openjournals / joss-reviews

Reviews for the Journal of Open Source Software
Creative Commons Zero v1.0 Universal
707 stars 37 forks source link

[REVIEW]: hdlib: A Python library for designing Vector-Symbolic Architectures #5704

Closed editorialbot closed 1 year ago

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@cumbof<!--end-author-handle-- (Fabio Cumbo) Repository: https://github.com/cumbof/hdlib Branch with paper.md (empty if default branch): joss Version: v.0.1.15 Editor: !--editor-->@danielskatz<!--end-editor-- Reviewers: @mahfuz05062, @anilbey Archive: 10.5281/zenodo.8331296

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/ef404bdbfd9428d01d2142820ab799c1"><img src="https://joss.theoj.org/papers/ef404bdbfd9428d01d2142820ab799c1/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/ef404bdbfd9428d01d2142820ab799c1/status.svg)](https://joss.theoj.org/papers/ef404bdbfd9428d01d2142820ab799c1)

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

@mahfuz05062 & @anilbey, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

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

Checklists

πŸ“ Checklist for @mahfuz05062

πŸ“ Checklist for @anilbey

editorialbot commented 1 year ago

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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

@editorialbot commands

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

@editorialbot generate pdf
editorialbot commented 1 year ago
Software report:

github.com/AlDanial/cloc v 1.88  T=0.05 s (270.0 files/s, 73716.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                           8            702           1228           1162
TeX                              1             22              0            210
Markdown                         3             82              0            140
Bourne Shell                     1              1              0              2
-------------------------------------------------------------------------------
SUM:                            13            807           1228           1514
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository
editorialbot commented 1 year ago
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.3390/a13090233 is OK
- 10.1007/978-3-030-59028-4_1 is OK
- 10.1109/DAC.2018.8465708 is OK
- 10.1007/s12559-009-9009-8 is OK
- 10.1007/s10462-021-10110-3 is OK
- 10.1109/TNNLS.2022.3211274 is OK
- 10.1109/IJCNN55064.2022.9892981 is OK
- 10.1145/3508352.3549477 is OK
- 10.48550/arXiv.2303.15604 is OK
- 10.1109/BIBM55620.2022.9995708 is OK
- 10.1109/DAC18074.2021.9586253 is OK
- 10.1109/FCCM53951.2022.9786145 is OK
- 10.23919/DATE48585.2020.9116397 is OK
- 10.1109/BIBE.2018.00046 is OK
- 10.1007/s12559-021-09974-y is OK
- 10.1109/ACCESS.2020.3001765 is OK
- 10.1109/ALLERTON.2014.7028470 is OK
- 10.1007/s13218-019-00623-z is OK
- 10.48550/arXiv.cs/0412059 is OK
- 10.1016/j.future.2020.04.005 is OK
- 10.48550/arXiv.2205.09208 is OK
- 10.1109/TC.2022.3179226 is OK
- 10.48550/arXiv.2206.04746 is OK

MISSING DOIs

- None

INVALID DOIs

- None
editorialbot commented 1 year ago

Wordcount for paper.md is 1319

editorialbot commented 1 year ago

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

danielskatz commented 1 year ago

@mahfuz05062 and @anilbey - Thanks for agreeing to review this submission. This is the review thread for the paper. All of our communications will happen here from now on.

As you can see above, you each should use the command @editorialbot generate my checklist to create your review checklist. @editorialbot commands need to be the first thing in a new comment.

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, reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#5704 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 either of you require some more time. We can also use editorialbot (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 (@danielskatz) if you have any questions/concerns.

mahfuz05062 commented 1 year ago

Review checklist for @mahfuz05062

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

anilbey commented 1 year ago

Review checklist for @anilbey

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

danielskatz commented 1 year ago

πŸ‘‹ @mahfuz05062 and @anilbey - I see the review is moving along, which is great!

Please keep up the progress, and let me know if there's anything that is blocking you.

cumbof commented 1 year ago

@editorialbot generate pdf

This is the new version of the manuscript. Actually the same as the previous one with a couple of fixes on grammatical mistakes as spotted by @mahfuz05062 in cumbof/hdlib#7

editorialbot commented 1 year ago

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

danielskatz commented 1 year ago

πŸ‘‹ @mahfuz05062 and @anilbey - How are things going? Is there anything blocking further progress on your reviews?

anilbey commented 1 year ago

Hi @danielskatz it is moving smoothly. There are only a few items remaining on my checklist.

mahfuz05062 commented 1 year ago

Hi @danielskatz it is moving well on my end too! I have to check the references and see if the method comparison could be better, both of which should be done in the coming weekend.

cumbof commented 1 year ago

@editorialbot generate pdf

Another minor fix based on https://github.com/cumbof/hdlib/issues/7#issuecomment-1711534272

editorialbot commented 1 year ago

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

anilbey commented 1 year ago

@danielskatz, I'm pleased to inform you that I've completed my checklist. All of my comments, have been addressed by @cumbof

mahfuz05062 commented 1 year ago

@danielskatz I'm also done with my checklist. All of my concerns have been addressed and I am happy with the changes made in response to @anilbey and me.

cumbof commented 1 year ago

Thanks @anilbey and @mahfuz05062, I really appreciate your time in reviewing our submission. All your comments have been very useful for improving code and documentation.

