Prepare v.0.3.0 release #180

ljvmiranda921 · 2018-07-25T00:30:03Z

Tasklist (Deadline: August 10, 2018)

Please write the changelog below for our release notes. It would be nice to follow this link.

Release v.0.3.0

We're proud to present the release of PySwarms version 0.3.0! Coinciding with this, we would like to welcome Aaron Moser (@whzup) as one of the project's maintainers! v.0.3.0 includes new topologies, a static option to configure a particle's neighbor/s, and a revamped plotters module. We would like to thank our contributors for helping us with this release.

Release notes

NEW: More basic particle topologies in the pyswarms.backend module - Created class for pyramid topology #142, Create GeneralOptimizer class and fix index error in Pyramid class #151, Add Random topology class #155, Add Von Neumann topology #177
NEW: Ability to make topologies static or dynamic - Add static/dynamic functionality for topologies #164
NEW: A GeneralOptimizerPSO class. The GeneralOptimizerPSO class has an additional attribute for the topology used in the optimization - Create GeneralOptimizer class and fix index error in Pyramid class #151
NEW: A plotters module for swarm visualization. The environments module is now deprecated - Add plotters module #135, Fix plotter module (#167) #172
FIX: Bugfix for optimizations not returning the best cost - Fix bug in topology classes #176
FIX: Bugfix for setup.py not running on Windows - Fix bug in setup.py #175
IMPROVED: Objective functions can now be parametrized. Helpful for your custom-objective functions - Feature parameterize obj #144. Thanks, @bradahoward!
IMPROVED: New single-objective functions - Add objective functions (#158) #168. Awesome work, @jayspeidell!

New Topologies and the `GeneralOptimizerPSO` Class

New topologies were added to improve the ability to customize how a swarm behaves during optimization. In addition, a GeneralOptimizerPSO class was added to enable switching-out various topologies. Check out the description below!

New Topology classes and the `static attribute`

The newly added topologies expand on the existing ones (Star and Ring topology) and increase the built-in variety of possibilities for users that want to build their custom swarm implementation from the pyswarms.backend module. The new topologies include:
- Pyramid topology: Computes the neighbours using a Delaunay triangulation of the particles.
- Random topology: Computes the neighbours randomly, but systematically.
- VonNeumann topology: Computes the neighbours using a Von Neumann topology (inherited from the Ring topology)
With these new topologies, the ability to change the behaviour of the topologies was added in form of a static argument that is passed when initializing a Topology class. The static parameter is a boolean that decides whether the neighbours in the topologies are computed every iteration (static=False) or only in the first one (static=True). It is passed as a parameter at the initialization of the topology and is False by default. Additionally, the LocalBestPSO now also takes a static parameter to pass this information to its Ring topology. For an example see below.

The `GeneralOptimizerPSO` class

The new topologies can also be easily used in the new GeneralOptimizerPSO class which extends the collection of optimizers. In addition to the parameters used in the GlobalBestPSO and LocalBestPSO classes, the GeneralOptimizerPSO uses a topology argument. This argument passes a Topology class to the GeneralOptimizerPSO.

from pyswarms.single import GeneralOptimizer
from pyswarms.backend.topology import Random

options = {"w": 1, "c1": 0.4, "c2": 0.5, "k": 3}
topology = Random(static=True)
optimizer = GeneralOptimizerPSO(n_particles=20, dimensions=4, options=options, bounds=bounds, topology=topology)

The `plotters` module

The environments module is now deprecated. Instead, we have a plotters module that takes a property of the optimizer and plots it with minimal effort. The whole module is built on top of matplotlib.

 import pyswarms as ps
 from pyswarms.utils.functions import single_obj as fx
 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=50, dimensions=2, options=options)
 optimizer.optimize(fx.sphere_func, iters=100)

 # Plot the cost
 plot_cost_history(optimizer.cost_history)
 plt.show()

We can also plot the animation...

from pyswarms.utils.plotters.formatters import Mesher
from pyswarms.utils.plotters.formatters import Designer
from pyswarms.utils.plotters import plot_contour, plot_surface

# 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'])

In 2D,

plot_contour(pos_history=optimizer.pos_history, mesher=m, mark=(0,0))

Or in 3D!

