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[REVIEW]: Satisfiability.jl: Satisfiability Modulo Theories in Julia #6757

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editorialbot opened this issue May 16, 2024 · 76 comments
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accepted Julia published Papers published in JOSS recommend-accept Papers recommended for acceptance in JOSS. review Shell TeX Track: 7 (CSISM) Computer science, Information Science, and Mathematics

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editorialbot commented May 16, 2024

Submitting author: @elsoroka (Emiko Soroka)
Repository: https://github.com/elsoroka/Satisfiability.jl
Branch with paper.md (empty if default branch): joss-paper
Version: 0.2.0
Editor: @diehlpk
Reviewers: @rafaelbailo, @dpsanders, @computablee
Archive: 10.6084/m9.figshare.26768461

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/68f75b3e24424e344dbb80af79dcab4b"><img src="https://joss.theoj.org/papers/68f75b3e24424e344dbb80af79dcab4b/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/68f75b3e24424e344dbb80af79dcab4b/status.svg)](https://joss.theoj.org/papers/68f75b3e24424e344dbb80af79dcab4b)

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

@rafaelbailo & @dpsanders & @computablee, 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 @diehlpk 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 @rafaelbailo

📝 Checklist for @computablee

📝 Checklist for @dpsanders

@editorialbot
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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

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Software report:

github.com/AlDanial/cloc v 1.90  T=0.05 s (1492.7 files/s, 139966.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                           31            750           1116           2470
Markdown                        16            229              0            834
TeX                              6             31             29            336
Lisp                             3             63              0            310
YAML                             5              6             12            108
JSON                             1              0              0             30
Bourne Shell                     3              4              0             21
TOML                             2              4              0             14
Dockerfile                       1              2              0              7
-------------------------------------------------------------------------------
SUM:                            68           1089           1157           4130
-------------------------------------------------------------------------------

Commit count by author:

   232	Emiko Soroka
     2	dependabot[bot]
     1	Mykel Kochenderfer
     1	Thomas Schmelzer

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Paper file info:

📄 Wordcount for paper.md is 1299

✅ The paper includes a Statement of need section

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License info:

✅ License found: MIT License (Valid open source OSI approved license)

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

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

OK DOIs

- 10.48550/arXiv.1410.4821 is OK
- 10.1007/s12532-023-00239-3 is OK
- 10.1145/1995376.1995394 is OK
- 10.1007/978-3-030-81688-9_9 is OK
- 10.1007/978-3-540-78800-3_24 is OK
- 10.1007/978-3-030-99524-9_24 is OK
- 10.3233/SAT190039 is OK
- 10.1145/3136000.3136004 is OK
- 10.1007/978-3-031-24950-1_5 is OK
- 10.1007/978-3-031-24950-1_12 is OK
- 10.1137/141000671 is OK
- 10.1007/978-3-030-80223-3_26 is OK

MISSING DOIs

- No DOI given, and none found for title: The calculus of computation: decision procedures w...
- No DOI given, and none found for title: Decision procedures
- No DOI given, and none found for title: PySMT: a solver-agnostic library for fast prototyp...
- No DOI given, and none found for title: PicoSAT.jl
- No DOI given, and none found for title: The SMT-LIB Standard: Version 2.6

INVALID DOIs

- None

@rafaelbailo
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rafaelbailo commented May 16, 2024

Review checklist for @rafaelbailo

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

General checks

  • Repository: Is the source code for this software available at the https://github.com/elsoroka/Satisfiability.jl?
  • License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
  • Contribution and authorship: Has the submitting author (@elsoroka) 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
  • Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
  • Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
  • Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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, who the target audience is, and its relation to other work?
  • 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?

@computablee
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computablee commented May 16, 2024

Review checklist for @computablee

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

General checks

  • Repository: Is the source code for this software available at the https://github.com/elsoroka/Satisfiability.jl?
  • License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
  • Contribution and authorship: Has the submitting author (@elsoroka) 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
  • Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
  • Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
  • Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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, who the target audience is, and its relation to other work?
  • 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?

@diehlpk
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diehlpk commented May 31, 2024

Hi @rafaelbailo, @dpsanders, @computablee how is your review going?

@computablee
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computablee commented May 31, 2024

@diehlpk I was just taking a look at this a couple days ago. Things have been very busy with work, but if all goes well I should be able to get a lot of review stuff done this weekend.

@rafaelbailo
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Hi @diehlpk, I've just posted my review in a separate issue. Thanks for your patience!

