[REVIEW]: Acanthophis: a comprehensive plant hologenomics pipeline

[editorialbot]

Submitting author: @kdm9 (Kevin Murray)
Repository: https://github.com/kdm9/Acanthophis
Branch with paper.md (empty if default branch):
Version: 1.0.0
Editor: @marcosvital
Reviewers: @bricoletc, @gbouras13, @abhishektiwari
Archive: 10.5281/zenodo.10795245

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/89901b387b0acb458c0efe6637fad366"><img src="https://joss.theoj.org/papers/89901b387b0acb458c0efe6637fad366/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/89901b387b0acb458c0efe6637fad366/status.svg)](https://joss.theoj.org/papers/89901b387b0acb458c0efe6637fad366)

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

@bricoletc & @gbouras13 & @abhishektiwari, 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 @marcosvital 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 @bricoletc

📝 Checklist for @abhishektiwari

📝 Checklist for @gbouras13

[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:

@editorialbot commands

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=0.08 s (818.1 files/s, 40579.1 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
YAML                             35             64            192            897
Markdown                          7            176              0            600
TeX                               1             28              0            484
Python                            7             71             58            303
Bourne Again Shell                4             23             26            113
Bourne Shell                      7              9             16             48
TOML                              1              1              0             11
Dockerfile                        1              1              0              4
--------------------------------------------------------------------------------
SUM:                             63            373            292           2460
--------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 980

[editorialbot]

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

OK DOIs

- 10.1101/2021.08.07.455511 is OK
- 10.21105/joss.05627 is OK
- 10.1038/nmeth.3176 is OK
- 10.1093/gigascience/giab008 is OK
- 10.1093/bioinformatics/btw354 is OK
- 10.48550/arXiv.2309.15884 is OK
- 10.1101/2022.04.08.487684 is OK
- 10.1101/gr.210641.116 is OK
- 10.1093/bioinformatics/bts480 is OK
- 10.5281/ZENODO.4677629 is OK
- 10.1093/bioinformatics/btp352 is OK
- 10.1093/bioinformatics/btr509 is OK
- 10.1093/bioinformatics/bty191 is OK
- 10.1093/bioinformatics/btab705 is OK
- 10.1186/1756-0500-5-337 is OK
- 10.7717/peerj-cs.104 is OK
- 10.1038/ncomms11257 is OK
- 10.1371/journal.pbio.1002311 is OK
- 10.1371/journal.pcbi.1005727 is OK
- 10.1111/mec.15287 is OK
- 10.1186/s13059-016-0997-x is OK
- 10.1093/bioinformatics/btx699 is OK
- 10.1038/s41396-020-0665-8 is OK
- 10.1186/s13104-016-1900-2 is OK
- 10.1093/bioinformatics/btt468 is OK
- 10.6084/m9.figshare.13174337.v1 is OK
- 10.1186/s13059-019-1891-0 is OK
- 10.5281/ZENODO.7728364 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[marcosvital]

Dear @bricoletc, @gbouras13 and @abhishektiwari, thank you again for accepting review this submission for JOSS.
The reviewing process is checklist based, and instructions were already posted above by the editorial bot - but let me know if you need any assistance, ok?
Also, you can tag @kdm9 if you have specific questions about the manuscript.

@kdm9, you can tag your co-authors GitHub accounts if you want, so they will be able to follow this issue and answer to questions as well.

[abhishektiwari]

Review checklist for @abhishektiwari

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/kdm9/Acanthophis?
• 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 (@kdm9) 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?

[bricoletc]

Review checklist for @bricoletc

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/kdm9/Acanthophis?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
  Yes, Mozilla Public Licence 2.0
• Contribution and authorship: Has the submitting author (@kdm9) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
  For the submitting author, yes, undeniably (from commit history); for the other authors, I cannot judge from the software repository and so trust the submitting author instead. In fact @marcosvital I'm surprised that there is no 'Author Contributions' section in the article proof, is this generally the case in JOSS papers?
• 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.
  No original data.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
  No original results.
• 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.
  No such data.

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

The documentation is very well-written and just missing one definition (see kdm9/Acanthophis#9)

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  Yes
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
  Yes; acanthophis pipeline available from PyPI and dependencies installable through conda/mamba
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
  Yes, the example config.yml in ./documentation.md explains all the options in comments.
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
  Yes, the tool is built around a highly-configurable Snakemake pipeline, whose steps and options can be selected and modified through config.yml
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
  Yes, I could run them successfully - see Unable to run tests: missing 'populate_metadata' in module 'acanthophis' kdm9/Acanthophis#7 .
• 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
  Yes, solved in Missing contribution/community guidelines kdm9/Acanthophis#8

Software paper

I have provided my comments to be addressed on the software paper in kdm9/Acanthophis#9

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
  Yes, after review
• 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?
  _Yes, after review
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
  Yes, after review
• 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?

[gbouras13]

Review checklist for @gbouras13

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/kdm9/Acanthophis?
• 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 (@kdm9) 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?

[bricoletc]

@kdm9, I've provided my main comments in three issues on your repo; I'll wait until they're addressed before checking in the corresponding items in my checklist

@marcosvital, I have two questions about JOSS: 1) why are there no 'Author contributions' sections in JOSS papers? This would help address checklist point 'contribution and authorship' 2) Can there be a 'Discussion' section in JOSS papers? I've provided two comments to that effect in kdm9/Acanthophis#9 ; but is fine if not - just curious why they don't exist in JOSS papers

[gbouras13]

Just as an FYI @marcosvital and @kdm9, I'll try and complete my initial review next week.

George

[marcosvital]

Hello everyone!

