[REVIEW]: UnROOT: an I/O library for the CERN ROOT file format written in Julia

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@tamasgal@danielskatz<!--end-editor-- Reviewers: @PerilousApricot, @jpata Archive: 10.5281/zenodo.7008076

Status

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HTML: <a href="https://joss.theoj.org/papers/bab42b0c60f9dc7ef3b8d6460bc7229c"><img src="https://joss.theoj.org/papers/bab42b0c60f9dc7ef3b8d6460bc7229c/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/bab42b0c60f9dc7ef3b8d6460bc7229c/status.svg)](https://joss.theoj.org/papers/bab42b0c60f9dc7ef3b8d6460bc7229c)

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

@PerilousApricot & @jpata, 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 @PerilousApricot

📝 Checklist for @jpata

editorialbot commented 2 years ago

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editorialbot commented 2 years ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.06 s (822.7 files/s, 108344.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                           14            638            311           3556
Markdown                         9            105              0            547
Python                          20             98             65            404
SVG                              1              0              0            173
TeX                              1              3              0            141
YAML                             4              4              4            119
Jupyter Notebook                 1              0            624             82
TOML                             2              4              0             59
C                                1              9              1             33
-------------------------------------------------------------------------------
SUM:                            53            861           1005           5114
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 2 years ago

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

OK DOIs

- 10.1137/141000671 is OK
- 10.1007/s41781-021-00053-3 is OK
- 10.5281/zenodo.5539722 is OK
- 10.5281/zenodo.6522027 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.5281/zenodo.3509134 is OK
- 10.1016/S0168-9002(97)00048-X is OK
- 10.1088/0954-3899/43/8/084001 is OK
- 10.1051/epjconf/202024506002 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 2 years ago

Wordcount for paper.md is 1079

danielskatz commented 2 years ago

@PerilousApricot and @jpata - 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#4452 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.

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:

PerilousApricot commented 2 years ago

Review checklist for @PerilousApricot

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/JuliaHEP/UnROOT.jl?
[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 (@tamasgal) 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 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?

danielskatz commented 2 years ago

Hi @PerilousApricot and @jpata - I just wanted to check in and see how things are going...

PerilousApricot commented 2 years ago

Hello @danielskatz Sorry for the delay! I need to set up a julia environment to get some of these checks. Soon!

jpata commented 2 years ago

Review checklist for @jpata

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/JuliaHEP/UnROOT.jl?
[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 (@tamasgal) 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?

jpata commented 2 years ago

From my side, I'm done with the initial paper review and have left some issues:

Contribution guidelines: https://github.com/JuliaHEP/UnROOT.jl/issues/170
Adding some more details and improving the writing in the paper: https://github.com/JuliaHEP/UnROOT.jl/issues/171

I'm also going to try out the library in the next days and check off the functionality/performance based on that.

danielskatz commented 2 years ago

👋 @tamasgal - you can work on the two issues from @jpata at this point if you want; you don't need to wait for one of both review to be complete.

tamasgal commented 2 years ago

Thanks, we are already working on the improvements!

danielskatz commented 2 years ago

👋 @PerilousApricot - Can I check in with you on the status of your review?

danielskatz commented 2 years ago

👋 @PerilousApricot - checking in again...

PerilousApricot commented 2 years ago

Errrr, apparently the Github email connector isn't working?? Sorry about that -- I tried to say earlier that I was on vacation until the 13th... I've nearly completed the review now and should be able to sign off on the paper in the next hour

PerilousApricot commented 2 years ago

LGTM! Great paper & great project all

danielskatz commented 2 years ago

👋 @PerilousApricot and @jpata - it looks like both of you have checked off all items on your lists. Please confirm that you are ready for this to be accepted.

PerilousApricot commented 2 years ago

@danielskatz I confirm that I am ready for this to be accepted

danielskatz commented 2 years ago

Ah, @jpata, I see that you didn't check off an item: "Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?"

What needs to be done for you to check this off?

Moelf commented 2 years ago

I think when he comes back from vacation and take a look at the PR that closed:

https://github.com/JuliaHEP/UnROOT.jl/issues/171

they probably can decide if we have more items to do

danielskatz commented 2 years ago

Ok, thanks - I didn't realize he was on vacation

danielskatz commented 2 years ago

👋 @jpata - can you check on the few comments above ☝️ and let us know if you think more work is needed or this is ready to go? (sorry for the delay on my part here - I was also on vacation the last 2 weeks)

jpata 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:

jpata commented 2 years ago

Sorry for the delay on my part due to vacations.

The paper has been improved significantly and all the content-related comments have been addressed, but I think it could still benefit from some language-level improvements. I'm not a native speaker, but here are some suggestions which could improve readability.

11. The High-Energy Physics (HEP) community, especially the group doing analysis, has facing the two-language problem for a long time. -> ... especially in data analysis, has been facing ...
14. is extremely hard to express in columnar -> can be challenging to express
16. leads to either writing C++ kernels and interface them -> ... and interfacing them
26. the existing usage often rely on -> often relies on
26. newer techniques such as automatic differentiation also works more smoothly without language barriers, allows physicists to DIY algorithms themselves. -> ... also work more smoothly without language barriers, allowing physicists to develop algorithms.
68. can be done with 0 code addition -> can be done with no code addition

If you want to go forward as-is, I will be happy to sign off, but I think a little bit of polishing of the language could make the paper even better.

danielskatz commented 2 years ago

Thanks @jpata!

@tamasgal - can you go ahead and address these language comments?

Also, I'll do a final proof-read when everything else seems ready.

jpata 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:

jpata commented 2 years ago

All items are checked off on my side!

danielskatz commented 2 years ago

thanks @jpata

@tamasgal - next I'll do a proof-read and then we can start the final steps in publication

danielskatz commented 2 years ago

@tamasgal - I suggest a number of changes in the paper and one in the bib in https://github.com/JuliaHEP/UnROOT.jl/pull/179

danielskatz commented 2 years ago

@editorialbot generate pdf

Thanks for merging the PR. At this point, assuming everything looks ok to you in the PDF that will soon be generated, can 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.

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:

tamasgal commented 2 years ago

Thanks @danielskatz and sorry for the late response (lot of traveling lately).

I fixed the Zenodo entry and created and archived a new version of UnROOT: 0.8.11

Here is the DOI: 10.5281/zenodo.7008076

danielskatz commented 2 years ago

@editorialbot set 0.8.11 as version

editorialbot commented 2 years ago

Done! version is now 0.8.11

danielskatz commented 2 years ago

@editorialbot set 10.5281/zenodo.7008076 as archive

editorialbot commented 2 years ago

Done! Archive is now 10.5281/zenodo.7008076

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

- 10.1137/141000671 is OK
- 10.1007/s41781-021-00053-3 is OK
- 10.5281/zenodo.5539722 is OK
- 10.5281/zenodo.6522027 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.5281/zenodo.3509134 is OK
- 10.1016/S0168-9002(97)00048-X is OK
- 10.1088/0954-3899/43/8/084001 is OK
- 10.1051/epjconf/202024506002 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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/3446, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

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/3447
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04452
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 @tamasgal (Tamás Gál) and co-authors!!

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

editorialbot commented 2 years ago

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tamasgal commented 2 years ago

Many thanks Daniel, and of course big thanks to the reviewers too! :)

openjournals / joss-reviews