[REVIEW]: Mallob: Scalable SAT Solving On Demand With Decentralized Job Scheduling

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@domschrei@danielskatz<!--end-editor-- Reviewers: @ARMartinelli, @massimotorquati Archive: 10.5281/zenodo.6890240

Status

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Markdown: [![status](https://joss.theoj.org/papers/700e9010c4080ffe8ae4df21cf1cc899/status.svg)](https://joss.theoj.org/papers/700e9010c4080ffe8ae4df21cf1cc899)

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

@ARMartinelli & @massimotorquati, 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

📝 Checklist for @ARMartinelli

📝 Checklist for @massimotorquati

editorialbot commented 2 years 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:

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

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editorialbot commented 2 years ago

Software report:

github.com/AlDanial/cloc v 1.88  T=2.34 s (113.5 files/s, 211333.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JSON                             4              2              0         427093
C/C++ Header                   129           7840          10522          30563
C++                             68           2083           1224          10027
Python                          26            520            305           2057
Bourne Shell                    31            352            206           1420
TeX                              1             46              0            374
Markdown                         3             79              0            270
CMake                            1             33              9            110
diff                             1              2             41             24
YAML                             1              1              4             18
Dockerfile                       1              4              3              9
-------------------------------------------------------------------------------
SUM:                           266          10962          12314         471965
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 2 years ago

Wordcount for paper.md is 786

editorialbot commented 2 years ago

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

OK DOIs

- 10.1109/tc.1985.5009385 is OK
- 10.1137/1.9781611974768.7 is OK
- 10.1109/tc.2006.58 is OK
- 10.1109/clustr.2007.4629252 is OK
- 10.7551/mitpress/12274.003.0036 is OK
- 10.1007/s10586-007-0032-9 is OK
- 10.1016/j.artint.2021.103572 is OK
- 10.1109/date.2001.915010 is OK
- 10.7551/mitpress/7056.001.0001 is OK
- 10.1109/hipc.2014.7116905 is OK
- 10.3233/sat190070 is OK
- 10.1609/aimag.v34i2.2450 is OK
- 10.1007/978-3-030-51825-7_9 is OK
- 10.1007/978-3-319-40970-2_15 is OK
- 10.1007/978-3-540-24644-2_20 is OK
- 10.1109/sbac-pad.2004.27 is OK
- 10.1007/978-3-030-32409-4_2 is OK
- 10.1016/j.artint.2021.103572 is OK
- 10.3233/faia200987 is OK
- 10.34727/2021/isbn.978-3-85448-046-4_33 is OK
- 10.1007/978-3-030-25209-0 is OK
- 10.1109/ipdps.2011.110 is OK
- 10.1007/978-3-642-32820-6_18 is OK
- 10.1613/jair.1.12520 is OK
- 10.1007/978-3-030-80223-3_35 is OK
- 10.1007/978-3-319-24318-4_12 is OK
- 10.1007/978-3-540-24605-3_37 is OK

MISSING DOIs

- None

INVALID DOIs

- 10.6084/m9.figshare.20000642 is INVALID

editorialbot 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:

danielskatz commented 2 years ago

👋 @ARMartinelli, @massimotorquati - 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#4591 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.

danielskatz commented 2 years ago

👋 @domschrei - note that one of your references has an invalid DOI. Please feel free to make changes to your .bib file, then use the command @editorialbot check references to check again, and the command @editorialbot generate pdf when the references are right to make a new PDF. editorialbot commands need to be the first entry in a new comment.

domschrei commented 2 years ago

Hi there! :wave: Thank you for reviewing our submission.

Regarding the invalid DOI, this is a figshare reference to our software reproducibility artifact which got us invited to the Euro-Par special issue. The DOI is not active yet, but it should become active together with the Euro-Par '22 proceedings.

