Merge branch 'release/0.3.2'

.gitignore

@@ -7,6 +7,9 @@ dist/
 wayward.egg-info/
 .mypy_cache/
 .pytest_cache/
+docs/_build
+docs/_static
+docs/_templates
 
 .dmypy.json
 .python-version

.readthedocs.yml

@@ -0,0 +1,23 @@
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+
+# Build documentation with MkDocs
+#mkdocs:
+#  configuration: mkdocs.yml
+
+# Optionally build your docs in additional formats such as PDF and ePub
+formats: all
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+  version: 3.7
+  install:
+    - requirements: docs/requirements.txt

CHANGELOG.md

@@ -6,6 +6,20 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+- 
+
+## [0.3.2] - 2019-06-09
+
+### Added
+
+- Package documentation:
+    - Transclude basic instructions from README.
+    - Generate API documentation.
+    - Configuration for Read the Docs.
+    - Incorporate changelog via symlink.
+    - Add a Dickens example page.
+- Docs build status and PyPI version badges in README.
+
 ## [0.3.1] - 2019-06-05
 
 ### Added

README.rst

@@ -1,15 +1,28 @@
 Wayward
 =======
 
+.. image:: https://readthedocs.org/projects/wayward/badge/?version=latest
+   :target: https://wayward.readthedocs.io/en/latest/?badge=latest
+   :alt: Documentation status
+
+.. image:: https://badge.fury.io/py/wayward.svg
+   :target: https://pypi.org/project/wayward/
+   :alt: PyPI package version
+
+
+.. docs-inclusion-marker
+
 **Wayward** is a Python package that helps to identify characteristic terms from
-single documents or groups of documents. It can be used to create word clouds.
+single documents or groups of documents. It can be used for keyword extraction
+and several related tasks, and can create efficient sparse representations for
+classifiers. It was originally created to provide term weights for word clouds.
 
-Rather than use simple term frequency, it weighs terms by statistical models
-known as *parsimonious language models*. These models are good at picking up
-the terms that distinguish a text document from other documents in a
-collection.
+Rather than use simple term frequency to estimate the importance of words and
+phrases, it weighs terms by statistical models known as *parsimonious language
+models*. These models are good at picking up the terms that distinguish a text
+document from other documents in a collection.
 
-For this to work, a preferably large amount of documents are needed
+For this to work, a preferably large amount of documents is needed
 to serve as a background collection, to compare the documents of interest to.
 This could be a random sample of newspaper articles, for instance, but for many
 applications it works better to take a natural collection, such as a periodical
@@ -29,14 +42,14 @@ Installation
 
 Either install the latest release from PyPI::
 
-    pip install wayward
+    $ pip install wayward
 
 or clone the git repository, and use `Poetry <https://poetry.eustace.io/docs/>`_
 to install the package in editable mode::
 
-    git clone https://github.com/aolieman/wayward.git
-    cd wayward/
-    poetry install
+    $ git clone https://github.com/aolieman/wayward.git
+    $ cd wayward/
+    $ poetry install
 
 Usage
 -----
@@ -53,7 +66,7 @@ Usage
 
 The ``ParsimoniousLM`` is initialized with all document tokens as a
 background corpus, and subsequently takes a single document's tokens
-as input. Its ``top`` method returns the top terms and their probabilities:
+as input. Its ``top()`` method returns the top terms and their probabilities:
 
 >>> from wayward import ParsimoniousLM
 >>> plm = ParsimoniousLM(doc_tokens, w=.1)
@@ -75,23 +88,26 @@ method returns the top terms and their probabilities:
 
 >>> from wayward import SignificantWordsLM
 >>> swlm = SignificantWordsLM(doc_tokens, lambdas=(.7, .1, .2))
->>> swlm.group_top(10, doc_tokens[-3:])
-[('in', 0.37875318027881),
- ('is', 0.07195732361699828),
- ('mortal', 0.07195732361699828),
- ('nature', 0.07195732361699828),
- ('all', 0.07110584778711342),
- ('we', 0.03597866180849914),
- ('true', 0.03597866180849914),
- ('lovers', 0.03597866180849914),
- ('strange', 0.03597866180849914),
- ('capers', 0.03597866180849914)]
-
-See ``example/dickens.py`` for a running example with more realistic data.
-
-Background
-----------
-This package started out as `WeighWords <https://github.com/larsmans/weighwords/>`_,
+>>> swlm.group_top(10, doc_tokens[-2:], fix_lambdas=True)
+[('much', 0.09077675276900632),
+ ('lover', 0.06298706244865138),
+ ('will', 0.06298706244865138),
+ ('you', 0.04538837638450315),
+ ('your', 0.04538837638450315),
+ ('rhymes', 0.04538837638450315),
+ ('speak', 0.04538837638450315),
+ ('neither', 0.04538837638450315),
+ ('rhyme', 0.04538837638450315),
+ ('nor', 0.04538837638450315)]
+
+See |example/dickens.py|_ for a runnable example with more realistic data.
+
+.. |example/dickens.py| replace:: ``example/dickens.py``
+.. _example/dickens.py: https://github.com/aolieman/wayward/blob/master/example/dickens.py
+
+Origin and Relaunch
+-------------------
+This package started out as WeighWords_,
 written by Lars Buitinck at the University of Amsterdam. It provides an efficient
 parsimonious LM implementation, and a very accessible API.
 
@@ -104,6 +120,11 @@ the background collection. The parsimonization algorithm discounts terms that ar
 already well explained by the background model, until the most wayward terms come
 out on top.
 
+See the Changelog_ for an overview of the most important changes.
+
+..  _WeighWords: https://github.com/larsmans/weighwords/
+..  _Changelog: https://wayward.readthedocs.io/en/develop/changelog.html
+
 References
 ----------
 D. Hiemstra, S. Robertson, and H. Zaragoza (2004). `Parsimonious Language Models

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     = .
+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/api_docs/wayward.logsum.rst

@@ -0,0 +1,7 @@
+logsum module
+=====================
+
+.. automodule:: wayward.logsum
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/api_docs/wayward.parsimonious.rst

@@ -0,0 +1,6 @@
+parsimonious module
+===========================
+
+.. automodule:: wayward.parsimonious
+   :members:
+   :show-inheritance:

docs/api_docs/wayward.significant_words.rst

@@ -0,0 +1,6 @@
+significant\_words module
+=================================
+
+.. automodule:: wayward.significant_words
+   :members:
+   :show-inheritance:

docs/api_docs/wayward.specific_term_estimators.rst

@@ -0,0 +1,8 @@
+specific\_term\_estimators module
+=========================================
+
+.. automodule:: wayward.specific_term_estimators
+   :members:
+   :undoc-members:
+   :show-inheritance:
+   :exclude-members: logger

docs/changelog.md

@@ -0,0 +1 @@
+../CHANGELOG.md

docs/conf.py

@@ -0,0 +1,67 @@
+# 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:
+# 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 -----------------------------------------------------
+import pkg_resources
+
+project = 'Wayward'
+copyright = (
+    '2019, TinQwise Stamkracht, University of Amsterdam'
+)
+author = 'Alex Olieman'
+
+# The full version, including alpha/beta/rc tags
+release = pkg_resources.get_distribution('wayward').version
+
+master_doc = 'index'
+
+# -- 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.napoleon',
+    'sphinx.ext.viewcode',
+    'recommonmark',
+]
+
+# 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']
+
+
+# -- 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'
+html_show_sourcelink = True
+
+# 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']
+
+html_theme_options = {
+    'collapse_navigation': False,
+}