add docstring generation files

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docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/source/conf.py

@@ -0,0 +1,76 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+import os
+import sys
+sys.path.append(os.path.abspath('../../tods'))
+sys.path.append(os.path.abspath('../../'))
+
+# -- Auto-doc Skip --------------------
+def skip_member(app, what, name, obj, skip, opts):
+ # we can document otherwise excluded entities here by returning False
+ # or skip otherwise included entities by returning True
+    if name == "__author" or name == "metadata":
+        return True
+    return None
+
+def setup(app):
+    app.connect('autodoc-skip-member', skip_member)
+
+# -- Project information -----------------------------------------------------
+
+project = 'Time Series Outlier Detection System'
+copyright = '2020, DataLab@Texas A&M University'
+author = 'DataLab@Texas A&M University'
+
+# The full version, including alpha/beta/rc tags
+release = '0.0.1'
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.doctest',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.todo',
+    'sphinx.ext.coverage',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.githubpages',
+    'sphinx.ext.napoleon',
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+source_suffix = '.rst'
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = []
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'alabaster'
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+

docs/source/index.rst

@@ -0,0 +1,20 @@
+.. Time Series Outlier Detection System documentation master file, created by
+   sphinx-quickstart on Wed Sep  9 22:52:15 2020.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to Time Series Outlier Detection System's documentation!
+================================================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/source/modules.rst

@@ -0,0 +1,7 @@
+tods
+====
+
+.. toctree::
+   :maxdepth: 3
+
+   tods

docs/source/tods.data_processing.rst

@@ -0,0 +1,69 @@
+tods.data\_processing package
+=============================
+
+Submodules
+----------
+
+tods.data\_processing.CategoricalToBinary module
+------------------------------------------------
+
+.. automodule:: tods.data_processing.CategoricalToBinary
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.data\_processing.ColumnFilter module
+-----------------------------------------
+
+.. automodule:: tods.data_processing.ColumnFilter
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.data\_processing.ContinuityValidation module
+-------------------------------------------------
+
+.. automodule:: tods.data_processing.ContinuityValidation
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.data\_processing.DatasetToDataframe module
+-----------------------------------------------
+
+.. automodule:: tods.data_processing.DatasetToDataframe
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.data\_processing.DuplicationValidation module
+--------------------------------------------------
+
+.. automodule:: tods.data_processing.DuplicationValidation
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.data\_processing.TimeIntervalTransform module
+--------------------------------------------------
+
+.. automodule:: tods.data_processing.TimeIntervalTransform
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.data\_processing.TimeStampValidation module
+------------------------------------------------
+
+.. automodule:: tods.data_processing.TimeStampValidation
+   :members:
+   :noindex:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: tods.data_processing
+   :members:
+   :noindex:
+   :show-inheritance:

docs/source/tods.detection_algorithm.rst

@@ -0,0 +1,189 @@
+tods.detection\_algorithm package
+=================================
+
+Submodules
+----------
+
+tods.detection\_algorithm.AutoRegODetect module
+-----------------------------------------------
+
+.. automodule:: tods.detection_algorithm.AutoRegODetect
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.detection\_algorithm.DeepLog module
+----------------------------------------
+
+.. automodule:: tods.detection_algorithm.DeepLog
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.detection\_algorithm.KDiscordODetect module
+------------------------------------------------
+
+.. automodule:: tods.detection_algorithm.KDiscordODetect
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.detection\_algorithm.LSTMODetect module
+--------------------------------------------
+
+.. automodule:: tods.detection_algorithm.LSTMODetect
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.detection\_algorithm.MatrixProfile module
+----------------------------------------------
+
+.. automodule:: tods.detection_algorithm.MatrixProfile
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.detection\_algorithm.PCAODetect module
+-------------------------------------------
+
+.. automodule:: tods.detection_algorithm.PCAODetect
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.detection\_algorithm.PyodABOD module
+-----------------------------------------
+
+.. automodule:: tods.detection_algorithm.PyodABOD
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.detection\_algorithm.PyodAE module
+---------------------------------------
+
+.. automodule:: tods.detection_algorithm.PyodAE
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.detection\_algorithm.PyodCBLOF module
+------------------------------------------
+
+.. automodule:: tods.detection_algorithm.PyodCBLOF
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.detection\_algorithm.PyodCOF module
+----------------------------------------
+
+.. automodule:: tods.detection_algorithm.PyodCOF
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.detection\_algorithm.PyodHBOS module
+-----------------------------------------
+
+.. automodule:: tods.detection_algorithm.PyodHBOS
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.detection\_algorithm.PyodIsolationForest module
+----------------------------------------------------
+
+.. automodule:: tods.detection_algorithm.PyodIsolationForest
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.detection\_algorithm.PyodKNN module
+----------------------------------------
+
+.. automodule:: tods.detection_algorithm.PyodKNN
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.detection\_algorithm.PyodLODA module
+-----------------------------------------
+
+.. automodule:: tods.detection_algorithm.PyodLODA
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.detection\_algorithm.PyodLOF module
+----------------------------------------
+
+.. automodule:: tods.detection_algorithm.PyodLOF
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.detection\_algorithm.PyodMoGaal module
+-------------------------------------------
+
+.. automodule:: tods.detection_algorithm.PyodMoGaal
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.detection\_algorithm.PyodOCSVM module
+------------------------------------------
+
+.. automodule:: tods.detection_algorithm.PyodOCSVM
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.detection\_algorithm.PyodSOD module
+----------------------------------------
+
+.. automodule:: tods.detection_algorithm.PyodSOD
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.detection\_algorithm.PyodSoGaal module
+-------------------------------------------
+
+.. automodule:: tods.detection_algorithm.PyodSoGaal
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.detection\_algorithm.PyodVAE module
+----------------------------------------
+
+.. automodule:: tods.detection_algorithm.PyodVAE
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.detection\_algorithm.Telemanom module
+------------------------------------------
+
+.. automodule:: tods.detection_algorithm.Telemanom
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.detection\_algorithm.UODBasePrimitive module
+-------------------------------------------------
+
+.. automodule:: tods.detection_algorithm.UODBasePrimitive
+   :members:
+   :noindex:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: tods.detection_algorithm
+   :members:
+   :noindex:
+   :show-inheritance:

docs/source/tods.feature_analysis.rst

@@ -0,0 +1,253 @@
+tods.feature\_analysis package
+==============================
+
+Submodules
+----------
+
+tods.feature\_analysis.AutoCorrelation module
+---------------------------------------------
+
+.. automodule:: tods.feature_analysis.AutoCorrelation
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.feature\_analysis.BKFilter module
+--------------------------------------
+
+.. automodule:: tods.feature_analysis.BKFilter
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.feature\_analysis.DiscreteCosineTransform module
+-----------------------------------------------------
+
+.. automodule:: tods.feature_analysis.DiscreteCosineTransform
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.feature\_analysis.FastFourierTransform module
+--------------------------------------------------
+
+.. automodule:: tods.feature_analysis.FastFourierTransform
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.feature\_analysis.HPFilter module
+--------------------------------------
+
+.. automodule:: tods.feature_analysis.HPFilter
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.feature\_analysis.NonNegativeMatrixFactorization module
+------------------------------------------------------------
+
+.. automodule:: tods.feature_analysis.NonNegativeMatrixFactorization
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.feature\_analysis.SKTruncatedSVD module
+--------------------------------------------
+
+.. automodule:: tods.feature_analysis.SKTruncatedSVD
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.feature\_analysis.SpectralResidualTransform module
+-------------------------------------------------------
+
+.. automodule:: tods.feature_analysis.SpectralResidualTransform
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.feature\_analysis.StatisticalAbsEnergy module
+--------------------------------------------------
+
+.. automodule:: tods.feature_analysis.StatisticalAbsEnergy
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.feature\_analysis.StatisticalAbsSum module
+-----------------------------------------------
+
+.. automodule:: tods.feature_analysis.StatisticalAbsSum
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.feature\_analysis.StatisticalGmean module
+----------------------------------------------
+
+.. automodule:: tods.feature_analysis.StatisticalGmean
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.feature\_analysis.StatisticalHmean module
+----------------------------------------------
+
+.. automodule:: tods.feature_analysis.StatisticalHmean
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.feature\_analysis.StatisticalKurtosis module
+-------------------------------------------------
+
+.. automodule:: tods.feature_analysis.StatisticalKurtosis
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.feature\_analysis.StatisticalMaximum module
+------------------------------------------------
+
+.. automodule:: tods.feature_analysis.StatisticalMaximum
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.feature\_analysis.StatisticalMean module
+---------------------------------------------
+
+.. automodule:: tods.feature_analysis.StatisticalMean
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.feature\_analysis.StatisticalMeanAbs module
+------------------------------------------------
+
+.. automodule:: tods.feature_analysis.StatisticalMeanAbs
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.feature\_analysis.StatisticalMeanAbsTemporalDerivative module
+------------------------------------------------------------------
+
+.. automodule:: tods.feature_analysis.StatisticalMeanAbsTemporalDerivative
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.feature\_analysis.StatisticalMeanTemporalDerivative module
+---------------------------------------------------------------
+
+.. automodule:: tods.feature_analysis.StatisticalMeanTemporalDerivative
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.feature\_analysis.StatisticalMedian module
+-----------------------------------------------
+
+.. automodule:: tods.feature_analysis.StatisticalMedian
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.feature\_analysis.StatisticalMedianAbsoluteDeviation module
+----------------------------------------------------------------
+
+.. automodule:: tods.feature_analysis.StatisticalMedianAbsoluteDeviation
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.feature\_analysis.StatisticalMinimum module
+------------------------------------------------
+
+.. automodule:: tods.feature_analysis.StatisticalMinimum
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.feature\_analysis.StatisticalSkew module
+---------------------------------------------
+
+.. automodule:: tods.feature_analysis.StatisticalSkew
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.feature\_analysis.StatisticalStd module
+--------------------------------------------
+
+.. automodule:: tods.feature_analysis.StatisticalStd
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.feature\_analysis.StatisticalVar module
+--------------------------------------------
+
+.. automodule:: tods.feature_analysis.StatisticalVar
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.feature\_analysis.StatisticalVariation module
+--------------------------------------------------
+
+.. automodule:: tods.feature_analysis.StatisticalVariation
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.feature\_analysis.StatisticalVecSum module
+-----------------------------------------------
+
+.. automodule:: tods.feature_analysis.StatisticalVecSum
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.feature\_analysis.StatisticalWillisonAmplitude module
+----------------------------------------------------------
+
+.. automodule:: tods.feature_analysis.StatisticalWillisonAmplitude
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.feature\_analysis.StatisticalZeroCrossing module
+-----------------------------------------------------
+
+.. automodule:: tods.feature_analysis.StatisticalZeroCrossing
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.feature\_analysis.TRMF module
+----------------------------------
+
+.. automodule:: tods.feature_analysis.TRMF
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.feature\_analysis.WaveletTransform module
+----------------------------------------------
+
+.. automodule:: tods.feature_analysis.WaveletTransform
+   :members:
+   :noindex:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: tods.feature_analysis
+   :members:
+   :noindex:
+   :show-inheritance:

docs/source/tods.reinforcement.rst

@@ -0,0 +1,21 @@
+tods.reinforcement package
+==========================
+
+Submodules
+----------
+
+tods.reinforcement.RuleBasedFilter module
+-----------------------------------------
+
+.. automodule:: tods.reinforcement.RuleBasedFilter
+   :members:
+   :noindex:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: tods.reinforcement
+   :members:
+   :noindex:
+   :show-inheritance:

docs/source/tods.rst

@@ -0,0 +1,24 @@
+tods package
+============
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   tods.data_processing
+   tods.detection_algorithm
+   tods.feature_analysis
+   tods.reinforcement
+   tods.searcher
+   tods.timeseries_processing
+
+
+Module contents
+---------------
+
+.. automodule:: tods
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/tods.searcher.rst

@@ -0,0 +1,37 @@
+tods.searcher package
+=====================
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   tods.searcher.search
+
+Submodules
+----------
+
+tods.searcher.schemas module
+----------------------------
+
+.. automodule:: tods.searcher.schemas
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tods.searcher.utils module
+--------------------------
+
+.. automodule:: tods.searcher.utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: tods.searcher
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/tods.searcher.search.rst

@@ -0,0 +1,21 @@
+tods.searcher.search package
+============================
+
+Submodules
+----------
+
+tods.searcher.search.brute\_force\_search module
+------------------------------------------------
+
+.. automodule:: tods.searcher.search.brute_force_search
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: tods.searcher.search
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/tods.timeseries_processing.rst

@@ -0,0 +1,85 @@
+tods.timeseries\_processing package
+===================================
+
+Submodules
+----------
+
+tods.timeseries\_processing.HoltSmoothing module
+------------------------------------------------
+
+.. automodule:: tods.timeseries_processing.HoltSmoothing
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.timeseries\_processing.HoltWintersExponentialSmoothing module
+------------------------------------------------------------------
+
+.. automodule:: tods.timeseries_processing.HoltWintersExponentialSmoothing
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.timeseries\_processing.MovingAverageTransform module
+---------------------------------------------------------
+
+.. automodule:: tods.timeseries_processing.MovingAverageTransform
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.timeseries\_processing.SKAxiswiseScaler module
+---------------------------------------------------
+
+.. automodule:: tods.timeseries_processing.SKAxiswiseScaler
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.timeseries\_processing.SKPowerTransformer module
+-----------------------------------------------------
+
+.. automodule:: tods.timeseries_processing.SKPowerTransformer
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.timeseries\_processing.SKQuantileTransformer module
+--------------------------------------------------------
+
+.. automodule:: tods.timeseries_processing.SKQuantileTransformer
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.timeseries\_processing.SKStandardScaler module
+---------------------------------------------------
+
+.. automodule:: tods.timeseries_processing.SKStandardScaler
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.timeseries\_processing.SimpleExponentialSmoothing module
+-------------------------------------------------------------
+
+.. automodule:: tods.timeseries_processing.SimpleExponentialSmoothing
+   :members:
+   :noindex:
+   :show-inheritance:
+
+tods.timeseries\_processing.TimeSeriesSeasonalityTrendDecomposition module
+--------------------------------------------------------------------------
+
+.. automodule:: tods.timeseries_processing.TimeSeriesSeasonalityTrendDecomposition
+   :members:
+   :noindex:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: tods.timeseries_processing
+   :members:
+   :noindex:
+   :show-inheritance: