Merge pull request #149 from chrislit/0.3.6

0.3.6
chrislit · Nov 17, 2018 · 71985bb · 71985bb
2 parents f435470 + c0060e6
commit 71985bb
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diff --git a/.codeclimate.yml b/.codeclimate.yml
@@ -22,4 +22,4 @@ exclude_patterns:
 - "docs/"
 - "setup.py"
 - "badge_update.py"
-- "_bmdata.py"
+- "_beider_morse_data.py"
diff --git a/.travis.yml b/.travis.yml
@@ -18,17 +18,17 @@ matrix:
 
 notifications:
   email: false
- 
+
 # Install packages
 install:
   - if [[ $TRAVIS_PYTHON_VERSION == 2* ]]; then travis_retry pip install pyliblzma; fi
   - travis_retry pip install coveralls
   - travis_retry python setup.py install
- 
+
 # Run test
 script:
   - nosetests --verbose --with-coverage --cover-erase --cover-branches --cover-package=abydos --logging-level=INFO --process-timeout=60 --process-restartworker
- 
+
 # Calculate coverage
 after_success:
   - coveralls --verbose --rcfile=.coveragerc
diff --git a/CODING_STANDARDS.rst b/CODING_STANDARDS.rst
@@ -1,6 +1,14 @@
 CODING STANDARDS
 ----------------
 
+- nosetest will be used for testing
+- flake8 will be used for best practice conformance
+- pydocstyle will be used to ensure documentation style conformance to PEP257
+  (for the most part) and NumPy documentation style
+- black will be used to keep code style consistent
+
+----
+
 git commits
 ~~~~~~~~~~~
 
@@ -15,6 +23,8 @@ git pushes
 A git push should be performed only under the following conditions:
 
 - library is syntactically correct (compiling correctly) in both Python 2 & 3
-- library passes all tests according to nosetests in both Python 2 & 3
+- library passes all tests and doctests according to nosetests in both Python 2
+  & 3
 - test coverage is 100% according to nosetests
-- using the included pylint.rc, pylint reports a 10/10 rating
+- flake8 and pydocstyle should report 0 issues
+- black code styling has been applied
diff --git a/HISTORY.rst b/HISTORY.rst
@@ -2,6 +2,22 @@ Release History
 ---------------
 
 
+0.3.6 (2018-11-17) *classy carl*
+++++++++++++++++++++++++++++++++
+
+doi:10.5281/zenodo.1490288
+
+Changes:
+
+- Most functions were encapsulated into classes.
+- Each class is broken out into its own file, with test files paralleling
+  library files.
+- Documentation was converted from Sphinx markup to Numpy style.
+- A tutorial was written for each subpackage.
+- Documentation was cleaned up, with math markup corrections and many
+  additional links.
+
+
 0.3.5 (2018-10-31) *cantankerous carl*
 ++++++++++++++++++++++++++++++++++++++
 

diff --git a/README.rst b/README.rst
@@ -8,13 +8,13 @@ Abydos
 +------------------+------------------------------------------------------+
 | Dependencies     | |requires| |snyk| |pyup| |fossa|                     |
 +------------------+------------------------------------------------------+
-| Local Analysis   | |pylint| |flake8| |black|                            |
+| Local Analysis   | |pylint| |flake8| |pydocstyle| |black|               |
 +------------------+------------------------------------------------------+
 | Usage            | |docs| |mybinder| |license| |sourcerank| |zenodo|    |
 +------------------+------------------------------------------------------+
 | Contribution     | |cii| |waffle| |openhub|                             |
 +------------------+------------------------------------------------------+
-| PyPI             | |pypi| |pypi-ver|                                    |
+| PyPI             | |pypi| |pypi-dl| |pypi-ver|                          |
 +------------------+------------------------------------------------------+
 | conda-forge      | |conda| |conda-dl| |conda-platforms|                 |
 +------------------+------------------------------------------------------+
@@ -71,14 +71,18 @@ Abydos
      :target: https://app.fossa.io/projects/git%2Bgithub.com%2Fchrislit%2Fabydos?ref=badge_shield
      :alt: FOSSA Status
 
-.. |pylint| image:: https://img.shields.io/badge/Pylint-9.5/10-green.svg
+.. |pylint| image:: https://img.shields.io/badge/Pylint-9.16/10-yellowgreen.svg
    :target: #
    :alt: Pylint Score
 
-.. |flake8| image:: https://img.shields.io/badge/flake8-2-green.svg
+.. |flake8| image:: https://img.shields.io/badge/flake8-0-brightgreen.svg
    :target: #
    :alt: flake8 Errors
 
+.. |pydocstyle| image:: https://img.shields.io/badge/pydocstyle-0-brightgreen.svg
+   :target: #
+   :alt: pydocstyle Errors
+
 .. |black| image:: https://img.shields.io/badge/code%20style-black-000000.svg
    :target: https://github.com/ambv/black
    :alt: black
@@ -91,16 +95,16 @@ Abydos
     :target: https://mybinder.org/v2/gh/chrislit/abydos/master?filepath=binder
     :alt: Binder
 
-.. |license| image:: https://img.shields.io/badge/License-GPL%20v3-blue.svg
+.. |license| image:: https://img.shields.io/badge/License-GPL%20v3+-blue.svg
     :target: https://www.gnu.org/licenses/gpl-3.0
-    :alt: License: GPL v3
+    :alt: License: GPL v3.0+
 
 .. |sourcerank| image:: https://img.shields.io/librariesio/sourcerank/pypi/abydos.svg
     :target: https://libraries.io/pypi/abydos
     :alt: Libraries.io SourceRank
 
-.. |zenodo| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.1462443.svg
-   :target: https://doi.org/10.5281/zenodo.1463204
+.. |zenodo| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.1490288.svg
+   :target: https://doi.org/10.5281/zenodo.1490288
    :alt: Zenodo
 
 .. |cii| image:: https://bestpractices.coreinfrastructure.org/projects/1598/badge
@@ -119,7 +123,11 @@ Abydos
     :target: https://pypi.python.org/pypi/abydos
     :alt: PyPI
 
-.. |pypi-ver| image:: 	https://img.shields.io/pypi/pyversions/abydos.svg
+.. |pypi-dl| image:: https://img.shields.io/pypi/dm/abydos.svg
+    :target: https://pypi.python.org/pypi/abydos
+    :alt: PyPI downloads/month
+
+.. |pypi-ver| image:: https://img.shields.io/pypi/pyversions/abydos.svg
     :target: https://pypi.python.org/pypi/abydos
     :alt: PyPI versions
 
@@ -138,11 +146,12 @@ Abydos
 |
 
 .. image:: https://raw.githubusercontent.com/chrislit/abydos/master/abydos-small.png
+    :target: https://github.com/chrislit/abydos
     :alt: abydos
     :align: right
 
 |
-| Abydos NLP/IR library
+| `Abydos NLP/IR library <https://github.com/chrislit/abydos>`_
 | Copyright 2014-2018 by Christopher C. Little
 
 Abydos is a library of phonetic algorithms, string distance measures & metrics,
@@ -188,6 +197,7 @@ stemmers, and string fingerprinters including:
     - SoundexBR
     - NRL English-to-phoneme
     - Beider-Morse Phonetic Matching
+
 - String distance metrics
     - Levenshtein distance
     - Optimal String Alignment distance
@@ -212,7 +222,7 @@ stemmers, and string fingerprinters including:
     - Monge-Elkan similarity & distance
     - Matrix similarity
     - Needleman-Wunsch score
-    - Smither-Waterman score
+    - Smith-Waterman score
     - Gotoh score
     - Length similarity
     - Prefix, Suffix, and Identity similarity & distance
@@ -226,6 +236,7 @@ stemmers, and string fingerprinters including:
     - Typo distance
     - Indel distance
     - Synoname
+
 - Stemmers
     - the Lovins stemmer
     - the Porter and Porter2 (Snowball English) stemmers
@@ -236,6 +247,7 @@ stemmers, and string fingerprinters including:
     - Paice-Husk Stemmer
     - Schinke Latin stemmer
     - S stemmer
+
 - String Fingerprints
     - string fingerprint
     - q-gram fingerprint
@@ -248,6 +260,7 @@ stemmers, and string fingerprinters including:
     - Cisłak & Grabowski's position fingerprint
     - Synoname Toolcode
 
+
 -----
 
 Installation
@@ -279,7 +292,7 @@ To install Abydos (latest release) from PyPI using pip::
 
    pip install abydos
 
-To install from `conda-forge <https://conda-forge.org/>`_::
+To install from `conda-forge <https://anaconda.org/conda-forge/abydos>`_::
 
    conda install abydos
 
@@ -292,10 +305,10 @@ To run the whole test-suite just call tox::
 
     tox
 
-The tox setup has the following environments: py27, py36, doctest,
-py27-regression, py36-regression, pylint, pycodestyle, flake8, doc8,
-badges, docs, py27-fuzz, & py36-fuzz. So if only want to generate documentation
-(in HTML, EPUB, & PDF formats), just call::
+The tox setup has the following environments: black, py36, py27, doctest,
+py36-regression, py27-regression, py36-fuzz, py27-fuzz, pylint, pycodestyle,
+pydocstyle, flake8, doc8, badges, docs, & dist. So if you only want to generate
+documentation (in HTML, EPUB, & PDF formats), just call::
 
     tox -e docs
 
@@ -304,4 +317,6 @@ In order to only run & generate Flake8 reports, call::
     tox -e flake8
 
 Contributions such as bug reports, PRs, suggestions, desired new features, etc.
-are welcome through the Github Issues & Pull requests.
+are welcome through Github
+`Issues <https://github.com/chrislit/abydos/issues>`_ &
+`Pull requests <https://github.com/chrislit/abydos/pulls>`_.
diff --git a/abydos/__init__.py b/abydos/__init__.py
@@ -19,8 +19,36 @@
 """abydos.
 
 Abydos NLP/IR library by Christopher C. Little
+
+
+There are nine major packages that make up Abydos:
+
+    - :py:mod:`.compression` for string compression classes
+    - :py:mod:`.corpus` for document corpus classes
+    - :py:mod:`.distance` for string distance measure & metric classes
+    - :py:mod:`.fingerprint` for string fingerprint classes
+    - :py:mod:`.phones` for functions relating to phones and phonemes
+    - :py:mod:`.phonetic` for phonetic algorithm classes
+    - :py:mod:`.stats` for statistical functions and a confusion table class
+    - :py:mod:`.stemmer` for stemming classes
+    - :py:mod:`.tokenizer` for tokenizer classes
+
+Classes with each package have consistent method names, as discussed below.
+A tenth package, :py:mod:`.util`, contains functions not intended for end-user
+use.
+
+----
+
 """
-__version__ = '0.3.5'
+
+from __future__ import (
+    absolute_import,
+    division,
+    print_function,
+    unicode_literals,
+)
+
+__version__ = '0.3.6'
 
 __all__ = [
     'compression',

diff --git a/abydos/compression/__init__.py b/abydos/compression/__init__.py
@@ -16,30 +16,51 @@
 # You should have received a copy of the GNU General Public License
 # along with Abydos. If not, see <http://www.gnu.org/licenses/>.
 
-"""abydos.compression.
+r"""abydos.compression.
 
 The compression package defines compression and compression-related functions
 for use within Abydos, including implementations of the following:
 
-    - arithmetic coding functions (ac_train, ac_encode, & ac_decode)
-    - Burrows-Wheeler transform encoder/decoder (bwt_encode & bwt_decode)
-    - Run-Length Encoding encoder/decoder (rle_encode & rle_decode)
+        - :py:class:`.Arithmetic` for arithmetic coding
+        - :py:class:`.BWT` for Burrows-Wheeler Transform
+        - :py:class:`.RLE` for Run-Length Encoding
+
+
+Each class exposes ``encode`` and ``decode`` methods for performing and
+reversing its encoding. For example, the Burrows-Wheeler Transform can be
+performed by creating a :py:class:`.BWT` object and then calling
+:py:meth:`.BWT.encode` on a string:
+
+>>> bwt = BWT()
+>>> bwt.encode('^BANANA')
+'ANNB^AA\x00'
+
+----
+
 """
 
-from __future__ import unicode_literals
+from __future__ import (
+    absolute_import,
+    division,
+    print_function,
+    unicode_literals,
+)
 
-from ._arithmetic import ac_decode, ac_encode, ac_train
-from ._bwt import bwt_decode, bwt_encode
-from ._rle import rle_decode, rle_encode
+from ._arithmetic import Arithmetic, ac_decode, ac_encode, ac_train
+from ._bwt import BWT, bwt_decode, bwt_encode
+from ._rle import RLE, rle_decode, rle_encode
 
 __all__ = [
+    'Arithmetic',
+    'ac_decode',
+    'ac_encode',
+    'ac_train',
+    'BWT',
     'bwt_decode',
     'bwt_encode',
+    'RLE',
     'rle_decode',
     'rle_encode',
-    'ac_decode',
-    'ac_encode',
-    'ac_train',
 ]