[REVIEW]: Opfi: A Python package for identifying gene clusters in large genomics and metagenomics data sets

[whedon]

Submitting author: @alexismhill3 (Alexis Hill)
Repository: https://github.com/wilkelab/Opfi
Version: 0.1.2
Editor: @csoneson
Reviewer: @Thomieh73, @afrubin
Archive: 10.5281/zenodo.5601741

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Status

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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

@Thomieh73 & @afrubin, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

1. Make sure you're logged in to your GitHub account
2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

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 ✨

Review checklist for @Thomieh73

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 repository url?
• 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 (@alexismhill3) 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 and who the target audience is?
• 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?

Review checklist for @afrubin

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 repository url?
• 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 (@alexismhill3) 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 and who the target audience is?
• 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?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @Thomieh73, @afrubin it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

2. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

For a list of things I can do to help you, just type:

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

[whedon]

Wordcount for paper.md is 1401

[whedon]

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

OK DOIs

- 10.1186/2042-5783-2-3 is OK
- 10.1038/nrg1709 is OK
- 10.1186/1471-2105-10-421 is OK
- 10.1038/nbt.3988 is OK
- 10.1038/s41592-021-01101-x is OK
- 10.1093/nar/gkz310 is OK
- 10.1093/nar/gky383 is OK
- 10.1093/nar/gkz192 is OK
- 10.1186/1471-2105-8-18 is OK
- 10.1093/bioinformatics/btaa213 is OK
- 10.1101/2021.08.16.456562 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.31 s (525.7 files/s, 84309.5 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
C++                              85           2266            585          12905
Python                           38           1095           1366           4350
C/C++ Header                     19            261             61           1418
Markdown                          5            109              0            305
XML                               1              0              0            210
TeX                               1             10              0            179
reStructuredText                  8            202            244            177
YAML                              3             11             12            103
Jupyter Notebook                  1              0            302             77
make                              2             12              8             28
Bourne Again Shell                1              1              0              4
--------------------------------------------------------------------------------
SUM:                            164           3967           2578          19756
--------------------------------------------------------------------------------


Statistical information for the repository 'fbe5dc8158f92bfb3e7b73b1' was
gathered on 2021/08/31.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Alexis Hill                    146         23336           3224           72.53
Jim Rybarski                   159          7274           2786           27.47

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Alexis Hill               19831           85.0         17.4                5.03
Jim Rybarski               4476           61.5         12.2                8.80

[whedon]

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

[csoneson]

👋🏼 @alexismhill3, @clauswilke, @Thomieh73, @afrubin - this is the review thread for the submission. All of our communications will happen here from now on.

Both reviewers have checklists at the top of this thread. 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!

[afrubin]

@csoneson not sure why, but I'm unable to check any of the boxes in my checklist.

[afrubin]

@alexismhill3 there are several (mostly old) open issues in the GitHub repository at this time. What is the status of these issues? Some of them seem worth fixing, especially the temp file (wilkelab/Opfi#181) and missing documentation (wilkelab/Opfi#30) issues.

It would be helpful to know before we start adding our own comments during the review.

[danielskatz]

@afrubin - did you accept the invitation mentioned at the start of this review issue?

[afrubin]

@danielskatz totally missed it, sorry about that! Looks like everything is working now.

[clauswilke]

@afrubin The vast majority of the old issues were stale and we have started closing them. The temp-file issue unfortunately is caused by a dependency and doesn't have an easy fix. Documentation has improved massively since spring 2020.

Any requests for improvement, new features, or bug fixes should be filed as new issues. Thanks!

[Thomieh73]

@csoneson Hi, I am having issues with notifications from this repo. I am receiving all notifications from this entire repo. I have pushed the button to unsubscribe from this thread, but somehow I am stil receiving all notifications from this repo. Any suggestions on how to solve this.
It drives me nuts to have 100 mails in my mailbox everyday that are not relevant.

[csoneson]

@Thomieh73 - check the instructions in the second post above: #3678 (comment)

[Thomieh73]

@csoneson Thanks I had completely forgotten about that option at github. :-)

[whedon]

👋 @Thomieh73, please update us on how your review is going (this is an automated reminder).

[whedon]

👋 @afrubin, please update us on how your review is going (this is an automated reminder).

