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[REVIEW]: sknet: A Python framework for Machine Learning in Complex Networks #3864

Closed whedon closed 2 years ago

whedon commented 3 years ago

Submitting author: @TNanukem (Tiago Toledo Junior) Repository: https://github.com/TNanukem/scikit-net/ Version: v0.0.1 Editor: @osorensen Reviewers: @dvysardana, @drj11, @imw Archive: 10.5281/zenodo.5783027

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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.)

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@dvysardana & @drj11, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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Review checklist for @dvysardana

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General checks

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Review checklist for @drj11

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Software paper

whedon commented 3 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @dvysardana, @drj11 it looks like you're currently assigned to review this paper :tada:.

:warning: JOSS reduced service mode :warning:

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whedon commented 3 years ago 
Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.06 s (1133.7 files/s, 66119.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          22            586            955           1207
reStructuredText                32            204            252            342
YAML                             5             18              1             79
HTML                             2              1              0             66
Bourne Shell                     1             31             16             62
Markdown                         3             26              0             52
DOS Batch                        1              8              1             26
CSS                              1              2              0             11
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            68            880           1232           1854
-------------------------------------------------------------------------------

Statistical information for the repository 'ab4397100d0d540f281a770c' was
gathered on 2021/10/28.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Tiago Toledo Junior             30          3619            786          100.00

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Tiago Toledo Junior        2833           78.3          3.3                6.99
whedon commented 3 years ago

PDF failed to compile for issue #3864 with the following error: 

 Can't find any papers to compile :-(
drj11 commented 3 years ago

@osorensen the PDF isn't compiling. Should it be? Is that where i would expect to find the full author list?

osorensen commented 3 years ago

Thanks for letting me know @drj11. The paper is in a separate branch, so we need some special syntax.

osorensen commented 3 years ago

@whedon generate pdf from branch docs/joss_paper

whedon commented 3 years ago 
Attempting PDF compilation from custom branch docs/joss_paper. Reticulating splines etc...
whedon commented 3 years ago

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

drj11 commented 3 years ago

Good work whedon!

dvysardana commented 3 years ago

@osorensen, @whedon, I have completed my review.

osorensen commented 3 years ago

Thanks @dvysardana. Do I understand correctly that you think a statement of need is missing but otherwise everything is fine?

dvysardana commented 3 years ago

Hello @osorensen

Yes, I have completed my review. The statement of need needs to be updated to clearly mention the target audience. Further, the paper lacks a description and comparison of other similar packages that already exist in the community.

Can you please confirm that all the review requirements are complete now?

Thanks Divya Sardana

On Sun, Oct 31, 2021 at 12:01 AM Øystein Sørensen @.***> wrote:

Thanks @dvysardana https://github.com/dvysardana. Do I understand correctly that you think a statement of need is missing but otherwise everything is fine?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/3864#issuecomment-955647768, or unsubscribe https://github.com/notifications/unsubscribe-auth/AE6FQXZNUKIWGDXEBZKIQXLUJTSTLANCNFSM5G4K4XNQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

osorensen commented 3 years ago

Thanks a lot for your review @dvysardana . I can confirm that you have done what is requested for now, but once the authors report in this thread that they have added a statement if need and a target audience, please come back and compete the review checklist. I will tag you in this thread to make sure you get notified.

TNanukem commented 3 years ago

@whedon generate pdf from branch docs/joss_paper

whedon commented 3 years ago 
Attempting PDF compilation from custom branch docs/joss_paper. Reticulating splines etc...
whedon commented 3 years ago

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

TNanukem commented 3 years ago

Hello @dvysardana

I've added more information about the target audience on the README and on the sphinx documentation. Also, I added more information about other packages on the paper.

Do those changes meet the criteria for your revision? If not, do you have any suggestions on how to improve it to make it acceptable?

Thank you for your review!

dvysardana commented 3 years ago

Hello @tnanukem

Thanks for adding the additional information. These changes look good to me. I have no other suggestions for improvement.

Best Regards Divya Sardana

On Tue, Nov 2, 2021 at 4:50 AM Tiago Toledo Junior @.***> wrote:

Hello @dvysardana https://github.com/dvysardana

I've added more information about the target audience on the README and on the sphinx documentation. Also, I added more information about other packages on the paper.

Do those changes meet the criteria for your revision? If not, do you have any suggestions on how to improve it to make it acceptable?

Thank you for your review!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/3864#issuecomment-957368556, or unsubscribe https://github.com/notifications/unsubscribe-auth/AE6FQX4DTPGPHTF3NHD7WV3UJ7GATANCNFSM5G4K4XNQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

TNanukem commented 3 years ago

Thank you @dvysardana.

