[REVIEW]: Lerche: Generating data file processors in Julia from EBNF grammars

[whedon]

Submitting author: @jamesrhester (James Hester)
Repository: https://github.com/jamesrhester/Lerche.jl
Version: 0.5.1
Editor: @sbenthall
Reviewer: @ziotom78, @eschnett
Archive: 10.5281/zenodo.5178771

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Markdown: [![status](https://joss.theoj.org/papers/155f7b318824375713eec08697c57b2a/status.svg)](https://joss.theoj.org/papers/155f7b318824375713eec08697c57b2a)

Reviewers and authors:

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Review checklist for @ziotom78

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 repository url?
• 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 (@jamesrhester) 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?

Review checklist for @eschnett

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 repository url?
• 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 (@jamesrhester) 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?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @ziotom78, @eschnett it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

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For a list of things I can do to help you, just type:

@whedon commands

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

@whedon generate pdf

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.04 s (802.2 files/s, 158794.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                           23            832            563           4366
Markdown                         4            168              0            477
YAML                             2              2              6             65
TOML                             4             12              1             40
-------------------------------------------------------------------------------
SUM:                            33           1014            570           4948
-------------------------------------------------------------------------------


Statistical information for the repository 'd12e38096882d091e4341ecf' was
gathered on 2021/07/15.
No commited files with the specified extensions were found.

[whedon]

PDF failed to compile for issue #3497 with the following error:

 Can't find any papers to compile :-(

[sbenthall]

@jamesrhester any ideas as to why there is a PDF compilation error? We'll need to fix this to enable to reviewers.

[jamesrhester]

See #3245. I believe the correct syntax is:
@whedon generate pdf from branch joss_paper

Which I've just done below.

[jamesrhester]

@whedon generate pdf from branch joss_paper

[whedon]

Attempting PDF compilation from custom branch joss_paper. Reticulating splines etc...

[whedon]

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

[ziotom78]

@jamesrhester , I am posting this here instead of opening an issue, because this is mostly relevant in the context of this review. I am not able to find any information about how to contribute to your code (see the point «Community guidelines» in the checklist and the JOSS guide).

[ziotom78]

@jamesrhester , I cannot find any performance claim of Lerche over Lark, and while this is not mandatory for a successful review at JOSS, it would make a valuable addition and would probably find its place in the Statement of need in the paper itself.

I created the simple JSON parser described in the Lerche.jl documentation and the same parser in Lark, and then I benchmarked the time required to open a ~500 KB file. Lerche.jl took ~0.3s, while Lark took 4s: Lerche.jl is an order of magnitude faster!

It would be nice to add a xstatement about this, of course after having validated these benchmarks.

[jamesrhester]

@jamesrhester , I am posting this here instead of opening an issue, because this is mostly relevant in the context of this review. I am not able to find any information about how to contribute to your code (see the point «Community guidelines» in the checklist and the JOSS guide).

I have just added two short sections "Issues" and "Contributions" to the top-level README. Hopefully these are sufficient.

[jamesrhester]

@jamesrhester , I cannot find any performance claim of Lerche over Lark, and while this is not mandatory for a successful review at JOSS, it would make a valuable addition and would probably find its place in the Statement of need in the paper itself.

I created the simple JSON parser described in the Lerche.jl documentation and the same parser in Lark, and then I benchmarked the time required to open a ~500 KB file. Lerche.jl took ~0.3s, while Lark took 4s: Lerche.jl is an order of magnitude faster!

It would be nice to add a xstatement about this, of course after having validated these benchmarks.

An earlier draft contained some performance claims but we decided that on balance comparing to interpreted Python was not very helpful when things like PyPy can dramatically improve Python execution speed. I will consult with my coauthor on suitable additional text, as it is true that most people do expect some statements about execution speed in the context of Julia.

