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[REVIEW]: MParT: Monotone Parameterization Toolkit #4843

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editorialbot opened this issue Oct 11, 2022 · 66 comments
Closed

[REVIEW]: MParT: Monotone Parameterization Toolkit #4843

editorialbot opened this issue Oct 11, 2022 · 66 comments
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accepted C++ CMake Dockerfile published Papers published in JOSS recommend-accept Papers recommended for acceptance in JOSS. review Track: 5 (DSAIS) Data Science, Artificial Intelligence, and Machine Learning

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editorialbot commented Oct 11, 2022

Submitting author: @mparno (Matthew Parno)
Repository: https://github.com/MeasureTransport/MParT
Branch with paper.md (empty if default branch):
Version: v1.3.0
Editor: @diehlpk
Reviewers: @ansgarwenzel, @f-t-s
Archive: 10.5281/zenodo.7435142

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/47379a12758596ff3f7799cb2d7fc2e5"><img src="https://joss.theoj.org/papers/47379a12758596ff3f7799cb2d7fc2e5/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/47379a12758596ff3f7799cb2d7fc2e5/status.svg)](https://joss.theoj.org/papers/47379a12758596ff3f7799cb2d7fc2e5)

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

@ansgarwenzel & @f-t-s, 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:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @diehlpk 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

Checklists

📝 Checklist for @f-t-s

📝 Checklist for @ansgarwenzel

@editorialbot editorialbot added C++ CMake Dockerfile review Track: 5 (DSAIS) Data Science, Artificial Intelligence, and Machine Learning labels Oct 11, 2022
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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:

@editorialbot commands

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

@editorialbot generate pdf

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Software report:

github.com/AlDanial/cloc v 1.88  T=0.12 s (1690.7 files/s, 221511.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C++                             81           2997            807           8805
C/C++ Header                    46           1759           2698           5670
MATLAB                          17            173             84            691
CMake                           11            165             79            539
reStructuredText                31            541            674            286
Python                           7             91             54            182
YAML                             5             29              0            172
TeX                              1             15              0            139
Markdown                         2             21              0             70
Dockerfile                       1             10              0             39
DOS Batch                        1              8              1             26
Bourne Shell                     1              2              2              9
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                           205           5815           4406          16637
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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Wordcount for paper.md is 907

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

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

OK DOIs

- 10.21105/joss.03076 is OK
- 10.1137/17m1134640 is OK
- 10.1137/17m1114867 is OK
- 10.1016/j.jpdc.2014.07.003 is OK
- 10.1007/978-3-319-20828-2 is OK
- 10.1007/978-3-319-11259-6_23-1 is OK

MISSING DOIs

- None

INVALID DOIs

- None

@diehlpk
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diehlpk commented Oct 28, 2022

@ansgarwenzel, @f-t-s how is your review going?

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f-t-s commented Oct 30, 2022

Review checklist for @f-t-s

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

General checks

  • Repository: Is the source code for this software available at the https://github.com/MeasureTransport/MParT?
  • 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 (@mparno) 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
  • Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
  • Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
  • Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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, who the target audience is, and its relation to other work?
  • 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?

@f-t-s
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f-t-s commented Oct 30, 2022

I worked my way through the checklist. I think this is a cool piece of software that will definitely be useful to my group's research. Do you need anything else from me for the review?

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diehlpk commented Oct 31, 2022

I worked my way through the checklist. I think this is a cool piece of software that will definitely be useful to my group's research. Do you need anything else from me for the review?

No thanks. That was quick. Good luck with your new collaboration.

@mparno
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mparno commented Nov 4, 2022

Thanks @f-t-s ! We fixed the bug you mentioned in Issue #40. MParT release v1.2 includes the fix and is currently making its way through conda and the julia package manager.

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diehlpk commented Nov 6, 2022

Hi @ansgarwenzel please let us know how your review is going?

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diehlpk commented Nov 18, 2022

Hi @ansgarwenzel please let us know how your review is going?

