Joss-reviews: [REVIEW]: Minimalist And Customizable Optimization Package

[whedon]

Submitting author: @jbuisine (Jérôme BUISINE)
Repository: https://github.com/jbuisine/macop
Version: v1.0.0
Editor: @melissawm
Reviewer: @stsievert, @torressa
Archive: Pending

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Status

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Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@stsievert & @torressa, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

1. Make sure you're logged in to your GitHub account
2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @melissawm know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Review checklist for @stsievert

Conflict of interest

• [x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• [x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• [x] Repository: Is the source code for this software available at the repository url?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Contribution and authorship: Has the submitting author (@jbuisine) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• [x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

• [ ] (not checked) Installation: Does installation proceed as outlined in the documentation?
• [ ] Functionality: Have the functional claims of the software been confirmed?
  
  
  
  • Specifically, this claim is made in paper.md: "Solutions modeling continuous problems can also be created by the anyone who wants to model his own problem", but I'm not seeing a continuous optimization problem in the examples or tests.
  
  
• [x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• [ ] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [ ] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• [ ] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
  
  
  
  • Yes, but these tests are not sufficient; some modules are untouched. See below for details.
  
  
• [ ] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support
  
  
  
  • Yes, there's some guidelines for contributing code/PRs but it's not super clear.
  
  
  • Yes, there is some guidelines for filing issues/bug reports but it only says "submit an issue with label ...".
  
  
  • There really aren't any guidelines for seeking support past "do not hestitate" when contacting.
  
  
  • I think this could be a lot clearer; I'm leaving this requirement unchecked.
  
  

Software paper

• [ ] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
  
  
  
  • Not really. It claims to solve every optimization problem; that seems a little to general. I don't know what job/data would motivate using this software.
  
  
• [ ] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [.] State of the field: Do the authors describe how this software compares to other commonly-used packages?
  
  
  
  • Marginally – I think this requirement is partially satisfied. The entirety of the comparison is "Available libraries in the literature did not allow this kind of implementation of an evaluation function quickly"
  
  
• [ ] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
  
  
  
  • See below for specific edits.
  
  
• [ ] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

Review checklist for @torressa

Conflict of interest

• [ ] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• [ ] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• [ ] Repository: Is the source code for this software available at the repository url?
• [ ] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [ ] Contribution and authorship: Has the submitting author (@jbuisine) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• [ ] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

• [ ] Installation: Does installation proceed as outlined in the documentation?
• [ ] Functionality: Have the functional claims of the software been confirmed?
• [ ] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• [ ] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [ ] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [ ] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [ ] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• [ ] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• [ ] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• [ ] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [ ] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [ ] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [ ] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [ ] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @stsievert, @torressa it looks like you're currently assigned to review this paper :tada:.

:warning: JOSS reduced service mode :warning:

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[whedon]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1007/0-306-48056-5_11 is OK
- 10.1109/TEVC.2007.892759 is OK
- 10.1016/j.cor.2006.02.008 is OK
- 10.1109/TEVC.2013.2239648 is OK
- 10.1007/s00158-004-0465-1 is OK
- 10.1109/ICMLA.2007.35 is OK
- 10.3390/rs10071117 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[melissawm]

👋🏼 @jbuisine @stsievert @torressa this is the review thread for the paper. All of our communications will happen here from now on.

Both reviewers have checklists at the top of this thread with the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#REVIEW_NUMER so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within about 2-4 weeks. Please let me know if any of you require some more time (@torressa has already done so). We can also use Whedon (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@melissawm) if you have any questions/concerns.

[whedon]

:wave: @stsievert, please update us on how your review is going.

[whedon]

:wave: @torressa, please update us on how your review is going.

[stsievert]

I'll try to have a review in by this weekend.

[stsievert]

@whedon generate pdf

[whedon]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[stsievert]

@whedon commands

[whedon]

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Ask Whedon to check the references for missing DOIs
@whedon check references

# Ask Whedon to check repository statistics for the submitted software
@whedon check repository

[stsievert]

@melissawm I have a review waiting. It looks like I didn't accept the invitation to collaborate on this repo in time, so I can't edit https://github.com/openjournals/joss-reviews/issues/2812#issue-734575770. Could you resend that invitation?

[melissawm]

Sure, no problem!

[melissawm]

@whedon re-invite @stsievert as reviewer

[whedon]

OK, the reviewer has been re-invited.

@stsievert please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

[stsievert]

My initial review: I do not believe this software project meets the [JOSS review requirements]. I welcome questions and comments from @jbuisine so provide clarification or be corrected on points below.

The most significant comments/questions are below. I have also edited https://github.com/openjournals/joss-reviews/issues/2812#issue-734575770 to check various boxes* and add some notes on specific items.

• The tests are not sufficient. I only found a single test in setup.py, and not a single doctest [as claimed]. In this one test, there are many untested classes.
• Target audience and statement of need. The main documentation do not identify a target audience or a statement of need. Only one feature of the software, maximum flexibility, is described. Who would want that and why? In paper.md, I see that there's a need for maximum flexibility mentioned in the paper, but why would a user want if they're not doing "thesis work"?

The documentation has some specific problems: it's very general and not detailed, is missing a good API description.

• Generality: optimization is very general. When is Macop not appropriate?
  
  
  
  • For example, could I use it for my favorite deep learning problem? Could it be used for a continuous convex optimization?
  
  
  • Or what if the optimization problem I'm using requires sparse arrays or GPUs?
  
  
• Detailed: the only information core classes have is their name – past that, there's not much detail.
  
  
  
  • For example, the documentation for IteratedLocalSearch is basically "[this class is] used to avoid local optima and increave EvE (Exploration vs Exploitation) compromise". What's "EvE", what effect does it have, and how do the various parameters balance it?
  
  
  • For example, what do C and exp_rate do in [UCBPolicy]? Does increasing C increase or decrease the importance of exploration? How does changing the value of exp_rate change the exploration/exploitation tradeoff?
  
  
• API: it's not clear what different policies, mutators and crossovers are used for. What's the data flow of one example? Detailing the input/output of these modules would be useful. I'd expect to see a clear definitions for non-experts.

Some specific questions/suggestions/typos for paper.md:

• "generic and implemented OR algorithms" This is the first definition of "OR".
• "Tools for modelling and solving discrete and continuous problems are proposed in the literature." This needs at least one citation.
• "Allowing students to quickly develop their own algorithms." This sentence is a sentence fragment: it doesn't express a complete thought.
• "finding a point $x \in X$ en that has" What does "en" mean?
• "implement the whole available algorithms in the literature" -> "which doesn't implement every algorithm in the literature"
• "but let you the possibility to quickly develop and test" -> "but provides the ability to ..."
• "The main objective of this package is to be the most flexible as possible and hence, to offer a maximum of implementation possibilities." This sentence doesn't make sense. I think you're trying to convey "The main objective of this package is to provide maximum flexibility, which allows for easy experimentation in implementation."
• The second paragraph in motivation needs cleaning up -- I'm having a hard time deciphering "Binary solution was used as appreciation for selected or non-selected feature from the available set of features. The solution was therefore a new model obtained and its fitness which is the score obtained on the test data set. "
• $\mathbb{N}$ should be used instead of $\mathbf{N}$

^{* a checked box ([x]) means "satisfied", an unchecked box ([ ]) means "not reviewed" and a crossed box ([ ]) means "not satisfied". A partially satisfied requirement is indicated with "[.]"}