diff --git a/.gitignore b/.gitignore index afe3b1aa6..d6bf048cb 100644 --- a/.gitignore +++ b/.gitignore @@ -64,3 +64,59 @@ target/ # Annoying stuff from contributors venv .DS_Store + +# Created by https://www.gitignore.io/api/pycharm + +### PyCharm ### +# Covers JetBrains IDEs: IntelliJ, RubyMine, PhpStorm, AppCode, PyCharm, CLion, Android Studio and Webstorm +# Reference: https://intellij-support.jetbrains.com/hc/en-us/articles/206544839 + +# User-specific stuff: +.idea/workspace.xml +.idea/tasks.xml +.idea/dictionaries +.idea/vcs.xml +.idea/jsLibraryMappings.xml + +# Sensitive or high-churn files: +.idea/dataSources.ids +.idea/dataSources.xml +.idea/dataSources.local.xml +.idea/sqlDataSources.xml +.idea/dynamic.xml +.idea/uiDesigner.xml + +# Gradle: +.idea/gradle.xml +.idea/libraries + +# Mongo Explorer plugin: +.idea/mongoSettings.xml + +## File-based project format: +*.iws + +## Plugin-specific files: + +# IntelliJ +/out/ + +# mpeltonen/sbt-idea plugin +.idea_modules/ + +# JIRA plugin +atlassian-ide-plugin.xml + +# Crashlytics plugin (for Android Studio and IntelliJ) +com_crashlytics_export_strings.xml +crashlytics.properties +crashlytics-build.properties +fabric.properties + +### PyCharm Patch ### +# Comment Reason: https://github.com/joeblau/gitignore.io/issues/186#issuecomment-215987721 + +# *.iml +# modules.xml +# .idea/misc.xml +# *.ipr diff --git a/docs/Makefile b/docs/Makefile new file mode 100644 index 000000000..0d0bca988 --- /dev/null +++ b/docs/Makefile @@ -0,0 +1,225 @@ +# Makefile for Sphinx documentation +# + +# You can set these variables from the command line. +SPHINXOPTS = +SPHINXBUILD = sphinx-build +PAPER = +BUILDDIR = _build + +# Internal variables. +PAPEROPT_a4 = -D latex_paper_size=a4 +PAPEROPT_letter = -D latex_paper_size=letter +ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . +# the i18n builder cannot share the environment and doctrees with the others +I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . + +.PHONY: help +help: + @echo "Please use \`make ' where is one of" + @echo " html to make standalone HTML files" + @echo " dirhtml to make HTML files named index.html in directories" + @echo " singlehtml to make a single large HTML file" + @echo " pickle to make pickle files" + @echo " json to make JSON files" + @echo " htmlhelp to make HTML files and a HTML help project" + @echo " qthelp to make HTML files and a qthelp project" + @echo " applehelp to make an Apple Help Book" + @echo " devhelp to make HTML files and a Devhelp project" + @echo " epub to make an epub" + @echo " epub3 to make an epub3" + @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter" + @echo " latexpdf to make LaTeX files and run them through pdflatex" + @echo " latexpdfja to make LaTeX files and run them through platex/dvipdfmx" + @echo " text to make text files" + @echo " man to make manual pages" + @echo " texinfo to make Texinfo files" + @echo " info to make Texinfo files and run them through makeinfo" + @echo " gettext to make PO message catalogs" + @echo " changes to make an overview of all changed/added/deprecated items" + @echo " xml to make Docutils-native XML files" + @echo " pseudoxml to make pseudoxml-XML files for display purposes" + @echo " linkcheck to check all external links for integrity" + @echo " doctest to run all doctests embedded in the documentation (if enabled)" + @echo " coverage to run coverage check of the documentation (if enabled)" + @echo " dummy to check syntax errors of document sources" + +.PHONY: clean +clean: + rm -rf $(BUILDDIR)/* + +.PHONY: html +html: + $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html + @echo + @echo "Build finished. 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The XML files are in $(BUILDDIR)/xml." + +.PHONY: pseudoxml +pseudoxml: + $(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml + @echo + @echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml." + +.PHONY: dummy +dummy: + $(SPHINXBUILD) -b dummy $(ALLSPHINXOPTS) $(BUILDDIR)/dummy + @echo + @echo "Build finished. Dummy builder generates no files." diff --git a/docs/_static/.gitkeep b/docs/_static/.gitkeep new file mode 100644 index 000000000..e69de29bb diff --git a/docs/_templates/.gitkeep b/docs/_templates/.gitkeep new file mode 100644 index 000000000..e69de29bb diff --git a/docs/api/modules.rst b/docs/api/modules.rst new file mode 100644 index 000000000..6814db03e --- /dev/null +++ b/docs/api/modules.rst @@ -0,0 +1,7 @@ +API Reference +============== + +.. toctree:: + :maxdepth: 4 + + yellowbrick diff --git a/docs/api/yellowbrick.rst b/docs/api/yellowbrick.rst new file mode 100644 index 000000000..c7b063df2 --- /dev/null +++ b/docs/api/yellowbrick.rst @@ -0,0 +1,94 @@ +yellowbrick package +=================== + +Submodules +---------- + +yellowbrick.anscombe module +--------------------------- + +.. automodule:: yellowbrick.anscombe + :members: + :undoc-members: + :show-inheritance: + +yellowbrick.base module +----------------------- + +.. automodule:: yellowbrick.base + :members: + :undoc-members: + :show-inheritance: + +yellowbrick.classifier module +----------------------------- + +.. automodule:: yellowbrick.classifier + :members: + :undoc-members: + :show-inheritance: + +yellowbrick.color_utils module +------------------------------ + +.. automodule:: yellowbrick.color_utils + :members: + :undoc-members: + :show-inheritance: + +yellowbrick.exceptions module +----------------------------- + +.. automodule:: yellowbrick.exceptions + :members: + :undoc-members: + :show-inheritance: + +yellowbrick.regressor module +---------------------------- + +.. automodule:: yellowbrick.regressor + :members: + :undoc-members: + :show-inheritance: + +yellowbrick.utils module +------------------------ + +.. automodule:: yellowbrick.utils + :members: + :undoc-members: + :show-inheritance: + +yellowbrick.version module +-------------------------- + +.. automodule:: yellowbrick.version + :members: + :undoc-members: + :show-inheritance: + +yellowbrick.yb_palettes module +------------------------------ + +.. automodule:: yellowbrick.yb_palettes + :members: + :undoc-members: + :show-inheritance: + +yellowbrick.yb_rcmod module +--------------------------- + +.. automodule:: yellowbrick.yb_rcmod + :members: + :undoc-members: + :show-inheritance: + + +Module contents +--------------- + +.. automodule:: yellowbrick + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/conf.py b/docs/conf.py new file mode 100644 index 000000000..4f14dbc3f --- /dev/null +++ b/docs/conf.py @@ -0,0 +1,348 @@ +#!/usr/bin/env python3 +# -*- coding: utf-8 -*- +# +# yellowbrick documentation build configuration file, created by +# sphinx-quickstart on Tue Jul 5 19:45:43 2016. +# +# This file is execfile()d with the current directory set to its +# containing dir. +# +# Note that not all possible configuration values are present in this +# autogenerated file. +# +# All configuration values have a default; values that are commented out +# serve to show the default. + +# 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('..')) + +# -- General configuration ------------------------------------------------ + +# If your documentation needs a minimal Sphinx version, state it here. +# +# needs_sphinx = '1.0' + +# 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.intersphinx', + 'sphinx.ext.coverage', + 'sphinx.ext.mathjax', + 'sphinx.ext.viewcode', +] + +# Add any paths that contain templates here, relative to this directory. +templates_path = ['_templates'] + +# The suffix(es) of source filenames. +# You can specify multiple suffix as a list of string: +# +# source_suffix = ['.rst', '.md'] +source_suffix = '.rst' + +# The encoding of source files. +# +# source_encoding = 'utf-8-sig' + +# The master toctree document. +master_doc = 'index' + +# General information about the project. +project = 'yellowbrick' +copyright = '2016, District Data Labs' +author = 'District Data Labs' + +# The version info for the project you're documenting, acts as replacement for +# |version| and |release|, also used in various other places throughout the +# built documents. +# +# The short X.Y version. +version = '0.1' +# The full version, including alpha/beta/rc tags. +release = '0.1' + +# The language for content autogenerated by Sphinx. Refer to documentation +# for a list of supported languages. +# +# This is also used if you do content translation via gettext catalogs. +# Usually you set "language" from the command line for these cases. +language = None + +# There are two options for replacing |today|: either, you set today to some +# non-false value, then it is used: +# +# today = '' +# +# Else, today_fmt is used as the format for a strftime call. +# +# today_fmt = '%B %d, %Y' + +# List of patterns, relative to source directory, that match files and +# directories to ignore when looking for source files. +# This patterns also effect to html_static_path and html_extra_path +exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] + +# The reST default role (used for this markup: `text`) to use for all +# documents. +# +# default_role = None + +# If true, '()' will be appended to :func: etc. cross-reference text. +# +# add_function_parentheses = True + +# If true, the current module name will be prepended to all description +# unit titles (such as .. function::). +# +# add_module_names = True + +# If true, sectionauthor and moduleauthor directives will be shown in the +# output. They are ignored by default. +# +# show_authors = False + +# The name of the Pygments (syntax highlighting) style to use. +pygments_style = 'sphinx' + +# A list of ignored prefixes for module index sorting. +# modindex_common_prefix = [] + +# If true, keep warnings as "system message" paragraphs in the built documents. +# keep_warnings = False + +# If true, `todo` and `todoList` produce output, else they produce nothing. +todo_include_todos = False + + +# -- 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 = 'sphinx_rtd_theme' + +# Theme options are theme-specific and customize the look and feel of a theme +# further. For a list of options available for each theme, see the +# documentation. +# +# html_theme_options = {} + +# Add any paths that contain custom themes here, relative to this directory. +# html_theme_path = [] + +# The name for this set of Sphinx documents. +# " v documentation" by default. +# +# html_title = 'yellowbrick v0.1' + +# A shorter title for the navigation bar. Default is the same as html_title. +# +# html_short_title = None + +# The name of an image file (relative to this directory) to place at the top +# of the sidebar. +# +# html_logo = None + +# The name of an image file (relative to this directory) to use as a favicon of +# the docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 +# pixels large. +# +# html_favicon = None + +# 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'] + +# Add any extra paths that contain custom files (such as robots.txt or +# .htaccess) here, relative to this directory. These files are copied +# directly to the root of the documentation. +# +# html_extra_path = [] + +# If not None, a 'Last updated on:' timestamp is inserted at every page +# bottom, using the given strftime format. +# The empty string is equivalent to '%b %d, %Y'. +# +# html_last_updated_fmt = None + +# If true, SmartyPants will be used to convert quotes and dashes to +# typographically correct entities. +# +# html_use_smartypants = True + +# Custom sidebar templates, maps document names to template names. +# +# html_sidebars = {} + +# Additional templates that should be rendered to pages, maps page names to +# template names. +# +# html_additional_pages = {} + +# If false, no module index is generated. +# +# html_domain_indices = True + +# If false, no index is generated. +# +# html_use_index = True + +# If true, the index is split into individual pages for each letter. +# +# html_split_index = False + +# If true, links to the reST sources are added to the pages. +# +# html_show_sourcelink = True + +# If true, "Created using Sphinx" is shown in the HTML footer. Default is True. +# +# html_show_sphinx = True + +# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. +# +# html_show_copyright = True + +# If true, an OpenSearch description file will be output, and all pages will +# contain a tag referring to it. The value of this option must be the +# base URL from which the finished HTML is served. +# +# html_use_opensearch = '' + +# This is the file name suffix for HTML files (e.g. ".xhtml"). +# html_file_suffix = None + +# Language to be used for generating the HTML full-text search index. +# Sphinx supports the following languages: +# 'da', 'de', 'en', 'es', 'fi', 'fr', 'h', 'it', 'ja' +# 'nl', 'no', 'pt', 'ro', 'r', 'sv', 'tr', 'zh' +# +# html_search_language = 'en' + +# A dictionary with options for the search language support, empty by default. +# 'ja' uses this config value. +# 'zh' user can custom change `jieba` dictionary path. +# +# html_search_options = {'type': 'default'} + +# The name of a javascript file (relative to the configuration directory) that +# implements a search results scorer. If empty, the default will be used. +# +# html_search_scorer = 'scorer.js' + +# Output file base name for HTML help builder. +htmlhelp_basename = 'yellowbrickdoc' + +# -- Options for LaTeX output --------------------------------------------- + +latex_elements = { + # The paper size ('letterpaper' or 'a4paper'). + # + # 'papersize': 'letterpaper', + + # The font size ('10pt', '11pt' or '12pt'). + # + # 'pointsize': '10pt', + + # Additional stuff for the LaTeX preamble. + # + # 'preamble': '', + + # Latex figure (float) alignment + # + # 'figure_align': 'htbp', +} + +# Grouping the document tree into LaTeX files. List of tuples +# (source start file, target name, title, +# author, documentclass [howto, manual, or own class]). +latex_documents = [ + (master_doc, 'yellowbrick.tex', 'yellowbrick Documentation', + 'District Data Labs', 'manual'), +] + +# The name of an image file (relative to this directory) to place at the top of +# the title page. +# +# latex_logo = None + +# For "manual" documents, if this is true, then toplevel headings are parts, +# not chapters. +# +# latex_use_parts = False + +# If true, show page references after internal links. +# +# latex_show_pagerefs = False + +# If true, show URL addresses after external links. +# +# latex_show_urls = False + +# Documents to append as an appendix to all manuals. +# +# latex_appendices = [] + +# If false, no module index is generated. +# +# latex_domain_indices = True + + +# -- Options for manual page output --------------------------------------- + +# One entry per manual page. List of tuples +# (source start file, name, description, authors, manual section). +man_pages = [ + (master_doc, 'yellowbrick', 'yellowbrick Documentation', + [author], 1) +] + +# If true, show URL addresses after external links. +# +# man_show_urls = False + + +# -- Options for Texinfo output ------------------------------------------- + +# Grouping the document tree into Texinfo files. List of tuples +# (source start file, target name, title, author, +# dir menu entry, description, category) +texinfo_documents = [ + (master_doc, 'yellowbrick', 'yellowbrick Documentation', + author, 'yellowbrick', 'One line description of project.', + 'Miscellaneous'), +] + +# Documents to append as an appendix to all manuals. +# +# texinfo_appendices = [] + +# If false, no module index is generated. +# +# texinfo_domain_indices = True + +# How to display URL addresses: 'footnote', 'no', or 'inline'. +# +# texinfo_show_urls = 'footnote' + +# If true, do not generate a @detailmenu in the "Top" node's menu. +# +# texinfo_no_detailmenu = False + + +# Locations of objects.inv files for intersphinx extension that auto links to external api docs. +intersphinx_mapping = {'python': ('https://docs.python.org/3', None), + 'matplotlib': ('http://matplotlib.org/', None), + 'scipy': ('http://scipy.github.io/devdocs/', None), + 'numpy': ('https://docs.scipy.org/doc/numpy-dev/', None), + 'cycler': ('http://matplotlib.org/cycler/', None), + 'seaborn': ('https://web.stanford.edu/~mwaskom/software/seaborn/', None)} diff --git a/docs/index.md b/docs/index.md deleted file mode 100644 index 6b647f28c..000000000 --- a/docs/index.md +++ /dev/null @@ -1,33 +0,0 @@ -# Welcome to Yellowbrick - -**A suite of visual analysis and diagnostic tools to facilitate feature selection, model selection, and parameter tuning for machine learning.** - -## Tools for feature analysis and selection - -- boxplots (box-and-whisker plots) -- violinplots -- histograms -- scatter plot matrices (sploms) -- radial visualizations (radviz) -- parallel coordinates -- jointplots -- diagonal correlation matrix - - -## Tools for model evaluation - -### Classification - -- ROC curves -- classification heatmaps - -### Regression - -- prediction error plots -- residual plots - - -## Tools for parameter tuning - -- validation curves -- gridsearch heatmap diff --git a/docs/index.rst b/docs/index.rst new file mode 100644 index 000000000..67aa52988 --- /dev/null +++ b/docs/index.rst @@ -0,0 +1,68 @@ +.. yellowbrick documentation master file, created by + sphinx-quickstart on Tue Jul 5 19:45:43 2016. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +Welcome to yellowbrick's documentation! +======================================= + +**Yellowbrick is a suite of visual analysis and diagnostic tools to facilitate feature selection, model selection, and parameter tuning for machine learning.** + +Tools for feature analysis and selection +------------------------------------------ + +- boxplots (box-and-whisker plots) +- violinplots +- histograms +- scatter plot matrices (sploms) +- radial visualizations (radviz) +- parallel coordinates +- jointplots +- diagonal correlation matrix + + +Tools for model evaluation +---------------------------- + +Classification +^^^^^^^^^^^^^^^ + +- ROC curves +- classification heatmaps + +Regression +^^^^^^^^^^^^ + +- prediction error plots +- residual plots + + +Tools for parameter tuning +---------------------------- + +- validation curves +- gridsearch heatmap + + + + + + +Contents: +========== + +.. toctree:: + :maxdepth: 2 + + setup + api/modules + + + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` + diff --git a/docs/setup.md b/docs/setup.rst similarity index 78% rename from docs/setup.md rename to docs/setup.rst index fe05ec7e2..0f8738742 100644 --- a/docs/setup.md +++ b/docs/setup.rst @@ -1,23 +1,22 @@ -# Welcome to yellowbrick - -## Quick Start +Quick Start +============== This quick start is intended to get you setup with Yellowbrick in development mode (since the project is still under development). 1. Fork and clone the repository. After clicking fork in the upper right corner for your own copy of yellowbrick to your github account. Clone it in a directory -of your choice. +of your choice.:: $ git clone https://github.com/[YOURUSERNAME]/yellowbrick $ cd yellowbrick -2. Create virtualenv and create the dependencies +2. Create virtualenv and create the dependencies:: $ virtualenv venv $ pip install -r requirements.txt -3. Fetch and switch to development. +3. Fetch and switch to development.:: $ git fetch $ git checkout develop diff --git a/mkdocs.yml b/mkdocs.yml deleted file mode 100644 index c8e810a23..000000000 --- a/mkdocs.yml +++ /dev/null @@ -1,10 +0,0 @@ -site_name: Yellowbrick -theme: readthedocs -repo_name: GitHub -repo_url: https://github.com/DistrictDataLabs/yellowbrick -site_description: A suite of visual analysis and diagnostic tools for machine learning. -site_author: District Data Labs -copyright: "© 2016 District Data Labs, All Rights Reserved" - -pages: - - "Introduction": index.md diff --git a/requirements.txt b/requirements.txt index 7016aacb5..46a4e65b8 100644 --- a/requirements.txt +++ b/requirements.txt @@ -24,3 +24,7 @@ cycler==0.10.0 #pip==8.1.2 #setuptools==22.0.5 #wsgiref==0.1.2 + +## Documentation (uncomment to build documentation) +#Sphinx==1.4.4 +#sphinx-rtd-theme==0.1.9 \ No newline at end of file diff --git a/yellowbrick/yb_palettes.py b/yellowbrick/yb_palettes.py index adaf24abd..d2e272fba 100644 --- a/yellowbrick/yb_palettes.py +++ b/yellowbrick/yb_palettes.py @@ -86,40 +86,58 @@ def as_hex(self): def color_palette(palette=None, n_colors=None, desat=None): """Return a list of colors defining a color palette. - Availible seaborn palette names: - accent, dark, paired, pastel, bold, muted - Availible seaborn palette names: - sns_deep, sns_muted, sns_bright, sns_pastel, sns_dark, sns_colorblind - Other options: - list of colors Calling this function with ``palette=None`` will return the current matplotlib color cycle. This function can also be used in a ``with`` statement to temporarily set the color cycle for a plot or set of plots. - Parameters - ---------- - palette: None, string, or sequence, optional + + :param palette: Name of palette or None to return current palette. If a sequence, input colors are used but possibly cycled and desaturated. - n_colors : int, optional + + Available seaborn palette names from :py:mod:`seaborn.palettes` are: + + .. hlist:: + :columns: 3 + + * :py:const:`deep` + * :py:const:`dark` + * :py:const:`paired` + * :py:const:`pastel` + * :py:const:`bold` + * :py:const:`muted` + * :py:const:`sns_deep` + * :py:const:`sns_muted` + * :py:const:`sns_bright` + * :py:const:`sns_pastel` + * :py:const:`sns_dark` + * :py:const:`sns_colorblind` + + :type palette: None or str or sequence + :param n_colors: Number of colors in the palette. If ``None``, the default will depend on how ``palette`` is specified. Named palettes default to 6 colors (except paired, which has 10), but grabbing the current palette or passing in a list of colors will not change the number of colors unless this is specified. Asking for more colors than exist in the palette will cause it to cycle. + :type n_colors: int or None + :param desat: + :type desat: - Returns - ------- - palette : list of RGB tuples. + :rtype: list(tuple) + :return: list of RGB tuples. Color palette. Behaves like a list, but can be used as a context - manager and possesses an ``as_hex`` method to convert to hex color + manager and possesses an :py:meth:`as_hex` method to convert to hex color codes. - See Also - -------- - set_palette : Set the default color cycle for all plots. - set_color_codes : Reassign color codes like ``"b"``, ``"g"``, etc. to - colors from one of the yellowbrick palettes. + + .. seealso:: + + :func:`.set_palette` + Set the default color cycle for all plots. + :func:`.set_color_codes` + Reassign color codes like ``"b"``, ``"g"``, etc. to + colors from one of the yellowbrick palettes. """ if palette is None: palette = get_color_cycle()