If anything else comes up I'm available for the changes proposed by you or @drj11 :)

osorensen commented 3 years ago

@dvysardana, please also remember to check the two reminaing boxes in your review checklist at the top of this issue.

dvysardana commented 3 years ago

@osorensen Checked all the boxes in my review.

On Thu, Nov 4, 2021 at 6:25 AM Øystein Sørensen @.***> wrote:

@dvysardana https://github.com/dvysardana, please also remember to check the two reminaing boxes in your review checklist at the top of this issue.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/3864#issuecomment-960921508, or unsubscribe https://github.com/notifications/unsubscribe-auth/AE6FQX2LSEM4HYBHFYEPWB3UKKCUDANCNFSM5G4K4XNQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

whedon commented 3 years ago

:wave: @drj11, please update us on how your review is going (this is an automated reminder).

drj11 commented 3 years ago

Oh good reminder @whedon I'll have a look this afternoon.

osorensen commented 2 years ago

@drj11, how is it going with your review? If there are issues which you think the authors should address, please mention them in this thread or by opening an issue in the source repository.

osorensen commented 2 years ago

Dear @drj11, could you please update us on how it is going with your review of this submission?

TNanukem commented 2 years ago

Hello @osorensen and @drj11. If there is anything I can do to make the reviewing process easier, just let me know.

osorensen commented 2 years ago

@TNanukem, thanks for reaching out. I'll see if we can find another reviewer, and hopefully we can finish this.

osorensen commented 2 years ago

:wave: @imw, would you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

imw commented 2 years ago

Yes, happy to do so by this weekend.

osorensen commented 2 years ago

Thanks a lot @imw!

osorensen commented 2 years ago

@whedon add @imw as reviewer

whedon commented 2 years ago

OK, @imw is now a reviewer

osorensen commented 2 years ago

@imw, I have added a review checklist for you at the top of this thread, which you can use for your review. You find the reviewer guidelines here. Please let me know if you need any assistance in the process.

drj11 commented 2 years ago

tbh this dropped off my radar. I'm happy to complete the review today (GMT) if you still want, but it looks like you've found another reviewer.

To be honest there is one concrete thing that you can change to improve the process slightly: put the review deadline either at the top, at the bottom, or in any of the nagging comments.

Sorry I dropped the ball on this one.

osorensen commented 2 years ago

Thanks for getting back to us @drj11. I've tried to ping you a few times, but I completely understand that it's easy to loose track of e-mails. It would be very much appreciated if you could complete your review, even though we have already secured a third reviewer. Having three reviewers rather than two is a good thing.

And thanks for your comment regarding deadlines. However, this might be slightly problematic to implement, since the reviews in JOSS are supposed to be interactive. Sometimes, when the reviewers have a large number of suggestions, it can take many months for the submitting authors to fix the issues proposed by the reviewers, so it's hard to set deadlines for reviews.

drj11 commented 2 years ago

@TNanukem I have opened a few issues, but only two block the review:

https://github.com/TNanukem/scikit-net/issues/35

https://github.com/TNanukem/scikit-net/issues/37

I think that these should be easy to resolve.

In the written paper I particularly appreciated the Statement of Need and the catalogue of implemented algorithms.

TNanukem commented 2 years ago

Hello @drj11. Thanks for the feedback, I will solve the issues during the weekend

imw commented 2 years ago

@TNanukem I also opened a couple of issues.: https://github.com/TNanukem/scikit-net/issues/39 https://github.com/TNanukem/scikit-net/issues/40 Also quite minor. Nice library!

TNanukem commented 2 years ago

@whedon generate pdf from branch docs/joss_paper

whedon commented 2 years ago 
Attempting PDF compilation from custom branch docs/joss_paper. Reticulating splines etc...
whedon commented 2 years ago

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

TNanukem commented 2 years ago

Hello @imw and @drj11

Thank you for your review! I think I solved most of the issues.

Only the one related to the warning on the unit tests is still open. Since it will change the expected value of the test, I will tackle it after. However, I think the blocking issues are all solved.

If there is any additional point I will be happy to work on it.

Have a good weekend everyone!

drj11 commented 2 years ago

@whedon @osorensen my review is complete and i have no further reasons to delay publication. Thank you to everyone involved!

whedon commented 2 years ago

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@whedon commands
osorensen commented 2 years ago

Thank you very much @drj11!

osorensen commented 2 years ago

@imw, when you have time, please let us know if the two Issues you opened in the source repository have been properly addressed.

imw commented 2 years ago

Yes, all addressed well!

osorensen commented 2 years ago

@TNanukem, I'll read through the manuscript once more, and get back to you if there are any suggested changes. In the meantime, could you please do the following?

osorensen commented 2 years ago

@whedon generate pdf from branch docs/joss_paper

whedon commented 2 years ago 
Attempting PDF compilation from custom branch docs/joss_paper. Reticulating splines etc...