ljvmiranda921 · ljvmiranda921 · Aug 9, 2018 · Jun 11, 2018 · Jun 11, 2018 · Jun 12, 2018
diff --git a/.flake8 b/.flake8
@@ -0,0 +1,5 @@
+[flake8]
+ignore = E203, E266, E501, W503, F403, F401
+max-line-length = 79
+max-complexity = 18
+select = B,C,E,F,W,T4,B9
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -0,0 +1,37 @@
+<!--- Provide a general summary of your changes in the Title above -->
+
+## Description
+<!--- Describe your changes in detail -->
+
+## Related Issue
+<!--- This project only accepts pull requests related to open issues -->
+<!--- If suggesting a new feature or change, please discuss it in an issue first -->
+<!--- If fixing a bug, there should be an issue describing it with steps to reproduce -->
+<!--- Please link to the issue here: -->
+
+## Motivation and Context
+<!--- Why is this change required? What problem does it solve? -->
+
+## How Has This Been Tested?
+<!--- Please describe in detail how you tested your changes. -->
+<!--- Include details of your testing environment, and the tests you ran to -->
+<!--- see how your change affects other areas of the code, etc. -->
+
+## Screenshots (if appropriate):
+
+## Types of changes
+<!--- What types of changes does your code introduce? Put an `x` in all the boxes that apply: -->
+- [ ] Bug fix (non-breaking change which fixes an issue)
+- [ ] New feature (non-breaking change which adds functionality)
+- [ ] Breaking change (fix or feature that would cause existing functionality to change)
+
+## Checklist:
+<!--- Go over all the following points, and put an `x` in all the boxes that apply. -->
+<!--- If you're unsure about any of these, don't hesitate to ask. We're here to help! -->
+- [ ] My code follows the code style of this project.
+- [ ] My change requires a change to the documentation.
+- [ ] I have updated the documentation accordingly.
+- [ ] I have read the **CONTRIBUTING** document.
+- [ ] I have added tests to cover my changes.
+- [ ] All new and existing tests passed.
+
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,10 @@
+repos:
+-   repo: https://github.com/ambv/black
+    rev: stable
+    hooks:
+    - id: black
+      language_version: python3.6
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v1.2.3
+    hooks:
+    - id: flake8
diff --git a/AUTHORS.rst b/AUTHORS.rst
@@ -9,20 +9,23 @@ The package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypacka
 .. _Cookiecutter: https://github.com/audreyr/cookiecutter
 .. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage
 
-Development Lead
-----------------
+Maintainers
+-----------
 
 * Lester James V. Miranda (`@ljvmiranda921`_)
+* Aaron Moser (`@whzup`_)
+* Siobhán K. Cronin (`@SioKCronin`_)
 
 Contributors
 ------------
 
 * Carl-K (`@Carl-K`_)
-* Siobhán K Cronin (`@SioKCronin`_)
 * Andrew Jarcho (`@jazcap53`_)
 * Charalampos Papadimitriou (`@CPapadim`_)
 * Mamady Nabé (`@mamadyonline`_)
 * Erik (`@slek120`_)
+* Jay Speidell (`@jayspeidell`_)
+* Bradahoward (`@bradahoward`_)
 * Thomas (`@ThomasCES`_)
 
 .. _`@ljvmiranda921`: https://github.com/ljvmiranda921
@@ -32,4 +35,7 @@ Contributors
 .. _`@CPapadim`: https://github.com/CPapadim
 .. _`@mamadyonline`: https://github.com/mamadyonline
 .. _`@slek120`: https://github.com/slek120
+.. _`@whzup`: https://github.com/whzup
+.. _`@jayspeidell`: https://github.com/jayspeidell
+.. _`@bradahoward`: https://github.com/bradahoward
 .. _`@ThomasCES`: https://github.com/ThomasCES
diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst
@@ -77,13 +77,15 @@ Ready to contribute? Here's how to set up `pyswarms` for local development.
 
    Now you can make your changes locally.
 
