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

whedon · 2021-10-28T09:06:06Z

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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Review checklist for @dvysardana

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Documentation

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Software paper

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✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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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.

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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 (@TNanukem) 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: Does the paper have a section titled 'Statement of Need' that clearly states 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?

Review checklist for @imw

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 (@TNanukem) 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: Does the paper have a section titled 'Statement of Need' that clearly states 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?

The text was updated successfully, but these errors were encountered:

whedon · 2021-10-28T09:06:12Z

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 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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whedon · 2021-10-28T09:06:18Z

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 · 2021-10-28T09:06:19Z

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

 Can't find any papers to compile :-(

drj11 · 2021-10-29T11:57:20Z

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

osorensen · 2021-10-29T11:58:52Z

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

osorensen · 2021-10-29T11:58:55Z

@whedon generate pdf from branch docs/joss_paper

whedon · 2021-10-29T11:58:58Z

Attempting PDF compilation from custom branch docs/joss_paper. Reticulating splines etc...

whedon · 2021-10-29T11:59:25Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

drj11 · 2021-10-29T12:17:03Z

Good work whedon!

dvysardana · 2021-10-30T23:30:16Z

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

osorensen · 2021-10-31T07:00:59Z

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

dvysardana · 2021-11-01T17:55:35Z

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 <#3864 (comment)>, 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 · 2021-11-01T19:59:44Z

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 · 2021-11-02T11:48:02Z

@whedon generate pdf from branch docs/joss_paper

whedon · 2021-11-02T11:48:05Z

Attempting PDF compilation from custom branch docs/joss_paper. Reticulating splines etc...

whedon · 2021-11-02T11:48:31Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

TNanukem · 2021-11-02T11:50:21Z

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 · 2021-11-02T17:25:33Z

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 <#3864 (comment)>, 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 · 2021-11-04T10:27:08Z

Thank you @dvysardana.

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

osorensen · 2021-11-04T13:25:10Z

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

dvysardana · 2021-11-04T18:01:36Z

@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 <#3864 (comment)>, 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 · 2021-11-11T09:06:31Z

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

drj11 · 2021-11-11T09:36:46Z

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

osorensen · 2021-11-17T07:25:35Z

@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.

whedon · 2021-12-15T10:05:40Z

Attempting PDF compilation from custom branch docs/joss_paper. Reticulating splines etc...

whedon · 2021-12-15T10:06:11Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

TNanukem · 2021-12-15T10:07:59Z

@whedon generate pdf from branch docs/joss_paper

whedon · 2021-12-15T10:08:02Z

Attempting PDF compilation from custom branch docs/joss_paper. Reticulating splines etc...

whedon · 2021-12-15T10:08:29Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

osorensen · 2021-12-15T10:56:43Z

@whedon set 10.5281/zenodo.5783027 as archive

whedon · 2021-12-15T10:56:46Z

OK. 10.5281/zenodo.5783027 is the archive.

osorensen · 2021-12-15T10:57:00Z

@whedon set v0.0.1 as version

whedon · 2021-12-15T10:57:04Z

OK. v0.0.1 is the version.

osorensen · 2021-12-15T10:58:32Z

@whedon recommend-accept

whedon · 2021-12-15T10:58:35Z

Attempting dry run of processing paper acceptance...

whedon · 2021-12-15T10:58:41Z

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

 Can't find any papers to compile :-(

osorensen · 2021-12-15T10:59:26Z

@whedon recommend-accept from branch docs/joss_paper

whedon · 2021-12-15T10:59:29Z

Attempting dry run of processing paper acceptance...

whedon · 2021-12-15T10:59:57Z

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#2825

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2825, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true from branch docs/joss_paper

whedon · 2021-12-15T11:00:15Z

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

OK DOIs

- 10.1007/978-3-319-17290-3 is OK
- 10.1016/j.neucom.2011.04.042 is OK
- 10.1016/j.neucom.2014.03.071 is OK
- 10.1109/TNNLS.2012.2195027 is OK
- 10.1109/TNNLS.2011.2181866 is OK

MISSING DOIs

- None

INVALID DOIs

- None

kyleniemeyer · 2021-12-15T21:44:30Z

@whedon accept deposit=true from branch docs/joss_paper

whedon · 2021-12-15T21:44:33Z

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

whedon · 2021-12-15T21:45:08Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon · 2021-12-15T21:45:10Z

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

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.03864 joss-papers#2829
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03864
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kyleniemeyer · 2021-12-15T21:46:44Z

Congratulations @TNanukem on your article's publication in JOSS!

Many thanks to @dvysardana, @drj11, and @imw for reviewing this, and @osorensen for editing.

whedon · 2021-12-15T21:46:47Z

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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.03864/status.svg)](https://doi.org/10.21105/joss.03864)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03864">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03864/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03864/status.svg
   :target: https://doi.org/10.21105/joss.03864

This is how it will look in your documentation:

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whedon added Python review labels Oct 28, 2021

whedon assigned osorensen Oct 28, 2021

whedon mentioned this issue Oct 28, 2021

[PRE REVIEW]: sknet: A Python framework for Machine Learning in Complex Networks #3830

Closed

whedon assigned drj11 and dvysardana Oct 29, 2021

whedon added the recommend-accept Papers recommended for acceptance in JOSS. label Dec 15, 2021

whedon added accepted published Papers published in JOSS labels Dec 15, 2021

kyleniemeyer closed this as completed Dec 15, 2021

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

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

Comments

whedon commented Oct 28, 2021 • edited Loading

Status

Reviewer instructions & questions

Review checklist for @dvysardana

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @drj11

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @imw

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented Oct 28, 2021

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whedon commented Oct 28, 2021

drj11 commented Oct 29, 2021

osorensen commented Oct 29, 2021

osorensen commented Oct 29, 2021

whedon commented Oct 29, 2021

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drj11 commented Oct 29, 2021

dvysardana commented Oct 30, 2021

osorensen commented Oct 31, 2021

dvysardana commented Nov 1, 2021 via email

osorensen commented Nov 1, 2021

TNanukem commented Nov 2, 2021

whedon commented Nov 2, 2021

whedon commented Nov 2, 2021

TNanukem commented Nov 2, 2021

dvysardana commented Nov 2, 2021 via email

TNanukem commented Nov 4, 2021

osorensen commented Nov 4, 2021

dvysardana commented Nov 4, 2021 via email

whedon commented Nov 11, 2021

drj11 commented Nov 11, 2021

osorensen commented Nov 17, 2021

whedon commented Dec 15, 2021

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TNanukem commented Dec 15, 2021

whedon commented Dec 15, 2021

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osorensen commented Dec 15, 2021

whedon commented Dec 15, 2021

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osorensen commented Dec 15, 2021

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kyleniemeyer commented Dec 15, 2021

whedon commented Dec 15, 2021

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whedon commented Dec 15, 2021

whedon commented Oct 28, 2021 •

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