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[REVIEW]: binary_c-python: A python-based stellar population synthesis tool and interface to binary_c
Submitting author: @ddhendriks (David Douwe Hendriks) Repository: https://gitlab.surrey.ac.uk/ri0005/binary_c-python Branch with paper.md (empty if default branch): master Version: v0.9.4 Editor: @eloisabentivegna Reviewers: @trappitsch, @schristophe Archive: Pending
Status
Status badge code:
HTML: <a href="https://joss.theoj.org/papers/7c43806e6d1f82c2945e12ae500f03b2"><img src="https://joss.theoj.org/papers/7c43806e6d1f82c2945e12ae500f03b2/status.svg"></a>
Markdown: [](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. 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 @eloisabentivegna 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
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:
@editorialbot commands
For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:
@editorialbot generate pdf
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
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
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@trappitsch, @schristophe, many thanks again for your help with this submission. Please let us know if I can clarify or facilitate anything.
Review checklist for @trappitsch
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://gitlab.surrey.ac.uk/ri0005/binary_c-python?
- [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 (@ddhendriks) 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
- [ ] Installation: Does installation proceed as outlined in the documentation?
- [ ] 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?
- [ ] 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?
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
@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?
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, @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.
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.
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 I have not yet received a reply from the open-research team here at the university, but I have sent them a reminder.
@ddhendriks, could you let us know whether there's any progress on the repository migration?
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
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
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.
@editorialbot set https://gitlab.com/binary_c/binary_c-python/ as repository
Review checklist for @schristophe
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://gitlab.com/binary_c/binary_c-python/?
- [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 (@ddhendriks) 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
- [x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
- [x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
- [x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.
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?