[afrubin]

I started with the installation instructions and have opened some related issues:
wilkelab/Opfi#198
wilkelab/Opfi#199
wilkelab/Opfi#200
wilkelab/Opfi#201

[alexismhill3]

Thanks @afrubin, I'll get started working on these

[Thomieh73]

Hi @alexismhill3,
I had created two issues when working on the installation and on your tutorial (which you already solved).
wilkelab/Opfi#202 - which is a suggestion of how one can create a conda environment with all the dependencies.

I did not find any other problems using the tool or checking the documentation

[Thomieh73]

@csoneson I am done with the checklist. It is an interesting tool due to the versatility of what you can research.

[alexismhill3]

Thanks everyone! @csoneson @afrubin I've added the Bioconda reference.

[csoneson]

@whedon check references

[whedon]

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

OK DOIs

- 10.1038/s41592-018-0046-7 is OK
- 10.1002/biot.201000181 is OK
- 10.1186/1471-2105-10-421 is OK
- 10.1038/nbt.3988 is OK
- 10.1038/s41592-021-01101-x is OK
- 10.1093/nar/gkz310 is OK
- 10.1093/nar/gky383 is OK
- 10.1093/nar/gkz192 is OK
- 10.1186/1471-2105-8-18 is OK
- 10.1104/pp.19.00386 is OK
- 10.1093/bioinformatics/btaa213 is OK
- 10.1101/2021.08.16.456562 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[clauswilke]

@csoneson Just wondering if you need anything else from us.

[csoneson]

@clauswilke, @alexismhill3 - apologies, busy week. I have gone through the submission and I have only a few minor suggestions:

• I would suggest to move the first line from the Statement of Need section to the Summary section, to explain what gene clusters are right from the start.
• line 54: alternatating -> alternating
• line 70: there seems to be an extra space in post- homology
• BAGEL4 reference: I'd suggest to put curly braces around {van Heel} and {de Jong}

You can generate a new proof with @whedon generate pdf. Then, could you please:

• Make a tagged release of the software, and list the version tag of the archived version here.
• Archive the reviewed software in Zenodo or a similar service
• Check that the archival deposit (e.g., in Zenodo) has the correct metadata. In particular, the title and author list should be identical to those of the paper. You can also add the authors' ORCID.
• Please list the DOI of the archived version here.

I can then move forward with accepting the submission.

[alexismhill3]

@whedon generate pdf

[whedon]

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

[clauswilke]

I believe we have done everything.

Release: https://github.com/wilkelab/Opfi/releases/tag/0.1.2

Zenodo DOI: https://doi.org/10.5281/zenodo.5601741

[csoneson]

@whedon set 0.1.2 as version

[whedon]

OK. 0.1.2 is the version.

[csoneson]

@whedon set 10.5281/zenodo.5601741 as archive

[whedon]

OK. 10.5281/zenodo.5601741 is the archive.

[csoneson]

Thanks, looks good! I'll hand over to an associate EiC for the final steps.

[csoneson]

@whedon recommend-accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1038/s41592-018-0046-7 is OK
- 10.1002/biot.201000181 is OK
- 10.1186/1471-2105-10-421 is OK
- 10.1038/nbt.3988 is OK
- 10.1038/s41592-021-01101-x is OK
- 10.1093/nar/gkz310 is OK
- 10.1093/nar/gky383 is OK
- 10.1093/nar/gkz192 is OK
- 10.1186/1471-2105-8-18 is OK
- 10.1104/pp.19.00386 is OK
- 10.1093/bioinformatics/btaa213 is OK
- 10.1101/2021.08.16.456562 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#2713

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2713, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[kthyng]

Everything is ready! Awesome!

[kthyng]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 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.03678 joss-papers#2715
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03678
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...

[kthyng]

Congrats on your new publication @alexismhill3! Many thanks to editor @csoneson and reviewers @Thomieh73 and @afrubin for your time, hard work, and expertise!

[whedon]

🎉🎉🎉 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.03678/status.svg)](https://doi.org/10.21105/joss.03678)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03678">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03678/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03678/status.svg
   :target: https://doi.org/10.21105/joss.03678

This is how it will look in your documentation:

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[clauswilke]

Thanks so much everybody!