[REVIEW]: Binette: a fast and accurate bin refinement tool to construct high quality Metagenome Assembled Genomes.

editorialbot commented 1 month ago

Submitting author: !--author-handle-->@JeanMainguy@arfon<!--end-editor-- Reviewers: @lskatz, @beardymcjohnface Archive: Pending

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/ad304709d59f1a51a31614393b09ba2b"><img src="https://joss.theoj.org/papers/ad304709d59f1a51a31614393b09ba2b/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/ad304709d59f1a51a31614393b09ba2b/status.svg)](https://joss.theoj.org/papers/ad304709d59f1a51a31614393b09ba2b)

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

@lskatz & @beardymcjohnface, 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 @arfon 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 @lskatz

📝 Checklist for @beardymcjohnface

editorialbot commented 1 month ago

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

editorialbot commented 1 month ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.03 s (1189.8 files/s, 155400.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          16            951            579           1875
Markdown                        10            249              0            459
TeX                              1             25              0            185
YAML                             6             40             44            172
TOML                             1              7              4             57
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            36           1284            635           2783
-------------------------------------------------------------------------------

Commit count by author:

   120  JeanMainguy
    79  Jean Mainguy

editorialbot commented 1 month ago

Paper file info:

📄 Wordcount for paper.md is 850

✅ The paper includes a Statement of need section

editorialbot commented 1 month ago

License info:

✅ License found: MIT License (Valid open source OSI approved license)

editorialbot commented 1 month ago

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

OK DOIs

- 10.1038/s41586-019-1058-x is OK
- 10.1038/s42003-021-02112-2 is OK
- 10.7717/peerj.7359 is OK
- 10.1038/nmeth.3103 is OK
- 10.1038/s41587-020-00777-4 is OK
- 10.1038/s41564-018-0171-1 is OK
- 10.1093/bioinformatics/btac694 is OK
- 10.1186/s40168-018-0541-1 is OK
- 10.1038/s41592-022-01431-4 is OK
- 10.1101/gr.186072.114 is OK
- 10.1038/s41592-023-01940-w is OK
- 10.1038/nmeth.3176 is OK
- 10.21105/joss.04296 is OK
- 10.1186/1471-2105-11-119 is OK
- 10.1038/s41592-018-0046-7 is OK
- 10.1038/s41592-018-0046-7 is OK

MISSING DOIs

- No DOI given, and none found for title: MetagWGS, a complete workflow to analyse metagenom...

INVALID DOIs

- None

editorialbot commented 1 month ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

arfon commented 1 month ago

@lskatz, @beardymcjohnface – This is the review thread for the paper. All of our communications will happen here from now on.

Please read the "Reviewer instructions & questions" in the first comment above. Please create your checklist typing:

@editorialbot generate my checklist

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, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention https://github.com/openjournals/joss-reviews/issues/6782 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 the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.

lskatz commented 1 month ago

Review checklist for @lskatz

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/genotoul-bioinfo/Binette?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@JeanMainguy) 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

[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.
[ ] 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)?
[ ] 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?

beardymcjohnface commented 1 month ago

Review checklist for @beardymcjohnface

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/genotoul-bioinfo/Binette?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@JeanMainguy) 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

[x] 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?
[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?

lskatz commented 3 weeks ago

Some general comments on the paper

Line 42: why is the weight set as 2?
Clarity on line 45: currently is " rather than CheckM1 as in the metaWRAP pipeline" but maybe " rather than CheckM1, which is what the metaWRAP pipeline uses"
Line 96: does JOSS allow for in preparation citations? (might be a question for the editor)

lskatz commented 1 week ago

Any questions/concerns please let @arfon know.

@arfon does JOSS allow for in preparation citations?

arfon commented 1 week ago

@arfon does JOSS allow for in preparation citations?

I think that's fine.

openjournals / joss-reviews