-5. When you're done making changes, check that your changes pass flake8 and the tests, including testing other Python versions with tox::
+5. When you're done making changes, check that your changes pass flake8 and the tests, including testing other Python versions with tox. In addition, ensure that your code is formatted using black::
 
     $ flake8 pyswarms tests
+    $ black pyswarms tests
     $ python setup.py test or py.test
     $ tox
 
-   To get flake8 and tox, just pip install them into your virtualenv.
+   To get flake8, black, and tox, just pip install them into your virtualenv. If you wish,
+   you can add pre-commit hooks for both flake8 and black to make all formatting easier.
 
 6. Commit your changes and push your branch to GitHub::
 

diff --git a/README.md b/README.md
@@ -8,6 +8,7 @@
 [![Documentation Status](https://readthedocs.org/projects/pyswarms/badge/?version=master)](https://pyswarms.readthedocs.io/en/master/?badge=development)
 [![License: MIT](https://img.shields.io/badge/license-MIT-blue.svg )](https://raw.githubusercontent.com/ljvmiranda921/pyswarms/master/LICENSE)
 [![DOI](http://joss.theoj.org/papers/10.21105/joss.00433/status.svg)](https://doi.org/10.21105/joss.00433)
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/ambv/black)
 [![Gitter Chat](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/pyswarms/Issues)
 
 PySwarms is an extensible research toolkit for particle swarm optimization
@@ -186,39 +187,67 @@ fresh run to plot the cost and create animation.
 ```python
 import pyswarms as ps
 from pyswarms.utils.functions import single_obj as fx
-from pyswarms.utils.environments import PlotEnvironment
+from pyswarms.utils.plotters import plot_cost_history
 # Set-up optimizer
 options = {'c1':0.5, 'c2':0.3, 'w':0.9}
-optimizer = ps.single.GlobalBestPSO(n_particles=10, dimensions=3, options=options)
-# Initialize plot environment
-plt_env = PlotEnvironment(optimizer, fx.sphere_func, 1000)
+optimizer = ps.single.GlobalBestPSO(n_particles=50, dimensions=2, options=options)
+optimizer.optimize(fx.sphere_func, iters=100)
 # Plot the cost
-plt_env.plot_cost(figsize=(8,6));
+plot_cost_history(optimizer.cost_history)
 plt.show()
 ```
 
-<img src="./docs/examples/output_9_0.png" width="460">
+<img src="./docs/examples/output_8_0.png" width="460">
 
-We can also plot the animation,
+We can also plot the animation...
 
 ```python
-plt_env.plot_particles2D(limits=((-1.2,1.2),(-1.2,1.2))
+from pyswarms.utils.plotters.formatters import Mesher
+from pyswarms.utils.plotters.formatters import Designer
+# Plot the sphere function's mesh for better plots
+m = Mesher(func=fx.sphere_func)
+# Adjust figure limits
+d = Designer(limits=[(-1,1), (-1,1), (-0.1,1)],
+             label=['x-axis', 'y-axis', 'z-axis'])
 ```
 
-<img src="./docs/examples/output_3d.gif" width="460">
+In 2D,
 
+```python
+plot_contour(pos_history=optimizer.pos_history, mesher=m, mark=(0,0))
+```
+
+![Contour](https://i.imgur.com/H3YofJ6.gif)
+
+Or in 3D!
+
+```python
+pos_history_3d = m.compute_history_3d(optimizer.pos_history) # preprocessing
+animation3d = plot_surface(pos_history=pos_history_3d,
+                           mesher=m, designer=d,
+                           mark=(0,0,0))    
+```
+
+![Surface](https://i.imgur.com/kRb61Hx.gif)
 
 ## Contributing
 
-PySwarms is currently maintained by a single person (me!) with the aid of a
-few but very helpful contributors. We would appreciate it if you can lend a
-hand with the following:
+PySwarms is currently maintained by a small yet dedicated team:
+- Lester James V. Miranda ([@ljvmiranda921](https://github.com/ljvmiranda921))
+- Siobhán K. Cronin ([@SioKCronin](https://github.com/SioKCronin))
+- Aaron Moser ([@whzup](https://github.com/whzup))
+
+And we would appreciate it if you can lend a hand with the following:
 
 * Find bugs and fix them
 * Update documentation in docstrings
 * Implement new optimizers to our collection
 * Make utility functions more robust.
 