@computablee
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Hello @diehlpk! Sorry for the late review, but I've checked most of the boxes and opened an issue over here with my full review.

@diehlpk
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diehlpk commented Jun 18, 2024

Hi @rafaelbailo how is your review going?

@rafaelbailo
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Hi @diehlpk, @elsoroka has began work addressing my comments in the review issue.

@diehlpk
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diehlpk commented Jun 28, 2024

Hi @elsoroka please let me know when you have done the changes.

@elsoroka
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elsoroka commented Jul 2, 2024

Hi @diehlpk apologies for the delay; I started a new internship a couple weeks ago and haven't had much time. I am targeting end of this week to make the changes because we have a couple days off for the holiday.

@dpsanders
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dpsanders commented Jul 4, 2024

Review checklist for @dpsanders

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

General checks

  • Repository: Is the source code for this software available at the https://github.com/elsoroka/Satisfiability.jl?
  • License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
  • Contribution and authorship: Has the submitting author (@elsoroka) 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
  • Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
  • Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
  • Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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, who the target audience is, and its relation to other work?
  • 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?

@dpsanders
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Apologies for the delay in my review. Here are some observations.

This is a very nice package, providing key functionality for the Julia ecosystem. The documentation is very well done, with nice motivating examples.

  • The package looks for a command-line z3 function. This should ideally be provided instead via BinaryBuilder. (E.g. Z3.jl does this.)

  • Does the command-line interface work on Windows?

  • On MacOS brew install z3 should work (assuming the user has Homebrew installed) to install Z3.

  • Why is the function called sat! instead of sat? It's not clear what it's mutating.

  • I suggest to add a simple usage example to the paper. This would help focus the reader's understanding of the functionality and API of the package.

  • There doesn’t seem to be any API documentation.

  • There don’t seem to be any contribution guidelines.

Overall this is a very nice piece of work!

@rafaelbailo
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@editorialbot generate pdf

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

@rafaelbailo
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Hi @diehlpk, all my queries have been satisfied, and I've ticked all the items on my checklist. As far as I'm concerned, the paper is good to go 👍🏻 .

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

OK DOIs

- 10.48550/arXiv.1410.4821 is OK
- 10.1007/s12532-023-00239-3 is OK
- 10.1145/1995376.1995394 is OK
- 10.1007/978-3-030-81688-9_9 is OK
- 10.1007/978-3-540-78800-3_24 is OK
- 10.1007/978-3-030-99524-9_24 is OK
- 10.3233/SAT190039 is OK
- 10.1145/3136000.3136004 is OK
- 10.1007/978-3-031-24950-1_5 is OK
- 10.1007/978-3-031-24950-1_12 is OK
- 10.1137/141000671 is OK
- 10.1007/978-3-030-80223-3_26 is OK

MISSING DOIs

- No DOI given, and none found for title: The calculus of computation: decision procedures w...
- No DOI given, and none found for title: Decision procedures
- No DOI given, and none found for title: PySMT: a solver-agnostic library for fast prototyp...
- No DOI given, and none found for title: PicoSAT.jl
- No DOI given, and none found for title: The SMT-LIB Standard: Version 2.6

INVALID DOIs

- None

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

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#5781, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

@editorialbot editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Aug 19, 2024
@danielskatz
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As track editor, I'll next proofread this and provide further instructions, if any are needed, probably in the next 12 or so hours.

@danielskatz
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@elsoroka - I just found 2 small changes needed in the references, as indicated in elsoroka/Satisfiability.jl#66

Please merge this, or let me now what you disagree with, then we can finish the publication process.

@elsoroka
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@danielskatz Thank you for catching that! I merged it in

@danielskatz
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@editorialbot recommend-accept

generating new proof - will check again and hopefully complete in a couple of hours...

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Attempting dry run of processing paper acceptance...

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

✅ OK DOIs

- 10.48550/arXiv.1410.4821 is OK
- 10.1007/s12532-023-00239-3 is OK
- 10.1145/1995376.1995394 is OK
- 10.1007/978-3-030-81688-9_9 is OK
- 10.1007/978-3-540-78800-3_24 is OK
- 10.1007/978-3-030-99524-9_24 is OK
- 10.3233/SAT190039 is OK
- 10.1145/3136000.3136004 is OK
- 10.1007/978-3-031-24950-1_5 is OK
- 10.1007/978-3-031-24950-1_12 is OK
- 10.1137/141000671 is OK
- 10.1007/978-3-030-80223-3_26 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: The calculus of computation: decision procedures w...
- No DOI given, and none found for title: Decision procedures
- No DOI given, and none found for title: PySMT: a solver-agnostic library for fast prototyp...
- No DOI given, and none found for title: PicoSAT.jl
- No DOI given, and none found for title: The SMT-LIB Standard: Version 2.6

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

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

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#5784, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

@danielskatz
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👋 @elsoroka - the changes I made in the PR didn't make it in to this proof, I think because I was working in your main branch but this review thread is working in joss-paper. Should JOSS be working in main now? If so, we can change this thread to point to main. If not, can you make the same two changes in the joss-paper branch?