@danielskatz I've just released hdlib v.0.1.15 which mainly includes my replies to the reviewers' issues.

Could you please update the package version here as well?

Also, please let me know if there is anything I'm supposed to do now. Thanks

danielskatz commented 1 year ago

@editorialbot set v.0.1.15 as version

editorialbot commented 1 year ago

Done! version is now v.0.1.15

danielskatz commented 1 year ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance

danielskatz commented 1 year ago

@cumbof - please do the author items above (some of which you might have already done)

cumbof commented 1 year ago

@danielskatz I'm done with the additional author tasks, you can mark them all as completed. Here is the link to the Zenodo entry https://doi.org/10.5281/zenodo.8331296

danielskatz commented 1 year ago

@editorialbot set 10.5281/zenodo.8331296 as archive

editorialbot commented 1 year ago

Done! archive is now 10.5281/zenodo.8331296

danielskatz commented 1 year ago

@editorialbot recommend-accept

I'll proofread this and let you know the next steps

editorialbot commented 1 year ago
Attempting dry run of processing paper acceptance...
editorialbot commented 1 year ago
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.3390/a13090233 is OK
- 10.1007/978-3-030-59028-4_1 is OK
- 10.1109/DAC.2018.8465708 is OK
- 10.1007/s12559-009-9009-8 is OK
- 10.1007/s10462-021-10110-3 is OK
- 10.1109/TNNLS.2022.3211274 is OK
- 10.1109/IJCNN55064.2022.9892981 is OK
- 10.1145/3508352.3549477 is OK
- 10.48550/arXiv.2303.15604 is OK
- 10.1109/BIBM55620.2022.9995708 is OK
- 10.1109/DAC18074.2021.9586253 is OK
- 10.1109/FCCM53951.2022.9786145 is OK
- 10.23919/DATE48585.2020.9116397 is OK
- 10.1109/BIBE.2018.00046 is OK
- 10.1007/s12559-021-09974-y is OK
- 10.1109/ACCESS.2020.3001765 is OK
- 10.1109/ALLERTON.2014.7028470 is OK
- 10.1007/s13218-019-00623-z is OK
- 10.48550/arXiv.cs/0412059 is OK
- 10.1016/j.future.2020.04.005 is OK
- 10.48550/arXiv.2205.09208 is OK
- 10.1109/TC.2022.3179226 is OK
- 10.48550/arXiv.2206.04746 is OK

MISSING DOIs

- None

INVALID DOIs

- None
editorialbot commented 1 year ago

:wave: @openjournals/csism-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/4541, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

danielskatz commented 1 year ago

πŸ‘‹ @cumbof - I've suggested a bunch of minor fixes for bib entries in https://github.com/cumbof/hdlib/pull/10 - please merge this, or let me know what you disagree with, then we can proceed to acceptance and publication

danielskatz commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago
Attempting dry run of processing paper acceptance...
editorialbot commented 1 year ago
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.3390/a13090233 is OK
- 10.1007/978-3-030-59028-4_1 is OK
- 10.1109/DAC.2018.8465708 is OK
- 10.1007/s12559-009-9009-8 is OK
- 10.1007/s10462-021-10110-3 is OK
- 10.1109/TNNLS.2022.3211274 is OK
- 10.1109/IJCNN55064.2022.9892981 is OK
- 10.1145/3508352.3549477 is OK
- 10.48550/arXiv.2303.15604 is OK
- 10.1109/BIBM55620.2022.9995708 is OK
- 10.1109/DAC18074.2021.9586253 is OK
- 10.1109/FCCM53951.2022.9786145 is OK
- 10.23919/DATE48585.2020.9116397 is OK
- 10.1109/BIBE.2018.00046 is OK
- 10.1007/s12559-021-09974-y is OK
- 10.1109/ACCESS.2020.3001765 is OK
- 10.1109/ALLERTON.2014.7028470 is OK
- 10.1007/s13218-019-00623-z is OK
- 10.48550/arXiv.cs/0412059 is OK
- 10.1016/j.future.2020.04.005 is OK
- 10.48550/arXiv.2205.09208 is OK
- 10.1109/TC.2022.3179226 is OK
- 10.48550/arXiv.2206.04746 is OK

MISSING DOIs

- None

INVALID DOIs

- None
cumbof commented 1 year ago

Thanks @danielskatz! I don't have any concerns about your PR. I've just merged it.

