Merge pull request #112 from JeffersonLab/release-v2.0.0

Merges in release v2.0.0 into master

.gitignore

@@ -67,8 +67,9 @@ coverage.xml
 *.log
 
 # Sphinx documentation
-doc/_build/
-doc/build/
+docs/_build/
+docs/build/
+/docs/output/
 
 # PyBuilder
 target/
@@ -79,3 +80,6 @@ virt3/
 
 # PyCharm
 .idea/
+
+# MyPy
+/.mypy_cache/

.travis.yml

@@ -3,13 +3,31 @@ language: python
 cache: pip
 python:
   - "2.7"
-  - "3.3"
   - "3.4"
   - "3.5"
+  - "3.6"
+  - "3.6-dev"
+  - "3.7-dev"
+  - "nightly"
+matrix:
+  allow_failures:
+    - python: "3.6-dev"
+    - python: "3.7-dev"
+    - python: "nightly"
+addons:
+  apt:
+    packages:
+      - "build-essential"
+      - "gfortran"
+      - "libatlas-base-dev"
 before_install:
   - python --version
   - uname -a
   - ls -a
+  - "pip install --upgrade pip setuptools wheel"
+  - "pip install --upgrade numpy scipy"
+  - "pip install --upgrade iminuit nestle ruamel.yaml tabulate appdirs"
+  - "pip install --upgrade fuzzywuzzy python-Levenshtein"
   - "pip install coveralls --upgrade"
   - "pip install coverage --upgrade"
   - "pip install pytest --upgrade"
@@ -24,9 +42,6 @@ after_success:
   - coveralls
   - head .coverage
 notifications:
-  emails: false
-  slack:
-    rooms:
-      - pypwa:qPFpdrleMXOkj6mE18RctZQR
+  emails:
     on_success: change
     on_failure: change

CHANGELOG.mg

@@ -0,0 +1,25 @@
+# Changelog
+All changes important to the user will be documented in this file.
+
+The format is based on [Keep a Changelog](http://keepachangelog.com/) 
+and this project adheres to [Semantic Versioning](http://semver.org/)
+
+## [2.0.0] - 2017-6-5
+### Added
+ - Plugin Subsystem
+ - Configurator Subsystem
+ - Data Plugin
+ - SV Plugin
+ - EVIL Plugin
+ - GAMP Plugin
+ - Data Caching
+ - Processing Plugin
+ - iMinuit plugin
+ - Nestle likelihood
+ - PyFit plugin
+ - Log Likelihood Plugin
+ - Chi-Squared Likelihood
+ - PySim plugin
+ - Packaging
+
+[2.0.0]: https://github.com/JeffersonLab/PyPWA/compare/v1.1...v2.0.0

CONTRIBUTORS.md

@@ -0,0 +1,15 @@
+# Contributors to PyPWA (in Chronological Order)
+
+## PyPWA Staff:
+ - Carlos Salgado <https://github.com/cwsalgado>
+ - Will Phelps <https://github.com/wphelps>
+ - Brandon DeMello <https://github.com/bdell>
+ - Stephanie Bramlett <https://github.com/skbramlett>
+ - Josh Pond <https://github.com/JTPond>
+ - Mark Jones <markjonestx@live.com> <https://github.com/Markjonestx>
+ - LaRay Hare <https://github.com/lmhare>
+
+High School Interns:
+
+ - Ryan Wright <https://github.com/painballking>
+   - Ran Amplitude benchmarks on the XeonPhi

PyPWA/__init__.py

@@ -1,38 +1,86 @@
-#    PyPWA, a scientific analysis toolkit.
-#    Copyright (C) 2016  JLab
+#  coding=utf-8
 #
-#    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.
+#  PyPWA, a scientific analysis toolkit.
+#  Copyright (C) 2016 JLab
 #
-#    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.
+#  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.
 #
-#    You should have received a copy of the GNU General Public License
-#    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#  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.  If not, see <http://www.gnu.org/licenses/>.
 
