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[PRE REVIEW]: pySLM2: A full-stack python package for holographic beam shaping #6205

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editorialbot opened this issue Jan 10, 2024 · 69 comments
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editorialbot commented Jan 10, 2024

Submitting author: @ldes89150 (Chung-You Shih)
Repository: https://github.com/QITI/pySLM2
Branch with paper.md (empty if default branch): paper
Version: v0.1.0
Editor: @HaoZeke
Reviewers: @brandondube, @sidihamady, @ktahar
Managing EiC: Kyle Niemeyer

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status

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HTML: <a href="https://joss.theoj.org/papers/70246ad674d3806798e343f6ecffa686"><img src="https://joss.theoj.org/papers/70246ad674d3806798e343f6ecffa686/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/70246ad674d3806798e343f6ecffa686/status.svg)](https://joss.theoj.org/papers/70246ad674d3806798e343f6ecffa686)

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Thanks for submitting your paper to JOSS @ldes89150. Currently, there isn't a JOSS editor assigned to your paper.

@ldes89150 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.

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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 10, 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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Checking the BibTeX entries failed with the following error:

No paper file path

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Software report:

github.com/AlDanial/cloc v 1.88  T=0.05 s (695.6 files/s, 66611.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          26            773            554           1888
YAML                             2              9              4             61
Markdown                         1             21              0             49
reStructuredText                 5             30             44             36
DOS Batch                        1              8              1             26
TOML                             1              2              0             17
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            37            847            610           2086
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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Failed to discover a Statement of need section in paper

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⚠️ An error happened when generating the pdf. Paper file not found.

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Hello @ldes89150, thanks for your submission to JOSS. We'll use this pre-review issue to assign an editor and find reviewers; unfortunately, we don't have any editors available to handle your submission right now, so I need to put this on our waitlist until someone can edit it.

In the meantime, any reviewer recommendations you can make would be welcome.

@kyleniemeyer kyleniemeyer added waitlisted Submissions in the JOSS backlog due to reduced service mode. and removed Python labels Jan 10, 2024
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@ldes89150 it looks like the JOSS paper is located on the paper.md branch, is that correct?

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Hi @kyleniemeyer ,

Yes, it is in the paper.md branch. Do you need me to make any changes?

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@editorialbot set paper.md as branch

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Done! branch is now paper.md

@openjournals openjournals deleted a comment from editorialbot Jan 10, 2024
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@editorialbot generate pdf

@openjournals openjournals deleted a comment from editorialbot Jan 10, 2024
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@ldes89150 we just needed to specify the branch, since our editorialbot looks for the paper in the main branch by default.

I'm not quite sure what is causing the error in building the PDF, though.

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@openjournals/dev @arfon do you understand this error in the PDF build job?

Run bundle exec ruby /home/runner/work/_actions/xuanxu/paper-action/main/get_paper.rb
/home/runner/work/_actions/xuanxu/paper-action/main/vendor/bundle/ruby/3.2.0/gems/commonmarker-0.23.10/lib/commonmarker.rb:38:in `render_doc': text must be a String; got a NilClass! (TypeError)

      raise TypeError, "text must be a String; got a #{text.class}!" unless text.is_a?(String)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
	from /home/runner/work/_actions/xuanxu/paper-action/main/vendor/bundle/ruby/3.2.0/gems/theoj-1.9.0/lib/theoj/submission.rb:189:in `plaintext'
	from /home/runner/work/_actions/xuanxu/paper-action/main/vendor/bundle/ruby/3.2.0/gems/theoj-1.9.0/lib/theoj/submission.rb:100:in `all_metadata'
	from /home/runner/work/_actions/xuanxu/paper-action/main/vendor/bundle/ruby/3.2.0/gems/theoj-1.9.0/lib/theoj/submission.rb:78:in `metadata_info'
	from /home/runner/work/_actions/xuanxu/paper-action/main/vendor/bundle/ruby/3.2.0/gems/theoj-1.9.0/lib/theoj/submission.rb:57:in `article_metadata'
	from /home/runner/work/_actions/xuanxu/paper-action/main/get_paper.rb:25:in `<main>'
Error: Process completed with exit code 1.

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xuanxu commented Jan 11, 2024

Probably the error comes from the branch being named paper.md. Git creates internal files with the names of every branch so there is a paper.md file that can confuse the bot if it finds it before the real paper file.
Renaming the branch should fix the error.

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@editorialbot set paper as branch

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Done! branch is now paper

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@editorialbot generate pdf

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

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Five most similar historical JOSS papers:

PySDM v1: particle-based cloud modeling package for warm-rain microphysics and aqueous chemistry
Submitting author: @piotrbartman
Handling editor: @dhhagan (Active)
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SkyPy: A package for modelling the Universe
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prysm: A Python optics module
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beamshapes: a Python package to generate directivity patterns for various sound source models
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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.