[ziotom78]

An earlier draft contained some performance claims but we decided that on balance comparing to interpreted Python was not very helpful when things like PyPy can dramatically improve Python execution speed. I will consult with my coauthor on suitable additional text, as it is true that most people do expect some statements about execution speed in the context of Julia.

I see. I just wanted to raise a flag because this is what people usually look after when they see a Python package ported to Julia, but I do not think it's mandatory to include this information.

[whedon]

👋 @ziotom78, please update us on how your review is going (this is an automated reminder).

[whedon]

👋 @eschnett, please update us on how your review is going (this is an automated reminder).

[ziotom78]

@ziotom78, please update us on how your review is going (this is an automated reminder).

My review is almost finished; there was just the issue whether to include some statement about the performance or not, but if the authors don't feel to do this, that's fine with me.

[eschnett]

I have reviewed the paper and the software. This paper is well written; it gives a brief overview of the software (the parser), but doesn't go into any details about its usage or functionality. I think this is fine, since the README and the documentation of the software do so. The software itself seems mature and has been used for a few years in a few projects. I hope that this publication will increase the reach of this Julia package – it could be useful for many other Julia packages as well.

[eschnett]

A remark to the editors: If software is hosted on Github, then several of the items on the checklist can be checked off almost automatically. Furthermore, if the software is written in Julia, then quite a few more can be checked off almost automatically, since the Julia packaging standards and templates almost automatically lead to well-designed and easy-to-use software.

[jamesrhester]

We have just added a paragraph about performance as it might be of interest.

[jamesrhester]

@whedon generate pdf from branch joss_paper

[whedon]

Attempting PDF compilation from custom branch joss_paper. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #3497 with the following error:

 Can't find any papers to compile :-(

[kthyng]

@whedon recommend-accept from branch joss_paper

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

PDF failed to compile for issue #3497 with the following error:

 Can't find any papers to compile :-(

[kthyng]

@whedon generate pdf from branch joss_paper

[whedon]

Attempting PDF compilation from custom branch joss_paper. Reticulating splines etc...

[whedon]

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

[kthyng]

@jamesrhester Please update the metadata in your Zenodo archive so that the title and author list exactly match your JOSS paper.

[kthyng]

@whedon check references

[kthyng]

The paper looks good, and version updated. This is ready to accept once the Zenodo archive is updated.

[danielskatz]

👋 @jamesrhester - note we just need you to update your zenodo metadata to proceed

[danielskatz]

Additionally, in proofreading the paper, your bib entries for software packages should each have a title field with the title of the package.

[danielskatz]

Finally, I suggest a number of small changes in jamesrhester/Lerche.jl#22

[jamesrhester]

I have updated the title and author list for the Zenodo metadata, merged Daniel's editorial fixes and added title fields where missing to the .bib file.

[danielskatz]

@whedon recommend-accept from branch joss_paper

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1107/S1600576715021871 is OK
- 10.1021/ci300076w is OK

MISSING DOIs

- 10.1038/nsb1203-980 may be a valid DOI for title: Announcing the worldwide Protein Data Bank

INVALID DOIs

- None

[whedon]

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

Check final proof 👉 openjournals/joss-papers#2528

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2528, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true from branch joss_paper 

[danielskatz]

@jamesrhester - I don't see anything different in the Zenodo metadata (title or author(s)):

[jamesrhester]

Sorry, pressed "Save" and not "Publish". Done now.

[danielskatz]

@whedon accept deposit=true from branch joss_paper

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 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.03497 joss-papers#2530
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03497
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...

[danielskatz]

Congratulations to @jamesrhester (James Hester) and co-author!!

And thanks to @sbenthall for editing, and @ziotom78 and @eschnett for reviewing!
We couldn't do this without you.

[whedon]

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

If you would like to include a link to your paper from your README use the following code snippets:

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  <img src="https://joss.theoj.org/papers/10.21105/joss.03497/status.svg" alt="DOI badge" >
</a>

reStructuredText:
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