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))

This commit makes the if-else statements in generators more concise. To be honest, I didn't know what came into my mind as to why I nested those if statements. It turns out that using the "and" operator is much, much better. Signed-off-by: Lester James V. Miranda <[email protected]>

Modify if-else statements in generators

In this commit, we add a DeprecationWarning for the PlotEnvironment module. Although useful, I realized that it might be a hassle when the environment still optimizes the optimizer if we just want to plot it. What if a swarm iteration takes a long time? Will plotting take the same amount of time? We want to decouple the optimization part from the visualization. It is better to just have the user supply the position and cost histories and we just have the module do what it knows. Signed-off-by: Lester James V. Miranda <[email protected]>

In this commit, we decided to remove the @Property in storing the dependency. I found this very redundant and violates Python's rule of having only one way of doing things. Instead, we just access the histories from the class/instance attributes Signed-off-by: Lester James V. Miranda <[email protected]>

In this commit, we updated the tests on the optimizers to reflect the changes on using @Property. It's much better now because our tests are parameterized than having multiple asserts. Signed-off-by: Lester James V. Miranda <[email protected]>

This coincides with the decision to deprecate the PlotEnvironment. The whole environments module is now unsupported, and users will now be required to use the plotters module instead. Signed-off-by: Lester James V. Miranda <[email protected]>

Reference: #130 This commit adds a plotters.py module to replace the environments module. We hope that we can actually decouple the optimization and visualization part, without having the environment to do another rollout of your PSO. Signed-off-by: Lester James V. Miranda <[email protected]>

Reference: #130 The problem before is that we tend to have many parameters in our plotting functions. The formatters module changes that. We have three types of formatters: Designer, Animator, and Mesher. There are defaults present, but the user can change and pass them to the ploting functions whenever needed. Signed-off-by: Lester James V. Miranda <[email protected]>

Sometimes your swarm can generate a pure 0 or pure 1 vector, we should account that. Signed-off-by: Lester James V. Miranda <[email protected]>

This commit adds the plotters module into ReadTheDocs index and adds a deprecated information on plot_environment.py Signed-off-by: Lester James V. Miranda <[email protected]>

This commit updates the docstrings in formatters.py and adds a legend attribute in plotters.py Signed-off-by: Lester James V. Miranda <[email protected]>

Resolves #130

This commit formats the majority of pyswarms code using the black formatter. This will be our new formatter from this point forward. Signed-off-by: Lester James V. Miranda <[email protected]>

This commit adds the .flake8 and pyproject.toml to specify flake8 and black configuration. In addition, we updated the code to reflect the warnings found in flake8. Signed-off-by: Lester James V. Miranda <[email protected]>

In this commit, we explicitly say that we are using black as our code formatter. Signed-off-by: Lester James V. Miranda <[email protected]>

Format code using black and add pre-commit hooks

@whzup

Resolves #136 Created an Inverse Kinematics Tutorial in a Jupyter Notebook. Committed with @whzup

@whzup

Reference: #129 Created a class for the implementation of a pyramid topology using Delaunay triangulation. Additionally, @whzup changed a small error in the description of the `compute_velocity()` method in the Ring class. Notes: - For v.0.2.0-dev.3. - TODO: Update README in dev Committed with: @whzup Signed-off-by: Lester James V. Miranda <[email protected]>

@bradahoward

Resolves #143 This commit adds a `**kwargs` parameter to the `optimize()` method to pass arguments directly on the objective function. Additional tests and documentation were also provided. Committed with @bradahoward Signed-off-by: Lester James V. Miranda <[email protected]>

Created a GeneralOptimizer class with a topology parameter so one can choose which topology to use. Some special additions implemented: - Added an error message in case the topology attribute has the wrong type. - Added a special case for the ring topology so it's the same as local optimization. Also, created the corresponding test file and updated the documentation as well as the RST files for the GeneralOptimizer as well as the Pyramid topology. Resolves: #148

Fixed an index error in the Pyramid class that occured because the type of the idx array did not match 'int'