@marvelousmonicaaa
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@kyleniemeyer changing the paper.md branch name to paper made the pdf work

@sidihamady
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@editorialbot generate my checklist

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Checklists can only be created once the review has started in the review issue

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HaoZeke commented Jan 31, 2024

@editorialbot add @sidihamady as reviewer

Hi @HaoZeke , I can review it. However, with the same remark as the colleague: I do not have access to the hardware part to test this functionality.

Excellent, thank you for the prompt response, testing only the software component will be fine.

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@sidihamady added to the reviewers list!

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HaoZeke commented Jan 31, 2024

@HaoZeke I can do a review from a general perspective on code quality, the paper, and so-on. But I do not have access to the hardware devices I believe the package is meant to control, and could not verify the functionality in a strict way

Hey @HaoZeke @brandondube ,

Just want to clarify on the hardware part: Most part of the software and majority of the functionalities don't require the hardware. All the hardware related code is in pySLM2/utils.

And @brandondube Thank you for your interest in reviewing the paper/repo!

@ldes89150, since we haven't found any reviewers for testing the hardware integration, would you be willing to add [not-reviewed] to the section describing the integration? If so, we can immediately go ahead and start the review.

Any suggestions for other reviewers for the hardware section would also be very welcome.

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@editorialbot generate my checklist

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Checklists can only be created once the review has started in the review issue

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HaoZeke commented Feb 1, 2024

Sorry @sidihamady, I need to wait for @ldes89150 to confirm the [not-reviewed] label for the hardware section before I can start this one.

The checklist can be generated after that, in the [REVIEW] thread.

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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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Hello @ldes89150, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

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

# 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 branch
@editorialbot set joss-paper as branch

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

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

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@editorialbot generate my checklist

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Checklists can only be created once the review has started in the review issue

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ldes89150 commented Feb 2, 2024

@HaoZeke What exactly do I need to do?
I confirm no review for the hardware section (pySLM2/utils).

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I added it to the paper. Let me know if there is still something I need to do.
https://github.com/QITI/pySLM2/blob/paper/paper.md#hardware-controls-not-reviewed

Thanks!

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@editorialbot generate pdf

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

1 similar comment
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👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

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Five most similar historical JOSS papers:

SkyPy: A package for modelling the Universe
Submitting author: @rrjbca
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Submitting author: @piotrbartman
Handling editor: @dhhagan (Active)
Reviewers: @darothen, @josephhardinee
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beamshapes: a Python package to generate directivity patterns for various sound source models
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Handling editor: @faroit (Active)
Reviewers: @nils-werner, @hagenw
Similarity score: 0.8144

prysm: A Python optics module
Submitting author: @brandondube
Handling editor: @xuanxu (Active)
Reviewers: @aquilesC
Similarity score: 0.8119

PiSCAT: A Python Package for Interferometric Scattering Microscopy
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Reviewers: @ziatdinovmax, @aquilesC
Similarity score: 0.8100

⚠️ 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.

1 similar comment
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Five most similar historical JOSS papers:

SkyPy: A package for modelling the Universe
Submitting author: @rrjbca
Handling editor: @arfon (Active)
Reviewers: @cescalara, @rmorgan10
Similarity score: 0.8171

PySDM v1: particle-based cloud modeling package for warm-rain microphysics and aqueous chemistry
Submitting author: @piotrbartman
Handling editor: @dhhagan (Active)
Reviewers: @darothen, @josephhardinee
Similarity score: 0.8155

beamshapes: a Python package to generate directivity patterns for various sound source models
Submitting author: @thejasvibr
Handling editor: @faroit (Active)
Reviewers: @nils-werner, @hagenw
Similarity score: 0.8144

prysm: A Python optics module
Submitting author: @brandondube
Handling editor: @xuanxu (Active)
Reviewers: @aquilesC
Similarity score: 0.8119

PiSCAT: A Python Package for Interferometric Scattering Microscopy
Submitting author: @po60nani
Handling editor: @emdupre (Active)
Reviewers: @ziatdinovmax, @aquilesC
Similarity score: 0.8100

⚠️ 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.

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ktahar commented Feb 2, 2024

I could review this paper but the situation is the same as the other reviewers; I don't have the hardware.
(This reply might be too late, sorry.)

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HaoZeke commented Feb 2, 2024

@editorialbot add @ktahar as reviewer

I could review this paper but the situation is the same as the other reviewers; I don't have the hardware.

That's alright, thanks for accepting the request to review.

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@ktahar added to the reviewers list!

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HaoZeke commented Feb 2, 2024

@editorialbot start review

@ldes89150 thanks for the quick turn-around. We can now proceed with the review.

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OK, I've started the review over in #6315.

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