Joss-reviews: [REVIEW]: PyMarket

[whedon]

Submitting author: @gus0k (Diego)
Repository: https://github.com/gus0k/pymarket
Version: v0.7.8
Editor: @alexhanna
Reviewer: @igarizio, @taqtiqa-mark
Archive: 10.5281/zenodo.3665175

Status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/2851d3edebf001a6784de629d3330532"><img src="http://joss.theoj.org/papers/2851d3edebf001a6784de629d3330532/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/2851d3edebf001a6784de629d3330532/status.svg)](http://joss.theoj.org/papers/2851d3edebf001a6784de629d3330532)

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

@igarizio & @taqtiqa-mark, 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 @alexhanna know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @igarizio

Conflict of interest

• [x] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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] Version: v0.7.8
• [x] Authorship: Has the submitting author (@gus0k) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
  
  
  
  • ~gus0k/pymarket/issues/13~
  
  
• [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

• [x] 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).
• [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• [x] Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
• [x] 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

• [x] Authors: Does the paper.md file include a list of authors with their affiliations?
• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @taqtiqa-mark

Conflict of interest

• [x] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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] Version: v0.7.8
  
  
  
  • gus0k/pymarket/issues/4
  
  
• [x] Authorship: Has the submitting author (@gus0k) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [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

• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  
  
  
  • ~gus0k/pymarket/issues/3~
  
  
• [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
  
  
  
  • gus0k/pymarket/issues/5
  
  
  • gus0k/pymarket/issues/7
  
  
• [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• [x] Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
• [x] 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

• [x] Authors: Does the paper.md file include a list of authors with their affiliations?
• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  
  
  
  • ~gus0k/pymarket/issues/3~
  
  
• [x] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?
  
  
  
  • ~gus0k/pymarket/issues/2~
  
  

[whedon]

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

:star: Important :star:

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

1. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

For a list of things I can do to help you, just type:

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[gus0k]

Hello,

Do you have anything so far that you would like me to fix or clarify?

Best regards,
K

[igarizio]

Hello @gus0k 👋,
Great work on PyMarket! It is really well written and nicely documented. Also, the idea behind it seems really useful.

Here are some of my comments:

• Software version: This may be silly, but I prefer to ask. The review states v0.7.4 but your last version is v0.7.5, I suppose you want to publish the last version, right? (@alexhanna if that is the case, is it possible to just change the version stated in this issue?)

• Authorship: Just wanted to check, but you own both @gus0k and @ellguso, right? (context: I was looking at the contributors part of your repo)

• Paper acknowledgement: Here I may be wrong, but I think the title "acknowledgement" may not be correct. What I generally see in the acknowledgement part is words of appreciation to other researchers, funding entities, etc. (@taqtiqa-mark, @alexhanna please let me know what you think).

• List of mechanisms: I think it would help people reading your paper if you added a list of the mechanisms implemented in the library (maybe you can even add this list to your README).

• Paper references: If you decide to add the list of mechanisms implemented, I think it would be appropriate to cite where those mechanisms come from (I think you already have those references inside huang_auction.py, muda_auction.py, etc.)

• Small detail: On the second page of the paper, it says "Figure 1: png".

I will continue to review the other items in the checklist and will post if necessary. Please let me know if you have any questions. 😃

[gus0k]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[gus0k]

@whedon set v0.7.5 as version

[whedon]

I'm sorry @gus0k, I'm afraid I can't do that. That's something only editors are allowed to do.

[gus0k]

@igarizio @taqtiqa-mark Thank you both so far for your input. I have updated the paper to list the implemented algorithms and their references.

@alexhanna Would it be possible to update the version number to 0.7.5?

Regarding the acknowledgements, Telecom ParisTech is paying for my PhD. In that sense, I feel it plays the same role as funding entities.

Best regards,
K

[gus0k]

@igarizio @taqtiqa-mark , can I help you in any way to advance in your reviews?
Best regards,
k

[alexhanna]

👋 @igarizio and @taqtiqa-mark, are you able to continue your reviews of this package?

[alexhanna]

@whedon set v0.7.5 as version

[whedon]

OK. v0.7.5 is the version.

[alexhanna]

@gus0k the version has been updated.

[gus0k]

Thank you.

[gus0k]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[gus0k]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[gus0k]

Hello,

What is the status on this?

Best regards,
Diego

[danielskatz]

👋 @alexhanna, it looks like reviewers still need to continue their reviews?

[alexhanna]

Hi @taqtiqa-mark, are you able to continue reviewing this?

👋 @igarizio, it looks like the last thing you need to check on the review is the functionality?

[igarizio]

👋 @alexhanna Yes, I am almost done.

[alexhanna]

Hi @taqtiqa-mark, checking in again. Can you confirm that the issues noted above have been adequately addressed?

[taqtiqa-mark]

No. I've opened gus0k/pymarket/issues/11 as an example of issues 5/7, and I've made a pull request providing reproducible example. I'll settle for just Ubuntu 16.04 instructions that work.

[gus0k]

@taqtiqa-mark Sorry for the dealy, it was a busy week. I have already addressed the issue. I think there was a problem with the python version you were using. I uploaded a working Docker with ubuntu 16.04

@igarizio Fixed the problem with too many bidders.

[gus0k]

@igarizio , it looks like you have finished. Is that ok?

[alexhanna]

Hi @taqtiqa-mark can you ensure that these issues have been addressed and check off the relevant boxes in your review?

[taqtiqa-mark]

@alexhanna As best I can tell the install instructions are not tested.
@gus0k previously waved his hands that things work on Linux, but has now qualified that to a couple of distributions. The install instructions have been updated to add some missing step. So we are making progress (painfully).

I've made another pull request, showing the install instructions will break the users pip installation on their computer - a big no-no.