@elsoroka
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elsoroka commented Aug 20, 2024

Hi @danielskatz - to solve this, I merged the changes from main into joss-paper. So now the two branches should be in sync elsoroka/Satisfiability.jl@main...joss-paper.
I think it's fine to work off either (I don't know the best practice). I do note that the previous changes before the bibliography edit were merged into main, so they made it into the software archive.

@danielskatz
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@editorialbot recommend-accept

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Attempting dry run of processing paper acceptance...

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

✅ OK DOIs

- 10.48550/arXiv.1410.4821 is OK
- 10.1007/s12532-023-00239-3 is OK
- 10.1145/1995376.1995394 is OK
- 10.1007/978-3-030-81688-9_9 is OK
- 10.1007/978-3-540-78800-3_24 is OK
- 10.1007/978-3-030-99524-9_24 is OK
- 10.3233/SAT190039 is OK
- 10.1145/3136000.3136004 is OK
- 10.1007/978-3-031-24950-1_5 is OK
- 10.1007/978-3-031-24950-1_12 is OK
- 10.1137/141000671 is OK
- 10.1007/978-3-030-80223-3_26 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: The calculus of computation: decision procedures w...
- No DOI given, and none found for title: Decision procedures
- No DOI given, and none found for title: PySMT: a solver-agnostic library for fast prototyp...
- No DOI given, and none found for title: PicoSAT.jl
- No DOI given, and none found for title: The SMT-LIB Standard: Version 2.6

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

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

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#5786, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

@danielskatz
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@editorialbot accept

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

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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: Soroka
  given-names: Emiko
  orcid: "https://orcid.org/0009-0001-2710-469X"
- family-names: Kochenderfer
  given-names: Mykel J.
  orcid: "https://orcid.org/0000-0002-7238-9663"
- family-names: Lall
  given-names: Sanjay
  orcid: "https://orcid.org/0000-0002-1783-5309"
contact:
- family-names: Soroka
  given-names: Emiko
  orcid: "https://orcid.org/0009-0001-2710-469X"
- family-names: Kochenderfer
  given-names: Mykel J.
  orcid: "https://orcid.org/0000-0002-7238-9663"
- family-names: Lall
  given-names: Sanjay
  orcid: "https://orcid.org/0000-0002-1783-5309"
doi: 10.6084/m9.figshare.26768461
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Soroka
    given-names: Emiko
    orcid: "https://orcid.org/0009-0001-2710-469X"
  - family-names: Kochenderfer
    given-names: Mykel J.
    orcid: "https://orcid.org/0000-0002-7238-9663"
  - family-names: Lall
    given-names: Sanjay
    orcid: "https://orcid.org/0000-0002-1783-5309"
  date-published: 2024-08-20
  doi: 10.21105/joss.06757
  issn: 2475-9066
  issue: 100
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6757
  title: "Satisfiability.jl: Satisfiability Modulo Theories in Julia"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06757"
  volume: 9
title: "Satisfiability.jl: Satisfiability Modulo Theories in Julia"

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.

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🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

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🚨🚨🚨 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 👉 Creating pull request for 10.21105.joss.06757 joss-papers#5787
  2. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06757
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

@editorialbot editorialbot added accepted published Papers published in JOSS labels Aug 20, 2024
@rafaelbailo
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Congratulations to the authors, and thank you everyone for your hard work! 🎉🎊

@computablee
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Congratulations on the publication!

@danielskatz
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Congratulations to @elsoroka (Emiko Soroka) and co-authors on your publication!!

And thanks to @rafaelbailo, @dpsanders, and @computablee for reviewing, and to @diehlpk for editing!
JOSS depends on volunteers and we couldn't do this without you

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🎉🎉🎉 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.06757/status.svg)](https://doi.org/10.21105/joss.06757)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06757">
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@elsoroka
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Thank you everyone for your help reviewing and editing and congratulations to co-authors @mykelk and @sanjaylall!

@dpsanders
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Congratulations to the authors for their nice work and paper!

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