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[PRE REVIEW]: A Planar Laser Induced Fluorescence Software Package #6196

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editorialbot opened this issue Jan 9, 2024 · 36 comments
Open

[PRE REVIEW]: A Planar Laser Induced Fluorescence Software Package #6196

editorialbot opened this issue Jan 9, 2024 · 36 comments
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Matlab pre-review TeX Track: 3 (PE) Physics and Engineering

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editorialbot commented Jan 9, 2024 •
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Submitting author: @TomosRich (Tomos Rich)
Repository: https://github.com/TomosRich/PLIF-Processing
Branch with paper.md (empty if default branch):
Version: 1.0
Editor: @jgostick
Reviewers: Pending
Managing EiC: Kyle Niemeyer

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/108896c8f5797f732efdeda4e98e4e4a"><img src="https://joss.theoj.org/papers/108896c8f5797f732efdeda4e98e4e4a/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/108896c8f5797f732efdeda4e98e4e4a/status.svg)](https://joss.theoj.org/papers/108896c8f5797f732efdeda4e98e4e4a)

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Thanks for submitting your paper to JOSS @TomosRich. Currently, there isn't a JOSS editor assigned to your paper.

@TomosRich if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

Editor instructions

The JOSS submission bot @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:

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@editorialbot editorialbot added pre-review Track: 3 (PE) Physics and Engineering labels Jan 9, 2024
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Hello human, 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=0.04 s (690.8 files/s, 129618.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
MATLAB                          22            448           1495           2684
Markdown                         2             93              0            159
TeX                              1              8              0            119
YAML                             2              9             15             36
-------------------------------------------------------------------------------
SUM:                            27            558           1510           2998
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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

OK DOIs

- 10.1007/s00348-008-0496-2 is OK
- 10.1007/s00348-016-2190-0 is OK
- 10.1007/s00348-014-1801-x is OK
- 10.1016/j.buildenv.2022.109763 is OK
- 10.1007/s00348-022-03439-0 is OK
- 10.1016/J.ATMOSENV.2017.06.035 is OK
- 10.1016/j.ijheatfluidflow.2020.108561 is OK
- 10.1007/s00348-007-0372-5 is OK
- 10.1007/s10546-016-0226-x is OK

MISSING DOIs

- None

INVALID DOIs

- None

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Wordcount for paper.md is 2277

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

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Five most similar historical JOSS papers:

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⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

@kyleniemeyer
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Hello @TomosRich, sorry for the delay in processing your submission. We'll use this issue to get the review set up, including finding an editor and then reviewers. Unfortunately, we don't have an editor available to handle this right now, so I have to put this on our waitlist. I'll get back to you soon, though.

@kyleniemeyer kyleniemeyer added the waitlisted Submissions in the JOSS backlog due to reduced service mode. label Jan 9, 2024
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Hello @TomosRich, I took a closer look at your submission, and I think there are some issues that need to be resolved based on our review criteria before we assign an editor and find reviewers.

We require more substantial documentation; currently, I see a very short README. I do see documented functions, and an example.m, but one issue is hardcoded paths in that file. Is it possible to structure this such that it can be installed somewhere centrally and called by users? (And add installation instructions describing this process?)

I do not see any sort of tests to objectively check the expected functionality of the software.

Also, right now the submission is just a directory with a large number of unorganized files, including some .png files that may not be part of the package (unclear to me). Can you organize this more?

@arfon
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arfon commented May 9, 2024

@kyleniemeyer – seems like the author might have abandoned this submission?

@TomosRich
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TomosRich commented May 9, 2024 via email

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OK, @TomosRich, I'll put this on pause until then.

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@editorialbot remind @TomosRich in 1 month

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Reminder set for @TomosRich in 1 month

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TomosRich commented Jun 10, 2024 via email

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👋 @TomosRich, please update us on how things are progressing here (this is an automated reminder).

