saqc.SaQC properly documented

funcSummaries/breaks.rst

+breaks
+======
+
+Detecting breaks in data.
+
+This module provides functions to detect and flag breaks in data, for example temporal
+gaps (:py:func:`flagMissing`), jumps and drops (:py:func:`flagJumps`) or temporal
+isolated values (:py:func:`flagIsolated`).
+
+.. currentmodule:: saqc
+
+.. autosummary::
+
+   ~SaQC.flagMissing
+   ~SaQC.flagIsolated
+   ~SaQC.flagJumps

funcSummaries/changepoints.rst

+changepoints
+============
+
+
+
+.. currentmodule:: saqc
+
+.. autosummary::
+
+   ~SaQC.flagChangePoints
+   ~SaQC.assignChangePointCluster

funcSummaries/constants.rst

+constants
+=========
+
+
+
+.. currentmodule:: saqc
+
+.. autosummary::
+
+   ~SaQC.flagConstants
+   ~SaQC.flagByVariance

funcSummaries/curvefit.rst

+curvefit
+========
+
+
+
+.. currentmodule:: saqc
+
+.. autosummary::
+
+   ~SaQC.fitPolynomial

funcSummaries/drift.rst

+drift
+=====
+
+
+
+.. currentmodule:: saqc
+
+.. autosummary::
+
+   ~SaQC.flagDriftFromNorm
+   ~SaQC.flagDriftFromReference
+   ~SaQC.flagDriftFromScaledNorm
+   ~SaQC.correctDrift
+   ~SaQC.correctRegimeAnomaly
+   ~SaQC.correctOffset
+   ~SaQC.flagRegimeAnomaly
+   ~SaQC.assignRegimeAnomaly

funcSummaries/flagtools.rst

+flagtools
+=========
+
+
+
+.. currentmodule:: saqc
+
+.. autosummary::
+
+   ~SaQC.forceFlags
+   ~SaQC.clearFlags
+   ~SaQC.flagUnflagged
+   ~SaQC.flagManual
+   ~SaQC.flagDummy

funcSummaries/generic.rst

+generic
+=======
+
+
+
+.. currentmodule:: saqc
+
+.. autosummary::
+
+   ~SaQC.processGeneric
+   ~SaQC.flagGeneric

funcSummaries/interpolation.rst

+interpolation
+=============
+
+
+
+.. currentmodule:: saqc
+
+.. autosummary::
+
+   ~SaQC.interpolateByRolling
+   ~SaQC.interpolateInvalid
+   ~SaQC.interpolateIndex

funcSummaries/noise.rst

+noise
+=====
+
+
+
+.. currentmodule:: saqc
+
+.. autosummary::
+
+   ~SaQC.flagByStatLowPass

funcSummaries/outliers.rst

+outliers
+========
+
+
+
+.. currentmodule:: saqc
+
+.. autosummary::
+
+   ~SaQC.flagByStray
+   ~SaQC.flagMVScores
+   ~SaQC.flagRaise
+   ~SaQC.flagMAD
+   ~SaQC.flagOffset
+   ~SaQC.flagByGrubbs
+   ~SaQC.flagRange
+   ~SaQC.flagCrossStatistic

funcSummaries/pattern.rst

+pattern
+=======
+
+
+
+.. currentmodule:: saqc
+
+.. autosummary::
+
+   ~SaQC.flagPatternByWavelet
+   ~SaQC.calculateDistanceByDTW
+   ~SaQC.flagPatternByDTW

funcSummaries/resampling.rst

+resampling
+==========
+
+
+
+.. currentmodule:: saqc
+
+.. autosummary::
+
+   ~SaQC.linear
+   ~SaQC.interpolate
+   ~SaQC.shift
+   ~SaQC.resample
+   ~SaQC.concatFlags

funcSummaries/residues.rst

+residues
+========
+
+
+
+.. currentmodule:: saqc
+
+.. autosummary::
+
+   ~SaQC.calculatePolynomialResidues
+   ~SaQC.calculateRollingResidues

funcSummaries/rolling.rst

+rolling
+=======
+
+
+
+.. currentmodule:: saqc
+
+.. autosummary::
+
+   ~SaQC.roll

funcSummaries/scores.rst

+scores
+======
+
+
+
+.. currentmodule:: saqc
+
+.. autosummary::
+
+   ~SaQC.assignKNNScore

funcSummaries/tools.rst

+tools
+=====
+
+
+
+.. currentmodule:: saqc
+
+.. autosummary::
+
+   ~SaQC.copyField
+   ~SaQC.dropField
+   ~SaQC.renameField
+   ~SaQC.maskTime
+   ~SaQC.plot

sphinx-doc/moduleAPIs/Functionstransformation.rst → funcSummaries/transformation.rst

 transformation
 ==============
 
-.. automodapi:: Functions.transformation
-   :no-heading:
+
+
+.. currentmodule:: saqc
+
+.. autosummary::
+
+   ~SaQC.transform

sphinx-doc/.gitignore

-
-_api/
-_build/
-_static/
-*.automodsumm
-_static/*
\ No newline at end of file

