[REVIEW]: CiteLang: Modeling the Research Software Ecosystem

[editorialbot]

Submitting author: @vsoch (Vanessa Sochat)
Repository: https://github.com/vsoch/citelang
Branch with paper.md (empty if default branch):
Version: 0.0.33
Editor: @faroit
Reviewers: @gflofst, @rmmilewi
Archive: https://doi.org/10.5281/zenodo.7048920

Status

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Markdown: [![status](https://joss.theoj.org/papers/3e3f4e819e6f9400ba204dbae4b9c3d5/status.svg)](https://joss.theoj.org/papers/3e3f4e819e6f9400ba204dbae4b9c3d5)

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

@gflofst & @rmmilewi, 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 @faroit 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 @gflofst

📝 Checklist for @rmmilewi

[editorialbot]

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]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.12 s (977.8 files/s, 91464.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          62           1175           1187           4292
Markdown                        19            152              0            635
HTML                             4            106              0            532
YAML                            12             79             16            464
reStructuredText                 8            533            545            443
SVG                              2              1             21            239
make                             1             28              6            143
TeX                              1             19              0            123
Bourne Shell                     4             29             20            105
CSS                              2             17              8             82
CMake                            1             11              6             44
XML                              1              0              0             30
JSON                             1              0              0             22
Dockerfile                       1              3              1             14
-------------------------------------------------------------------------------
SUM:                           119           2153           1810           7168
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1398

[editorialbot]

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

OK DOIs

- 10.5334/jors.by is OK
- 10.1016/S0950-5849(02)00049-6 is OK
- 10.1109/MS.2020.2973362 is OK
- 10.48550/ARXIV.1905.08674 is OK
- 10.1109/MIC.2014.88 is OK
- 10.1109/CHASE.2019.00039 is OK
- 10.7717/peerj-cs.86 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[faroit]

👋🏼 @vsoch @gflofst @rmmilewi this is the review thread for the paper. All of our communications will happen here from now on.

As a reviewer, the first step is to create a checklist for your review by entering

@editorialbot generate my checklist

as the top of a new comment in this thread.

These checklists contain the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. The first comment in this thread also contains 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, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#4458 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 any 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 (@faroit) if you have any questions/concerns.

[vsoch]

Hey @faroit ! 👋 Just wanted to check in and see if you need anything from me? Happy Saturday! 🥤

[faroit]

@gflofst @rmmilewi please update us on the status of the review.

We aim for reviews to be completed within about 2-4 weeks which is why I will start reminding you using our editorial bot. Let me know if you have problems completing the review or need other help from my side or the authors.

[rmmilewi]

To be clear, I am in fact going to review this paper. I was without reliable internet for a few days while moving houses. But I'm back online and should have this review done in the next day or two!

[vsoch]

Congrats on your move! 🏡

[faroit]

@editorialbot remind @rmmilewi in seven days

[editorialbot]

Reminder set for @rmmilewi in seven days

[faroit]

@editorialbot remind @gflofst in seven days

[editorialbot]

Reminder set for @gflofst in seven days

[gflofst]

I was on travel for a week and then the US holiday on Monday. This week I'll get started.

[gflofst]

Review checklist for @gflofst

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/vsoch/citelang?
• 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 (@vsoch) 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, 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?

[gflofst]

@vsoch I do not see any automated testing support. That is the only thing that might be missing as far as I can see.

[vsoch]

We do have automated tests! They are run via GitHub workflows:

• test-action tests the GitHub actions provided, which also means testing the underlying badge, contrib, and gen commands
• main has linting (black and pyflakes) along with running the test suite at the end - both via pytest and a bash tester that tests the same but via the command line client
• build-deploy ensures the container build is working that is automatically deployed to the repo
• codql is GitHub's code QL analyzer - I'm not convinced yet this is super useful, but I haven't had any errors from it, so maybe that's it.

And here is an example of the "main" test run - if you look under "Run Tests" you'll see lots of output that shows what is going on. https://github.com/vsoch/citelang/runs/6640961948?check_suite_focus=true You can also see the tests here: https://github.com/vsoch/citelang/tree/main/citelang/tests

As an addition, citlelang runs weekly to update the rsepedia, and although it's not an official test, I check that the results look as I'd expect. That's probably a sanity check for a more complex usecase that combines many of the subcommands!

Let me know if you have any questions!

[gflofst]

That is excellent. If you could copy and lightly edit that into the installation instructions, it'll be 100% complete.

[vsoch]

Will do - probably first thing after the work day. Ty!

[vsoch]

okay all set! Added a new test section: https://vsoch.github.io/citelang/getting_started/installation.html#testing

[gflofst]

This looks great! All requirements are passed for me.

[vsoch]

Thank you @rmmilewi ! ❤️

[faroit]

@editorialbot generate pdf

[faroit]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.5334/jors.by is OK
- 10.1016/S0950-5849(02)00049-6 is OK
- 10.1109/MS.2020.2973362 is OK
- 10.48550/ARXIV.1905.08674 is OK
- 10.1109/MIC.2014.88 is OK
- 10.1109/CHASE.2019.00039 is OK
- 10.7717/peerj-cs.86 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[faroit]

@vsoch Everything looks good from my side. For the next steps, please make a new release of the package and archive it, for example on zenodo. Once you complete those tasks, please report here the version number and doi. Please ensure that the archive's author names and title match exactly those of the paper.pdf.

[vsoch]

okay DOI is created, added to the repository along with a CITATION.cff! https://github.com/vsoch/citelang

I think Zenodo might be lagged in actually creating the page for it - there is a notification at the top about uploading issues. So I can't edit the metadata and ensure the author/title are OK, but I'll keep checking it today and update when I can. I can also ping you here when it is fully formed if you like! Thankfully we have the metadata

• Version number: 0.0.33
• DOI: https://doi.org/10.5281/zenodo.7048920 (not working yet)

[vsoch]

Update: is working! And I've fixed the title and my author name! https://zenodo.org/record/7048920

[faroit]

@editorialbot set https://doi.org/10.5281/zenodo.7048920 as archive

[editorialbot]

Done! Archive is now https://doi.org/10.5281/zenodo.7048920

[faroit]

@editorialbot set 0.0.33 as version

[editorialbot]

Done! version is now 0.0.33

[faroit]

@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

- 10.5334/jors.by is OK
- 10.1016/S0950-5849(02)00049-6 is OK
- 10.1109/MS.2020.2973362 is OK
- 10.48550/ARXIV.1905.08674 is OK
- 10.1109/MIC.2014.88 is OK
- 10.1109/CHASE.2019.00039 is OK
- 10.7717/peerj-cs.86 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/joss-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#3493, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[arfon]

@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.04458 joss-papers#3499
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04458
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...

[arfon]

@gflofst, @rmmilewi – many thanks for your reviews here and to @faroit for editing this submission! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@vsoch – your paper is now accepted and published in JOSS ⚡🚀💥 This is such a neat piece of work – I'm hoping I get to use it!

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[faroit]

@vsoch congrats and thanks for all your patience! I am not very happy with duration of the review process so I want to apologize for the delay also were coming from my side. I hope you will choose JOSS again and I will try harder to speed up the process next time.

[vsoch]

it's okay @faroit - thank you so kindly for moving it along! I have a pretty cool project under development called tunel that I'll eventually submit, so I'll definitely be back for a next time! I'm trying to limit myself to one paper / year to not overwhelm the process - I'm just really appreciative for JoSS! I tend to not be a fan of publication as a means to derive our worth but I think y'all are doing it right - a focus on reviewing the code, testing, and documentation. Happy Monday!