[REVIEW]: GEMMI: A library for structural biology

[editorialbot]

Submitting author: @wojdyr (Marcin Wojdyr)
Repository: https://github.com/project-gemmi/gemmi/
Branch with paper.md (empty if default branch): paper
Version: v0.5.1
Editor: @kellyrowland
Reviewers: @jamesrhester, @dominiquesydow
Archive: 10.6084/m9.figshare.19678776

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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

@jamesrhester & @dominiquesydow, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
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✨ 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 @jamesrhester

📝 Checklist for @dominiquesydow

[editorialbot]

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

⚠️ JOSS reduced service mode ⚠️

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[editorialbot]

Checking the BibTeX entries failed with the following error:

No paper file path

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.46 s (973.5 files/s, 226542.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C/C++ Header                   266           7164           6870          51133
C++                             86           1088            491          13443
reStructuredText                10           3191           3870           4837
Python                          50            507            499           3759
C                                8            429            768           3235
JSON                             3              0              0            884
YAML                             7             68             27            444
CMake                            1             73             38            324
Bourne Shell                     7             43             70            279
Markdown                         2             24              0             68
make                             2             19              7             52
Fortran 90                       2              3              4             42
CSS                              1              3              3             13
JavaScript                       1              1              0             12
-------------------------------------------------------------------------------
SUM:                           446          12613          12647          78525
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Failed to discover a Statement of need section in paper

[kellyrowland]

@editorialbot generate pdf from branch paper

[editorialbot]

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

[danielskatz]

@editorialbot set custom-branch-with-paper as paper

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[danielskatz]

👋 @openjournals/dev - Looks like something isn't working right

[xuanxu]

@editorialbot set paper as branch

[editorialbot]

Done! branch is now paper

[xuanxu]

@editorialbot generate pdf

[editorialbot]

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

[kellyrowland]

This needs to be updated: https://joss.readthedocs.io/en/latest/editorial_bot.html#compiling-papers-from-a-specific-branch

[jamesrhester]

Review checklist for @jamesrhester

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 https://github.com/project-gemmi/gemmi/?
• 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 (@wojdyr) 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?

[jamesrhester]

@wojdyr I can't find anything that might be interpreted as "community guidelines" in either the README.md or the Introduction on readthedocs. I would be satisifed with a couple of headings along the lines of "Contributing to GEMMI" explaining how to contribute, and another header "Support" explaining support options. The former would make sense in the README.md and the latter in the introduction to the documentation, I think.

[jamesrhester]

Another minor comment: I think it is worth mentioning somewhere in the Summary which major platforms the software compiles and runs on, or maybe just insert the word "cross-platform" somewhere.

[wojdyr]

@jamesrhester Thanks a lot for the review.

We indeed don't have any guidelines or suggestions regarding contributing to GEMMI. Default Github's Community Guidelines apply. I think it makes reporting bugs easier – the user doesn't need to read and conform to a given protocol. Contributing code to GEMMI has not been formalized yet. To formalize it we'd need to decide how to handle copyrights (should we have CLA and copyright assignment from contributors?), and this would need to be discussed with all stakeholders in the project. Which would take time. As for the support, some users open issue or discussion on Github, other use email. The main page of the documentation (here) encourages to ask question by email, but I don't really have a preferred mode of communication.

"cross-platform" – makes sense, I'll add it (I guess I should wait for the second review before updating the paper).

Thanks again for reviewing the paper!

[jamesrhester]

Perhaps then a header "Contributing" with just a "See Github Community Guidelines" link underneath. "Support" could have "Please open an issue (link) or contact via email". Just something minimal like this should be enough.

[wojdyr]

@jamesrhester I misunderstood community guidelines. I thought about Github guidelines which recommend that people are nice and don't offend each other. When the user open a new issue, they see a footnote:
_{Remember, contributions to this repository should follow our GitHub Community Guidelines.}

But I see that the community guidelines in the review process are specifically about guidelines how to seek support, report problems, etc. So I added this to README.md:

To report problems or ask questions either use GitHub Issues, or email [email protected]. If you consider a major code contribution, please get in touch beforehand.

Thanks for the time you spend on this review.

[dominiquesydow]

Review checklist for @dominiquesydow

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 https://github.com/project-gemmi/gemmi/?
• 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 (@wojdyr) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
  • See commit counts listed in [PRE REVIEW]: GEMMI: A library for structural biology #4089 (comment)
• 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?
  • Tested conda and pip installations.
• 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?
  • Wait for: JOSS review on documentation - statement of need project-gemmi/gemmi#203
• 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).
  • Possible addition suggested here: JOSS review on documentation - show case? project-gemmi/gemmi#202
• 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
  • Wait for: JOSS review on documentation - community guidelines project-gemmi/gemmi#204

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?
  • Wait for: JOSS review on software paper project-gemmi/gemmi#201
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
  • Wait for: JOSS review on software paper project-gemmi/gemmi#201
• 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?
  • Wait for: JOSS review on software paper project-gemmi/gemmi#201

[dominiquesydow]

Hi @wojdyr, thanks for your updates! This completes my review and I recommend this work to be accepted.

[jamesrhester]

My review is also complete.

[kellyrowland]

Excellent, thank you both for your work in reviewing this submission.

[kellyrowland]

@editorialbot generate pdf

[editorialbot]

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

[kellyrowland]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1107/S2059798321009475 is OK
- 10.21105/joss.00350 is OK
- 10.1107/S160057672100755X is OK
- 10.1107/S2059798317016035 is OK
- 10.1107/S2059798317014565 is OK
- 10.1107/S2059798321003934 is OK
- 10.1093/bioinformatics/bty191 is OK
- 10.1002/jcc.21439 is OK
- 10.1088/1742-6596/430/1/012007 is OK
- 10.1107/S0021889801017824 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[kellyrowland]

@wojdyr I'm ready to recommend this for acceptance. Please create an archive of the tagged release you wish to have the paper associated with (I see we started at v0.5.1 but the software is up to v0.5.4) and archive it (on Zenodo, figshare, or elsewhere) and post the DOI here.

[wojdyr]

Thank you all!
I uploaded v0.5.1 here:
https://doi.org/10.6084/m9.figshare.19678776

[kellyrowland]

@editorialbot set 10.6084/m9.figshare.19678776 as archive

[editorialbot]

Done! Archive is now 10.6084/m9.figshare.19678776

[kellyrowland]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1107/S2059798321009475 is OK
- 10.21105/joss.00350 is OK
- 10.1107/S160057672100755X is OK
- 10.1107/S2059798317016035 is OK
- 10.1107/S2059798317014565 is OK
- 10.1107/S2059798321003934 is OK
- 10.1093/bioinformatics/bty191 is OK
- 10.1002/jcc.21439 is OK
- 10.1088/1742-6596/430/1/012007 is OK
- 10.1107/S0021889801017824 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

Check final proof 👉 openjournals/joss-papers#3182

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3182, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[kyleniemeyer]

@editorialbot accept

[editorialbot]

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

[editorialbot]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[editorialbot]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.04200 joss-papers#3196
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04200
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[kyleniemeyer]

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

Many thanks to @jamesrhester and @dominiquesydow for reviewing this, and @kellyrowland for editing.

[editorialbot]

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

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[wojdyr]

Thanks a lot @jamesrhester @dominiquesydow @kellyrowland and @kyleniemeyer !

[kellyrowland]

Congratulations @wojdyr ! 🎉