Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[REVIEW]: Koverage: Read-coverage analysis for massive (meta)genomics datasets #6235

Closed
editorialbot opened this issue Jan 17, 2024 · 51 comments
Assignees
Labels
accepted published Papers published in JOSS Python recommend-accept Papers recommended for acceptance in JOSS. review TeX Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials

Comments

@editorialbot
Copy link
Collaborator

editorialbot commented Jan 17, 2024

Submitting author: @beardymcjohnface (Michael J. Roach)
Repository: https://github.com/beardymcjohnface/Koverage
Branch with paper.md (empty if default branch): JOSS
Version: 0.1.11
Editor: @csoneson
Reviewers: @lparsons, @telatin
Archive: 10.5281/zenodo.10633263

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/c17433374e2f3927cc63313ee2d69ee3"><img src="https://joss.theoj.org/papers/c17433374e2f3927cc63313ee2d69ee3/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/c17433374e2f3927cc63313ee2d69ee3/status.svg)](https://joss.theoj.org/papers/c17433374e2f3927cc63313ee2d69ee3)

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

@lparsons & @telatin, 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 @csoneson 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 @lparsons

📝 Checklist for @telatin

@editorialbot editorialbot added Python review TeX Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials waitlisted Submissions in the JOSS backlog due to reduced service mode. labels Jan 17, 2024
@editorialbot
Copy link
Collaborator Author

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
Copy link
Collaborator Author

Software report:

github.com/AlDanial/cloc v 1.88  T=0.04 s (1049.2 files/s, 101075.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          18            362            341           1609
SVG                              1              1              1            663
Markdown                        10            195              0            545
YAML                            15             43             16            353
TeX                              1              0              0            206
-------------------------------------------------------------------------------
SUM:                            45            601            358           3376
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

@editorialbot
Copy link
Collaborator Author

Wordcount for paper.md is 2060

@editorialbot
Copy link
Collaborator Author

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

OK DOIs

- 10.12688/f1000research.29032.1 is OK
- 10.1371/journal.pcbi.1010705 is OK
- 10.1093/bioinformatics/bty191 is OK
- 10.1093/bioinformatics/btr011 is OK
- 10.1093/gigascience/giab008 is OK
- 10.25957/FLINDERS.HPC.DEEPTHOUGHT is OK
- 10.1186/s13015-021-00185-6 is OK
- 10.1089/cmb.2022.0262 is OK
- 10.1101/2023.04.19.537311 is OK
- 10.1007/s00248-022-02094-6 is OK
- 10.1093/bioinformatics/btad586 is OK
- 10.1101/2022.05.15.492003 is OK

MISSING DOIs

- None

INVALID DOIs

- None

@editorialbot
Copy link
Collaborator Author

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

@csoneson
Copy link
Member

👋🏼 @beardymcjohnface, @lparsons, @telatin - this is the review thread for the submission. All of our communications will happen here from now on.

Please check the post at the top of the issue for instructions on how to generate your own review 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 directly in the software repository. If you do so, please mention this thread so that a link is created (and I can keep an eye on what is happening). Please also feel free to comment and ask questions in this thread. It is often easier to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

Please feel free to ping me (@csoneson) if you have any questions or concerns. Thanks!

@csoneson csoneson removed the waitlisted Submissions in the JOSS backlog due to reduced service mode. label Jan 17, 2024
@lparsons
Copy link

lparsons commented Jan 26, 2024

Review checklist for @lparsons

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

General checks

  • Repository: Is the source code for this software available at the https://github.com/beardymcjohnface/Koverage?
  • License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
  • Contribution and authorship: Has the submitting author (@beardymcjohnface) 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
  • 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.
  • Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
  • 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?

@telatin
Copy link

telatin commented Jan 27, 2024

Howdy,

Great package, I think this can be very useful.

I started testing the package, but I cannot see the checklist here.

@csoneson
Copy link
Member

@telatin You have to generate your own review checklist; see the first post in this issue for instructions.

@telatin
Copy link

telatin commented Jan 27, 2024

Review checklist for @telatin

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

General checks

  • Repository: Is the source code for this software available at the https://github.com/beardymcjohnface/Koverage?
  • License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
  • Contribution and authorship: Has the submitting author (@beardymcjohnface) 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
  • 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.
  • Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
  • 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?

@csoneson
Copy link
Member

👋🏻 @telatin and @lparsons - I see you have both ticked off all the boxes in your checklists above, and the linked issues are closed. Could you let me know what your status is - are you happy with the submission, are you waiting for input, or do you have additional comments for the author? Thanks!!

@telatin
Copy link

telatin commented Feb 20, 2024

LGTM!

@lparsons
Copy link

Same, LGTM.

@csoneson
Copy link
Member

Ok, thanks both for your reviews!
@beardymcjohnface - I will also take a look at the submission shortly, and get back to you with the next steps.

@csoneson
Copy link
Member

@editorialbot check references

@editorialbot
Copy link
Collaborator Author

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

OK DOIs

- 10.12688/f1000research.29032.1 is OK
- 10.1371/journal.pcbi.1010705 is OK
- 10.1093/bioinformatics/bty191 is OK
- 10.1093/bioinformatics/btr011 is OK
- 10.1093/gigascience/giab008 is OK
- 10.25957/FLINDERS.HPC.DEEPTHOUGHT is OK
- 10.1186/s13015-021-00185-6 is OK
- 10.1089/cmb.2022.0262 is OK
- 10.1101/2023.04.19.537311 is OK
- 10.1007/s00248-022-02094-6 is OK
- 10.1093/bioinformatics/btad586 is OK
- 10.1101/2022.05.15.492003 is OK

MISSING DOIs

- None

INVALID DOIs

- None

@csoneson
Copy link
Member

@editorialbot generate pdf

@editorialbot
Copy link
Collaborator Author

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

@csoneson
Copy link
Member

👋🏻 @beardymcjohnface - I have gone through your submission and overall it looks good. I made a PR here with some small suggestions for the paper.

In addition to that, note that your paper is currently significantly longer than the recommendations in the JOSS guidelines (250-1,000 words, yours is over 2,000). If you could look into trimming the manuscript a bit to get closer to the recommended length, that would be great. Once that is done, you can generate a new proof here with @editorialbot generate pdf.

I will make another post below with the other remaining steps (some for you, some for me).

@csoneson
Copy link
Member

csoneson commented Feb 25, 2024

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

  • Double check authors and affiliations (including ORCIDs)
  • Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
  • Archive the release on Zenodo/figshare/etc and post the DOI here.
  • Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
  • Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

  • Read the text of the paper and offer comments/corrections (as either a list or a pull request)
  • Check that the archive title, author list, version tag, and the license are correct
  • Set archive DOI with @editorialbot set <DOI here> as archive
  • Set version with @editorialbot set <version here> as version
  • Double check rendering of paper with @editorialbot generate pdf
  • Specifically check the references with @editorialbot check references and ask author(s) to update as needed
  • Recommend acceptance with @editorialbot recommend-accept

@editorialbot
Copy link
Collaborator Author

Wordcount for paper.md is 1764

@csoneson
Copy link
Member

@editorialbot set 0.1.11 as version

@editorialbot
Copy link
Collaborator Author

Done! version is now 0.1.11

@csoneson
Copy link
Member

@editorialbot check references

@editorialbot
Copy link
Collaborator Author

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

OK DOIs

- 10.12688/f1000research.29032.1 is OK
- 10.1371/journal.pcbi.1010705 is OK
- 10.1093/bioinformatics/bty191 is OK
- 10.1093/bioinformatics/btr011 is OK
- 10.1093/gigascience/giab008 is OK
- 10.25957/FLINDERS.HPC.DEEPTHOUGHT is OK
- 10.1186/s13015-021-00185-6 is OK
- 10.1089/cmb.2022.0262 is OK
- 10.1101/2023.04.19.537311 is OK
- 10.1007/s00248-022-02094-6 is OK
- 10.1093/bioinformatics/btad586 is OK
- 10.1101/2022.05.15.492003 is OK

MISSING DOIs

- None

INVALID DOIs

- None

@csoneson
Copy link
Member

Thanks @beardymcjohnface - could you please fix the title of the Zenodo archive so that it's the same as the paper title?

@beardymcjohnface
Copy link

Thanks @beardymcjohnface - could you please fix the title of the Zenodo archive so that it's the same as the paper title?

Done!

@csoneson
Copy link
Member

@editorialbot set 10.5281/zenodo.10633263 as archive

@editorialbot
Copy link
Collaborator Author

Done! archive is now 10.5281/zenodo.10633263

@csoneson
Copy link
Member

Great, thank you @beardymcjohnface - I will hand off to the track AEiC for the last steps. Thank you for submitting to JOSS!

@csoneson
Copy link
Member

@editorialbot recommend-accept

@editorialbot
Copy link
Collaborator Author

Attempting dry run of processing paper acceptance...

@editorialbot
Copy link
Collaborator Author

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

OK DOIs

- 10.12688/f1000research.29032.1 is OK
- 10.1371/journal.pcbi.1010705 is OK
- 10.1093/bioinformatics/bty191 is OK
- 10.1093/bioinformatics/btr011 is OK
- 10.1093/gigascience/giab008 is OK
- 10.25957/FLINDERS.HPC.DEEPTHOUGHT is OK
- 10.1186/s13015-021-00185-6 is OK
- 10.1089/cmb.2022.0262 is OK
- 10.1101/2023.04.19.537311 is OK
- 10.1007/s00248-022-02094-6 is OK
- 10.1093/bioinformatics/btad586 is OK
- 10.1101/2022.05.15.492003 is OK

MISSING DOIs

- None

INVALID DOIs

- None

@editorialbot
Copy link
Collaborator Author

👋 @openjournals/bcm-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#5054, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

@editorialbot editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Feb 26, 2024
@beardymcjohnface
Copy link

Thank you so much @csoneson, @lparsons, and @telatin for your work in reviewing and editing the paper, it is greatly appreciated!

@Kevin-Mattheus-Moerman
Copy link
Member

@beardymcjohnface as AEiC will now process final steps for acceptance in JOSS. I have just checked the paper, the archive link, your repository, and this review. All seems in order so I will now proceed to accept this paper in JOSS.

@Kevin-Mattheus-Moerman
Copy link
Member

@editorialbot accept

@editorialbot
Copy link
Collaborator Author

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

@editorialbot
Copy link
Collaborator Author

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: Roach
  given-names: Michael J.
  orcid: "https://orcid.org/0000-0003-1488-5148"
- family-names: Hart
  given-names: Bradley J.
  orcid: "https://orcid.org/0000-0001-8110-2460"
- family-names: Beecroft
  given-names: Sarah J.
  orcid: "https://orcid.org/0000-0002-3935-2279"
- family-names: Papudeshi
  given-names: Bhavya
  orcid: "https://orcid.org/0000-0001-5359-3100"
- family-names: Inglis
  given-names: Laura K.
  orcid: "https://orcid.org/0000-0001-7919-8563"
- family-names: Grigson
  given-names: Susanna R.
  orcid: "https://orcid.org/0000-0003-4738-3451"
- family-names: Mallawaarachchi
  given-names: Vijini
  orcid: "https://orcid.org/0000-0002-2651-8719"
- family-names: Bouras
  given-names: George
  orcid: "https://orcid.org/0000-0002-5885-4186"
- family-names: Edwards
  given-names: Robert A.
  orcid: "https://orcid.org/0000-0001-8383-8949"
contact:
- family-names: Roach
  given-names: Michael J.
  orcid: "https://orcid.org/0000-0003-1488-5148"
doi: 10.5281/zenodo.10633263
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Roach
    given-names: Michael J.
    orcid: "https://orcid.org/0000-0003-1488-5148"
  - family-names: Hart
    given-names: Bradley J.
    orcid: "https://orcid.org/0000-0001-8110-2460"
  - family-names: Beecroft
    given-names: Sarah J.
    orcid: "https://orcid.org/0000-0002-3935-2279"
  - family-names: Papudeshi
    given-names: Bhavya
    orcid: "https://orcid.org/0000-0001-5359-3100"
  - family-names: Inglis
    given-names: Laura K.
    orcid: "https://orcid.org/0000-0001-7919-8563"
  - family-names: Grigson
    given-names: Susanna R.
    orcid: "https://orcid.org/0000-0003-4738-3451"
  - family-names: Mallawaarachchi
    given-names: Vijini
    orcid: "https://orcid.org/0000-0002-2651-8719"
  - family-names: Bouras
    given-names: George
    orcid: "https://orcid.org/0000-0002-5885-4186"
  - family-names: Edwards
    given-names: Robert A.
    orcid: "https://orcid.org/0000-0001-8383-8949"
  date-published: 2024-02-27
  doi: 10.21105/joss.06235
  issn: 2475-9066
  issue: 94
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6235
  title: "Koverage: Read-coverage analysis for massive (meta)genomics
    datasets"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06235"
  volume: 9
title: "Koverage: Read-coverage analysis for massive (meta)genomics
  datasets"

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
Copy link
Collaborator Author

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

@editorialbot
Copy link
Collaborator Author

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.06235 joss-papers#5059
  2. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06235
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

@editorialbot editorialbot added accepted published Papers published in JOSS labels Feb 27, 2024
@Kevin-Mattheus-Moerman
Copy link
Member

@beardymcjohnface congratulations on this JOSS publication!

Thanks for the flawless editing @csoneson!

And a special thanks to the reviewers: @lparsons, @telatin !!

@editorialbot
Copy link
Collaborator Author

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

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

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.06235/status.svg)](https://doi.org/10.21105/joss.06235)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06235">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06235/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06235/status.svg
   :target: https://doi.org/10.21105/joss.06235

This is how it will look in your documentation:

DOI

We need your help!

The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
accepted published Papers published in JOSS Python recommend-accept Papers recommended for acceptance in JOSS. review TeX Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials
Projects
None yet
Development

No branches or pull requests

6 participants