sphinx-doc/Makefile

-# 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     = .
-BUILDDIR      = _build
-
-# sphinx build controll:
-# Function documentations will be acessible through: FUNCTIONS.saqc
-FUNCTIONS     = Functions
-CORE          = Core
-# List of folders containing markdown content to include into the build
-MDLIST		  = getting_started_md how_to_doc_md cook_books_md misc_md
-# Put it first so that "make" without argument is like "make help".
-help:
-	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
-
-.PHONY: help Makefile clean
-
-test:
-	for k in $(MDLIST); do echo sphinx-doc/"$$k"; done
-
-# clean sphinx generated stuff
-clean:
-	rm -rf _build _static
-	rm -rf ../$(FUNCTIONS)
-	rm -rf ../$(CORE)
-	mkdir _static
-	# for k in $(MDLIST); do rm -r "$$k"_m2r; done
-	rm -f *.automodsumm
-	rm -f *.automodapi
-	rm -f moduleAPIs/*.automodsumm
-	rm -f moduleAPIs/*.automodapi
-	rm -f */*.automodsumm
-
-# trigger (saqc) customized documentation pipeline
-doc:
-	# generate parent fake module for the functions to be documented
-	python scripts/make_doc_module.py -p "saqc/funcs" -t "$(FUNCTIONS)" -sr ".."
-	# generate environment table from dictionary
-	python scripts/make_env_tab.py
-	# make rest folders from markdown folders
-	# for k in $(MDLIST); do python scripts/make_md_to_rst.py -p sphinx-doc/"$$k" -sr ".."; done
-	# make the html build
-	@$(SPHINXBUILD) -M html "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
-
-# 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)
-

sphinx-doc/conf.py

-# 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.insert(0, os.path.abspath(".."))
-package_path = os.path.abspath("..")
-os.environ["PYTHONPATH"] = ":".join((package_path, os.environ.get("PYTHONPATH", "")))
-
-
-# -- Project information -----------------------------------------------------
-
-project = "SaQC"
-copyright = (
-    "2020, Bert Palm, David Schäfer, Peter Lünenschloß, Lennart Schmidt, Juliane Geller"
-)
-author = "Bert Palm, David Schäfer, Peter Lünenschloß, Lennart Schmidt, Juliane Geller"
-
-# The full version, including alpha/beta/rc tags
-release = f"2.0"
-
-
-# -- 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.autosummary",
-    "sphinx.ext.doctest",
-    # "sphinx.ext.extlinks",
-    # "sphinx.ext.todo",
-    # "sphinx.ext.intersphinx",
-    # "sphinx.ext.coverage",
-    # "sphinx.ext.mathjax",
-    # "sphinx.ext.ifconfig",
-    "sphinx.ext.autosectionlabel",
-    # link source code
-    "sphinx.ext.viewcode",
-    # add suupport for NumPy style docstrings
-    "sphinx.ext.napoleon",
-    # Doc a whole module
-    # see https://sphinx-automodapi.readthedocs.io/en/latest/
-    "sphinx_automodapi.automodapi",
-    # 'sphinx_automodapi.smart_resolver',
-    # see https://sphinxcontrib-fulltoc.readthedocs.io/en/latest/
-    "sphinxcontrib.fulltoc",
-    # Markdown sources support
-    # https://recommonmark.readthedocs.io/en/latest/
-    "recommonmark",
-    # https://github.com/ryanfox/sphinx-markdown-tables
-    "sphinx_markdown_tables",
-    # snippet plotting
-    "matplotlib.sphinxext.plot_directive",
-    # jupyter code execution
-    "jupyter_sphinx",
-    # "sphinx_autodoc_typehints",
-    # "numpydoc"
-]
-
-
-# -- Params of the extensions ------------------------------------------------
-autosummary_ignore_module_all = True
-autosummary_imported_members = False
-add_module_names = False
-numpydoc_show_class_members = False
-plot_html_show_formats = False
-automodsumm_inherited_members = True
-# write out the files generated by automodapi, mainly for debugging
-automodsumm_writereprocessed = True
-automodapi_writereprocessed = True
-automodapi_inheritance_diagram = False
-automodapi_toctreedirnm = "_api"
-autosectionlabel_prefix_document = True
-
-autodoc_typehints = "none"
-
-doctest_global_setup = """
-import saqc
-import pandas as pd
-import numpy as np
-from saqc.constants import *
-"""
-# -- Other options -----------------------------------------------------------
-
-# Add any paths that contain templates here, relative to this directory.
-templates_path = ["_templates"]
-
-# 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 = ["_build", "Thumbs.db", ".DS_Store"]
-
-source_suffix = [".rst", ".md"]
-
-
-# -- Options for HTML output -------------------------------------------------
-
-# The name of the Pygments (syntax highlighting) style to use.
-pygments_style = "sphinx"
-
-# The theme to use for HTML and HTML Help pages.  See the documentation for
-# a list of builtin themes.
-html_theme = "nature"
-
-# use pandas theme
-# html_theme = "pydata_sphinx_theme"
-
-
-# html_theme_options = {
-# }
-
-# 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", "css"]
-
-# -- RST options -------
-rst_prolog = """
-.. |ufzLogo| image:: /ressources/images/Representative/UFZLogo.jpg
-   :width: 40 %
-   :target: https://www.ufz.de/
-
-.. |rdmLogo| image:: /ressources/images/Representative/RDMlogo.jpg
-   :width: 18 %
-   :target: https://www.ufz.de/index.php?de=45348
-   :class: align-right
-
-|ufzLogo| |rdmLogo|
-"""