Let me know if I can do anything else.

Also, I was wondering if I'm supposed to maintain the joss branch in the hdlib repo even after the publication. Since it is out of sync with the main branch, except for the paper folder, I was planning to push the paper in the main branch and get rid of the joss branch.

Please let me know if this is possible.

editorialbot commented 1 year ago

:wave: @openjournals/csism-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/4547, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

danielskatz commented 1 year ago

@cumbof - yes, that's fine. We don't have a requirement for a paper branch at all, some submissions have the paper in main from the start. But please don't do this until after the publication is done.

danielskatz commented 1 year ago

@cumbof - can you change the dna in the Cumbo reference to {DNA} - sorry I missed this one.

cumbof commented 1 year ago

@danielskatz - Sure, no problem. Done

danielskatz commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago
Attempting dry run of processing paper acceptance...
editorialbot commented 1 year ago
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.3390/a13090233 is OK
- 10.1007/978-3-030-59028-4_1 is OK
- 10.1109/DAC.2018.8465708 is OK
- 10.1007/s12559-009-9009-8 is OK
- 10.1007/s10462-021-10110-3 is OK
- 10.1109/TNNLS.2022.3211274 is OK
- 10.1109/IJCNN55064.2022.9892981 is OK
- 10.1145/3508352.3549477 is OK
- 10.48550/arXiv.2303.15604 is OK
- 10.1109/BIBM55620.2022.9995708 is OK
- 10.1109/DAC18074.2021.9586253 is OK
- 10.1109/FCCM53951.2022.9786145 is OK
- 10.23919/DATE48585.2020.9116397 is OK
- 10.1109/BIBE.2018.00046 is OK
- 10.1007/s12559-021-09974-y is OK
- 10.1109/ACCESS.2020.3001765 is OK
- 10.1109/ALLERTON.2014.7028470 is OK
- 10.1007/s13218-019-00623-z is OK
- 10.48550/arXiv.cs/0412059 is OK
- 10.1016/j.future.2020.04.005 is OK
- 10.48550/arXiv.2205.09208 is OK
- 10.1109/TC.2022.3179226 is OK
- 10.48550/arXiv.2206.04746 is OK

MISSING DOIs

- None

INVALID DOIs

- None
editorialbot commented 1 year ago

:wave: @openjournals/csism-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/4549, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

danielskatz commented 1 year ago

@editorialbot accept

editorialbot commented 1 year ago
Doing it live! Attempting automated processing of paper acceptance...
editorialbot commented 1 year ago

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

``` cff-version: "1.2.0" authors: - family-names: Cumbo given-names: Fabio orcid: "https://orcid.org/0000-0003-2920-5838" - family-names: Weitschek given-names: Emanuel orcid: "https://orcid.org/0000-0002-8045-2925" - family-names: Blankenberg given-names: Daniel orcid: "https://orcid.org/0000-0002-6833-9049" contact: - family-names: Cumbo given-names: Fabio orcid: "https://orcid.org/0000-0003-2920-5838" doi: 10.5281/zenodo.8331296 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Cumbo given-names: Fabio orcid: "https://orcid.org/0000-0003-2920-5838" - family-names: Weitschek given-names: Emanuel orcid: "https://orcid.org/0000-0002-8045-2925" - family-names: Blankenberg given-names: Daniel orcid: "https://orcid.org/0000-0002-6833-9049" date-published: 2023-09-11 doi: 10.21105/joss.05704 issn: 2475-9066 issue: 89 journal: Journal of Open Source Software publisher: name: Open Journals start: 5704 title: "hdlib: A Python library for designing Vector-Symbolic Architectures" type: article url: "https://joss.theoj.org/papers/10.21105/joss.05704" volume: 8 title: "hdlib: A Python library for designing Vector-Symbolic Architectures" ```

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

editorialbot commented 1 year ago

🐘🐘🐘 πŸ‘‰ Toot for this paper πŸ‘ˆ 🐘🐘🐘

editorialbot commented 1 year ago

🚨🚨🚨 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/4550
  2. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05704
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! πŸŽ‰πŸŒˆπŸ¦„πŸ’ƒπŸ‘»πŸ€˜

Any issues? Notify your editorial technical team...

danielskatz commented 1 year ago

Congratulations to @cumbof (Fabio Cumbo) and co-authors on your publication!!

And thanks to @mahfuz05062 and @anilbey for reviewing! JOSS is based on volunteers, and we couldn't do this without you

editorialbot commented 1 year ago

: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.05704/status.svg)](https://doi.org/10.21105/joss.05704)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05704">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05704/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05704/status.svg
   :target: https://doi.org/10.21105/joss.05704

This is how it will look in your documentation:

DOI

We need your help!

The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following: