[REVIEW]: CircuitGraph: A Python package for Boolean circuits

whedon commented 4 years ago

Submitting author: @jpsety (Joseph Sweeney) Repository: https://github.com/circuitgraph/circuitgraph Version: v0.0.3 Editor: @danielskatz Reviewer: @skadio, @prw99r, @r-a-hoggarth Archive: 10.5281/zenodo.4302741

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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

@skadio & @prw99r & @r-a-hoggarth, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

Make sure you're logged in to your GitHub account
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 @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 ✨

Review checklist for @skadio

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 (@jpsety) 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

[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?
[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 functionality 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] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[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] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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 @prw99r

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 (@jpsety) 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

[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?
[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 functionality 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] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[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] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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 @r-a-hoggarth

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 (@jpsety) 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

[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?
[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 functionality 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] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[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] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

prw99r commented 3 years ago

I agree with the highlighted contribution that @skadio notes above - I think that @jpsety has gone partially down the road of dealing with my concerns and added some useful clarifications. The purpose of our comments has always been to provide positive criticism to improve the software and the paper. It can be tough to take sometimes, especially if there is a lot of time and effort already invested in the work, but it is worth taking the time to do it right.

One nice aspect of this approach (JOSS) is that the issues are there for all to see, and therefore it is left to the reader to make their own mind up as to whether the paper (and ultimately the software) will do what they need it to do, and if the paper is unclear, that they can ask the authors to clarify further. The last thing I want to do, personally, is get in the way of others using the library. In many respects that will be a/ the proof that it is any good and b/ provide useful wider feedback.

I stand by my review comments, JOSS is a Journal after all, albeit in a different format, and I don't see anything wrong with being rigorous and demanding, However I do not have a problem with the library being released for use by the design community, if that is the consensus, and therefore I am happy to accept the submission now.

Peter

On Mon, Nov 23, 2020 at 4:15 PM skadio notifications@github.com wrote:

@danielskatz https://github.com/danielskatz

First of all, I would like to thank @jpsety https://github.com/jpsety for the updates and improvements. Most of these comments were not immediate blockers for me but I shared with you in a positive spirit to improve the work for the next/intended users beyond the lead developer. It's nice to see that some are incorporated and others can be added as well.

Without going into a discussion of assessing the exact amount of work involved here, the author highlights an important aspect that I also agree with: "the large amount of work in converting between formats, adding interfaces to generate circuits, transforms that enable SAT calls".

I consider this as a valuable contribution since it can help bring consistency across different research applications and for "reproducibility" purposes. In light of that, I don't see an immediate reason why should the research community be barred from learning about this tool and benefit from its functionality. Hence, I would be happy to accept this submission with minor edits from the list above, if any remaining.

Best, Serdar

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/2646#issuecomment-732264025, or unsubscribe https://github.com/notifications/unsubscribe-auth/AESJLSSEKHVHDBFSWWEBFI3SRKDBFANCNFSM4Q74WFHQ .

danielskatz commented 3 years ago

Thanks @skadio and @prw99r - Can I ask that you check off any remaining items in your checklists in this case? If there's anything that you feel you can't check off, let's talk about it here so that it's clear what is needed for acceptance (vs future enhancements that would be good but are not needed for acceptance)

Also, please feel free to open any needed issues in the source repo as that will be more of a record of potential future enhancement than this review issue, which will close (but remain available) after the review finishes.

skadio commented 3 years ago

Revised the Checklist, no need for opening source repo issues from my side.

danielskatz commented 3 years ago

👋 @prw99r - Can I ask that you check off any remaining items in your checklist in this case? If there's anything that you feel you can't check off, let's talk about it here so that it's clear what is needed for acceptance (vs future enhancements that would be good but are not needed for acceptance)

Also, please feel free to open any needed issues in the source repo as that will be more of a record of potential future enhancement than this review issue, which will close (but remain available) after the review finishes.

prw99r commented 3 years ago

@danielskatz I have checked off my list now - my comments were for the paper more than the repo, so we are good to go.

danielskatz commented 3 years ago

Ok! Thanks very much to everyone (@jpsety, @skadio, @prw99r, @r-a-hoggarth) for working through this process. I think it's improved the software, and led to a good JOSS paper.

danielskatz commented 3 years ago

👋 @jpsety - At this point could you:

[ ] Proofread the paper, and make sure you are happy with it (which I will also do after this part of the process)
[ ] 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 processing the submission.

jpsety commented 3 years ago

I've proofread the paper and followed the above instructions.

Tagged release: https://github.com/circuitgraph/circuitgraph/releases/tag/v0.0.3

DOI: 10.5281/zenodo.4302741 https://zenodo.org/record/4302741#.X8gtyc1KhjE

danielskatz commented 3 years ago

@whedon set v0.0.3 as version

whedon commented 3 years ago

OK. v0.0.3 is the version.

danielskatz commented 3 years ago

@whedon set 10.5281/zenodo.4302741 as archive

whedon commented 3 years ago

OK. 10.5281/zenodo.4302741 is the archive.

danielskatz commented 3 years ago

@whedon generate pdf

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:

danielskatz commented 3 years ago

@whedon check references

whedon commented 3 years ago

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

OK DOIs

- 10.1007/978-3-319-94144-8_26 is OK

MISSING DOIs

- None

INVALID DOIs

- None

danielskatz commented 3 years ago

👋 @jpsety - some small final changes are needed in the paper and bib - please merge https://github.com/circuitgraph/circuitgraph/pull/22 or let me know what you disagree with.

jpsety commented 3 years ago

Merged the changes. Thanks

danielskatz commented 3 years ago

@whedon generate pdf

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:

danielskatz commented 3 years ago

sorry - one more change which I thought was in the PR but apparently wasn't - https://github.com/circuitgraph/circuitgraph/pull/23

danielskatz commented 3 years ago

@whedon generate pdf

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:

danielskatz commented 3 years ago

@jpsety - sorry, I missed a closing paren in the SciPy2008 bib entry - can you add it and then let me know - this really will be the last change...

jpsety commented 3 years ago

All set

danielskatz commented 3 years ago

@whedon generate pdf

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:

danielskatz commented 3 years ago

@whedon accept

whedon commented 3 years ago

Attempting dry run of processing paper acceptance...

whedon commented 3 years ago

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

OK DOIs

- 10.1007/978-3-319-94144-8_26 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 3 years ago

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1963

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1963, 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 commented 3 years ago

@whedon accept deposit=true

whedon commented 3 years ago

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

whedon commented 3 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 3 years ago

🚨🚨🚨 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 :point_right: https://github.com/openjournals/joss-papers/pull/1964
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02646
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

danielskatz commented 3 years ago

Congratulations to @jpsety (Joseph Sweeney) and co-authors!!

And thanks very much to reviewers @skadio, @prw99r, @r-a-hoggarth!

whedon commented 3 years 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.02646/status.svg)](https://doi.org/10.21105/joss.02646)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02646">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02646/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02646/status.svg
   :target: https://doi.org/10.21105/joss.02646

This is how it will look in your documentation:

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skadio commented 3 years ago

@danielskatz thank you as well for the organization and guiding us within a reasonable time-bounded review process.

Congrats to @jpsety and the team!

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