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

whedon commented 3 years ago

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

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Review checklist for @szorowi1

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] 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?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] 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?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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 commented 3 years ago

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 :tada:.

:warning: JOSS reduced service mode :warning:

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.

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whedon commented 3 years ago

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

 Can't find any papers to compile :-(

arokem commented 3 years ago

@whedon generate pdf from branch paper-joss

whedon commented 3 years ago

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

whedon commented 3 years ago

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 commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

arokem commented 3 years ago

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 commented 3 years ago

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

arokem commented 3 years ago

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

yarikoptic commented 3 years ago

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

jkanche commented 3 years ago

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

danielskatz commented 3 years ago

@Whedon re-assign @jkanche as reviewer

whedon commented 3 years ago

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

@whedon commands

danielskatz commented 3 years ago

@Whedon commands

whedon commented 3 years ago

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
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# 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 
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# Compile the paper
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danielskatz commented 3 years ago

@whedon re-invite @jkanche as reviewer

whedon commented 3 years ago

The reviewer already has a pending invite.

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

jkanche commented 3 years ago

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

whedon commented 3 years ago

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

whedon commented 3 years ago

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

mih commented 3 years ago

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 https://github.com/datalad/datalad/issues/5685

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

Thx and best!

arokem commented 3 years ago

👋 @szorowi1 : have you had a chance to take a look?

szorowi1 commented 3 years ago

Very sorry for the delay! I've worked through my review.

It's a very impressive piece of software. I've read through much of the documentation and several of the helpful tutorial videos. I haven't been able to test every aspect of its functionality, but I've successfully been able to install Datalad and work through the tutorials. I especially like the conversational style of the docs -- makes it very easy to read and follow.

I have no quibbles. It's very clear how much effort has gone into the documentation and software to make it user-friendly and easy-to-use.

arokem commented 3 years ago

Thanks @szorowi1!

@jkanche : I see that there are only two remaining check boxes in your list. Do you have any comments regarding the description of the state of the art or references included (or not included) in the article?

jkanche commented 3 years ago

This is really cool and I 100% agree with @szorowi1. I've been using it and it's been a great experience so far. The documentation is very thorough and has been super helpful to understand how things work.

Thanks for the awesome work!

yarikoptic commented 3 years ago

Thank you @szorowi1 @jkanche and @arokem ! Meanwhile, we ran into a paper which might be giving even a better presentation to the DataLad that we had prepared for JOSS https://psyarxiv.com/w8trm . I assume we still have a possibility to adjust the manuscript with more references?

mih commented 3 years ago

Wonderful! Thanks @jkanche and @szorowi1 for your assessment and the time and energy spent to wade through the materials!

arokem commented 3 years ago

Thanks @jkanche and @szorowi1!

As the reviewers have approved the submission, the next steps are for me to give this one more read, to make sure that there are no errors or issues. Then, we'll make sure that the metadata for the software/paper match and pass this on to approval by the EiCs. I'll provide guidance at every step.

For now, @yarikoptic : yes - you can add more references. Could you please add the reference now, and then let me know when you are ready for me to give it a read through?

yarikoptic commented 3 years ago

@whedon generate pdf from branch paper-joss

@arokem pushed, but give us till tomorrow to finalize , and we will buzz you. Thank you

whedon commented 3 years ago

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

whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

yarikoptic commented 3 years ago

Sorry whedon, you were faster than my fingers. Try now

@whedon generate pdf from branch paper-joss

mih commented 3 years ago

@whedon generate pdf from branch paper-joss

whedon commented 3 years ago

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

whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

mih commented 3 years ago

@whedon generate pdf from branch paper-joss

whedon commented 3 years ago

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

whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

mih commented 3 years ago

I have now updated the manuscript with the following changes:

spelling fixes
add citation for another system that uses datalad
a highres version of figure 2
list the datalad UKBiobank extension too

It should hopefully be acceptable for publication now. Thx for given us the opportunity for these last-minute updates.

yarikoptic commented 3 years ago

a promised (but forgotten to be done) ping @arokem . Cheers and thank you !

arokem commented 3 years ago

Hello! Overall, looks good. I have a couple of small suggestions:

I think that the section title "Overview of the DataLad and its ecosystem" should be "Overview of DataLad and its ecosystem" or "Overview of the DataLad software and its ecosystem" (I would prefer the former), unless there is some intention in this wording that I am missing.
https://github.com/datalad/datalad/pull/5766

yarikoptic commented 3 years ago

Thank you @arokem!

took the former (removing "the")
included the change to bib - not sure how it came to be @misc ;)

yarikoptic commented 3 years ago

@whedon generate pdf from branch paper-joss

whedon commented 3 years ago

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

whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

arokem commented 3 years ago

@whedon commands

whedon commented 3 years ago

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 recommend-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

arokem commented 3 years ago

@whedon check references

arokem commented 3 years ago

@whedon check references from branch paper-joss

whedon commented 3 years ago

Attempting to check references... from custom branch paper-joss

openjournals / joss-reviews