@whzup

Reference: #129 Added a new topology with random neighbors. Added documentation and a test file for it and reworked the documentation of the GeneralOptimizer class to incorporate all available topologies. Simplified the fixture function for the GeneralOptimizer class. Cited the relevant paper for the algorithm implemented. Updated the documentation of the Random class. Especially the __compute_neighbor() method. Added the comments inside the method to the docstring and deleted irrelevant comments. Changed the nested for-loops to one loop with the itertools library. Added a new test for the return value of the __compute_neighbor() method, which checks the shape and the symmetry. Added a new test for the return value of the __compute_neighbors() method, which compares the returned matrix with a preset comparison matrix using a seed. Signed-off-by: Lester James V. Miranda <[email protected]> Committed-by: @whzup

@whzup

Reference: #129 Added two new attributes to the topologies. `static` decides whether the topology is a static or a dynamic one, it is initialized together with the class. `neighbor_idx` is an array that stores the indices of the neighbors of every particle. Changed all occurrences of topologies to fit the new initialization. Reworked the tests to fit the new functionality and added more parametrization of fixture functions. Updated the documentation to incorporate the new functionality. Signed-off-by: Lester James V. Miranda <[email protected]> Commited-by: @whzup

whzup

Release Status

I guess it's all fine from my side. The tests run and the GeneralOptimizerclass with all the topologies look fine. I'll go ahead and beat the topologies a bit more until 12. August, hopefully without finding a bug 😄. I've written the first draft for my changelog, where shall I deposit it?

ljvmiranda921 · 2018-07-31T03:08:27Z

Yes, I think you're fine and it's my turn to finish all other admin tasks. Let me do them next week, I'll now move between cities this weekend! 👍

For the Changelog, you can just copy paste them below the TaskList above. 👍

ljvmiranda921 · 2018-07-31T07:39:47Z

Awesome work, can you also link the corresponding PR/s for each feature? Thank you so much and sorry for the hassle.

This commit updates all image source from local to Imgur. Turns out that whenever we create a setup file, the docs directory is excluded, thus, the images are nowhere to be found. By sourcing them from Imgur, we can resolve this problem. Signed-off-by: Lester James V. Miranda <[email protected]>

ljvmiranda921 · 2018-07-31T08:56:35Z

Release Status

Everything is fine on my end. We are ready to release on August 10, 2018.
If there are any bugs before that time, hopefully we can resolve them. If not,
let's just make patch releases (e.g. 0.3.1, 0.3.2, etc.) in the future.

For boundary conditions, let's just put that on v.0.4.0. It coincides with other features
we are actually planning so it might be a better fit.

I think the Release Notes are fine. We can even edit that after releasing so there's no pressure
to make it perfect from the get-go.

cc: @whzup @SioKCronin

whzup · 2018-07-31T16:55:38Z

How did you make the fancy pictures in the release notes for 0.2.0? Maybe we could use something similar for this one 😋 BTW, have you updated this part of the documentation with the new features?

whzup · 2018-07-31T17:15:03Z

I added this

from pyswarms.utils.plotters import plot_contour, plot_surface

to the changelog for completeness 👍

whzup · 2018-07-31T17:57:52Z

These parts of the documentation are outdated:

https://pyswarms.readthedocs.io/en/master/dev.optimizer.html#writing-unit-tests We don't use the unittest module anymore
https://pyswarms.readthedocs.io/en/master/api/pyswarms.base.html#module-pyswarms.base.base_single We should include the GeneralOptimizerPSO class in the "See also"

ljvmiranda921 · 2018-08-01T02:30:14Z

Hi @whzup ,

How did you make the fancy pictures in the release notes for 0.2.0?

LaTeX with TikZ 👍 There's a steep learning curve though, haha!

Maybe we could use something similar for this one

What kind of diagram do you propose? Sure no problem!

BTW, have you updated this part of the documentation with the new features?

I think there's no need. This part only describes the general API. And our new version doesn't really break that. We can leave this one out for now. 👍

ljvmiranda921 · 2018-08-01T02:31:23Z

Hi @whzup ,

These parts of the documentation are outdated:

You are correct and thanks for catching these! Would you like to make a PR? I can, but I might be able to fix this next week 😕

Thanks a lot @whzup ! I'm excited for the new release!

whzup · 2018-08-03T19:41:08Z

Hey @ljvmiranda921, I was a bit inactive the last few days due to some issues with my computer and time management 😄 I started working on the deprecated parts of the docs and I thought while on it, I could integrate the roadmap? We could put it in the General section, what do you think?

