Update to release v3.0.0a1

Author: markjonestx

.coveragerc

@@ -4,6 +4,7 @@ omit =
     */site-packages/nose/*
     */tests/*
     *.pyi
+    PyPWA/libs/logger.py
 
 exclude_lines =
     raise NotImplementedError

.gitignore

@@ -1,6 +1,7 @@
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
+.pytest_cache/
 
 # C extensions
 *.so
@@ -74,14 +75,6 @@ docs/build/
 # PyBuilder
 target/
 
-# Virtualenv
-virt/
-virt3/
-venv/
-venv2/
-
-# PyCharm
-.idea/
-
 # MyPy
 /.mypy_cache/
+

.travis.yml

@@ -1,42 +1,35 @@
 sudo: false
+dist: xenial
 language: python
 cache: pip
 python:
-  - "2.7"
-  - "3.4"
-  - "3.5"
-  - "3.6"
-  - "3.6-dev"
+  - "3.7"
+  - "3.8-dev"
 matrix:
   allow_failures:
-    - python: "3.6-dev"
+    - python: "3.8-dev"
 addons:
   apt:
     packages:
       - "build-essential"
       - "gfortran"
       - "libatlas-base-dev"
+      - "libopenblas-dev"
+      - "liblapack-dev"
+      - "python-dev"
+      - "cython"
 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"
-  - "pip install pytest-runner --upgrade"
-  - "pip install pytest-cov --upgrade"
-  - "pip install pytest-logging --upgrade"
+  - "pip install --upgrade coveralls coverage"
+  - "pip install --upgrade pytest pytest-runner pytest-cov"
 install:
-  - "pip install -e ."
-script: "py.test --cov=PyPWA tests/ -vvvv"
+  - "pip install --upgrade -e ."
+script: "pytest --cov=PyPWA tests --cov-report="
 after_success:
-  - ls -a
   - coveralls
-  - head .coverage
 notifications:
   emails:
     on_success: change

CHANGELOG.md

@@ -5,6 +5,39 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/)
 and this project adheres to [Semantic Versioning](http://semver.org/)
 
 
+## [3.0.0a1] - 2019-6-17
+### Added
+ - Added numpy reader and writer.
+ - Adds a helper script to clean the project directory of caches.
+ - Adds initial documentation for PyPWA.
+ - Added support for 3 Vectors, 4 Vectors, and Particles
+ - Added ParticlePool to aid in working with multiple Particles
+ - Added a binning utility that supports multiple binning variables and
+   dimensions
+ - Added PyTables support, so that large datasets can be easily managed
+### Changed
+ - All program names have been lowercased
+ - Configuration package has been compressed into a single module
+ - PySimulate now is a library that has no UI, and has a UI portion
+   that exclusively works with interfacing
+ - Fuzzywuzzy is now optional
+ - Process package is now a single module. Interface no longer uses IS_DUPLEX
+ - Bulk of program functionality moved to libs, progs being just for UI
+ - Builtin Plugins moved to libs, old plugin's plugins have still reside
+   in plugins, but under a package with the appropriate name. I.E. data
+   plugins are in plugins/data.
+ - All file related libs have been moved to libs/file
+ - Combined optimizers with fit library
+ - GAMP was updated to use Particles and ParticlePool
+ - Files with extra newline should parse correctly now
+ - CSV and TSV files will be lf instead of crlf on linux systems now
+### Removed
+ - Nestle Minimization. There is currently no clear way to have Minuit and
+   Nestle to operate with each other nicely. Implementation for multiple
+   optimizers will remain, as well as new associated issues created.
+ - Removed support for all version of Python before 3.7
+
+
 ## [2.2.1] - 2017-10-16
 ### Fixed
  - Setup would pull in unstable Yaml parser
@@ -26,7 +59,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/)
    on the interfaces purpose.
  - PyFit no longer assumes bins are named 'BinN' you must specify Bin names 
    in 'internal data'.
- - Multipler effect for the Miminzers has been moved to the individual
+ - Multiplier effect for the Minimizers has been moved to the individual
    likelihoods.
  - PyMask defaults to AND operations instead of or now.
 ### Fixed
@@ -77,7 +110,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/)
  - Packaging
 
 
-[Unreleased]: https://github.com/JeffersonLab/PyPWA/compare/v2.2.0...development
+[Unreleased]: https://github.com/JeffersonLab/PyPWA/compare/v3.0.0a1...development
+[3.0.0a1]: https://github.com/JeffersonLab/PyPWA/compare/v2.2.1...v3.0.0a1
 [2.2.1]: https://github.com/JeffersonLab/PyPWA/compare/v2.2.0...v2.2.1
 [2.2.0]: https://github.com/JeffersonLab/PyPWA/compare/v2.1.0...v2.2.0
 [2.1.0]: https://github.com/JeffersonLab/PyPWA/compare/v2.0.0...v2.1.0

CONTRIBUTORS.md

@@ -1,16 +1,17 @@
 # Contributors to PyPWA (in Chronological Order)
 
-## PyPWA Staff:
+### Current PyPWA Staff:
  - Carlos Salgado <https://github.com/cwsalgado>
  - Will Phelps <https://github.com/wphelps>
+ - Mark Jones <markjonestx@live.com> <https://github.com/Markjonestx>
+ 
+### Previous PyPWA Staff:
  - 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>
  - Christopher Banks <https://github.com/cjbanks>
 
-High School Interns:
-
+### High School Interns:
  - Ryan Wright <https://github.com/painballking>
    - Ran Amplitude benchmarks on the XeonPhi

PyPWA/__init__.py

@@ -38,18 +38,18 @@
 - PyIntensities - Just the calculation half of PySimulate.
 
 - 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.
 
 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 
+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
@@ -77,18 +77,14 @@
 respectively.
 """
 
+
 __author__ = "PyPWA Team and Contributors"
 __credits__ = ["Mark Jones"]
-__version__ = "2.2.0"
+__version__ = "3.0.0.dev"
 
 
-EMAIL = "pypwa@jlab.org"
 LICENSE = "GPLv3"
-STATUS = "stable"
+STATUS = "development"
 MAINTAINER = "Mark Jones"
 AUTHOR = __author__
 VERSION = __version__
-
-
-from PyPWA.builtin_plugins.data.iterator import Iterator
-from PyPWA.builtin_plugins.data.memory import Memory