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TomosRich commented Jun 15, 2024 via email

@kyleniemeyer
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@editorialbot invite @jgostick as editor

Hi @jgostick, could you edit this? You are our primary (if only!) image processing person.

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Invitation to edit this submission sent!

@jgostick
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jgostick commented Jul 3, 2024

@editorialbot assign @jgostick as editor

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Assigned! @jgostick is now the editor

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jgostick commented Jul 3, 2024 •
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Hi @TomosRich
I will be honest here...I'm not looking forward to editing this package because it seems to be rather far from ready to publish. Our review process requires that the reviewers go over a predefined checklist of things too look for, and as far as I can tell your submission will not check many of the boxes. The checklist is below....please put yourself in the reviewer's shoes and see how many of these items your current submission satisfies...

Review checklist for

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/ANP-Granular/ParticleTracking?
  • 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 (@a-niem) 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?

@kyleniemeyer kyleniemeyer removed paused waitlisted Submissions in the JOSS backlog due to reduced service mode. labels Jul 3, 2024
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TomosRich commented Jul 9, 2024 via email

@jgostick
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Hi @TomosRich
Have you had a look at the checklist above? Any thoughts?

@TomosRich
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TomosRich commented Jul 31, 2024 via email

@jgostick
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I think the documentation needs to be quite detailed, usually more than a readme can contain, so typically there is a separate documentation site. Alternatively, the documentation can be in the form of a PDF that is included with the package. However, there are plenty of cases where the readme describes the entire package.

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TomosRich commented Aug 1, 2024 via email

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TomosRich commented Aug 9, 2024 via email

@jgostick
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I have checked out the new readme and I'm still not quite sure about it. Firstly, it would be helpful if you could put all the code snippets inside backticks, like `code`, which will be rendered as code by Github. This is obviously a minor nit, but would help a lot.

The reason I'm still not sure is that regarding the reviewer checklist I posted above, I still think that the reviewers will have trouble to actually run your code. They almost certainly will not have this equipment or any of their own images, so there needs to be a very clear example with example data for them to use. However, they probably won't have "readimx-v2.1.9" installed, so including the im7 files in the test data folder is not enough. You should make it frictionless.

As an aside, and this is just my opinion, I think your program should only work on some standard file formats, like png or tif, and leave it to the user to convert im7 to these formats. Having your code depend on readimx-v2.1.9 means that if LaVision ever stops distributing their software, then yours is dead. At the moment your workflow is:

  • user runs package
  • package converts images
  • package does analysis
    But it should be:
  • user converts images
  • user runs package
  • package does analysis
    Does this make sense?

Now back to my point about making it reviewer-ready, have you asked a colleague or friend who is familiar with matlab but has never used your software, to get it running with no help from you?

@kyleniemeyer
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I would add that, while we do allow hardware-specific software packages, we do require that the authors find reviewers who have access to the hardware needed to fully run/test the software.

@TomosRich
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TomosRich commented Aug 16, 2024 via email

@jgostick
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@TomosRich How are things coming? It's been several months since we last heard from you.

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TomosRich commented Oct 28, 2024 via email

@TomosRich
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TomosRich commented Nov 4, 2024 via email

@jgostick
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jgostick commented Nov 9, 2024

OK, I'll take another look at things, and we can see about converting this to an actual submission. I am having trouble finding the time this fall though, so apologies if it drags out a bit.

@TomosRich
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TomosRich commented Nov 9, 2024 via email

@jgostick
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jgostick commented Jan 6, 2025

Hi @TomosRich, happy new year. I am happy to report that my overwhelming fall teaching load is behind me. I am now ready to move this submission along.

A few questions:

  • Because this software is meant to work with a rather specific piece of hardware, can you point me to a few vendors of this hardware so I can learn more about it?
  • Can you also suggest to me the names of some people who might have this hardware, so they can act as reviewers for this submission? I think it would be challenging for someone to evaluate it properly without this background/context.

Thanks
Jeff

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