[REVIEW]: SampleDB: A sample and measurement metadata database

[whedon]

Submitting author: @FlorianRhiem (Florian Rhiem)
Repository: https://github.com/sciapp/sampledb
Version: 0.17.0
Editor: @arfon
Reviewer: @stuartcampbell, @dvanic
Archive: 10.5281/zenodo.4529206

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/3769b983ef954e66bf7e3e7d064e7c7e"><img src="https://joss.theoj.org/papers/3769b983ef954e66bf7e3e7d064e7c7e/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/3769b983ef954e66bf7e3e7d064e7c7e/status.svg)](https://joss.theoj.org/papers/3769b983ef954e66bf7e3e7d064e7c7e)

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

@stuartcampbell & @dvanic, 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 @trallard know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @stuartcampbell

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 (@FlorianRhiem) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state 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 @dvanic

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 (@FlorianRhiem) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state 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. @eteq, @dvanic it looks like you're currently assigned to review this paper 🎉.

⭐ 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]

Reference check summary:

OK DOIs

- None

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👉 Check article proof 📄 👈

[danielskatz]

👋 @eteq, @dvanic - It doesn't look like there's been any progress on this review in about 3 1/2 weeks - Can everyone please check in and provide an estimate of when your reviews might be started/finished?

[FlorianRhiem]

@trallard SampleDB v0.9.0 has been released yesterday. I've updated the paper.json. Could you please run @whedon set v0.9.0 as version to update the version here?

[trallard]

@whedon set v0.9.0 as version

[whedon]

OK. v0.9.0 is the version.

[trallard]

@eteq and @dvanic any chance you could check in an give any updates re
your review?

[arfon]

Dear authors and reviewers

We wanted to notify you that in light of the current COVID-19 pandemic, JOSS has decided to suspend submission of new manuscripts and to handle existing manuscripts (such as this one) on a "best efforts basis". We understand that you may need to attend to more pressing issues than completing a review or updating a repository in response to a review. If this is the case, a quick note indicating that you need to put a "pause" on your involvement with a review would be appreciated but is not required.

Thanks in advance for your understanding.

Arfon Smith, Editor in Chief, on behalf of the JOSS editorial team.

[arfon]

👋 @eteq & @dvanic, just a friendly check-in to see how things are going with your reviews?

[FlorianRhiem]

@trallard I have just released SampleDB v0.10.0. Could you please run @whedon set v0.10.0 as version so that it is updated here? Thank you!

[arfon]

@whedon set v0.10.0 as version

[whedon]

OK. v0.10.0 is the version.

[arfon]

👋 @eteq & @dvanic - today we reopened JOSS for new submissions and are checking in on our existing reviews. Do you think you might be able to wrap up your reviews in the next 2-3 weeks?

[trallard]

Hi folks just checking in on the status as per Arfon's message.
Any updates on the reviews @eteq @dvanic

[dvanic]

@whedon commands

[whedon]

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

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

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

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

# 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

[dvanic]

@whedon I need a new invitation:

[whedon]

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

@whedon commands

[dvanic]

@whedon generate pdf

[dvanic]

@whedon check references

[dvanic]

@whedon check repository

[whedon]

Reference check summary:

OK DOIs

- None

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.84  T=1.34 s (345.2 files/s, 64768.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                         223           6529           3385          30001
JavaScript                      76           2128           2083          17229
CSS                             16             58             74          10764
HTML                            96            204             12           5965
SVG                              2              0              0           2959
JSON                            31              0              0           2604
reStructuredText                11            678           1092            391
YAML                             1              8             11            112
Markdown                         3             38              0            101
TeX                              1              0              0             28
Dockerfile                       1              9              7             20
-------------------------------------------------------------------------------
SUM:                           461           9652           6664          70174
-------------------------------------------------------------------------------


Statistical information for the repository '2107' was gathered on 2020/06/10.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Daniel Kaiser                    1            84             12            0.10
Dorothea Henkel                 56          5257           2195            7.54
Florian Rhiem                  360         74066          16361           91.49
peters@iff242                    5           720            141            0.87

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
Daniel Kaiser                72           85.7         20.0                0.00
Dorothea Henkel            2187           41.6         37.2                9.37
Florian Rhiem             58985           79.6         27.9                6.16
peters@iff242               185           25.7         20.8                0.00

[arfon]

@stuartcampbell - many thanks!

@FlorianRhiem – At this point could you make a new release of this software that includes the changes that have resulted from this review. Then, please make an archive of the software in Zenodo/figshare/other service and update this thread with the DOI of the archive? For the Zenodo/figshare archive, please make sure that:

• The title of the archive is the same as the JOSS paper title
• That the authors of the archive are the same as the JOSS paper authors

I can then move forward with accepting the submission.

[FlorianRhiem]

@arfon Thank you, I have created a new release (version 0.17.0), updated the paper.json accordingly and updated the auto-generated Zenodo entry to have the correct title and author: https://doi.org/10.5281/zenodo.4529206

[arfon]

@whedon set 10.5281/zenodo.4529206 as archive

[whedon]

OK. 10.5281/zenodo.4529206 is the archive.

[arfon]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

Check final proof 👉 openjournals/joss-papers#2082

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2082, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[whedon]

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

OK DOIs

- 10.1038/sdata.2016.18 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[arfon]

@FlorianRhiem - please give the paper proof linked to in openjournals/joss-papers#2082 a final proof read (I will do the same).

[FlorianRhiem]

The proof looks good to me. 👍 The top whedon post here still has version 0.11.0, but I didn't find that version referenced in either the paper or the crossref XML, so I guess that's fine and just for reviewing?

[arfon]

@whedon set 0.17.0 as version

[whedon]

OK. 0.17.0 is the version.

[arfon]

@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.02107 joss-papers#2083
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02107
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]

@stuartcampbell, @dvanic - many thanks for your reviews here! JOSS relies upon the volunteer efforts of folks like yourselves and we simply wouldn't be able to do this without you ✨

@FlorianRhiem - 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:
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HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.02107/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02107/status.svg
   :target: https://doi.org/10.21105/joss.02107

This is how it will look in your documentation:

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[eteq]

While know this is like 1-2 years after the fact, it came up in a search for my recently and I just want to publicly apologies for ghosting y'all here. This was definitely a victim of COVID/childcare/inability to keep up with committments in 2020, but I apologize all the same.