+We would also like to acknowledge [all our
+contributors](http://pyswarms.readthedocs.io/en/latest/authors.html), past and
+present, for making this project successful!
+
 If you wish to contribute, check out our [contributing guide].
 Moreover, you can also see the list of features that need some help in our
 [Issues] page.

diff --git a/docs/api/_pyswarms.utils.rst b/docs/api/_pyswarms.utils.rst
@@ -1,12 +1,13 @@
 Utilities
 =========
 
-This includes various utilities to help in optimization. In the future,
-parameter search and plotting techniques will be incoroporated in this
-module.
+This includes various utilities to help in optimization. Some utilities
+include benchmark objective functions, hyperparameter search, and plotting
+functionalities.
 
 .. toctree::
 
    pyswarms.utils.functions
    pyswarms.utils.search
-   pyswarms.utils.environments
+   pyswarms.utils.plotters
+   pyswarms.utils.environments
diff --git a/docs/api/pyswarms.single.rst b/docs/api/pyswarms.single.rst
@@ -21,4 +21,14 @@ pyswarms.single.local_best module
    :undoc-members:
    :show-inheritance:
    :private-members:
-   :special-members: __init__
+   :special-members: __init__
+
+pyswarms.single.general_optimizer module
+---------------------------------
+
+.. automodule:: pyswarms.single.general_optimizer
+   :members:
+   :undoc-members:
+   :show-inheritance:
+   :private-members:
+   :special-members: __init__
diff --git a/docs/api/pyswarms.topology.rst b/docs/api/pyswarms.topology.rst
@@ -34,4 +34,31 @@ pyswarms.backend.topology.ring module
    :members:
    :undoc-members:
    :show-inheritance:
-   :special-members: __init__
+   :special-members: __init__
+
+pyswarms.backend.topology.von_neumann module
+--------------------------------------
+
+.. automodule:: pyswarms.backend.topology.von_neumann
+   :members:
+   :undoc-members:
+   :show-inheritance:
+   :special-members: __init__
+
+pyswarms.backend.topology.pyramid module
+--------------------------------------
+
+.. automodule:: pyswarms.backend.topology.pyramid
+   :members:
+   :undoc-members:
+   :show-inheritance:
+   :special-members: __init__
+
+pyswarms.backend.topology.random module
+--------------------------------------
+
+.. automodule:: pyswarms.backend.topology.random
+   :members:
+   :undoc-members:
+   :show-inheritance:
+   :special-members: __init__
diff --git a/docs/api/pyswarms.utils.environments.rst b/docs/api/pyswarms.utils.environments.rst
@@ -3,6 +3,10 @@ pyswarms.utils.environments package
 
 .. automodule:: pyswarms.utils.environments
 
+.. deprecated:: 0.2.1
+   This module will be deprecated in the next release. Please use
+   :mod:`pyswarms.utils.plotters` instead.
+
 pyswarms.utils.environments.plot_environment module
 ----------------------------------------------------
 

diff --git a/docs/api/pyswarms.utils.plotters.rst b/docs/api/pyswarms.utils.plotters.rst
@@ -0,0 +1,20 @@
+pyswarms.utils.plotters package
+================================
+
+.. automodule:: pyswarms.utils.plotters
+
+pyswarms.utils.plotters.plotters module
+----------------------------------------
+
+.. automodule:: pyswarms.utils.plotters.plotters
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pyswarms.utils.plotters.formatters module
+------------------------------------------
+
+.. automodule:: pyswarms.utils.plotters.formatters
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/assets/inheritance.aux b/docs/assets/inheritance.aux
@@ -0,0 +1,2 @@
+\relax 
+\gdef \sa@multi@numpages {0}