Updated the documentation of the base class to include the GeneralOptimizer. Additionally, changed the chapter "Writing unit test" in the dev.optimizer.rst because we don't use the unittest module anymore. I replaced the "unittest" module with the "pytest" module and rewrote some parts of the paragraph so it reads a bit more easily. Also, added a link to the pytest docs for the running of tests.

ljvmiranda921 · 2018-08-04T02:41:41Z

I started working on the deprecated parts of the docs and I thought while on it, I could integrate the roadmap? We could put it in the General section, what do you think?

Oh, you mean put the roadmap in the documentation? Sure I think that's a nice idea but our roadmap seems to be a "live" document that we'll keep on updating. Normally I'll start with something general and then we make it more specific etc.

But yeah sure, we can put a "Roadmap" section under general (last part) and then we update them after every release!

whzup · 2018-08-06T04:46:52Z

Hi @ljvmiranda921, I just saw the release notes for GitHub Desktop and I really like their formatting. We could use some of their elements, for example:

NEW: Basic particle topologies in the pyswarms.backend module - Created class for pyramid topology #142, Add Random topology class #155, Fix bug in topology classes #176, Add Von Neumann topology #177
NEW: Ability to make the topologies static or dynamic - Add static/dynamic functionality for topologies #164

I guess the labels (new, fixed, etc.) are made with images.

ljvmiranda921 · 2018-08-06T04:51:05Z

This looks interesting @whzup . Wanna do it for v.0.3.0? I think we can get by with bold labels. 👍

whzup · 2018-08-06T16:29:29Z

I changed the release notes above. They look pretty slick now, don't they?😋

ljvmiranda921 · 2018-08-07T00:19:55Z

This is awesome, @whzup ! Do you have edit access on the release notes here? It would be nice if the formatting is uniform.

I guess this kind of formatting will work in our History I can do this on Friday night or on the weekend. 👍

whzup · 2018-08-07T04:24:59Z

I do have access! Shall I do this today? I'd have some spare time 😄 For the History we could use coloured labels like the GitHub Desktop example, what do you think? If so, we should style them differently though 😋

ljvmiranda921 · 2018-08-07T04:28:36Z

Shall I do this today? I'd have some spare time smile

Sure! If you want, then much better!

For the History we could use coloured labels like the GitHub Desktop example, what do you think? If so, we should style them differently though

How can we achieve this? Small image labels or just colored text? If the icons look ugly then using bold letters may suffice. 👍

whzup · 2018-08-07T17:44:11Z

@ljvmiranda921, I reformatted the release notes on GitHub. In my opinion, they look pretty slick now 😄 I unified the formatting to fit our "standard" for 0.3.0 and corrected some spelling and grammar errors. I noticed that in the History tab at RTD you mixed up two PRs (113 and 114 in 0.2.0) and a link is visible in the 0.2.1 notes.

ljvmiranda921 · 2018-08-08T01:12:04Z

I reformatted the release notes on GitHub. In my opinion, they look pretty slick now smile I unified the formatting to fit our "standard" for 0.3.0 and corrected some spelling and grammar errors.

Understood. Yes, they look much cleaner now!

I noticed that in the History tab at RTD you mixed up two PRs (113 and 114 in 0.2.0) and a link is visible in the 0.2.1 notes.

Will you make a PR on this (+ similar standard on our Release Notes)? If not, we can just do this on v.0.4.0. Really sorry for I've been quite busy due to internship. 😭

Added the GeneralOptimizer and the plotters module to the features.rst file and provided a deprecation warning in the environment package. Updated the HISTORY.rst file with the new release note format based on the notes in #180.

ljvmiranda921 · 2018-08-08T23:58:46Z

Hi @whzup , this looks good already. I will merge to master today so that tomorrow I can just upload the tarballs and wheel files and then we'll be all set!

ljvmiranda921 and others added 30 commits June 11, 2018 18:59

Merge pull request #128 from ljvmiranda921/better-lookup

4e4b474

Modify if-else statements in generators

Update test on optimizers

5343a1c

In this commit, we updated the tests on the optimizers to reflect the changes on using @Property. It's much better now because our tests are parameterized than having multiple asserts. Signed-off-by: Lester James V. Miranda <[email protected]>

Mark environment tests as expected failures

b128fa2

This coincides with the decision to deprecate the PlotEnvironment. The whole environments module is now unsupported, and users will now be required to use the plotters module instead. Signed-off-by: Lester James V. Miranda <[email protected]>

Add tests for plotters module

435db1c

Fix bad behavior in discrete swarm generation

054570e

Sometimes your swarm can generate a pure 0 or pure 1 vector, we should account that. Signed-off-by: Lester James V. Miranda <[email protected]>

Add plotters to docs index (#130)

a56c50e

This commit adds the plotters module into ReadTheDocs index and adds a deprecated information on plot_environment.py Signed-off-by: Lester James V. Miranda <[email protected]>

Update docstrings in plotters.py (#130)

d007009

This commit updates the docstrings in formatters.py and adds a legend attribute in plotters.py Signed-off-by: Lester James V. Miranda <[email protected]>

Add demo and documentation for plotters

9a4aa45

Merge branch 'feature-add-plotters'

e533ad6

[ci skip] Update README

8249ce2

Merge pull request #135 from ljvmiranda921/feature-plotters-module

adcf626

Resolves #130

Merge branch 'master' into development

853772f

Format code using black (#139)

a863fb8

This commit formats the majority of pyswarms code using the black formatter. This will be our new formatter from this point forward. Signed-off-by: Lester James V. Miranda <[email protected]>

Add pre-commit hook configurations (#139)

fbe052d

This commit adds the .flake8 and pyproject.toml to specify flake8 and black configuration. In addition, we updated the code to reflect the warnings found in flake8. Signed-off-by: Lester James V. Miranda <[email protected]>

Mention black in README and CONTRIBUTING (#139)

297a403

In this commit, we explicitly say that we are using black as our code formatter. Signed-off-by: Lester James V. Miranda <[email protected]>

Merge pull request #137 from ljvmiranda921/format-code

f59e73c

Format code using black and add pre-commit hooks

Add PULL_REQUEST_TEMPLATE.md

2dd5966

Create Inverse Kinematics tutorial (#141)

b643bfd

Resolves #136 Created an Inverse Kinematics Tutorial in a Jupyter Notebook. Committed with @whzup

Fix index error in the Pyramid class

38546d6

Fixed an index error in the Pyramid class that occured because the type of the idx array did not match 'int'

Merge pull request #151 from whzup/gen_opt

3d5e346

ljvmiranda921 modified the milestone: Version Release (v0.2.0) Jul 30, 2018

whzup approved these changes Jul 30, 2018

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ljvmiranda921 mentioned this pull request Jul 31, 2018

Bump version and setup.py #191

Merged

ljvmiranda921 added 2 commits July 31, 2018 17:10

Bump version to v.0.3.0 (#191)

f7ce89d

whzup mentioned this pull request Aug 8, 2018

Update features.rst and HISTORY.rst #199

Merged

10 tasks

Update features.rst and HISTORY.rst (#199)

b96a08d

Added the GeneralOptimizer and the plotters module to the features.rst file and provided a deprecation warning in the environment package. Updated the HISTORY.rst file with the new release note format based on the notes in #180.

ljvmiranda921 merged commit f58d308 into master Aug 9, 2018

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Prepare v.0.3.0 release #180

Prepare v.0.3.0 release #180

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Prepare v.0.3.0 release #180

Prepare v.0.3.0 release #180

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ljvmiranda921 commented Jul 25, 2018 • edited Loading

Tasklist (Deadline: August 10, 2018)

Release v.0.3.0

Release notes

New Topologies and the GeneralOptimizerPSO Class

New Topology classes and the static attribute

The GeneralOptimizerPSO class

The plotters module

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New Topologies and the `GeneralOptimizerPSO` Class

New Topology classes and the `static attribute`

The `GeneralOptimizerPSO` class

The `plotters` module

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