ARMartinelli commented 2 years ago

Review checklist for @ARMartinelli

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] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Repository: Is the source code for this software available at the https://github.com/domschrei/mallob?
[x] Contribution and authorship: Has the submitting author (@domschrei) 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: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
[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?

danielskatz commented 2 years ago

Regarding the invalid DOI, this is a figshare reference to our software reproducibility artifact which got us invited to the Euro-Par special issue. The DOI is not active yet, but it should become active together with the Euro-Par '22 proceedings.

ok, thanks - let's leave it as is then

massimotorquati commented 2 years ago

Review checklist for @massimotorquati

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 https://github.com/domschrei/mallob?
[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 (@domschrei) 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: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
[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?

ARMartinelli commented 2 years ago

@danielskatz, I have finished my review. I have no complaints.

danielskatz commented 2 years ago

Thanks @ARMartinelli

danielskatz commented 2 years ago

@massimotorquati - I notice your review is almost complete as well - is there anything blocking you from checking the last criterion?

massimotorquati commented 2 years ago

Yes, I completed the missing points. I have no objections; the work is OK with me.

danielskatz commented 2 years ago

@domschrei - I'm suggesting some minor changes in https://github.com/domschrei/mallob/pull/8. (note that this includes removing the funding agency logo at the end, which would be appropriate on slides or a poster, but not in a paper) Please merge this, or let me know what you disagree with, and we can move forward on acceptance.

danielskatz commented 2 years ago

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.

domschrei commented 2 years ago

I created a tagged release v1.1.0 and uploaded that version on Zenodo. The DOI is: https://doi.org/10.5281/zenodo.6890240

danielskatz commented 2 years ago

@editorialbot set 10.5281/zenodo.6890240 as archive

editorialbot commented 2 years ago

Done! Archive is now 10.5281/zenodo.6890240

danielskatz commented 2 years ago

@editorialbot set v1.1.0 as archive

editorialbot commented 2 years ago

Done! Archive is now v1.1.0

danielskatz commented 2 years ago

@editorialbot recommend-accept

editorialbot commented 2 years ago

Attempting dry run of processing paper acceptance...

editorialbot commented 2 years ago

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

OK DOIs

- 10.1109/tc.1985.5009385 is OK
- 10.1137/1.9781611974768.7 is OK
- 10.1109/tc.2006.58 is OK
- 10.1109/clustr.2007.4629252 is OK
- 10.7551/mitpress/12274.003.0036 is OK
- 10.1007/s10586-007-0032-9 is OK
- 10.1016/j.artint.2021.103572 is OK
- 10.1109/date.2001.915010 is OK
- 10.7551/mitpress/7056.001.0001 is OK
- 10.1109/hipc.2014.7116905 is OK
- 10.3233/sat190070 is OK
- 10.1609/aimag.v34i2.2450 is OK
- 10.1007/978-3-030-51825-7_9 is OK
- 10.1007/978-3-319-40970-2_15 is OK
- 10.1007/978-3-540-24644-2_20 is OK
- 10.1109/sbac-pad.2004.27 is OK
- 10.1007/978-3-030-32409-4_2 is OK
- 10.1016/j.artint.2021.103572 is OK
- 10.3233/faia200987 is OK
- 10.34727/2021/isbn.978-3-85448-046-4_33 is OK
- 10.1007/978-3-030-25209-0 is OK
- 10.1109/ipdps.2011.110 is OK
- 10.1007/978-3-642-32820-6_18 is OK
- 10.1613/jair.1.12520 is OK
- 10.1007/978-3-030-80223-3_35 is OK
- 10.1007/978-3-319-24318-4_12 is OK
- 10.1007/978-3-540-24605-3_37 is OK

MISSING DOIs

- None

INVALID DOIs

- 10.6084/m9.figshare.20000642 is INVALID

editorialbot commented 2 years ago

:warning: Error prepararing paper acceptance. The generated XML metadata file is invalid.

