[REVIEW]: anndata: Access and store annotated data matrices #4371

editorialbot · 2022-05-04T18:31:52Z

Submitting author: @falexwolf (F. Alexander Wolf)
Repository: https://github.com/scverse/anndata
Branch with paper.md (empty if default branch): paper
Version: 0.10.9
Editor: @luizirber
Reviewers: @nlhepler, @rcannood
Archive: 10.5281/zenodo.13643180

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/8b1f66b60f7af653cc09ff32fee77d83/status.svg)](https://joss.theoj.org/papers/8b1f66b60f7af653cc09ff32fee77d83)

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

@nlhepler & @rcannood, 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:

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✨ 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 @nlhepler

📝 Checklist for @rcannood

The text was updated successfully, but these errors were encountered:

editorialbot · 2022-05-04T18:31:55Z

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:

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

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editorialbot · 2022-05-04T18:31:56Z

Checking the BibTeX entries failed with the following error:

No paper file path

editorialbot · 2022-05-04T18:31:56Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.17 s (629.4 files/s, 102055.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          65           2795           2286          10220
reStructuredText                29            271            228            574
YAML                             5             19              2            129
TOML                             1              8              4            110
make                             1              5              6             14
Jupyter Notebook                 1              0            171             12
Markdown                         1              3              0              6
SVG                              1              0              0              1
-------------------------------------------------------------------------------
SUM:                           104           3101           2697          11066
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2022-05-04T18:31:58Z

Failed to discover a Statement of need section in paper

editorialbot · 2022-05-04T18:32:24Z

⚠️ An error happened when generating the pdf. Paper file not found.

nlhepler · 2022-05-04T18:35:56Z

Review checklist for @nlhepler

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/theislab/anndata?
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 (@falexwolf) 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?

rcannood · 2022-05-04T18:45:48Z

Review checklist for @rcannood

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/theislab/anndata?
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 (@falexwolf) 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?

luizirber · 2022-05-04T18:56:31Z

@editorialbot set paper as branch

editorialbot · 2022-05-04T18:56:32Z

Done! branch is now paper

luizirber · 2022-05-04T18:57:01Z

@editorialbot generate pdf

editorialbot · 2022-05-04T18:58:05Z

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

arfon · 2022-06-17T06:25:54Z

👋 @nlhepler – how are you getting along with your review here?

falexwolf · 2022-06-19T06:02:45Z

@arfon We moved the repository from theislab/anndata to https://github.com/scverse/anndata. Could you update the metadata here?

nlhepler · 2022-06-20T10:52:33Z

@arfon apologies for the delay. I aim to have it done today, certainly no later than tomorrow.

falexwolf · 2022-06-20T10:54:48Z

Let me try to generate an up-to-date version that includes our response to @rcannood:

@editorialbot generate pdf

danielskatz · 2022-06-20T11:45:54Z

editorialbot commands need to be the first entry in a new comment.

falexwolf · 2022-06-20T12:31:48Z

@editorialbot generate pdf

editorialbot · 2022-06-20T12:33:35Z

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

nlhepler · 2022-06-20T20:05:30Z

@falexwolf, I see that @rcannood has opened scverse/anndata#769, would you prefer I piggy-back my comments there or open a separate issue?

falexwolf · 2022-06-20T20:07:49Z

Thanks for checking! It'd be great if you added your comments to the existing thread! It's more efficient if we address both of your comments in ideally one additional pass on the paper (or as many it takes until your happy)! 😅

arfon · 2022-08-05T17:23:30Z

👋 folks. Just checking how things are going here? @nlhepler, @rcannood – it looks like you're well on your way to completing your reviews, have you had a chance to provide all of your feedback to @falexwolf?

nlhepler · 2022-08-05T19:23:32Z

👋 Hi @arfon, the conversation is mostly happening in scverse/anndata#769 -- we're still going back and forth

falexwolf · 2022-08-06T09:03:56Z

Yes, all reviews are there! Isaac was on a several-week-long conference and holiday trip.

He just got back last week and we want to get back to reviews this Monday.

arfon · 2022-10-01T12:13:41Z

👋 folks. Just checking in again here – @nlhepler, @rcannood – are your reviews mostly complete?

Kevin-Mattheus-Moerman · 2024-09-05T08:47:40Z

@editorialbot set 0.10.9 as version

editorialbot · 2024-09-05T08:47:42Z

Done! version is now 0.10.9

Kevin-Mattheus-Moerman · 2024-09-05T08:48:06Z

@editorialbot check references

Kevin-Mattheus-Moerman · 2024-09-05T08:48:34Z

@editorialbot generate pdf

editorialbot · 2024-09-05T08:48:56Z

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

✅ OK DOIs

- 10.1186/s13059-017-1382-0 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1038/nmeth.3252 is OK
- 10.5281/zenodo.264282 is OK
- 10.48550/arXiv.1309.0238 is OK
- 10.1016/j.cell.2021.04.048 is OK
- 10.21105/joss.03021 is OK
- 10.25080/majora-92bf1922-00a is OK
- 10.1007/bf02985802 is OK
- 10.1101/2021.02.19.431994 is OK
- 10.1101/2021.04.05.438318 is OK
- 10.1101/2021.04.28.441833 is OK
- 10.1038/s41587-020-0591-3 is OK
- 10.1101/2021.06.01.445670 is OK
- 10.1158/0008-5472.can-17-0344 is OK
- 10.5281/zenodo.3773450 is OK
- 10.18129/B9.bioc.tidySummarizedExperiment is OK
- 10.48550/arXiv.1802.03426 is OK
- 10.1038/s41592-019-0654-x is OK
- 10.48550/arXiv.1912.01703 is OK
- 10.1101/2023.12.11.23299816 is OK
- 10.1186/s13059-021-02519-4 is OK
- 10.14778/3025111.3025117 is OK
- 10.1038/s41586-019-1629-x is OK
- 10.7554/eLife.27041 is OK
- 10.32614/cran.package.anndata is OK
- 10.18129/B9.bioc.zellkonverter is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Scikit-learn: Machine Learning in Python
- No DOI given, and none found for title: Machine Learning: A Probabalistic Perspective
- No DOI given, and none found for title: Tidy data
- No DOI given, and none found for title: Python and HDF5
- No DOI given, and none found for title: The relational model for database management: vers...
- No DOI given, and none found for title: airspeed velocity
- No DOI given, and none found for title: A sandbox for prediction and integration of DNA, R...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

editorialbot · 2024-09-05T08:49:32Z

⚠️ An error happened when generating the pdf.

Kevin-Mattheus-Moerman · 2024-09-05T09:00:39Z

@openjournals/dev can you help with this paper compilation error? It seems to be related to affiliations but I can't quite make out what is wrong. Thanks

Kevin-Mattheus-Moerman · 2024-09-05T09:02:42Z

@falexwolf

Can you please edit the archive listed license to be 0.10.9, it currently says v2. There is no need to create a new archive link any more at this point, you can manually edit the listing and version tag.

danielskatz · 2024-09-05T09:04:54Z

This isn't the issue with compiling, but looking at the affiliations, they should all have the final period "." removed, and have the country added. The period at the end of the note for Wolf should also be removed.

falexwolf · 2024-09-05T09:10:09Z

Can you please edit the archive listed license to be 0.10.9, it currently says v2. There is no need to create a new archive link any more at this point, you can manually edit the listing and version tag.

Done!

This isn't the issue with compiling, but looking at the affiliations, they should all have the final period "." removed, and have the country added. The period at the end of the note for Wolf should also be removed.

I'll try this right away.

falexwolf · 2024-09-05T09:13:17Z

Removed the periods and added the countries: scverse/anndata@4ca388a

danielskatz · 2024-09-05T10:17:18Z

@Kevin-Mattheus-Moerman - the problem might be related to openjournals/joss#1353

rcannood · 2024-09-06T08:15:55Z

@editorialbot generate pdf

editorialbot · 2024-09-06T08:17:16Z

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

rcannood · 2024-09-08T05:03:13Z

@Kevin-Mattheus-Moerman Does the proof look good to you?

Kevin-Mattheus-Moerman · 2024-09-10T08:02:20Z

@rcannood thanks for your help with this review. I'll pick this up shortly.

I was wondering, can you please re-confirm if you have anything that an outsider might perceive as a conflict of interest with this submission? You are not listed as an author, but do you actively work with the authors? I see you are a contributor to the project, was that during this review or before? Thanks.

rcannood · 2024-09-10T09:59:56Z

@Kevin-Mattheus-Moerman I'd say back in May 2022 when I first reviewed the publication, I did not have any COIs related to the manuscript. Back then, I had probably already talked to some of the manuscript authors via GitHub issues, but did not know any of the authors personally.

Since then, I have become an avid user of the package, and use it in a lot of my projects. I did not contribute to the conceptualisation, development, or maintenance of this package, other than my review and one minor contribution I made in Dec 2020 (See below).

My enthusiasm related to wanting this paper published comes from my general affinity towards OSS and by extension JOSS, and also my belief that anndata is a useful package and its publication deserves publication.

However, for full transparency, I did start development on an R package called laminlabs/laminr last month in for Lamin Labs, whose CEO is @falexwolf -- the submitter of this manuscript.

I hope this addresses any concerns you may have.

TL;DR: I did not at the time of the review, I suppose that I do now.

Additional information

In Dec 2020 I made a small open-source contribution (scverse/anndata#463) related to an issue that I was encountering (scverse/anndata#464).

This issue I encountered while creating an R package also called 'anndata' (CRAN) which exposes the Python interface to users via reticulate. This was developed fully by myself without input from the scverse organisation (dynverse/anndata).

I did end up creating scverse/anndataR in collaboration with other non-scverse members lazappi LouiseDck and mtmorgan. However, this work was started in April 2023 as part of the scverse hackathon in Heidelberg (https://scverse.org/events/2023_04_hackathon/), which is way past my initial review.

Kevin-Mattheus-Moerman · 2024-09-16T08:29:01Z

@rcannood thanks for the clarification. Since the COI did not exist at the time of review we can accept this. However at this point it would be good to step down here, in terms of involvement, and let the authors handle queries and communication with me.

Kevin-Mattheus-Moerman · 2024-09-16T08:46:57Z

@falexwolf I believe all is in order now, so we will now proceed to process this for acceptance. It was unfortunately that this was a much longer than usual review process. We apologies for any delays from our end.

Kevin-Mattheus-Moerman · 2024-09-16T08:47:03Z

@editorialbot accept

editorialbot · 2024-09-16T08:47:04Z

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

falexwolf · 2024-09-16T08:52:51Z

@Kevin-Mattheus-Moerman, thank you for accepting the paper and not dropping this submission after such a long time. I apologize for the delays caused by me in the process.

editorialbot · 2024-09-16T08:54:34Z

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: Virshup
  given-names: Isaac
  orcid: "https://orcid.org/0000-0002-1710-8945"
- family-names: Rybakov
  given-names: Sergei
  orcid: "https://orcid.org/0000-0002-4944-6586"
- family-names: Theis
  given-names: Fabian J.
  orcid: "https://orcid.org/0000-0002-2419-1943"
- family-names: Angerer
  given-names: Philipp
  orcid: "https://orcid.org/0000-0002-0369-2888"
- family-names: Wolf
  given-names: F. Alexander
  orcid: "https://orcid.org/0000-0002-8760-7838"
doi: 10.5281/zenodo.13643180
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Virshup
    given-names: Isaac
    orcid: "https://orcid.org/0000-0002-1710-8945"
  - family-names: Rybakov
    given-names: Sergei
    orcid: "https://orcid.org/0000-0002-4944-6586"
  - family-names: Theis
    given-names: Fabian J.
    orcid: "https://orcid.org/0000-0002-2419-1943"
  - family-names: Angerer
    given-names: Philipp
    orcid: "https://orcid.org/0000-0002-0369-2888"
  - family-names: Wolf
    given-names: F. Alexander
    orcid: "https://orcid.org/0000-0002-8760-7838"
  date-published: 2024-09-16
  doi: 10.21105/joss.04371
  issn: 2475-9066
  issue: 101
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 4371
  title: "anndata: Access and store annotated data matrices"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.04371"
  volume: 9
title: "anndata: Access and store annotated data matrices"

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 · 2024-09-16T08:54:39Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2024-09-16T08:54:40Z

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

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.04371 joss-papers#5883
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04371
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

Kevin-Mattheus-Moerman · 2024-09-16T09:07:17Z

@falexwolf congratulations on this JOSS publication.

@luizirber thanks for editing!

And a special thank you to the reviewers: @nlhepler, @rcannood !!

editorialbot · 2024-09-16T09:07:20Z

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

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editorialbot added Python review labels May 4, 2022

editorialbot assigned luizirber May 4, 2022

editorialbot mentioned this issue May 4, 2022

[PRE REVIEW]: anndata: Annotated data #4006

Closed

rcannood mentioned this issue May 5, 2022

[JOSS] Comments scverse/anndata#769

Closed

11 tasks

editorialbot added the Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials label Sep 10, 2022

editorialbot added accepted published Papers published in JOSS labels Sep 16, 2024

Kevin-Mattheus-Moerman closed this as completed Sep 16, 2024

[REVIEW]: anndata: Access and store annotated data matrices #4371

[REVIEW]: anndata: Access and store annotated data matrices #4371

Comments

editorialbot commented May 4, 2022 • edited Loading

Status

Reviewer instructions & questions

Checklists

editorialbot commented May 4, 2022

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nlhepler commented May 4, 2022 • edited Loading

Review checklist for @nlhepler

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

rcannood commented May 4, 2022 • edited Loading

Review checklist for @rcannood

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

luizirber commented May 4, 2022

editorialbot commented May 4, 2022

luizirber commented May 4, 2022

editorialbot commented May 4, 2022

arfon commented Jun 17, 2022

falexwolf commented Jun 19, 2022

nlhepler commented Jun 20, 2022

falexwolf commented Jun 20, 2022

danielskatz commented Jun 20, 2022

falexwolf commented Jun 20, 2022

editorialbot commented Jun 20, 2022

nlhepler commented Jun 20, 2022

falexwolf commented Jun 20, 2022

arfon commented Aug 5, 2022

nlhepler commented Aug 5, 2022 • edited Loading

falexwolf commented Aug 6, 2022

arfon commented Oct 1, 2022

Kevin-Mattheus-Moerman commented Sep 5, 2024

editorialbot commented Sep 5, 2024

Kevin-Mattheus-Moerman commented Sep 5, 2024

Kevin-Mattheus-Moerman commented Sep 5, 2024

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Kevin-Mattheus-Moerman commented Sep 5, 2024

Kevin-Mattheus-Moerman commented Sep 5, 2024 • edited Loading

danielskatz commented Sep 5, 2024

falexwolf commented Sep 5, 2024

falexwolf commented Sep 5, 2024

danielskatz commented Sep 5, 2024

rcannood commented Sep 6, 2024

editorialbot commented Sep 6, 2024

rcannood commented Sep 8, 2024

Kevin-Mattheus-Moerman commented Sep 10, 2024

rcannood commented Sep 10, 2024

Additional information

Kevin-Mattheus-Moerman commented Sep 16, 2024

Kevin-Mattheus-Moerman commented Sep 16, 2024

Kevin-Mattheus-Moerman commented Sep 16, 2024

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falexwolf commented Sep 16, 2024

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Kevin-Mattheus-Moerman commented Sep 16, 2024

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