Given the package is currently so small and has limited use cases, I have suggested to @gus0k that simply providing a link to a working Docker Container, and removing references to claims to work on Linux is the fastest path forward.

[labarba]

@gus0k — Could we have a status update of your work on responding to reviewer comments? Let me know if you want us to set a reminder for you.

[gus0k]

Hello,

I think I managed to fix the problem: provide working installation instructions and specify for which platforms does it work.
I just addressed @taqtiqa-mark last comment.

Best regards,
Diego

[alexhanna]

:wave: @taqtiqa-mark -- have you been able to have a look at these changes?

[taqtiqa-mark]

The install instructions now appear to work. I haven't had time to check the remaning items. Expect to this weekend.

[alexhanna]

👋 @taqtiqa-mark - have you been able to check the remaining items?

[taqtiqa-mark]

Apologies. One of my parents has just died and am dealing with that - likely two weeks.

[gus0k]

@taqtiqa-mark I am very sorry to hear this. Please, take all the time you need.

[alexhanna]

Sorry to hear this, @taqtiqa-mark. Yes, please take your time.

[Kevin-Mattheus-Moerman]

@taqtiqa-mark we are sorry to hear about your loss. Let @alexhanna know whenever you are ready to resume this review. Thanks again for your help!

[taqtiqa-mark]

My apologies. I clean forgot about this. LGTM.

[danielskatz]

Sorry for the delay here - it now looks like this is ready to publish, which I will proceed with the steps for. If there's anything that's missing, either of the reviewers (@taqtiqa-mark or @igarizio) or the editor (@alexhanna) should speak up soon

[danielskatz]

👋 @gus0k - At this point could you:

• [ ] Make a tagged release of your software, and list the version tag of the archived version here.
• [ ] Archive the reviewed software in Zenodo or a similar service (e.g. figshare, an institutional repository)
• [ ] Check the archival deposit (e.g., in Zenodo) has the correct metadata, this includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it); you may also add the authors' ORCID.
• [ ] Please list the DOI of the archived version here.

I can then move forward with accepting the submission. As part of this, I will also be doing a careful proof read of the paper.

[danielskatz]

@whedon accept

[whedon]

No archive DOI set. Exiting...

[danielskatz]

@whedon generate pdf

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[danielskatz]

some suggested changes for the paper are in https://github.com/gus0k/pymarket/pull/18 and for the bib are in https://github.com/gus0k/pymarket/pull/19

[danielskatz]

@whedon check references

[whedon]

Reference check summary:

OK DOIs

- 10.1109/EEM.2017.7981938 is OK
- 10.1109/SmartGridComm.2017.8340728 is OK
- 10.1111/1467-8640.t01-1-00206 is OK
- 10.1088/1469-7688/2/5/303 is OK
- 10.1088/1469-7688/1/2/307 is OK

MISSING DOIs

- https://doi.org/10.1109/isgt.2019.8791585 may be missing for title: Strategy-proof local energy market with sequential stochastic decision process for battery control
- https://doi.org/10.1111/1467-937x.00171 may be missing for title: A decentralized market with common values uncertainty: Non-steady states

INVALID DOIs

- None

[danielskatz]

Also, please add the 2 missing DOIs above to the .bib file

[danielskatz]

@whedon check references

[whedon]

Reference check summary:

OK DOIs

- 10.1109/EEM.2017.7981938 is OK
- 10.1109/SmartGridComm.2017.8340728 is OK
- 10.1109/ISGT.2019.8791585 is OK
- 10.1111/1467-937X.00171 is OK
- 10.1111/1467-8640.t01-1-00206 is OK
- 10.1088/1469-7688/2/5/303 is OK
- 10.1088/1469-7688/1/2/307 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[danielskatz]

@whedon generate pdf

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[danielskatz]

sorry, missed one in the bib - please merge https://github.com/gus0k/pymarket/pull/20 as well

[danielskatz]

also, be aware that you can do @whedon generate pdf to check the PDF when you choose to

[gus0k]

@whedon generate pdf

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[gus0k]

@whedon generate pdf

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[gus0k]

@danielskatz
Created the tagged version (0.78) and uploaded it to zenodo:

10.5281/zenodo.3665175

[danielskatz]

@whedon set v0.7.8 as version

[whedon]

OK. v0.7.8 is the version.

[danielskatz]

@whedon set 10.5281/zenodo.3665175 as archive

[whedon]

OK. 10.5281/zenodo.3665175 is the archive.

[danielskatz]

Please change the metadata in the zenodo repository so that the title is the same as the title of the paper

[gus0k]

Done

[danielskatz]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Reference check summary:

OK DOIs

- 10.1109/EEM.2017.7981938 is OK
- 10.1109/SmartGridComm.2017.8340728 is OK
- 10.1109/ISGT.2019.8791585 is OK
- 10.1111/1467-937X.00171 is OK
- 10.1111/1467-8640.t01-1-00206 is OK
- 10.1088/1469-7688/2/5/303 is OK
- 10.1088/1469-7688/1/2/307 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1299

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1299, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

[danielskatz]

@whedon accept deposit=true

[whedon]

Doing it live! Attempting automated processing of paper acceptance...

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/1300
2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01591
3. If everything looks good, then close this review issue.

4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

   Any issues? notify your editorial technical team...

[danielskatz]

Thanks to @igarizio & @taqtiqa-mark for reviewing!
And to @alexhanna for editing!

Congratulations to @gus0k and co-authors!

[whedon]

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.01591/status.svg)](https://doi.org/10.21105/joss.01591)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01591">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01591/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01591/status.svg
   :target: https://doi.org/10.21105/joss.01591

This is how it will look in your documentation:

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[gus0k]

Thank you all!