ID ref-froleyks2021sat already defined

danielskatz commented 2 years ago

👋 @domschrei - I see that you have a duplicate bib entry for froleyks2021sat - Can you remove the first one, then we can try again.

domschrei commented 2 years ago

Done!

danielskatz commented 2 years ago

@editorialbot recommend-accept

editorialbot commented 2 years ago

Attempting dry run of processing paper acceptance...

editorialbot commented 2 years ago

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

OK DOIs

- 10.1109/tc.1985.5009385 is OK
- 10.1137/1.9781611974768.7 is OK
- 10.1109/tc.2006.58 is OK
- 10.1109/clustr.2007.4629252 is OK
- 10.7551/mitpress/12274.003.0036 is OK
- 10.1007/s10586-007-0032-9 is OK
- 10.1109/date.2001.915010 is OK
- 10.7551/mitpress/7056.001.0001 is OK
- 10.1109/hipc.2014.7116905 is OK
- 10.3233/sat190070 is OK
- 10.1609/aimag.v34i2.2450 is OK
- 10.1007/978-3-030-51825-7_9 is OK
- 10.1007/978-3-319-40970-2_15 is OK
- 10.1007/978-3-540-24644-2_20 is OK
- 10.1109/sbac-pad.2004.27 is OK
- 10.1007/978-3-030-32409-4_2 is OK
- 10.1016/j.artint.2021.103572 is OK
- 10.3233/faia200987 is OK
- 10.34727/2021/isbn.978-3-85448-046-4_33 is OK
- 10.1007/978-3-030-25209-0 is OK
- 10.1109/ipdps.2011.110 is OK
- 10.1007/978-3-642-32820-6_18 is OK
- 10.1613/jair.1.12520 is OK
- 10.1007/978-3-030-80223-3_35 is OK
- 10.1007/978-3-319-24318-4_12 is OK
- 10.1007/978-3-540-24605-3_37 is OK

MISSING DOIs

- None

INVALID DOIs

- 10.6084/m9.figshare.20000642 is INVALID

editorialbot commented 2 years ago

:wave: @openjournals/joss-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/3395, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

danielskatz commented 2 years ago

Current status:

paper is proofread, and content is ready to publish
missing DOI is ok, it's a DOI that will be associate with a to-be-published paper
As a Euro-Par associated paper, we need to fix the left column to add appropriate language and logo before final publishing

We're now on hold until the last item is figured out.

danielskatz commented 2 years ago

@arfon - can you explain to @domschrei how to finalize the work on this to add the Euro-Par connection?

arfon commented 2 years ago

@danielskatz – we need a PR to the paper.md for this submission that looks like this: https://github.com/yogi-tud/space_gpu/pull/5/files

Then you need to do @editorialbot accept

I don't think I know what the Euro-Par DOI is though for this submission?

danielskatz commented 2 years ago

👋 @massimotorquati - can you tell us the DOI for the Euro-Par paper this is associated with? (knowing that it's not yet active)

domschrei commented 2 years ago

Maybe I can help. There's two DOIs associated with this work:

DOI of the Figshare repository of our Euro-Par artifact: https://doi.org/10.6084/m9.figshare.20000642 (not active yet)
DOI of the Euro-Par publication itself as given by Springer: https://doi.org/10.1007/978-3-031-12597-3_8 (active)

massimotorquati commented 2 years ago

That's right. Thanks @domschrei !

domschrei commented 2 years ago

And regarding the PR @arfon referenced, the DOI of the publication itself seems to be the correct one to insert. Should I just go ahead and add this line to paper.md?

danielskatz commented 2 years ago

yes, please do

domschrei commented 2 years ago

@danielskatz Done! https://github.com/domschrei/mallob/commit/0d5889ae6e6d5f3bad184996e6081624f2cd843d

danielskatz commented 2 years ago

@editorialbot generate pdf

editorialbot 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:

danielskatz commented 2 years ago

@editorialbot accept

editorialbot commented 2 years ago

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

editorialbot commented 2 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot commented 2 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/3419
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04591
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 2 years ago

Congratulations to @domschrei (Dominik Schreiber) and co-author!!

And thanks to @ARMartinelli and @massimotorquati for reviewing! We couldn't do this without you

editorialbot commented 2 years ago

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

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HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.04591/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04591/status.svg
   :target: https://doi.org/10.21105/joss.04591

This is how it will look in your documentation:

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domschrei commented 2 years ago

Great! Thanks a lot for your work and your help, @danielskatz @ARMartinelli @massimotorquati !

openjournals / joss-reviews