@gbouras13, any news on your review? Let me know if you need any kind of assistance, ok?

@kdm9, let us know when you are able to address @bricoletc comments.

@abhishektiwari, let us know if you make any advances on your review.

[marcosvital]

@marcosvital, I have two questions about JOSS: 1) why are there no 'Author contributions' sections in JOSS papers? This would help address checklist point 'contribution and authorship' 2) Can there be a 'Discussion' section in JOSS papers? I've provided two comments to that effect in kdm9/Acanthophis#9 ; but is fine if not - just curious why they don't exist in JOSS papers

Sorry about the delayed reply.

About a space for Author contributions, I'll take that to our editorial team so we can discuss that. Feels like a good suggestions to me.

About a Discussion section: it can be included - beside the mandatory sections from all papers, the authors can include specific sections that are needed for their work. We usually won't find a Discussion section in a JOSS paper because the journal is devoted to publishing the research software, but not the research findings.

[kdm9]

many many thanks for the review @bricoletc

I was planning on addressing all reviews at once in the new year, if that's OK @marcosvital

[marcosvital]

I was planning on addressing all reviews at once in the new year, if that's OK @marcosvital

Yes, that's perfectly fine, @kdm9, thanks for letting me know.

[gbouras13]

@marcosvital apologies things got away from me - I'll aim to have my review done by early in the new year so @kdm9 can go through them all together.

George

[kdm9]

@gbouras13 perfect, and many thanks in advance.

[kdm9]

@gbouras13 a friendly new years reminder about this :)

happy new year all!

[Kevin-Mattheus-Moerman]

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

[Kevin-Mattheus-Moerman]

@marcosvital thanks for editing here. Just a comment, please run @editorialbot create post-review checklist in the future (sorry if you did and I missed it) and ensure all steps are checked/completed (for instance the archive title doesn't match the paper title at present, the license does not match the project license, and also the version tag listed here does not match the repository listed version tag). No worries though, I'll take it from here now.

[Kevin-Mattheus-Moerman]

@editorialbot set 1.0.0 as version

[editorialbot]

Done! version is now 1.0.0

[Kevin-Mattheus-Moerman]

@kdm9 as AEiC I will now help to process this work for acceptance in JOSS. I have checked this review, your repository, the paper, and the archive. Most seems in order, I only have the below point that needs your attention:

• Please edit the archive title to match the full paper title.
• Please edit the archive listed license to match your software license.

[Kevin-Mattheus-Moerman]

@kdm9 👋 could you have a look at the above? Thanks

[kdm9]

@Kevin-Mattheus-Moerman apologies, to confirm: I need to change the Zenodo DOI tarball name to the full paper title?

[kdm9]

I've now done that, so if that wasn't what was needed please let me know what was :)

[Kevin-Mattheus-Moerman]

@kdm9 Not the zip/tarrball but the actual title and license listed for the archive. See the red highlighted bits in this screenshot:

[Kevin-Mattheus-Moerman]

@kdm9 okay, looks like you did it 😄 our messages crossed paths

[kdm9]

brilliant, many thanks. Any remaining issues?

[Kevin-Mattheus-Moerman]

@kdm9 no, I think now it is all set. Thanks.

[Kevin-Mattheus-Moerman]

@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:
- email: [email protected]
  family-names: Murray
  given-names: Kevin D.
  orcid: "https://orcid.org/0000-0002-2466-1917"
- family-names: Borevitz
  given-names: Justin O.
  orcid: "https://orcid.org/0000-0001-8408-3699"
- family-names: Weigel
  given-names: Detlef
  orcid: "https://orcid.org/0000-0002-2114-7963"
- family-names: Warthmann
  given-names: Norman
  orcid: "https://orcid.org/0000-0002-1178-8409"
contact:
- email: [email protected]
  family-names: Murray
  given-names: Kevin D.
  orcid: "https://orcid.org/0000-0002-2466-1917"
- family-names: Warthmann
  given-names: Norman
  orcid: "https://orcid.org/0000-0002-1178-8409"
doi: 10.5281/zenodo.10795245
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - email: [email protected]
    family-names: Murray
    given-names: Kevin D.
    orcid: "https://orcid.org/0000-0002-2466-1917"
  - family-names: Borevitz
    given-names: Justin O.
    orcid: "https://orcid.org/0000-0001-8408-3699"
  - family-names: Weigel
    given-names: Detlef
    orcid: "https://orcid.org/0000-0002-2114-7963"
  - family-names: Warthmann
    given-names: Norman
    orcid: "https://orcid.org/0000-0002-1178-8409"
  date-published: 2024-03-25
  doi: 10.21105/joss.06062
  issn: 2475-9066
  issue: 95
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6062
  title: "Acanthophis: a comprehensive plant hologenomics pipeline"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06062"
  volume: 9
title: "Acanthophis: a comprehensive plant hologenomics pipeline"

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]

🐘🐘🐘 👉 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.06062 joss-papers#5169
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06062
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...

[kdm9]

brilliant, many thanks again to you all: @bricoletc @gbouras13 @abhishektiwari @marcosvital and @Kevin-Mattheus-Moerman

[Kevin-Mattheus-Moerman]

@kdm9 congratulations on this publication!

Thanks for editing @marcosvital, and a special thank you to the reviewers: @bricoletc, @gbouras13, @abhishektiwari !!

[editorialbot]

🎉🎉🎉 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.06062/status.svg)](https://doi.org/10.21105/joss.06062)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06062">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06062/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06062/status.svg
   :target: https://doi.org/10.21105/joss.06062

This is how it will look in your documentation:

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