🚧 [MAINT] New year, CI build corrections, and links (#23)

Fix formatting by running black on the rfgb directory. Fix 2017-2018 -> 2017-2019 Fix links that pointed to old repository locations Drop 3.3/3.4 from .travis.yml Add 3.8-dev to .travis.yml Add dist: xenial to .travis.yml Add Documentation/Tracker/Code links to setup.py Fix variable style (pre-pylint) for _log_prior in rfgb/boosting.py
hayesall · Aug 12, 2019 · 947f5c4 · 947f5c4
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diff --git a/.travis.yml b/.travis.yml
@@ -1,21 +1,19 @@
 sudo: false
-
+dist: xenial
 language: python
 
 env:
   - SH=bash
 
 python:
   - "2.7"
-  - "3.3"
-  - "3.4"
   - "3.5"
-  - "3.5-dev"
   - "3.6"
-  - "3.6-dev"
-  - "3.7-dev"
+  - "3.7"
+  - "3.8-dev"
 
-cache: pip
+cache:
+  pip: true
 
 install:
   - "pip install -r rfgb/tests/requirements.txt"
@@ -27,4 +25,4 @@ before_install:
   pip install codecov
 
 after_success:
-  codecov
+  codecov
diff --git a/README.rst b/README.rst
@@ -1,20 +1,33 @@
-Relational Functional Gradient Boosting (RFGB)
-==============================================
+##############################################
+Relational Functional Gradient Boosting (rfgb)
+##############################################
 
-*Relational Functional Gradient Boosting in Python.*
+|PyPi|_ |License|_ |Travis|_ |Codecov|_ |ReadTheDocs|_
 
-  .. image:: https://img.shields.io/github/license/starling-lab/rfgb.py.svg?style=flat-square
-	   :target: https://github.com/starling-lab/rfgb.py/blob/master/LICENSE
-  .. image:: https://img.shields.io/github/tag/starling-lab/rfgb.py.svg?style=flat-square
-	   :target: https://github.com/starling-lab/rfgb.py/releases
-  .. image:: https://img.shields.io/travis/starling-lab/rfgb.py.svg?style=flat-square
-	   :target: https://travis-ci.org/starling-lab/rfgb.py
-  .. image:: https://img.shields.io/codecov/c/github/starling-lab/rfgb.py/master.svg?style=flat-square
-	   :target: https://codecov.io/gh/starling-lab/rfgb.py?branch=master
-  .. image:: https://readthedocs.org/projects/rfgbpy/badge/?version=stable&style=flat-square
-	   :target: https://rfgbpy.readthedocs.io/en/stable/
+.. |PyPi| image:: https://img.shields.io/pypi/v/rfgb.svg
+  :alt: Python Package Index (PyPi) latest version.
+.. _PyPi: https://pypi.org/project/rfgb/
 
-**Kaushik Roy** (`@kkroy36`_) and **Alexander L. Hayes** (`@batflyer`_)
+.. |License| image:: https://img.shields.io/github/license/hayesall/rfgb.svg
+  :alt: License.
+.. _License: https://github.com/hayesall/rfgb/blob/master/LICENSE
+
+.. |Travis| image:: https://travis-ci.org/hayesall/rfgb.svg?branch=master
+  :alt: Master branch build status.
+.. _Travis: https://travis-ci.org/hayesall/rfgb
+
+.. |Codecov| image:: https://codecov.io/gh/hayesall/rfgb/branch/master/graphs/badge.svg?branch=master
+  :alt: Master branch code coverage.
+.. _Codecov: https://codecov.io/github/hayesall/rfgb?branch=master
+
+.. |ReadTheDocs| image:: https://readthedocs.org/projects/rfgb/badge/?version=latest
+  :alt: Documentation build status and link to documentation.
+.. _ReadTheDocs: http://rfgb.readthedocs.io/en/latest/
+
+**rfgb**: Relational Functional Gradient Boosting (in Python).
+
+- **Documentation**: https://rfgb.readthedocs.io/en/latest/
+- **Questions?** Contact `Alexander L. Hayes (hayesall) <https://hayesall.com>`_
 
 Installation
 ------------
@@ -29,8 +42,8 @@ Or develop further by cloning the repository
 
 .. code-block:: bash
 
-		git clone https://github.com/starling-lab/rfgb.py.git
-		cd rfgb.py/
+		git clone https://github.com/hayesall/rfgb.git
+		cd rfgb/
 		python setup.py develop
 
 Quick-Start
@@ -117,12 +130,4 @@ This program is free software: you can redistribute it and/or modify it under th
 
 This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
 
-A full `copy of the license <https://github.com/starling-lab/rfgb.py/blob/master/LICENSE>`_ is available in the base of this repository. For more information, see https://www.gnu.org/licenses/
-
-Acknowledgements
-----------------
-
-The authors would like to thank Professor Sriraam Natarajan, Professor Gautam Kunapuli, and fellow members of the `StARLinG Lab <https://starling.utdallas.edu>`_ at the University of Texas at Dallas.
-
-  .. _`@kkroy36`: https://github.com/kkroy36/
-  .. _`@batflyer`: https://github.com/batflyer/
+A full `copy of the license <https://github.com/hayesall/rfgb/blob/master/LICENSE>`_ is available in the base of this repository. For more information, see https://www.gnu.org/licenses/
diff --git a/contributors.md b/contributors.md
@@ -1,11 +1,11 @@
-# RFGB Contributors
+# rfgb Contributors
 
+* [Alexander L. Hayes](https://hayesall.com) ([hayesall](https://github.com/hayesall))
 * Kaushik Roy ([kkroy36](https://github.com/kkroy36))
-* Alexander L. Hayes ([batflyer](https://github.com/batflyer))
+* Changbin ([Hugo101](https://github.com/Hugo101))
 * Vignesh ([vignesh0710](https://github.com/vignesh0710))
 
 ## Credits
 
-* RFGB is based on BoostSRL, which is developed by Jude Shavlik, Tushar Khot, Sriraam Natarajan, Phillip Odom, Shuo Yang, Mayukh Das, Devendra Singh Dhami, Kaushik Roy, Alexander L. Hayes, Nandini Ramanan, Srijita Das, and Navdeep Kaur.
-
-* Sriraam Natarajan, Tushar Khot, Kristian Kersting, and Jude Shavlik, "Boosted Statistical Relational Learners: From Benchmarks to Data-Driven Medicine." SpringerBriefs in Computer Science, ISBN: 978-3-319-13643-1, 2015.
+- RFGB is based on BoostSRL, which is developed by Jude Shavlik, Tushar Khot, Sriraam Natarajan, Phillip Odom, Shuo Yang, Mayukh Das, Devendra Singh Dhami, Kaushik Roy, Alexander L. Hayes, Nandini Ramanan, Srijita Das, and Navdeep Kaur.
+- Sriraam Natarajan, Tushar Khot, Kristian Kersting, and Jude Shavlik, "Boosted Statistical Relational Learners: From Benchmarks to Data-Driven Medicine." SpringerBriefs in Computer Science, ISBN: 978-3-319-13643-1, 2015.
diff --git a/docs/source/commandline/01_workflow.rst b/docs/source/commandline/01_workflow.rst
@@ -12,7 +12,7 @@ Some of the ideas built here are shamelessly inspired by Git, so the workflows f
                 $ rfgb --help
                 usage: rfgb [-h] [-V] {init,learn,infer} ...
 
-                rfgb.py: Relational Functional Gradient Boosting is a gradient-boosting
+                rfgb: Relational Functional Gradient Boosting is a gradient-boosting
                 approach to learning statistical relational models.
 
                 optional arguments:

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 #
-# rfgb.py documentation build configuration file, created by
+# rfgb documentation build configuration file, created by
 # sphinx-quickstart on Thu Jun  7 13:09:12 2018.
 #
 # This file is execfile()d with the current directory set to its
@@ -48,25 +48,14 @@
 master_doc = 'index'
 
 # General information about the project.
-project = 'rfgb.py'
-copyright = '2018, Kaushik Roy (@kkroy36), Alexander L. Hayes (@batflyer)'
-author = 'Kaushik Roy (@kkroy36), Alexander L. Hayes (@batflyer)'
+project = 'rfgb'
+copyright = '2019 Alexander L. Hayes (@hayesall)'
+author = 'Alexander L. Hayes (@hayesall)'
 
-# 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 = '0.2.2'
-# The full version, including alpha/beta/rc tags.
-release = '0.2.2'
+from rfgb._metadata import __version__
 
-# 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
+version = __version__
+release = __release__
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -114,38 +103,14 @@
 }
 
 
-# -- Options for HTMLHelp output ------------------------------------------
-
-# Output file base name for HTML help builder.
-htmlhelp_basename = 'rfgbpydoc'
-
-
 # -- 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, 'rfgbpy.tex', 'rfgb.py Documentation',
-     'Kaushik Roy (@kkroy36), Alexander L. Hayes (@batflyer)', 'manual'),
+    (master_doc, 'rfgb.tex', 'rfgb Documentation',
+     'Alexander L. Hayes (@hayesall)', 'manual'),
 ]
 
 
@@ -154,7 +119,7 @@
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    (master_doc, 'rfgbpy', 'rfgb.py Documentation',
+    (master_doc, 'rfgb', 'rfgb Documentation',
      [author], 1)
 ]
 
@@ -165,7 +130,7 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'rfgbpy', 'rfgb.py Documentation',
-     author, 'rfgbpy', 'One line description of project.',
+    (master_doc, 'rfgb', 'rfgb Documentation',
+     author, 'rfgb', 'One line description of project.',
      'Miscellaneous'),
 ]
diff --git a/docs/source/development/01_contributing.rst b/docs/source/development/01_contributing.rst
@@ -26,12 +26,12 @@ Development Cheat-Sheet
 
    .. code-block:: bash
 
-		   git clone https://github.com/starling-lab/rfgb.py.git
+		   git clone https://github.com/hayesall/rfgb.git
 
 2. **Building local copy of documentation**
 
    We use Sphinx autodoc with a combination of inline docstrings and reStructuredText for documenting this project. Pull requests and further updates should include appropriate documentation.
-   
+
    A local copy of the documentation may be built from the Makefile:
 
    .. code-block:: bash

diff --git a/docs/source/getting_started/02_getting_started.rst b/docs/source/getting_started/02_getting_started.rst
@@ -17,17 +17,17 @@ Installation
 
 		   pip install rfgb
 
-2. Development builds on `GitHub <https://github.com/starling-lab/rfgb.py>`_
+2. Development builds on `GitHub <https://github.com/hayesall/rfgb>`_
 
    .. code-block:: bash
 
-		   pip install git+git://github.com/starling-lab/rfgb.py.git
+		   pip install git+git://github.com/hayesall/rfgb.git
 
-3. Bleeding-edge development builds on the `GitHub Development Branch <https://github.com/starling-lab/rfgb.py/tree/development>`_
+3. Bleeding-edge development builds on the `GitHub Development Branch <https://github.com/hayesall/rfgb/tree/development>`_
 
    .. code-block:: bash
 
-		   pip install git+git://github.com/starling-lab/rfgb.py.git@development
+		   pip install git+git://github.com/hayesall/rfgb.git@development
 
 
 Background
@@ -38,7 +38,7 @@ The main function of ``rfgb`` is to learn relational dependency networks [#]_ vi
 .. image:: rfgb.svg
 
 This algorithm is implemented as the ``__main__`` method for the ``rfgb`` package.
-	   
+
 .. code-block:: python
 
 		# rfgb.__main__
@@ -48,7 +48,7 @@ This algorithm is implemented as the ``__main__`` method for the ``rfgb`` packag
 		from .utils import Utils
 
 		# ... class Arguments:
-		
+
 		parameters = Arguments().args
 
 		for target in parameters.target:

diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -1,11 +1,6 @@
-.. rfgb.py documentation master file, created by
-   sphinx-quickstart on Thu Jun  7 13:09:12 2018.
-   You can adapt this file completely to your liking, but it should at least
-   contain the root `toctree` directive.
-
-=======
-rfgb.py
-=======
+====
+rfgb
+====
 
 .. toctree::
    :glob:

diff --git a/rfgb/__init__.py b/rfgb/__init__.py
@@ -1,23 +1,24 @@
+# -*- coding: utf-8 -*-
 
-# Copyright (C) 2017-2018 RFGB Contributors
-
+# Copyright © 2017-2019 rfgb Contributors
+#
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
 # the Free Software Foundation, either version 3 of the License, or
 # (at your option) any later version.
-
+#
 # This program is distributed in the hope that it will be useful,
 # but WITHOUT ANY WARRANTY; without even the implied warranty of
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
 # GNU General Public License for more details.
-
+#
 # You should have received a copy of the GNU General Public License
 # along with this program (at the base of this repository). If not,
 # see <http://www.gnu.org/licenses/>
 
 """
-rfgb.py
-=======
+rfgb
+====
 
 Provides
     1. The ability to perform Relational Functional Gradient Boosting (RFGB)
@@ -30,21 +31,20 @@
 code, mostly consisting of high-level overviews and some usage examples.
 
 As this grows in complexity, documentation will likely be found in either
-the doc strings for individual functions (i.e. rfgb.__doc__), or online as
-https://starling.utdallas.edu/
+the doc strings for individual functions (i.e. rfgb.__doc__), or online.
 """
 
-from rfgb.utils import Utils
-from rfgb.tree import node
-from rfgb.boosting import updateGradients
-from rfgb.boosting import performInference
-import rfgb._metadata
-import rfgb.cmd
-
-__author__ = rfgb._metadata.__author__
-__copyright__ = rfgb._metadata.__copyright__
-__license__ = rfgb._metadata.__license__
-__version__ = rfgb._metadata.__version__
-__maintainer__ = rfgb._metadata.__maintainer__
-__email__ = rfgb._metadata.__email__
-__status__ = rfgb._metadata.__status__
+from .utils import Utils
+from .tree import node
+from .boosting import updateGradients
+from .boosting import performInference
+
+from ._metadata import (
+    __author__,
+    __maintainer__,
+    __email__,
+    __copyright__,
+    __license__,
+    __version__,
+    __status__,
+)