 """
-PyPWA is an attempt to have a set multiprocessing tools to easy the
-Partial Wave Analysis process.
+============
+General Docs
+============
+
+PyPWA is statistical analysis toolkit that was built with Partial Wave
+Analysis in mind, however you should be able to use the tools included for
+anything statistical analysis.
+
+Currently there are 4 different applications defined inside this package:
+
+- PyFit - Fitting with any likelihood.
+
+- PyLikelihood - Fitting with the log-likelihood.
+
+- PyChiSquared - Fitting with the ChiSquared likelihood.
+
+- PySimulate - Simulation of an amplitude.
+
+- PyIntensities - Just the calculation half of PySimulate.
 
-Current there is a multiprocessing tool for both the Acceptance Rejection
-Model, and the Maximum-Likelihood Estimation for fitting.
+- PyRejection - Just the rejection-method half of PySimulate.
+    
+For information about how to use each of the programs, look in the docs folder
+included with the source code, or check the user docs at ReadTheDocs.io.
 
-The tools work with Kinematic Variables defined in standard text files,
-Comma Separated Variables, and Tab Separated Variables.
+Developer Docs
+==============
+
+To attempt to achieve a flexible fitter that could be quickly adapted to
+changing needs, we actually built the entire package around a generalized 
+plugin loader. The "main" objects ore defined as plugins, along with each 
+task that needed to be solved. This means that fitting, data loading, 
+the processing module, simulation, optimizers, etc are all defined as 
+plugins internally.
+
+Package purposes
+----------------
+
+- builtin_plugins - This is where each internal plugin is defined, 
+  the optimizers, the processing module, and the builtin parser and reader are
+  all defined here.
+
+- core - The true main of the program, this is where all the interfaces are
+  defined, the plugin loaders, plugin storage modules, and the main execution
+  logic that takes a simple YML file and translates it into executing code.
+
+- entries - The various entry points for each program contained in this 
+  package are here, each function defined here is a starting point for 
+  setuptools.
+ 
+- shell - This is where PySimulate and PyFit are defined.
+
+For more information on how each module works, view their documentation
+respectively.
 """
 
-__author__ = ["Mark Jones"]
+__author__ = "PyPWA Team and Contributors"
 __credits__ = ["Mark Jones"]
-__license__ = "GPLv3"
-__email__ = "maj@jlab.org"
-__status__ = "development"
-__maintainer__ = ["Mark Jones"]
-__version__ = "2.0.0-rc5"
+__version__ = "2.0.0"
+
 
+EMAIL = "pypwa@jlab.org"
+LICENSE = "GPLv3"
+STATUS = "development"
+MAINTAINER = "Mark Jones"
+AUTHOR = __author__
 VERSION = __version__
-STATUS = __status__
-LICENSE = __license__

PyPWA/builtin_plugins/__init__.py

@@ -1,31 +1,42 @@
-#    PyPWA, a scientific analysis toolkit.
-#    Copyright (C) 2016  JLab
+#  coding=utf-8
 #
-#    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.
+#  PyPWA, a scientific analysis toolkit.
+#  Copyright (C) 2016 JLab
 #
-#    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.
+#  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.
 #
-#    You should have received a copy of the GNU General Public License
-#    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#  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.  If not, see <http://www.gnu.org/licenses/>.
 
 """
-This module holds the built in Plugins for the program along with various
-needed libraries.
+All the plugins that come packaged with PyPWA by default.
+---------------------------------------------------------
+
+- data - A not so basic data plugin that supports caching, different file 
+  types, can be extended, and even supports both parsing and iterating.
+
+- minuit - A python / cython minimizer based on ROOT's PyPWA.
+
+- nestle - A python maximizer based off of Multinest.
+
+- process - A Kernel based multiprocessing module. Allows for an 
+  embarrassingly parallel calculation to be expanded across multiple cores.
+  
+For more information about how these plugins work, see their documentation 
+as well.
 """
 
 
-from PyPWA import VERSION, LICENSE, STATUS
+from PyPWA import AUTHOR, VERSION
 
-__author__ = ["Mark Jones"]
 __credits__ = ["Mark Jones"]
-__maintainer__ = ["Mark Jones"]
-__email__ = "maj@jlab.org"
-__status__ = STATUS
-__license__ = LICENSE
+__author__ = AUTHOR
 __version__ = VERSION