDistribution:24: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.InclusionExclusionList.writeTargets:7: ERROR: Unknown target name: "map".
docstring of pyopenms.pyopenms_1.IndexedMzMLDecoder:5: WARNING: Title underline too short.

A class to analyze indexedmzML files and extract the offsets of individual tags
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docstring of pyopenms.pyopenms_1.IndexedMzMLDecoder:5: CRITICAL: Unexpected section title.

A class to analyze indexedmzML files and extract the offsets of individual tags
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docstring of pyopenms.IndexedMzMLDecoder.findIndexListOffset:16: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.IndexedMzMLFileLoader.store:4: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.IndexedMzMLFileLoader.store:11: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.InspectInfile.handlePTMs:3: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.InspectOutfile.getWantedRecords:3: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.InspectOutfile.load:3: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.pyopenms_6.IntegerDataArray:5: WARNING: Block quote ends without a blank line; unexpected unindent.
docstring of pyopenms.InternalCalibration.calibrate:10: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.InternalCalibration.fillCalibrants:15: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.InternalCalibration.fillCalibrants:44: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.InternalCalibration.fillCalibrants:67: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.InternalCalibration.getCalibrationPoints:6: CRITICAL: Unexpected section title or transition.

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docstring of pyopenms.pyopenms_7.__static_IonIdentityMolecularNetworking_annotateConsensusMap:10: CRITICAL: Unexpected section title.

Parameters
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docstring of pyopenms.pyopenms_7.__static_IonIdentityMolecularNetworking_writeSupplementaryPairTable:8: CRITICAL: Unexpected section title.

Parameters
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jpfeuffer commented 2 years ago

Partly done in https://github.com/OpenMS/OpenMS/pull/6414

jpfeuffer commented 1 year ago

And in #333

jpfeuffer commented 1 year ago

Still missing: