add first pass at documentation

Author: ddbourgin

docs/Makefile

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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SOURCEDIR     = .
+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/conf.py

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+# -*- coding: utf-8 -*-
+#
+# Configuration file for the Sphinx documentation builder.
+#
+# This file does only contain a selection of the most common options. For a
+# full list see the documentation:
+# http://www.sphinx-doc.org/en/master/config
+
+# -- 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(".."))
+
+
+# -- Project information -----------------------------------------------------
+
+project = "numpy-ml"
+copyright = "2019, David Bourgin"
+author = "David Bourgin"
+
+# The short X.Y version
+version = ""
+# The full version, including alpha/beta/rc tags
+release = ""
+
+
+# -- 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.doctest",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.todo",
+    "sphinx.ext.coverage",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.ifconfig",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.githubpages",
+    "sphinx.ext.napoleon",
+    #  "numpydoc",
+]
+
+# Napoleon settings
+# https://sphinxcontrib-napoleon.readthedocs.io/en/latest/sphinxcontrib.napoleon.html#sphinxcontrib.napoleon.Config
+napoleon_google_docstring = False
+napoleon_numpy_docstring = True
+napoleon_include_init_with_doc = False
+napoleon_include_private_with_doc = False
+napoleon_include_special_with_doc = False
+napoleon_use_admonition_for_examples = False
+napoleon_use_admonition_for_notes = False
+napoleon_use_admonition_for_references = False
+napoleon_use_ivar = True
+napoleon_use_param = True
+napoleon_use_rtype = False
+napoleon_use_keyword = True
+
+
+# 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 master toctree document.
+master_doc = "index"
+
+# 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
+
+# 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"]
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = "friendly"
+
+autoclass_content = "both"
+
+
+# -- 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"
+
+# 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 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"]
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# The default sidebars (for documents that don't match any pattern) are
+# defined by theme itself.  Builtin themes are using these templates by
+# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
+# 'searchbox.html']``.
+#
+html_sidebars = {
+    "**": [
+        "about.html",
+        "navigation.html",
+        "relations.html",
+        "searchbox.html",
+        "donate.html",
+    ]
+}
+
+html_theme_options = {
+    #  'logo': 'logo.png',
+    "github_user": "ddbourgin",
+    "github_repo": "numpy-ml",
+    "description": "Machine learning, in NumPy",
+    #  'analytics_id': "", XXX: TODO
+    "github_button": True,
+    "show_powered_by": False,
+}
+
+
+# -- Options for HTMLHelp output ---------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = "numpy-mldoc"
+
+
+# -- 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, "numpy-ml.tex", "numpy-ml Documentation", "David Bourgin", "manual")
+]
+
+
+# -- 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, "numpy-ml", "numpy-ml Documentation", [author], 1)]
+
+
+# -- 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,
+        "numpy-ml",
+        "numpy-ml Documentation",
+        author,
+        "numpy-ml",
+        "Machine learning, in NumPy.",
+        "Miscellaneous",
+    )
+]
+
+
+# -- Options for Epub output -------------------------------------------------
+
+# Bibliographic Dublin Core info.
+epub_title = project
+
+# The unique identifier of the text. This can be a ISBN number
+# or the project homepage.
+#
+# epub_identifier = ''
+
+# A unique identification for the text.
+#
+# epub_uid = ''
+
+# A list of files that should not be packed into the epub file.
+epub_exclude_files = ["search.html"]
+
+autodoc_member_order = "bysource"
+
+
+# -- Extension configuration -------------------------------------------------
+
+# -- Options for intersphinx extension ---------------------------------------
+
+# Example configuration for intersphinx: refer to the Python standard library.
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/", None),
+    "numpy": ("http://docs.scipy.org/doc/numpy/", None),
+}
+
+# -- Options for todo extension ----------------------------------------------
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = True
+
+# -- Options for numpydocs extension -----------------------------------------
+# https://numpydoc.readthedocs.io/en/latest/install.html
+
+# Whether to produce plot:: directives for Examples sections that contain
+# import matplotlib or from matplotlib import.
+numpydoc_use_plots = True
+
+# Whether to show all members of a class in the Methods and Attributes sections
+# automatically. True by default.
+numpydoc_show_class_members = True
+
+#  Whether to show all inherited members of a class in the Methods and
+#  Attributes sections automatically. If it’s false, inherited members won’t
+#  shown. True by default.
+numpydoc_show_inherited_class_members = True
+
+#  Whether to create a Sphinx table of contents for the lists of class methods
+#  and attributes. If a table of contents is made, Sphinx expects each entry to
+#  have a separate page. True by default.
+numpydoc_class_members_toctree = False
+
+# A regular expression matching citations which should be mangled to avoid
+# conflicts due to duplication across the documentation. Defaults to [\w-]+.
+numpydoc_citation_re = r"[\w-]+"
+
+# Until version 0.8, parameter definitions were shown as blockquotes, rather
+# than in a definition list. If your styling requires blockquotes, switch this
+# config option to True. This option will be removed in version 0.10.
+numpydoc_use_blockquotes = False
+
+# Whether to format the Attributes section of a class page in the same way as
+# the Parameter section. If it's False, the Attributes section will be
+# formatted as the Methods section using an autosummary table. True by default.
+numpydoc_attributes_as_param_list = False
+
+# Whether to create cross-references for the parameter types in the Parameters,
+# Other Parameters, Returns and Yields sections of the docstring. False by
+# default.
+numpydoc_xref_param_type = False
+
+#  Mappings to fully qualified paths (or correct ReST references) for the
+#  aliases/shortcuts used when specifying the types of parameters. The keys
+#  should not have any spaces. Together with the intersphinx extension, you can
+#  map to links in any documentation. The default is an empty dict.  This
+#  option depends on the numpydoc_xref_param_type option being True.
+numpydoc_xref_aliases = {}
+
+#  Words not to cross-reference. Most likely, these are common words used in
+#  parameter type descriptions that may be confused for classes of the same
+#  name. For example: {'type', 'optional', 'default'}. The default is an empty
+#  set.
+numpydoc_xref_ignore = set([])
+
+#  Deprecated since version edit: your HTML template instead Whether to insert
+#  an edit link after docstrings.
+numpydoc_edit_link: bool

docs/img/gmm.png

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+Welcome to numpy-ml
+===================
+`numpy-ml`_ is a growing collection of machine learning models, algorithms, and
+tools written exclusively in `NumPy`_ and the Python `standard library`_. 
+
+The purpose of the project is to provide reference implementations of common
+machine learning components for rapid prototyping and experimentation. 
+
+.. _numpy-ml: http://www.github.com/ddbourgin/numpy-ml
+.. _NumPy: http://numpy.scipy.org/
+.. _standard library: https://docs.python.org/3/library/
+
+API Reference
+-------------
+.. toctree::
+   :maxdepth: 3
+
+   numpy_ml.hmm
+
+   numpy_ml.gmm
+
+   numpy_ml.lda
+
+   numpy_ml.ngram
+
+   numpy_ml.trees
+
+   numpy_ml.utils
+
+   numpy_ml.rl_models
+
+   numpy_ml.neural_nets
+
+   numpy_ml.linear_models
+
+   numpy_ml.nonparametric
+
+   numpy_ml.preprocessing
+
+##########
+Disclaimer	
+##########	
+	
+This software is provided as-is: there are no guarantees that it fits your
+purposes or that it is bug-free. Use it at your own risk!

docs/img/gmm_model.png

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+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+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%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+
+:end
+popd