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ansgarwenzel commented Nov 28, 2022 via email

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diehlpk commented Nov 28, 2022

@editorialbot commands

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Hello @diehlpk, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

# Add to this issue's reviewers list
@editorialbot add @username as reviewer

# Remove from this issue's reviewers list
@editorialbot remove @username from reviewers

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Assign a user as the editor of this submission
@editorialbot assign @username as editor

# Remove the editor assigned to this submission
@editorialbot remove editor

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

# Check the references of the paper for missing DOIs
@editorialbot check references

# Perform checks on the repository
@editorialbot check repository

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for version
@editorialbot set v1.0.0 as version

# Set a value for archive
@editorialbot set 10.21105/zenodo.12345 as archive

# Set a value for branch
@editorialbot set joss-paper as branch

# Set a value for repository
@editorialbot set https://github.com/organization/repo as repository

# Mention the EiCs for the correct track
@editorialbot ping track-eic

# Generates the pdf paper
@editorialbot generate pdf

# Recommends the submission for acceptance
@editorialbot recommend-accept

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Flag submission with questionable scope
@editorialbot query scope

# Get a link to the complete list of reviewers
@editorialbot list reviewers

# Open the review issue
@editorialbot start review

@diehlpk
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diehlpk commented Nov 28, 2022

@ansgarwenzel Can you please post @editorialbot generate my checklist in a comment and fill the checklist.

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ansgarwenzel commented Dec 5, 2022

@editorialbot generate my checklist

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ansgarwenzel commented Dec 5, 2022

Review checklist for @ansgarwenzel

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

General checks

  • Repository: Is the source code for this software available at the https://github.com/MeasureTransport/MParT?
  • 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 (@mparno) 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
  • Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
  • Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
  • Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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, who the target audience is, and its relation to other work?
  • 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?

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diehlpk commented Dec 5, 2022

@editorialbot check references

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diehlpk commented Dec 5, 2022

@editorialbot generate paper

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

@editorialbot commands

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diehlpk commented Dec 5, 2022

@editorialbot generate pdf

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

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Done! version is now v1.3.0

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diehlpk commented Dec 14, 2022

@editorialbot set 10.5281/zenodo.7435142 as archive

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Done! Archive is now 10.5281/zenodo.7435142

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diehlpk commented Dec 14, 2022

@editorialbot recommend-accept

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Attempting dry run of processing paper acceptance...

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

OK DOIs

- 10.21105/joss.03076 is OK
- 10.1137/17m1134640 is OK
- 10.1137/17m1114867 is OK
- 10.1016/j.jpdc.2014.07.003 is OK
- 10.1007/978-3-319-20828-2 is OK
- 10.1007/978-3-319-11259-6_23-1 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3806, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

@editorialbot editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Dec 14, 2022
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arfon commented Dec 15, 2022

@mparno, just checking your paper here. The following sentence reads weirdly:

The Monotone Parameterization Toolkit (MParT), pronounced aims to provide performance-portable implementations of such parameterizations.

Is pronounced meant to be in this sentence? If so, I'm not sure I quite know how to parse it :-)

@mparno
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mparno commented Dec 15, 2022

@arfon Yikes! How did that slip through? You're correct, "pronounced" should be removed. Would you like me to update the paper in our repo?

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diehlpk commented Dec 19, 2022

@mparno Yes, please update the paper.

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mparno commented Dec 21, 2022

@diehlpk @arfon This has been fixed in MParT's main branch. Thanks for your patience!

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diehlpk commented Dec 21, 2022

@editorialbot recommend-accept

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Attempting dry run of processing paper acceptance...

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

OK DOIs

- 10.21105/joss.03076 is OK
- 10.1137/17m1134640 is OK
- 10.1137/17m1114867 is OK
- 10.1016/j.jpdc.2014.07.003 is OK
- 10.1007/978-3-319-20828-2 is OK
- 10.1007/978-3-319-11259-6_23-1 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3842, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

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mparno commented Dec 22, 2022

I've reviewed the final proof and everything looks good on my end.

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arfon commented Dec 26, 2022

@editorialbot accept

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

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🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

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

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.04843 joss-papers#3849
  2. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04843
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

@editorialbot editorialbot added accepted published Papers published in JOSS labels Dec 26, 2022
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mparno commented Dec 26, 2022

@diehlpk @arfon @ansgarwenzel @f-t-s Thank you all!

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arfon commented Dec 28, 2022

@ansgarwenzel, @f-t-s – many thanks for your reviews here and to @diehlpk 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 ✨

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

@arfon arfon closed this as completed Dec 28, 2022
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🎉🎉🎉 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.04843/status.svg)](https://doi.org/10.21105/joss.04843)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.04843">
  <img src="https://joss.theoj.org/papers/10.21105/joss.04843/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04843/status.svg
   :target: https://doi.org/10.21105/joss.04843

This is how it will look in your documentation:

DOI

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