[REVIEW]: DataLad: distributed system for joint management of code, data, and their relationship

[whedon]

Submitting author: @yarikoptic (Yaroslav Halchenko)
Repository: https://github.com/datalad/datalad
Version: 0.14.3
Editor: @arokem
Reviewer: @szorowi1, @jkanche
Archive: 10.5281/zenodo.5034875

⚠️ 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

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/be6dfc853d7993c156456a6450b24dbc/status.svg)](https://joss.theoj.org/papers/be6dfc853d7993c156456a6450b24dbc)

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

@szorowi1 & @jkanche, 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

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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 ✨

Review checklist for @szorowi1

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 (@yarikoptic) 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 @jkanche

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 (@yarikoptic) 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. @szorowi1, @jkanche 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]

PDF failed to compile for issue #3262 with the following error:

 Can't find any papers to compile :-(

[arokem]

@whedon generate pdf from branch paper-joss

[whedon]

Attempting PDF compilation from custom branch paper-joss. Reticulating splines etc...

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=1.98 s (213.3 files/s, 62014.4 lines/s)
-----------------------------------------------------------------------------------
Language                         files          blank        comment           code
-----------------------------------------------------------------------------------
Python                             330          14272          28216          62740
reStructuredText                    18           1451            460           4920
Markdown                             6            992              0           3622
YAML                                13             99            239           2257
Bourne Shell                        25            230             83            937
Bourne Again Shell                  18            202            301            922
JSON                                 2             19              0            253
make                                 2             45             13            190
Windows Resource File                1              9              0             53
INI                                  1              6              0             42
Logos                                1             13             25             20
DOS Batch                            3              0              9             13
PowerShell                           1              1              2              5
TOML                                 1              0              1              2
-----------------------------------------------------------------------------------
SUM:                               422          17339          29349          75976
-----------------------------------------------------------------------------------


Statistical information for the repository '7e02e43ced864e434f290d6d' was
gathered on 2021/05/07.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Adina Wagner                   101           992            384            0.25
Alejandro de la Vega             5             7              7            0.00
Alex Waite                       2            12             13            0.00
Andy Connolly                    7            44             30            0.01
Benjamin Poldrack             1525         57087          25544           14.85
Christian Mönch                  9           271             43            0.06
Christopher J. Marki             4           169             46            0.04
Dave MacFarlane                 35           490            126            0.11
Debanjum Singh Solan           168         42529           4831            8.51
Gergana Alteva                 158          2903           1470            0.79
Horea Christian                  1             2              0            0.00
Jason Gors                      52           998            461            0.26
John T. Wodder II               26           726            848            0.28
Kusti Skytén                     2             2              0            0.00
Kyle Meyer                    1594         36680          15014            9.29
Matt Cieslak                     2             6              3            0.00
Matteo Visconti dOC              2            20              2            0.00
Michael Hanke                 3669        103152         133292           42.49
Nell Hardcastle                  1             1              1            0.00
Neuroimaging Communi             2            39             46            0.02
Nolan Nichols                    8            36             10            0.01
Robin Schneider                  1             2              2            0.00
Soichi Hayashi                   1             1              1            0.00
Taylor Olson                     7            55             30            0.02
Vanessa Sochat                   3            14              6            0.00
Yarchael                         2            12             10            0.00
Yaroslav Halchenko            3125         91283          36752           23.01

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
Adina Wagner                533           53.7         14.7                8.44
Alex Waite                    4           33.3         44.4               25.00
Andy Connolly                31           70.5         11.9                3.23
Benjamin Poldrack         11710           20.5         33.7               22.67
Christian Mönch             236           87.1          6.9               13.98
Christopher J. Marki        122           72.2         23.7               14.75
Dave MacFarlane             309           63.1         33.7               18.45
Debanjum Singh Solan        404            0.9         57.3               15.35
Gergana Alteva              131            4.5         57.3               15.27
Jason Gors                  269           27.0         68.7               12.64
John T. Wodder II            57            7.9          7.1                7.02
Kyle Meyer                17849           48.7         20.9               14.95
Matt Cieslak                  3           50.0          2.3              100.00
Matteo Visconti dOC           5           25.0         41.1                0.00
Michael Hanke             40833           39.6         28.7               17.88
Neuroimaging Communi         14           35.9          0.0                0.00
Nolan Nichols                16           44.4          9.3                6.25
Robin Schneider               2          100.0          1.7                0.00
Soichi Hayashi                1          100.0         17.4                0.00
Taylor Olson                  7           12.7         39.2               28.57
Yarchael                      4           33.3         32.0                0.00
Yaroslav Halchenko        32238           35.3         43.6               19.29
vsoch                         5          100.0         31.6                0.00

[whedon]

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

[arokem]

Question for @yarikoptic and @mih: I see that you are both "co-first author", but one of you is also the last author. I am not sure how that's supposed to work. Could you please explain what you intended here?

[yarikoptic]

"Contributed equally" would be more appropriate indeed given current authors ordering. Can/should we adjust manuscript and re-render here right away?

[arokem]

No hurry. You can do that on the next round of edits, after reviewers have had a chance to take a look.

[yarikoptic]

cool, so we don't forget I just committed/pushed to the original repo for now

[jkanche]

@arokem seems like I need to be assigned to check things on my review list

[danielskatz]

@whedon re-assign @jkanche as reviewer

[whedon]

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@whedon commands

[danielskatz]

@whedon commands

[whedon]

Here are some things you can ask me to do:

# List all of Whedon's capabilities
@whedon commands

# Assign a GitHub user as the sole reviewer of this submission
@whedon assign @username as reviewer

# Add a GitHub user to the reviewers of this submission
@whedon add @username as reviewer

# Re-invite a reviewer (if they can't update checklists)
@whedon re-invite @username as reviewer

# Remove a GitHub user from the reviewers of this submission
@whedon remove @username as reviewer

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

# Change editorial assignment
@whedon assign @username as editor

# Set the software archive DOI at the top of the issue e.g.
@whedon set 10.0000/zenodo.00000 as archive

# Set the software version at the top of the issue e.g.
@whedon set v1.0.1 as version

# Open the review issue
@whedon start review

EDITORIAL TASKS

# All commands can be run on a non-default branch, to do this pass a custom 
# branch name by following the command with `from branch custom-branch-name`.
# For example:

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Remind an author or reviewer to return to a review after a
# certain period of time (supported units days and weeks)
@whedon remind @reviewer in 2 weeks

# Ask Whedon to do a dry run of accepting the paper and depositing with Crossref
@whedon accept

# Ask Whedon to check the references for missing DOIs
@whedon check references

# Ask Whedon to check repository statistics for the submitted software
@whedon check repository

EiC TASKS

# Invite an editor to edit a submission (sending them an email)
@whedon invite @editor as editor

# Reject a paper
@whedon reject

# Withdraw a paper
@whedon withdraw

# Ask Whedon to actually accept the paper and deposit with Crossref
@whedon accept deposit=true

[danielskatz]

@whedon re-invite @jkanche as reviewer

[whedon]

The reviewer already has a pending invite.

@jkanche please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

[jkanche]

thank you @danielskatz! I am now able to review.

[whedon]

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

[whedon]

👋 @szorowi1, please update us on how your review is going (this is an automated reminder).

[mih]

Hey! Thanks in advance to the reviewers for wading through our code and docs -- certainly not a quick thing. I would nevertheless like to ask if there is anything we can do to streamline the process. I am only aware of one issue having been reported datalad/datalad#5685

Have @jkanche @szorowi1 found something that we could proactively tackle?

Thx and best!

[yarikoptic]

We have been meticulously archiving datalad on zenodo (and pypi and debian and neurodebian and their snapshots repos) through the years and https://zenodo.org/record/5034875#.YNsmFXWYXjE is the one for recent datalad/datalad: 0.14.6. Would it be sufficient (given the relaxed prefer for the metadata)?

[arokem]

Yes. I think this is fine.

[arokem]

@whedon set 10.5281/zenodo.5034875 as archive

[whedon]

OK. 10.5281/zenodo.5034875 is the archive.

[arokem]

@openjournals/joss-eics : I believe this article is ready for your review.

[arfon]

@whedon recommend-accept

☝️ @arokem – we have this dedicated command now for flagging submissions as ready to hand over to the EiC team.

[whedon]

Attempting dry run of processing paper acceptance...

[arfon]

@whedon recommend-accept from branch paper-joss

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1515/nf-2020-0037 is OK
- 10.5281/zenodo.4773629 is OK
- 10.5281/ZENODO.2431914 is OK
- 10.5281/ZENODO.2558512 is OK
- 10.5281/ZENODO.3874225 is OK
- 10.5281/ZENODO.3900277 is OK
- 10.5281/ZENODO.4495560 is OK
- 10.1038/sdata.2016.18 is OK
- 10.1038/s41467-021-21970-2 is OK
- 10.21203/rs.3.rs-264855/v1 is OK
- 10.1038/sdata.2016.44 is OK
- 10.31234/osf.io/w8trm 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#2425

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2425, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true from branch paper-joss 

[arfon]

@whedon accept deposit=true from branch paper-joss

[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.03262 joss-papers#2426
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03262
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...

[arfon]

@szorowi1, @jkanche – many thanks for your reviews here and to @arokem for editing this submission! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@yarikoptic – your paper is now accepted and published in JOSS ⚡🚀💥

[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.03262/status.svg)](https://doi.org/10.21105/joss.03262)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03262">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03262/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03262/status.svg
   :target: https://doi.org/10.21105/joss.03262

This is how it will look in your documentation:

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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:

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[yarikoptic]

Thank you @arfon @szorowi1, @jkanche and the last but not least @arokem for making this mundane Thursday a "once in a life time" special occasion ;)
The idea for the "DataLad paper" was painful (we exercised a number of concepts to pursue), and the goals, format and structure of JOSS publication and review process helped us tremendously to finally make it happen!

FWIW, if might come handy for some, https://github.com/datalad/datalad-git-bug-dumps/tree/master/tools provides some extra helper we used (on top of git-bug dump) to decide on co-authors etc to invite! No JOSS paper is expected to come for that ;) But may be it could give ideas to establish some JOSS-tools collection of helpers on how to objectively figure out the list of co-authors to invite etc.