[REVIEW]: binary_c-python: A python-based stellar population synthesis tool and interface to binary_c

[editorialbot]

Submitting author: @ddhendriks (David Douwe Hendriks)
Repository: https://gitlab.com/binary_c/binary_c-python/
Branch with paper.md (empty if default branch): master
Version: 1.0.0
Editor: @eloisabentivegna
Reviewers: @trappitsch, @schristophe
Archive: 10.5281/zenodo.7974135

Status

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Markdown: [![status](https://joss.theoj.org/papers/7c43806e6d1f82c2945e12ae500f03b2/status.svg)](https://joss.theoj.org/papers/7c43806e6d1f82c2945e12ae500f03b2)

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

@trappitsch & @schristophe, 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 @trappitsch

📝 Checklist for @schristophe

[editorialbot]

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.64 s (471.3 files/s, 195813.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                           106           5402            418          41330
Python                          60           4497           6696          27421
JavaScript                      32           2506           2607          10058
SVG                              5              0              0           2787
XML                             18              8              0           2751
reStructuredText                29            757            148           2610
CSS                              7            497            118           2260
Jupyter Notebook                15              0           6246           1780
XSD                              2            100             10           1080
TeX                              9            126             65            818
C                                1            232            277            816
Markdown                         2             55              0            119
Bourne Shell                     7             31             49             84
make                             3             31             23             77
C/C++ Header                     1             19             11             59
DOS Batch                        1              8              1             26
XSLT                             1              0              5             10
YAML                             1              1              0             10
TOML                             1              1              2              3
-------------------------------------------------------------------------------
SUM:                           301          14271          16676          94099
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

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

OK DOIs

- 10.1111/j.1365-2966.2004.07446.x is OK
- 10.1051/0004-6361:20066129 is OK
- 10.1051/0004-6361/200912827 is OK
- 10.1093/mnras/stx2355 is OK
- 10.1086/670067 is OK
- 10.1093/mnras/staa278 is OK
- 10.1051/0004-6361/201322068 is OK
- 10.3847/1538-3881/aabc4f is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

Wordcount for paper.md is 779

[editorialbot]

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

[eloisabentivegna]

@trappitsch, @schristophe, many thanks again for your help with this submission. Please let us know if I can clarify or facilitate anything.

[schristophe]

EDIT: Checklist updated with the new repo location is below.

[trappitsch]

Review checklist for @trappitsch

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://gitlab.surrey.ac.uk/ri0005/binary_c-python?
• 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 (@ddhendriks) 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?

[ddhendriks]

Dear @trappitsch @schristophe

Thank you for picking up my submission. I see that the checklists are not entirely completed, but I am unsure about what the implies. Does my submission not meet the unchecked requirements, or is this a matter of not having had time to check these requirements?

Kind regards,

David

[trappitsch]

@ddhendriks: Definitely the latter, slowly but surely working through the checklist, code, and testing. Will be raising issues as requested in the target repository. One problem with that though: I seem to require access in order to post issues in the target repository. The University of Surrey gitlab site says:

External collaborators
Sign in using a Google account. After initializing your account your University of Surrey contact will need to inform IT Services to authorize your access.

or

Ask your Surrey contact to request a GitLab account from IT Services on your behalf. You will need to provide an e-mail address.

@ddhendriks: Could you clarify how @schristophe and I can raise questions in the target repo?

[ddhendriks]

Dear @trappitsch , @schristophe ,

We are currently developing the code through our university enterprise Gitlab environment, which indeed requires either a Surrey University account or a google account workaround. To still allow anyone to submit issues we have a mirror repository on the normal Gitlab platform: https://gitlab.com/binary_c/binary_c-python/-/issues/new. While this is not the actual repository, it is a mirror and will contain the same code. We are considering actually migrating but we will not do so yet. Hopefully this is a good solution for everyone. I updated the link for submitting issues in the docs.

[schristophe]

@eloisabentivegna Is it ok if we submit issues in a mirror repository?

[eloisabentivegna]

@schristophe, @ddhendriks, I am not a fan of this solution. Depending of what will happen to the two versions after the review, the double repository incurs the risk of compromising reproducibility and proper crediting the reviewers for their contributions, two of our key goals. I'd much rather leave @ddhendriks some time to consolidate the package into a single repository compatible with the journal requirements, and start the review at that point.

Having said that, I'd like to loop in the @openjournals/joss-editors to see what they recommend.

[jgostick]

The situation as is will never pass the "Community Guidelines" requirement. The users can neither contribute, raise issues, or discuss the code using the private Gitlab instance. However, there is no perscription as to HOW this should be done. For instance, scikit-image uses some privately hosted forum for user help. Also, the convenience of linking bug reports to pull requests all within the same repo is great, but not mandatory. So this mirror repo could solve 2/3 problems. However, it does not let anyone contribute code, at least not in a way that allows for credit. Someone could email a file to the devs, but this is not really viable IMO. So, ultimately, I don't think that a mirror repo is actually a full solution.

[ddhendriks]

Dear @jgostick, thank you for looking into this.

The users can neither contribute, raise issues, or discuss the code using the private Gitlab instance.
However, it does not let anyone contribute code, at least not in a way that allows for credit.

While this is not totally the case, see quote below

External collaborators:
Sign in using a Google account. After initializing your account, your University of Surrey contact will need to inform IT Services to authorize your access.

it is arguably quite an impractical way of collaborating, and would require switching of accounts and probably cause git/ssh configuration hassle. So I would prefer a solution where we have a single repository myself as well.

@eloisabentivegna I have contacted the open-research group at my university to discuss this matter and find out what the actual policy is for situations like this. I will come back to this when I know more.

[eloisabentivegna]

Thanks, @ddhendriks. Please keep us posted.

[ddhendriks]

@eloisabentivegna I have not yet received a reply from the open-research team here at the university, but I have sent them a reminder.

[trappitsch]

any updates on this?

[eloisabentivegna]

@ddhendriks, could you let us know whether there's any progress on the repository migration?

[ddhendriks]

Dear @trappitsch @eloisabentivegna ,

First of all my apologies for the delay in this matter. End-of-PhD period together with delayed replies from university IT made this take longer than it should. After several back and forths with our university IT we came to the conclusion that no good solution will be found in the near future regarding allowing outside user (accounts) access to university repositories. With that being the case, the issues highlighted earlier in this thread won't be properly solved.

We have therefore decided to make a migration to a public, non enterprise Gitlab repository, so we can further this review process and allow anyone to make issues and submit feedback. I am currently looking into whether the current Gitlab repository (https://gitlab.com/binary_c/binary_c-python/) can be used for this. I will have solved this by the end of this week, and will update you when this is done.

Kind regards,

David

[eloisabentivegna]

Thanks for the update, @ddhendriks. Any news on the migration?

[ddhendriks]

Hello @eloisabentivegna

We have now migrated fully to the new repository (https://gitlab.com/binary_c/binary_c-python/)! Hopefully we can start continue the submission process. I will try to pick up flagged issues as soon as possible.

Best,

David

[eloisabentivegna]

Thanks, @ddhendriks! I will change the submission repository accordingly.

@trappitsch, @schristophe, could you restart your reviews from the new location? I appreciate your help and patience with the transition.

[ddhendriks]

Hello @drvinceknight,

I am not fully sure what each of these steps mean. I have created a git tag archive/JOSS_release associated with the formal release 1.0.0.

version number: 1.0.0
DOI: Gitlab sadly still does not provide DOI's upon release. Is there an alternative way to get a DOI for this? (other than migrating to Github). 10.5281/zenodo.7974135

Please make sure the archive deposit has the correct metadata (title and author list) which should match the paper.

The paper is stored in papers/joss/, containing the same information as the above article proofs contain. Is this sufficient?

My apologies, I don't think I fully understood your request, please correct me if any of my above assumptions are wrong.

Kind regards,

David Hendriks

edits: updated DOI

[drvinceknight]

DOI: Gitlab sadly still does not provide DOI's upon release. Is there an alternative way to get a DOI for this? (other than migrating to Github).

Yup there is. You can create a DOI for the release using Zenodo https://zenodo.org. You can upload the project repo there. If I can clarify anything let me know.

[ddhendriks]

Thank you @drvinceknight

the DOI:

10.5281/zenodo.7974135

[eloisabentivegna]

@editorialbot set 10.5281/zenodo.7974135 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.7974135

[eloisabentivegna]

@editorialbot set 1.0.0 as version

[editorialbot]

Done! version is now 1.0.0

[eloisabentivegna]

@ddhendriks, could you make sure the Zenodo title matches exactly the title of your submission?

[ddhendriks]

@eloisabentivegna I updated the Zenodo title

[eloisabentivegna]

@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

- 10.1111/j.1365-2966.2004.07446.x is OK
- 10.1051/0004-6361:20066129 is OK
- 10.1051/0004-6361/200912827 is OK
- 10.1093/mnras/stx2355 is OK
- 10.1093/mnras/stac2899 is OK
- 10.1086/670067 is OK
- 10.1093/mnras/staa278 is OK
- 10.1051/0004-6361/201322068 is OK
- 10.3847/1538-3881/aabc4f is OK
- 10.21105/joss.01987 is OK
- 10.1051/0004-6361/201321753 is OK
- 10.1093/mnras/sty2848 is OK
- 10.5281/zenodo.3482915 is OK
- 10.21105/joss.03838 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/aass-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#4272, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[eloisabentivegna]

Thanks @trappitsch and @schristophe for your helpful comments and suggestions! And thanks @ddhendriks for thoroughly responding to the feedback and adjusting the package to the journal requirements. Great submission!

[dfm]

@editorialbot accept

[editorialbot]

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

[editorialbot]

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: Hendriks
  given-names: D. D.
  orcid: "https://orcid.org/0000-0002-8717-6046"
- family-names: Izzard
  given-names: R. G.
  orcid: "https://orcid.org/0000-0003-0378-4843"
doi: 10.5281/zenodo.7974135
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Hendriks
    given-names: D. D.
    orcid: "https://orcid.org/0000-0002-8717-6046"
  - family-names: Izzard
    given-names: R. G.
    orcid: "https://orcid.org/0000-0003-0378-4843"
  date-published: 2023-05-30
  doi: 10.21105/joss.04642
  issn: 2475-9066
  issue: 85
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 4642
  title: "binary_c-python: A Python-based stellar population synthesis
    tool and interface to binary_c"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.04642"
  volume: 8
title: "`binary_c-python`: A Python-based stellar population synthesis
  tool and interface to `binary_c`"

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.

[editorialbot]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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🐘🐘🐘 👉 Toot 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.04642 joss-papers#4273
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04642
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...

[dfm]

Many thanks to @trappitsch and @schristophe for reviewing and to @eloisabentivegna for editing! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you!!

@ddhendriks — Your paper is now accepted and published in JOSS! ⚡🚀💥

[editorialbot]

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

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</a>

reStructuredText:
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   :target: https://doi.org/10.21105/joss.04642

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[ddhendriks]

@editorialbot generate preprint

[editorialbot]

📄 Preprint file created: Find it here in the Artifacts list 📄

[ddhendriks]

@editorialbot generate preprint

[editorialbot]

📄 Preprint file created: Find it here in the Artifacts list 📄